FASTQC :: [Fri Jul 6 10:02:00 2018] Checking Examples/basic_examples/miRNAs/Known_miRNAs/results/ for FastQC analysis FASTQC :: [Fri Jul 6 10:02:00 2018] Executing mkdir -p Examples/basic_examples/miRNAs/Known_miRNAs/results//Pre_fastqc_results/ ; fastqc -f fastq -t 4 Examples/basic_examples/miRNAs/reads//SRR873382.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873383.fq.gz Examples/basic_examples/miRNAs/reads//SRR873384.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873385.fq.gz Examples/basic_examples/miRNAs/reads//SRR873386.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873387.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873388.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873389.fastq.gz -o Examples/basic_examples/miRNAs/Known_miRNAs/results//Pre_fastqc_results/ >> Examples/basic_examples/miRNAs/Known_miRNAs/results//miARma_logfile.2498.log 2>&1 Started analysis of SRR873382.fastq.gz Approx 5% complete for SRR873382.fastq.gz Approx 10% complete for SRR873382.fastq.gz Approx 15% complete for SRR873382.fastq.gz Approx 20% complete for SRR873382.fastq.gz Started analysis of SRR873383.fq.gz Approx 25% complete for SRR873382.fastq.gz Approx 5% complete for SRR873383.fq.gz Approx 30% complete for SRR873382.fastq.gz Approx 10% complete for SRR873383.fq.gz Approx 35% complete for SRR873382.fastq.gz Approx 15% complete for SRR873383.fq.gz Approx 40% complete for SRR873382.fastq.gz Approx 20% complete for SRR873383.fq.gz Started analysis of SRR873384.fastq.gz Approx 45% complete for SRR873382.fastq.gz Approx 25% complete for SRR873383.fq.gz Approx 5% complete for SRR873384.fastq.gz Approx 10% complete for SRR873384.fastq.gz Approx 30% complete for SRR873383.fq.gz Approx 50% complete for SRR873382.fastq.gz Approx 15% complete for SRR873384.fastq.gz Approx 55% complete for SRR873382.fastq.gz Approx 35% complete for SRR873383.fq.gz Approx 20% complete for SRR873384.fastq.gz Approx 60% complete for SRR873382.fastq.gz Approx 40% complete for SRR873383.fq.gz Approx 25% complete for SRR873384.fastq.gz Started analysis of SRR873385.fq.gz Approx 65% complete for SRR873382.fastq.gz Approx 45% complete for SRR873383.fq.gz Approx 30% complete for SRR873384.fastq.gz Approx 5% complete for SRR873385.fq.gz Approx 70% complete for SRR873382.fastq.gz Approx 35% complete for SRR873384.fastq.gz Approx 50% complete for SRR873383.fq.gz Approx 10% complete for SRR873385.fq.gz Approx 75% complete for SRR873382.fastq.gz Approx 40% complete for SRR873384.fastq.gz Approx 55% complete for SRR873383.fq.gz Approx 15% complete for SRR873385.fq.gz Approx 80% complete for SRR873382.fastq.gz Approx 45% complete for SRR873384.fastq.gz Approx 60% complete for SRR873383.fq.gz Approx 20% complete for SRR873385.fq.gz Approx 50% complete for SRR873384.fastq.gz Approx 85% complete for SRR873382.fastq.gz Approx 65% complete for SRR873383.fq.gz Approx 25% complete for SRR873385.fq.gz Approx 55% complete for SRR873384.fastq.gz Approx 70% complete for SRR873383.fq.gz Approx 90% complete for SRR873382.fastq.gz Approx 30% complete for SRR873385.fq.gz Approx 60% complete for SRR873384.fastq.gz Approx 75% complete for SRR873383.fq.gz Approx 95% complete for SRR873382.fastq.gz Approx 35% complete for SRR873385.fq.gz Approx 65% complete for SRR873384.fastq.gz Approx 80% complete for SRR873383.fq.gz Approx 40% complete for SRR873385.fq.gz Approx 100% complete for SRR873382.fastq.gz Analysis complete for SRR873382.fastq.gz Approx 70% complete for SRR873384.fastq.gz Approx 85% complete for SRR873383.fq.gz Approx 45% complete for SRR873385.fq.gz Approx 75% complete for SRR873384.fastq.gz Approx 90% complete for SRR873383.fq.gz Approx 50% complete for SRR873385.fq.gz Approx 80% complete for SRR873384.fastq.gz Approx 95% complete for SRR873383.fq.gz Approx 55% complete for SRR873385.fq.gz Approx 60% complete for SRR873385.fq.gz Approx 85% complete for SRR873384.fastq.gz Approx 100% complete for SRR873383.fq.gz Analysis complete for SRR873383.fq.gz Approx 65% complete for SRR873385.fq.gz Approx 70% complete for SRR873385.fq.gz Approx 90% complete for SRR873384.fastq.gz Approx 75% complete for SRR873385.fq.gz Approx 80% complete for SRR873385.fq.gz Approx 95% complete for SRR873384.fastq.gz Approx 85% complete for SRR873385.fq.gz Approx 90% complete for SRR873385.fq.gz Approx 95% complete for SRR873385.fq.gz Approx 100% complete for SRR873384.fastq.gz Analysis complete for SRR873384.fastq.gz Approx 100% complete for SRR873385.fq.gz Analysis complete for SRR873385.fq.gz Started analysis of SRR873386.fastq.gz Approx 5% complete for SRR873386.fastq.gz Approx 10% complete for SRR873386.fastq.gz Approx 15% complete for SRR873386.fastq.gz Approx 20% complete for SRR873386.fastq.gz Approx 25% complete for SRR873386.fastq.gz Started analysis of SRR873387.fastq.gz Approx 30% complete for SRR873386.fastq.gz Approx 5% complete for SRR873387.fastq.gz Approx 35% complete for SRR873386.fastq.gz Approx 10% complete for SRR873387.fastq.gz Approx 40% complete for SRR873386.fastq.gz Approx 15% complete for SRR873387.fastq.gz Approx 45% complete for SRR873386.fastq.gz Approx 20% complete for SRR873387.fastq.gz Approx 50% complete for SRR873386.fastq.gz Approx 25% complete for SRR873387.fastq.gz Approx 55% complete for SRR873386.fastq.gz Approx 30% complete for SRR873387.fastq.gz Approx 60% complete for SRR873386.fastq.gz Started analysis of SRR873388.fastq.gz Approx 35% complete for SRR873387.fastq.gz Approx 5% complete for SRR873388.fastq.gz Approx 65% complete for SRR873386.fastq.gz Approx 40% complete for SRR873387.fastq.gz Approx 10% complete for SRR873388.fastq.gz Approx 70% complete for SRR873386.fastq.gz Approx 45% complete for SRR873387.fastq.gz Approx 15% complete for SRR873388.fastq.gz Approx 75% complete for SRR873386.fastq.gz Approx 80% complete for SRR873386.fastq.gz Started analysis of SRR873389.fastq.gz Approx 50% complete for SRR873387.fastq.gz Approx 20% complete for SRR873388.fastq.gz Approx 5% complete for SRR873389.fastq.gz Approx 85% complete for SRR873386.fastq.gz Approx 55% complete for SRR873387.fastq.gz Approx 25% complete for SRR873388.fastq.gz Approx 10% complete for SRR873389.fastq.gz Approx 90% complete for SRR873386.fastq.gz Approx 30% complete for SRR873388.fastq.gz Approx 60% complete for SRR873387.fastq.gz Approx 15% complete for SRR873389.fastq.gz Approx 95% complete for SRR873386.fastq.gz Approx 65% complete for SRR873387.fastq.gz Approx 35% complete for SRR873388.fastq.gz Approx 20% complete for SRR873389.fastq.gz Approx 100% complete for SRR873386.fastq.gz Analysis complete for SRR873386.fastq.gz Approx 40% complete for SRR873388.fastq.gz Approx 70% complete for SRR873387.fastq.gz Approx 25% complete for SRR873389.fastq.gz Approx 45% complete for SRR873388.fastq.gz Approx 30% complete for SRR873389.fastq.gz Approx 75% complete for SRR873387.fastq.gz Approx 50% complete for SRR873388.fastq.gz Approx 35% complete for SRR873389.fastq.gz Approx 80% complete for SRR873387.fastq.gz Approx 55% complete for SRR873388.fastq.gz Approx 40% complete for SRR873389.fastq.gz Approx 85% complete for SRR873387.fastq.gz Approx 60% complete for SRR873388.fastq.gz Approx 45% complete for SRR873389.fastq.gz Approx 90% complete for SRR873387.fastq.gz Approx 65% complete for SRR873388.fastq.gz Approx 50% complete for SRR873389.fastq.gz Approx 95% complete for SRR873387.fastq.gz Approx 70% complete for SRR873388.fastq.gz Approx 55% complete for SRR873389.fastq.gz Approx 100% complete for SRR873387.fastq.gz Analysis complete for SRR873387.fastq.gz Approx 75% complete for SRR873388.fastq.gz Approx 60% complete for SRR873389.fastq.gz Approx 80% complete for SRR873388.fastq.gz Approx 65% complete for SRR873389.fastq.gz Approx 85% complete for SRR873388.fastq.gz Approx 70% complete for SRR873389.fastq.gz Approx 90% complete for SRR873388.fastq.gz Approx 75% complete for SRR873389.fastq.gz Approx 95% complete for SRR873388.fastq.gz Approx 80% complete for SRR873389.fastq.gz Approx 100% complete for SRR873388.fastq.gz Analysis complete for SRR873388.fastq.gz Approx 85% complete for SRR873389.fastq.gz Approx 90% complete for SRR873389.fastq.gz Approx 95% complete for SRR873389.fastq.gz Approx 100% complete for SRR873389.fastq.gz Analysis complete for SRR873389.fastq.gz CUTADAPT :: [Fri Jul 6 10:02:15 2018] Executing mkdir -p Examples/basic_examples/miRNAs/Known_miRNAs/results///cutadapt_results/ ; cut_adapt -b ATCTCGTATGCCGTCTTCTGCTTGAA -m 15 -M 35 -q 0 Examples/basic_examples/miRNAs/reads///SRR873382.fastq.gz > Examples/basic_examples/miRNAs/Known_miRNAs/results///cutadapt_results/SRR873382_cut.fastq 2>> Examples/basic_examples/miRNAs/Known_miRNAs/results//miARma_stat.2498.log FASTQC :: [Fri Jul 6 10:08:04 2018] Checking Examples/basic_examples/miRNAs/Known_miRNAs/results/ for FastQC analysis FASTQC :: [Fri Jul 6 10:08:04 2018] Executing mkdir -p Examples/basic_examples/miRNAs/Known_miRNAs/results//Pre_fastqc_results/ ; fastqc -f fastq -t 4 Examples/basic_examples/miRNAs/reads//SRR873382.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873383.fq.gz Examples/basic_examples/miRNAs/reads//SRR873384.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873385.fq.gz Examples/basic_examples/miRNAs/reads//SRR873386.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873387.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873388.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873389.fastq.gz -o Examples/basic_examples/miRNAs/Known_miRNAs/results//Pre_fastqc_results/ >> Examples/basic_examples/miRNAs/Known_miRNAs/results//miARma_logfile.2498.log 2>&1 Started analysis of SRR873382.fastq.gz Approx 5% complete for SRR873382.fastq.gz Approx 10% complete for SRR873382.fastq.gz Approx 15% complete for SRR873382.fastq.gz Approx 20% complete for SRR873382.fastq.gz Started analysis of SRR873383.fq.gz Approx 5% complete for SRR873383.fq.gz Approx 25% complete for SRR873382.fastq.gz Approx 10% complete for SRR873383.fq.gz Approx 30% complete for SRR873382.fastq.gz Approx 15% complete for SRR873383.fq.gz Approx 35% complete for SRR873382.fastq.gz Approx 20% complete for SRR873383.fq.gz Approx 40% complete for SRR873382.fastq.gz Started analysis of SRR873384.fastq.gz Approx 25% complete for SRR873383.fq.gz Approx 45% complete for SRR873382.fastq.gz Approx 5% complete for SRR873384.fastq.gz Approx 30% complete for SRR873383.fq.gz Approx 50% complete for SRR873382.fastq.gz Approx 10% complete for SRR873384.fastq.gz Approx 35% complete for SRR873383.fq.gz Approx 55% complete for SRR873382.fastq.gz Approx 15% complete for SRR873384.fastq.gz Approx 40% complete for SRR873383.fq.gz Approx 60% complete for SRR873382.fastq.gz Approx 20% complete for SRR873384.fastq.gz Approx 45% complete for SRR873383.fq.gz Approx 65% complete for SRR873382.fastq.gz Started analysis of SRR873385.fq.gz Approx 25% complete for SRR873384.fastq.gz Approx 50% complete for SRR873383.fq.gz Approx 5% complete for SRR873385.fq.gz Approx 70% complete for SRR873382.fastq.gz Approx 30% complete for SRR873384.fastq.gz Approx 55% complete for SRR873383.fq.gz Approx 10% complete for SRR873385.fq.gz Approx 75% complete for SRR873382.fastq.gz Approx 35% complete for SRR873384.fastq.gz Approx 60% complete for SRR873383.fq.gz Approx 15% complete for SRR873385.fq.gz Approx 80% complete for SRR873382.fastq.gz Approx 40% complete for SRR873384.fastq.gz Approx 65% complete for SRR873383.fq.gz Approx 20% complete for SRR873385.fq.gz Approx 85% complete for SRR873382.fastq.gz Approx 45% complete for SRR873384.fastq.gz Approx 70% complete for SRR873383.fq.gz Approx 25% complete for SRR873385.fq.gz Approx 90% complete for SRR873382.fastq.gz Approx 50% complete for SRR873384.fastq.gz Approx 75% complete for SRR873383.fq.gz Approx 30% complete for SRR873385.fq.gz Approx 95% complete for SRR873382.fastq.gz Approx 55% complete for SRR873384.fastq.gz Approx 80% complete for SRR873383.fq.gz Approx 35% complete for SRR873385.fq.gz Approx 100% complete for SRR873382.fastq.gz Analysis complete for SRR873382.fastq.gz Approx 60% complete for SRR873384.fastq.gz Approx 85% complete for SRR873383.fq.gz Approx 40% complete for SRR873385.fq.gz Approx 45% complete for SRR873385.fq.gz Approx 65% complete for SRR873384.fastq.gz Approx 50% complete for SRR873385.fq.gz Approx 90% complete for SRR873383.fq.gz Approx 55% complete for SRR873385.fq.gz Approx 60% complete for SRR873385.fq.gz Approx 70% complete for SRR873384.fastq.gz Approx 65% complete for SRR873385.fq.gz Approx 95% complete for SRR873383.fq.gz Approx 70% complete for SRR873385.fq.gz Approx 75% complete for SRR873384.fastq.gz Approx 75% complete for SRR873385.fq.gz Approx 100% complete for SRR873383.fq.gz Analysis complete for SRR873383.fq.gz Approx 80% complete for SRR873385.fq.gz Approx 80% complete for SRR873384.fastq.gz Approx 85% complete for SRR873385.fq.gz Approx 85% complete for SRR873384.fastq.gz Approx 90% complete for SRR873385.fq.gz Approx 90% complete for SRR873384.fastq.gz Approx 95% complete for SRR873385.fq.gz Approx 95% complete for SRR873384.fastq.gz Approx 100% complete for SRR873385.fq.gz Analysis complete for SRR873385.fq.gz Approx 100% complete for SRR873384.fastq.gz Analysis complete for SRR873384.fastq.gz Started analysis of SRR873386.fastq.gz Approx 5% complete for SRR873386.fastq.gz Approx 10% complete for SRR873386.fastq.gz Approx 15% complete for SRR873386.fastq.gz Started analysis of SRR873387.fastq.gz Approx 5% complete for SRR873387.fastq.gz Approx 20% complete for SRR873386.fastq.gz Approx 25% complete for SRR873386.fastq.gz Approx 10% complete for SRR873387.fastq.gz Approx 30% complete for SRR873386.fastq.gz Approx 15% complete for SRR873387.fastq.gz Approx 35% complete for SRR873386.fastq.gz Approx 20% complete for SRR873387.fastq.gz Approx 40% complete for SRR873386.fastq.gz Approx 25% complete for SRR873387.fastq.gz Started analysis of SRR873388.fastq.gz Approx 5% complete for SRR873388.fastq.gz Approx 45% complete for SRR873386.fastq.gz Approx 30% complete for SRR873387.fastq.gz Approx 50% complete for SRR873386.fastq.gz Approx 10% complete for SRR873388.fastq.gz Approx 35% complete for SRR873387.fastq.gz Approx 55% complete for SRR873386.fastq.gz Approx 40% complete for SRR873387.fastq.gz Approx 15% complete for SRR873388.fastq.gz Approx 60% complete for SRR873386.fastq.gz Approx 20% complete for SRR873388.fastq.gz Approx 45% complete for SRR873387.fastq.gz Approx 65% complete for SRR873386.fastq.gz Started analysis of SRR873389.fastq.gz Approx 50% complete for SRR873387.fastq.gz Approx 25% complete for SRR873388.fastq.gz Approx 70% complete for SRR873386.fastq.gz Approx 5% complete for SRR873389.fastq.gz Approx 55% complete for SRR873387.fastq.gz Approx 30% complete for SRR873388.fastq.gz Approx 75% complete for SRR873386.fastq.gz Approx 10% complete for SRR873389.fastq.gz Approx 35% complete for SRR873388.fastq.gz Approx 60% complete for SRR873387.fastq.gz Approx 15% complete for SRR873389.fastq.gz Approx 80% complete for SRR873386.fastq.gz Approx 40% complete for SRR873388.fastq.gz Approx 65% complete for SRR873387.fastq.gz Approx 85% complete for SRR873386.fastq.gz Approx 20% complete for SRR873389.fastq.gz Approx 45% complete for SRR873388.fastq.gz Approx 70% complete for SRR873387.fastq.gz Approx 25% complete for SRR873389.fastq.gz Approx 90% complete for SRR873386.fastq.gz Approx 50% complete for SRR873388.fastq.gz Approx 75% complete for SRR873387.fastq.gz Approx 30% complete for SRR873389.fastq.gz Approx 95% complete for SRR873386.fastq.gz Approx 55% complete for SRR873388.fastq.gz Approx 80% complete for SRR873387.fastq.gz Approx 35% complete for SRR873389.fastq.gz Approx 100% complete for SRR873386.fastq.gz Analysis complete for SRR873386.fastq.gz Approx 60% complete for SRR873388.fastq.gz Approx 85% complete for SRR873387.fastq.gz Approx 40% complete for SRR873389.fastq.gz Approx 65% complete for SRR873388.fastq.gz Approx 90% complete for SRR873387.fastq.gz Approx 45% complete for SRR873389.fastq.gz Approx 70% complete for SRR873388.fastq.gz Approx 95% complete for SRR873387.fastq.gz Approx 50% complete for SRR873389.fastq.gz Approx 75% complete for SRR873388.fastq.gz Approx 100% complete for SRR873387.fastq.gz Analysis complete for SRR873387.fastq.gz Approx 55% complete for SRR873389.fastq.gz Approx 80% complete for SRR873388.fastq.gz Approx 60% complete for SRR873389.fastq.gz Approx 85% complete for SRR873388.fastq.gz Approx 65% complete for SRR873389.fastq.gz Approx 90% complete for SRR873388.fastq.gz Approx 70% complete for SRR873389.fastq.gz Approx 95% complete for SRR873388.fastq.gz Approx 75% complete for SRR873389.fastq.gz Approx 100% complete for SRR873388.fastq.gz Analysis complete for SRR873388.fastq.gz Approx 80% complete for SRR873389.fastq.gz Approx 85% complete for SRR873389.fastq.gz Approx 90% complete for SRR873389.fastq.gz Approx 95% complete for SRR873389.fastq.gz Approx 100% complete for SRR873389.fastq.gz Analysis complete for SRR873389.fastq.gz CUTADAPT :: [Fri Jul 6 10:08:16 2018] Executing mkdir -p Examples/basic_examples/miRNAs/Known_miRNAs/results///cutadapt_results/ ; cut_adapt -b ATCTCGTATGCCGTCTTCTGCTTGAA -m 15 -M 35 -q 0 Examples/basic_examples/miRNAs/reads///SRR873382.fastq.gz > Examples/basic_examples/miRNAs/Known_miRNAs/results///cutadapt_results/SRR873382_cut.fastq 2>> Examples/basic_examples/miRNAs/Known_miRNAs/results//miARma_stat.2498.log FASTQC :: [Fri Jul 6 10:16:54 2018] Checking Examples/basic_examples/miRNAs/Known_miRNAs/results/ for FastQC analysis FASTQC :: [Fri Jul 6 10:16:54 2018] Executing mkdir -p Examples/basic_examples/miRNAs/Known_miRNAs/results//Pre_fastqc_results/ ; fastqc -f fastq -t 4 Examples/basic_examples/miRNAs/reads//SRR873382.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873383.fq.gz Examples/basic_examples/miRNAs/reads//SRR873384.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873385.fq.gz Examples/basic_examples/miRNAs/reads//SRR873386.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873387.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873388.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873389.fastq.gz -o Examples/basic_examples/miRNAs/Known_miRNAs/results//Pre_fastqc_results/ >> Examples/basic_examples/miRNAs/Known_miRNAs/results//miARma_logfile.2498.log 2>&1 Started analysis of SRR873382.fastq.gz Approx 5% complete for SRR873382.fastq.gz Approx 10% complete for SRR873382.fastq.gz Approx 15% complete for SRR873382.fastq.gz Approx 20% complete for SRR873382.fastq.gz Started analysis of SRR873383.fq.gz Approx 25% complete for SRR873382.fastq.gz Approx 5% complete for SRR873383.fq.gz Approx 30% complete for SRR873382.fastq.gz Approx 10% complete for SRR873383.fq.gz Approx 35% complete for SRR873382.fastq.gz Approx 15% complete for SRR873383.fq.gz Approx 40% complete for SRR873382.fastq.gz Approx 20% complete for SRR873383.fq.gz Started analysis of SRR873384.fastq.gz Approx 45% complete for SRR873382.fastq.gz Approx 25% complete for SRR873383.fq.gz Approx 5% complete for SRR873384.fastq.gz Approx 50% complete for SRR873382.fastq.gz Approx 30% complete for SRR873383.fq.gz Approx 10% complete for SRR873384.fastq.gz Approx 55% complete for SRR873382.fastq.gz Approx 35% complete for SRR873383.fq.gz Approx 60% complete for SRR873382.fastq.gz Approx 15% complete for SRR873384.fastq.gz Approx 40% complete for SRR873383.fq.gz Approx 20% complete for SRR873384.fastq.gz Approx 65% complete for SRR873382.fastq.gz Started analysis of SRR873385.fq.gz Approx 45% complete for SRR873383.fq.gz Approx 25% complete for SRR873384.fastq.gz Approx 70% complete for SRR873382.fastq.gz Approx 5% complete for SRR873385.fq.gz Approx 50% complete for SRR873383.fq.gz Approx 30% complete for SRR873384.fastq.gz Approx 75% complete for SRR873382.fastq.gz Approx 10% complete for SRR873385.fq.gz Approx 55% complete for SRR873383.fq.gz Approx 35% complete for SRR873384.fastq.gz Approx 80% complete for SRR873382.fastq.gz Approx 15% complete for SRR873385.fq.gz Approx 60% complete for SRR873383.fq.gz Approx 40% complete for SRR873384.fastq.gz Approx 85% complete for SRR873382.fastq.gz Approx 20% complete for SRR873385.fq.gz Approx 65% complete for SRR873383.fq.gz Approx 45% complete for SRR873384.fastq.gz Approx 90% complete for SRR873382.fastq.gz Approx 25% complete for SRR873385.fq.gz Approx 70% complete for SRR873383.fq.gz Approx 50% complete for SRR873384.fastq.gz Approx 95% complete for SRR873382.fastq.gz Approx 30% complete for SRR873385.fq.gz Approx 75% complete for SRR873383.fq.gz Approx 55% complete for SRR873384.fastq.gz Approx 100% complete for SRR873382.fastq.gz Approx 35% complete for SRR873385.fq.gz Analysis complete for SRR873382.fastq.gz Approx 80% complete for SRR873383.fq.gz Approx 60% complete for SRR873384.fastq.gz Approx 40% complete for SRR873385.fq.gz Approx 65% complete for SRR873384.fastq.gz Approx 45% complete for SRR873385.fq.gz Approx 70% complete for SRR873384.fastq.gz Approx 85% complete for SRR873383.fq.gz Approx 50% complete for SRR873385.fq.gz Approx 75% complete for SRR873384.fastq.gz Approx 55% complete for SRR873385.fq.gz Approx 80% complete for SRR873384.fastq.gz Approx 90% complete for SRR873383.fq.gz Approx 60% complete for SRR873385.fq.gz Approx 85% complete for SRR873384.fastq.gz Approx 65% complete for SRR873385.fq.gz Approx 90% complete for SRR873384.fastq.gz Approx 70% complete for SRR873385.fq.gz Approx 95% complete for SRR873383.fq.gz Approx 95% complete for SRR873384.fastq.gz Approx 75% complete for SRR873385.fq.gz Approx 100% complete for SRR873384.fastq.gz Analysis complete for SRR873384.fastq.gz Approx 80% complete for SRR873385.fq.gz Approx 100% complete for SRR873383.fq.gz Approx 85% complete for SRR873385.fq.gz Analysis complete for SRR873383.fq.gz Approx 90% complete for SRR873385.fq.gz Approx 95% complete for SRR873385.fq.gz Approx 100% complete for SRR873385.fq.gz Analysis complete for SRR873385.fq.gz Started analysis of SRR873386.fastq.gz Approx 5% complete for SRR873386.fastq.gz Approx 10% complete for SRR873386.fastq.gz Approx 15% complete for SRR873386.fastq.gz Approx 20% complete for SRR873386.fastq.gz Approx 25% complete for SRR873386.fastq.gz Approx 30% complete for SRR873386.fastq.gz Approx 35% complete for SRR873386.fastq.gz Started analysis of SRR873387.fastq.gz Approx 40% complete for SRR873386.fastq.gz Approx 5% complete for SRR873387.fastq.gz Approx 45% complete for SRR873386.fastq.gz Approx 10% complete for SRR873387.fastq.gz Approx 50% complete for SRR873386.fastq.gz Approx 15% complete for SRR873387.fastq.gz Approx 55% complete for SRR873386.fastq.gz Approx 20% complete for SRR873387.fastq.gz Approx 60% complete for SRR873386.fastq.gz Approx 25% complete for SRR873387.fastq.gz Approx 65% complete for SRR873386.fastq.gz Approx 30% complete for SRR873387.fastq.gz Started analysis of SRR873388.fastq.gz Approx 70% complete for SRR873386.fastq.gz Approx 35% complete for SRR873387.fastq.gz Approx 5% complete for SRR873388.fastq.gz Approx 75% complete for SRR873386.fastq.gz Approx 40% complete for SRR873387.fastq.gz Approx 10% complete for SRR873388.fastq.gz Approx 80% complete for SRR873386.fastq.gz Approx 15% complete for SRR873388.fastq.gz Approx 45% complete for SRR873387.fastq.gz Approx 85% complete for SRR873386.fastq.gz Approx 20% complete for SRR873388.fastq.gz Started analysis of SRR873389.fastq.gz Approx 50% complete for SRR873387.fastq.gz Approx 90% complete for SRR873386.fastq.gz Approx 25% complete for SRR873388.fastq.gz Approx 5% complete for SRR873389.fastq.gz Approx 55% complete for SRR873387.fastq.gz Approx 95% complete for SRR873386.fastq.gz Approx 30% complete for SRR873388.fastq.gz Approx 10% complete for SRR873389.fastq.gz Approx 60% complete for SRR873387.fastq.gz Approx 100% complete for SRR873386.fastq.gz Approx 35% complete for SRR873388.fastq.gz Analysis complete for SRR873386.fastq.gz Approx 15% complete for SRR873389.fastq.gz Approx 65% complete for SRR873387.fastq.gz Approx 40% complete for SRR873388.fastq.gz Approx 20% complete for SRR873389.fastq.gz Approx 70% complete for SRR873387.fastq.gz Approx 45% complete for SRR873388.fastq.gz Approx 25% complete for SRR873389.fastq.gz Approx 75% complete for SRR873387.fastq.gz Approx 50% complete for SRR873388.fastq.gz Approx 30% complete for SRR873389.fastq.gz Approx 80% complete for SRR873387.fastq.gz Approx 55% complete for SRR873388.fastq.gz Approx 35% complete for SRR873389.fastq.gz Approx 85% complete for SRR873387.fastq.gz Approx 60% complete for SRR873388.fastq.gz Approx 40% complete for SRR873389.fastq.gz Approx 90% complete for SRR873387.fastq.gz Approx 65% complete for SRR873388.fastq.gz Approx 45% complete for SRR873389.fastq.gz Approx 95% complete for SRR873387.fastq.gz Approx 70% complete for SRR873388.fastq.gz Approx 50% complete for SRR873389.fastq.gz Approx 100% complete for SRR873387.fastq.gz Analysis complete for SRR873387.fastq.gz Approx 75% complete for SRR873388.fastq.gz Approx 55% complete for SRR873389.fastq.gz Approx 80% complete for SRR873388.fastq.gz Approx 60% complete for SRR873389.fastq.gz Approx 85% complete for SRR873388.fastq.gz Approx 65% complete for SRR873389.fastq.gz Approx 90% complete for SRR873388.fastq.gz Approx 70% complete for SRR873389.fastq.gz Approx 95% complete for SRR873388.fastq.gz Approx 75% complete for SRR873389.fastq.gz Approx 100% complete for SRR873388.fastq.gz Analysis complete for SRR873388.fastq.gz Approx 80% complete for SRR873389.fastq.gz Approx 85% complete for SRR873389.fastq.gz Approx 90% complete for SRR873389.fastq.gz Approx 95% complete for SRR873389.fastq.gz Approx 100% complete for SRR873389.fastq.gz Analysis complete for SRR873389.fastq.gz CUTADAPT :: [Fri Jul 6 10:17:06 2018] Executing mkdir -p Examples/basic_examples/miRNAs/Known_miRNAs/results///cutadapt_results/ ; cut_adapt -b ATCTCGTATGCCGTCTTCTGCTTGAA -m 15 -M 35 -q 0 Examples/basic_examples/miRNAs/reads///SRR873382.fastq.gz > Examples/basic_examples/miRNAs/Known_miRNAs/results///cutadapt_results/SRR873382_cut.fastq 2>> Examples/basic_examples/miRNAs/Known_miRNAs/results//miARma_stat.2498.log FASTQC :: [Fri Jul 6 10:23:23 2018] Checking Examples/basic_examples/miRNAs/Known_miRNAs/results/ for FastQC analysis FASTQC :: [Fri Jul 6 10:23:23 2018] Executing mkdir -p Examples/basic_examples/miRNAs/Known_miRNAs/results//Pre_fastqc_results/ ; fastqc -f fastq -t 4 Examples/basic_examples/miRNAs/reads//SRR873382.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873383.fq.gz Examples/basic_examples/miRNAs/reads//SRR873384.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873385.fq.gz Examples/basic_examples/miRNAs/reads//SRR873386.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873387.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873388.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873389.fastq.gz -o Examples/basic_examples/miRNAs/Known_miRNAs/results//Pre_fastqc_results/ >> Examples/basic_examples/miRNAs/Known_miRNAs/results//miARma_logfile.2498.log 2>&1 Started analysis of SRR873382.fastq.gz Approx 5% complete for SRR873382.fastq.gz Approx 10% complete for SRR873382.fastq.gz Approx 15% complete for SRR873382.fastq.gz Approx 20% complete for SRR873382.fastq.gz Started analysis of SRR873383.fq.gz Approx 25% complete for SRR873382.fastq.gz Approx 5% complete for SRR873383.fq.gz Approx 30% complete for SRR873382.fastq.gz Approx 10% complete for SRR873383.fq.gz Approx 35% complete for SRR873382.fastq.gz Approx 15% complete for SRR873383.fq.gz Approx 40% complete for SRR873382.fastq.gz Approx 20% complete for SRR873383.fq.gz Started analysis of SRR873384.fastq.gz Approx 45% complete for SRR873382.fastq.gz Approx 25% complete for SRR873383.fq.gz Approx 5% complete for SRR873384.fastq.gz Approx 50% complete for SRR873382.fastq.gz Approx 30% complete for SRR873383.fq.gz Approx 10% complete for SRR873384.fastq.gz Approx 35% complete for SRR873383.fq.gz Approx 55% complete for SRR873382.fastq.gz Approx 15% complete for SRR873384.fastq.gz Approx 40% complete for SRR873383.fq.gz Approx 60% complete for SRR873382.fastq.gz Approx 20% complete for SRR873384.fastq.gz Approx 45% complete for SRR873383.fq.gz Approx 65% complete for SRR873382.fastq.gz Started analysis of SRR873385.fq.gz Approx 25% complete for SRR873384.fastq.gz Approx 50% complete for SRR873383.fq.gz Approx 70% complete for SRR873382.fastq.gz Approx 5% complete for SRR873385.fq.gz Approx 30% complete for SRR873384.fastq.gz Approx 55% complete for SRR873383.fq.gz Approx 75% complete for SRR873382.fastq.gz Approx 10% complete for SRR873385.fq.gz Approx 35% complete for SRR873384.fastq.gz Approx 60% complete for SRR873383.fq.gz Approx 15% complete for SRR873385.fq.gz Approx 80% complete for SRR873382.fastq.gz Approx 40% complete for SRR873384.fastq.gz Approx 65% complete for SRR873383.fq.gz Approx 20% complete for SRR873385.fq.gz Approx 85% complete for SRR873382.fastq.gz Approx 45% complete for SRR873384.fastq.gz Approx 25% complete for SRR873385.fq.gz Approx 70% complete for SRR873383.fq.gz Approx 90% complete for SRR873382.fastq.gz Approx 50% complete for SRR873384.fastq.gz Approx 30% complete for SRR873385.fq.gz Approx 75% complete for SRR873383.fq.gz Approx 95% complete for SRR873382.fastq.gz Approx 55% complete for SRR873384.fastq.gz Approx 35% complete for SRR873385.fq.gz Approx 100% complete for SRR873382.fastq.gz Approx 80% complete for SRR873383.fq.gz Analysis complete for SRR873382.fastq.gz Approx 60% complete for SRR873384.fastq.gz Approx 40% complete for SRR873385.fq.gz Approx 65% complete for SRR873384.fastq.gz Approx 45% complete for SRR873385.fq.gz Approx 85% complete for SRR873383.fq.gz Approx 50% complete for SRR873385.fq.gz Approx 70% complete for SRR873384.fastq.gz Approx 55% complete for SRR873385.fq.gz Approx 90% complete for SRR873383.fq.gz Approx 75% complete for SRR873384.fastq.gz Approx 60% complete for SRR873385.fq.gz Approx 80% complete for SRR873384.fastq.gz Approx 85% complete for SRR873384.fastq.gz Approx 65% complete for SRR873385.fq.gz Approx 95% complete for SRR873383.fq.gz Approx 90% complete for SRR873384.fastq.gz Approx 70% complete for SRR873385.fq.gz Approx 95% complete for SRR873384.fastq.gz Approx 75% complete for SRR873385.fq.gz Approx 100% complete for SRR873383.fq.gz Analysis complete for SRR873383.fq.gz Approx 100% complete for SRR873384.fastq.gz Analysis complete for SRR873384.fastq.gz Approx 80% complete for SRR873385.fq.gz Approx 85% complete for SRR873385.fq.gz Approx 90% complete for SRR873385.fq.gz Approx 95% complete for SRR873385.fq.gz Approx 100% complete for SRR873385.fq.gz Analysis complete for SRR873385.fq.gz Started analysis of SRR873386.fastq.gz Approx 5% complete for SRR873386.fastq.gz Approx 10% complete for SRR873386.fastq.gz Approx 15% complete for SRR873386.fastq.gz Approx 20% complete for SRR873386.fastq.gz Started analysis of SRR873387.fastq.gz Approx 25% complete for SRR873386.fastq.gz Approx 5% complete for SRR873387.fastq.gz Approx 30% complete for SRR873386.fastq.gz Approx 10% complete for SRR873387.fastq.gz Approx 35% complete for SRR873386.fastq.gz Approx 15% complete for SRR873387.fastq.gz Approx 40% complete for SRR873386.fastq.gz Approx 20% complete for SRR873387.fastq.gz Approx 45% complete for SRR873386.fastq.gz Approx 25% complete for SRR873387.fastq.gz Started analysis of SRR873388.fastq.gz Approx 50% complete for SRR873386.fastq.gz Approx 5% complete for SRR873388.fastq.gz Approx 30% complete for SRR873387.fastq.gz Approx 10% complete for SRR873388.fastq.gz Approx 55% complete for SRR873386.fastq.gz Approx 35% complete for SRR873387.fastq.gz Approx 15% complete for SRR873388.fastq.gz Approx 60% complete for SRR873386.fastq.gz Approx 40% complete for SRR873387.fastq.gz Approx 20% complete for SRR873388.fastq.gz Approx 45% complete for SRR873387.fastq.gz Approx 65% complete for SRR873386.fastq.gz Approx 25% complete for SRR873388.fastq.gz Started analysis of SRR873389.fastq.gz Approx 50% complete for SRR873387.fastq.gz Approx 70% complete for SRR873386.fastq.gz Approx 5% complete for SRR873389.fastq.gz Approx 30% complete for SRR873388.fastq.gz Approx 55% complete for SRR873387.fastq.gz Approx 75% complete for SRR873386.fastq.gz Approx 10% complete for SRR873389.fastq.gz Approx 35% complete for SRR873388.fastq.gz Approx 60% complete for SRR873387.fastq.gz Approx 80% complete for SRR873386.fastq.gz Approx 40% complete for SRR873388.fastq.gz Approx 15% complete for SRR873389.fastq.gz Approx 65% complete for SRR873387.fastq.gz Approx 85% complete for SRR873386.fastq.gz Approx 20% complete for SRR873389.fastq.gz Approx 45% complete for SRR873388.fastq.gz Approx 70% complete for SRR873387.fastq.gz Approx 25% complete for SRR873389.fastq.gz Approx 50% complete for SRR873388.fastq.gz Approx 90% complete for SRR873386.fastq.gz Approx 75% complete for SRR873387.fastq.gz Approx 30% complete for SRR873389.fastq.gz Approx 55% complete for SRR873388.fastq.gz Approx 95% complete for SRR873386.fastq.gz Approx 80% complete for SRR873387.fastq.gz Approx 35% complete for SRR873389.fastq.gz Approx 60% complete for SRR873388.fastq.gz Approx 100% complete for SRR873386.fastq.gz Approx 85% complete for SRR873387.fastq.gz Analysis complete for SRR873386.fastq.gz Approx 40% complete for SRR873389.fastq.gz Approx 65% complete for SRR873388.fastq.gz Approx 90% complete for SRR873387.fastq.gz Approx 45% complete for SRR873389.fastq.gz Approx 70% complete for SRR873388.fastq.gz Approx 95% complete for SRR873387.fastq.gz Approx 50% complete for SRR873389.fastq.gz Approx 75% complete for SRR873388.fastq.gz Approx 100% complete for SRR873387.fastq.gz Approx 55% complete for SRR873389.fastq.gz Analysis complete for SRR873387.fastq.gz Approx 80% complete for SRR873388.fastq.gz Approx 60% complete for SRR873389.fastq.gz Approx 85% complete for SRR873388.fastq.gz Approx 65% complete for SRR873389.fastq.gz Approx 90% complete for SRR873388.fastq.gz Approx 70% complete for SRR873389.fastq.gz Approx 95% complete for SRR873388.fastq.gz Approx 75% complete for SRR873389.fastq.gz Approx 100% complete for SRR873388.fastq.gz Analysis complete for SRR873388.fastq.gz Approx 80% complete for SRR873389.fastq.gz Approx 85% complete for SRR873389.fastq.gz Approx 90% complete for SRR873389.fastq.gz Approx 95% complete for SRR873389.fastq.gz Approx 100% complete for SRR873389.fastq.gz Analysis complete for SRR873389.fastq.gz CUTADAPT :: [Fri Jul 6 10:23:35 2018] Executing mkdir -p Examples/basic_examples/miRNAs/Known_miRNAs/results///cutadapt_results/ ; cut_adapt -b ATCTCGTATGCCGTCTTCTGCTTGAA -m 15 -M 35 -q 0 Examples/basic_examples/miRNAs/reads///SRR873382.fastq.gz > Examples/basic_examples/miRNAs/Known_miRNAs/results///cutadapt_results/SRR873382_cut.fastq 2>> Examples/basic_examples/miRNAs/Known_miRNAs/results//miARma_stat.2498.log FASTQC :: [Fri Jul 6 11:01:25 2018] Checking Examples/basic_examples/miRNAs/Known_miRNAs/results/ for FastQC analysis FASTQC :: [Fri Jul 6 11:01:25 2018] Executing mkdir -p Examples/basic_examples/miRNAs/Known_miRNAs/results//Pre_fastqc_results/ ; fastqc -f fastq -t 4 Examples/basic_examples/miRNAs/reads//SRR873382.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873383.fq.gz Examples/basic_examples/miRNAs/reads//SRR873384.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873385.fq.gz Examples/basic_examples/miRNAs/reads//SRR873386.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873387.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873388.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873389.fastq.gz -o Examples/basic_examples/miRNAs/Known_miRNAs/results//Pre_fastqc_results/ >> Examples/basic_examples/miRNAs/Known_miRNAs/results//miARma_logfile.2498.log 2>&1 Started analysis of SRR873382.fastq.gz Approx 5% complete for SRR873382.fastq.gz Approx 10% complete for SRR873382.fastq.gz Approx 15% complete for SRR873382.fastq.gz Started analysis of SRR873383.fq.gz Approx 20% complete for SRR873382.fastq.gz Approx 5% complete for SRR873383.fq.gz Approx 25% complete for SRR873382.fastq.gz Approx 10% complete for SRR873383.fq.gz Approx 30% complete for SRR873382.fastq.gz Approx 15% complete for SRR873383.fq.gz Approx 35% complete for SRR873382.fastq.gz Started analysis of SRR873384.fastq.gz Approx 20% complete for SRR873383.fq.gz Approx 40% complete for SRR873382.fastq.gz Approx 5% complete for SRR873384.fastq.gz Approx 25% complete for SRR873383.fq.gz Approx 45% complete for SRR873382.fastq.gz Approx 10% complete for SRR873384.fastq.gz Approx 50% complete for SRR873382.fastq.gz Approx 30% complete for SRR873383.fq.gz Approx 55% complete for SRR873382.fastq.gz Approx 15% complete for SRR873384.fastq.gz Approx 35% complete for SRR873383.fq.gz Approx 60% complete for SRR873382.fastq.gz Approx 20% complete for SRR873384.fastq.gz Approx 40% complete for SRR873383.fq.gz Approx 65% complete for SRR873382.fastq.gz Started analysis of SRR873385.fq.gz Approx 25% complete for SRR873384.fastq.gz Approx 45% complete for SRR873383.fq.gz Approx 70% complete for SRR873382.fastq.gz Approx 5% complete for SRR873385.fq.gz Approx 30% complete for SRR873384.fastq.gz Approx 50% complete for SRR873383.fq.gz Approx 10% complete for SRR873385.fq.gz Approx 75% complete for SRR873382.fastq.gz Approx 35% complete for SRR873384.fastq.gz Approx 55% complete for SRR873383.fq.gz Approx 15% complete for SRR873385.fq.gz Approx 80% complete for SRR873382.fastq.gz Approx 40% complete for SRR873384.fastq.gz Approx 60% complete for SRR873383.fq.gz Approx 20% complete for SRR873385.fq.gz Approx 85% complete for SRR873382.fastq.gz Approx 45% complete for SRR873384.fastq.gz Approx 65% complete for SRR873383.fq.gz Approx 25% complete for SRR873385.fq.gz Approx 90% complete for SRR873382.fastq.gz Approx 50% complete for SRR873384.fastq.gz Approx 70% complete for SRR873383.fq.gz Approx 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SRR873389.fastq.gz Approx 80% complete for SRR873389.fastq.gz Approx 85% complete for SRR873389.fastq.gz Approx 90% complete for SRR873389.fastq.gz Approx 95% complete for SRR873389.fastq.gz Approx 100% complete for SRR873389.fastq.gz Analysis complete for SRR873389.fastq.gz BOWTIE 1 :: [Fri Jul 6 11:01:37 2018] Executing mkdir -p Examples/basic_examples/miRNAs/Known_miRNAs/results//Bowtie1_results/ ;bowtie --sam -p 4 Genomes/Indexes/bowtie1/human/bw1_homo_sapiens19 Examples/basic_examples/miRNAs/Known_miRNAs/results//cutadapt_results/SRR873382_cut.fastq Examples/basic_examples/miRNAs/Known_miRNAs/results//Bowtie1_results/SRR873382_cut_nat_bw1.bam 2>> Examples/basic_examples/miRNAs/Known_miRNAs/results//miARma_stat.2498.log File:Examples/basic_examples/miRNAs/Known_miRNAs/results//cutadapt_results/SRR873382_cut.fastq SEQCOUNT :: [Fri Jul 6 11:02:53 2018] Reading counts from Examples/basic_examples/miRNAs/Known_miRNAs/results//Bowtie1_results/SRR873382_cut_nat_bw1.bam SEQCOUNT :: [Fri Jul 6 11:02:53 2018] Executing mkdir -p Examples/basic_examples/miRNAs/Known_miRNAs/results//nat_bw1_readcount_results/ ;featureCounts -s 1 -t miRNA -g transcript_id -T 4 -a Examples/basic_examples/miRNAs/data/miRBase_Annotation_20_for_hsa_mature_miRNA.gtf -o Examples/basic_examples/miRNAs/Known_miRNAs/results//nat_bw1_readcount_results/SRR873382_cut_nat_bw1.tab Examples/basic_examples/miRNAs/Known_miRNAs/results//Bowtie1_results/SRR873382_cut_nat_bw1.bam 2>> Examples/basic_examples/miRNAs/Known_miRNAs/results//miARma_logfile.2498.log ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.5.0-p1 //========================== featureCounts setting ===========================\\ || || || Input files : 1 SAM file || || S Examples/basic_examples/miRNAs/Known_miRNA ... || || || || Output file : Examples/basic_examples/miRNAs/Known_miRNAs/ ... || || Annotations : Examples/basic_examples/miRNAs/data/miRBase_ ... || || || || Threads : 4 || || Level : meta-feature level || || Paired-end : no || || Strand specific : yes || || Multimapping reads : not counted || || Multi-overlapping reads : not counted || || Read orientations : fr || || || \\===================== http://subread.sourceforge.net/ ======================// //================================= Running ==================================\\ || || || Load annotation file Examples/basic_examples/miRNAs/data/miRBase_Annot ... || || Features : 2794 || || Meta-features : 2576 || || Chromosomes/contigs : 24 || || || || Process SAM file Examples/basic_examples/miRNAs/Known_miRNAs/results// ... || || Single-end reads are included. || || Assign reads to features... || || Total reads : 0 || || Successfully assigned reads : 0 || || Running time : 0.00 minutes || || || || Read assignment finished. || || || \\===================== http://subread.sourceforge.net/ ======================// SEQCOUNT :: [Fri Jul 6 11:02:53 2018] Please check the folder: Examples/basic_examples/miRNAs/Known_miRNAs/results//Readcount_results/. QC_EdgeR :: [Fri Jul 6 11:02:54 2018] Executing source("./lib/CbBio/RNASeq/R-Scripts/QC_EdgeR.R") setwd("/home/leila/apps/miARma/cbbio-miarma-42e187a7f514/Examples/basic_examples/miRNAs/Known_miRNAs/results/Readcount_results") resultsfiles<-QC_EdgeR(projectdir="/home/leila/apps/miARma/cbbio-miarma-42e187a7f514/Examples/basic_examples/miRNAs/Known_miRNAs/results",dir="/home/leila/apps/miARma/cbbio-miarma-42e187a7f514/Examples/basic_examples/miRNAs/Known_miRNAs/results/Readcount_results", file="nat_bw1-ReadCount.tab", targetfile="/home/leila/apps/miARma/cbbio-miarma-42e187a7f514/Examples/basic_examples/miRNAs/data/targets.txt", label="Hypoxia_nat_bw1", filter="yes") FASTQC :: [Sun Jul 8 19:01:00 2018] Checking Examples/basic_examples/miRNAs/Known_miRNAs/results/ for FastQC analysis FASTQC :: [Sun Jul 8 19:01:00 2018] Executing mkdir -p Examples/basic_examples/miRNAs/Known_miRNAs/results//Pre_fastqc_results/ ; fastqc -f fastq -t 4 Examples/basic_examples/miRNAs/reads//SRR873382.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873383.fq.gz Examples/basic_examples/miRNAs/reads//SRR873384.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873385.fq.gz Examples/basic_examples/miRNAs/reads//SRR873386.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873387.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873388.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873389.fastq.gz -o Examples/basic_examples/miRNAs/Known_miRNAs/results//Pre_fastqc_results/ >> Examples/basic_examples/miRNAs/Known_miRNAs/results//miARma_logfile.2498.log 2>&1 Started analysis of SRR873382.fastq.gz Approx 5% complete for SRR873382.fastq.gz Approx 10% complete for SRR873382.fastq.gz Approx 15% complete for SRR873382.fastq.gz Started analysis of SRR873383.fq.gz Approx 20% complete for SRR873382.fastq.gz Approx 5% complete for SRR873383.fq.gz Approx 25% complete for SRR873382.fastq.gz Approx 10% complete for SRR873383.fq.gz Approx 30% complete for SRR873382.fastq.gz Approx 15% complete for 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SRR873389.fastq.gz CUTADAPT :: [Sun Jul 8 19:01:15 2018] Executing mkdir -p Examples/basic_examples/miRNAs/Known_miRNAs/results///cutadapt_results/ ; cut_adapt -b ATCTCGTATGCCGTCTTCTGCTTGAA -m 15 -M 35 -q 0 Examples/basic_examples/miRNAs/reads///SRR873382.fastq.gz > Examples/basic_examples/miRNAs/Known_miRNAs/results///cutadapt_results/SRR873382_cut.fastq 2>> Examples/basic_examples/miRNAs/Known_miRNAs/results//miARma_stat.2498.log FASTQC :: [Sun Jul 8 19:01:38 2018] Checking Examples/basic_examples/miRNAs/Known_miRNAs/results/ for FastQC analysis FASTQC :: [Sun Jul 8 19:01:38 2018] Executing mkdir -p Examples/basic_examples/miRNAs/Known_miRNAs/results//Pre_fastqc_results/ ; fastqc -f fastq -t 4 Examples/basic_examples/miRNAs/reads//SRR873382.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873383.fq.gz Examples/basic_examples/miRNAs/reads//SRR873384.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873385.fq.gz Examples/basic_examples/miRNAs/reads//SRR873386.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873387.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873388.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873389.fastq.gz -o Examples/basic_examples/miRNAs/Known_miRNAs/results//Pre_fastqc_results/ >> Examples/basic_examples/miRNAs/Known_miRNAs/results//miARma_logfile.2498.log 2>&1 Started analysis of SRR873382.fastq.gz Approx 5% complete for SRR873382.fastq.gz Approx 10% complete for SRR873382.fastq.gz Approx 15% complete for SRR873382.fastq.gz Approx 20% complete for SRR873382.fastq.gz Started analysis of SRR873383.fq.gz Approx 25% complete for SRR873382.fastq.gz Approx 5% complete for SRR873383.fq.gz Approx 30% complete for SRR873382.fastq.gz Approx 10% complete for SRR873383.fq.gz Approx 35% complete for SRR873382.fastq.gz Approx 15% complete for SRR873383.fq.gz Approx 40% complete for SRR873382.fastq.gz Approx 20% complete for SRR873383.fq.gz Started analysis of SRR873384.fastq.gz Approx 45% complete for SRR873382.fastq.gz Approx 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complete for SRR873389.fastq.gz Approx 90% complete for SRR873386.fastq.gz Approx 30% complete for SRR873389.fastq.gz Approx 70% complete for SRR873387.fastq.gz Approx 50% complete for SRR873388.fastq.gz Approx 95% complete for SRR873386.fastq.gz Approx 35% complete for SRR873389.fastq.gz Approx 75% complete for SRR873387.fastq.gz Approx 55% complete for SRR873388.fastq.gz Approx 100% complete for SRR873386.fastq.gz Analysis complete for SRR873386.fastq.gz Approx 40% complete for SRR873389.fastq.gz Approx 80% complete for SRR873387.fastq.gz Approx 60% complete for SRR873388.fastq.gz Approx 45% complete for SRR873389.fastq.gz Approx 85% complete for SRR873387.fastq.gz Approx 65% complete for SRR873388.fastq.gz Approx 50% complete for SRR873389.fastq.gz Approx 90% complete for SRR873387.fastq.gz Approx 70% complete for SRR873388.fastq.gz Approx 55% complete for SRR873389.fastq.gz Approx 95% complete for SRR873387.fastq.gz Approx 75% complete for SRR873388.fastq.gz Approx 60% complete for SRR873389.fastq.gz Approx 100% complete for SRR873387.fastq.gz Analysis complete for SRR873387.fastq.gz Approx 80% complete for SRR873388.fastq.gz Approx 65% complete for SRR873389.fastq.gz Approx 85% complete for SRR873388.fastq.gz Approx 70% complete for SRR873389.fastq.gz Approx 75% complete for SRR873389.fastq.gz Approx 90% complete for SRR873388.fastq.gz Approx 80% complete for SRR873389.fastq.gz Approx 95% complete for SRR873388.fastq.gz Approx 100% complete for SRR873388.fastq.gz Approx 85% complete for SRR873389.fastq.gz Analysis complete for SRR873388.fastq.gz Approx 90% complete for SRR873389.fastq.gz Approx 95% complete for SRR873389.fastq.gz Approx 100% complete for SRR873389.fastq.gz Analysis complete for SRR873389.fastq.gz BOWTIE 1 :: [Sun Jul 8 19:01:51 2018] Executing mkdir -p Examples/basic_examples/miRNAs/Known_miRNAs/results//Bowtie1_results/ ;bowtie --sam -p 4 Genomes/Indexes/bowtie1/human/bw1_homo_sapiens19 Examples/basic_examples/miRNAs/Known_miRNAs/results//cutadapt_results/SRR873382_cut.fastq Examples/basic_examples/miRNAs/Known_miRNAs/results//Bowtie1_results/SRR873382_cut_nat_bw1.bam 2>> Examples/basic_examples/miRNAs/Known_miRNAs/results//miARma_stat.2498.log File:Examples/basic_examples/miRNAs/Known_miRNAs/results//cutadapt_results/SRR873382_cut.fastq SEQCOUNT :: [Sun Jul 8 19:03:10 2018] Reading counts from Examples/basic_examples/miRNAs/Known_miRNAs/results//Bowtie1_results/SRR873382_cut_nat_bw1.bam SEQCOUNT :: [Sun Jul 8 19:03:10 2018] Executing mkdir -p Examples/basic_examples/miRNAs/Known_miRNAs/results//nat_bw1_readcount_results/ ;featureCounts -s 1 -t miRNA -g transcript_id -T 4 -a Examples/basic_examples/miRNAs/data/miRBase_Annotation_20_for_hsa_mature_miRNA.gtf -o Examples/basic_examples/miRNAs/Known_miRNAs/results//nat_bw1_readcount_results/SRR873382_cut_nat_bw1.tab Examples/basic_examples/miRNAs/Known_miRNAs/results//Bowtie1_results/SRR873382_cut_nat_bw1.bam 2>> Examples/basic_examples/miRNAs/Known_miRNAs/results//miARma_logfile.2498.log ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.5.0-p1 //========================== featureCounts setting ===========================\\ || || || Input files : 1 SAM file || || S Examples/basic_examples/miRNAs/Known_miRNA ... || || || || Output file : Examples/basic_examples/miRNAs/Known_miRNAs/ ... || || Annotations : Examples/basic_examples/miRNAs/data/miRBase_ ... || || || || Threads : 4 || || Level : meta-feature level || || Paired-end : no || || Strand specific : yes || || Multimapping reads : not counted || || Multi-overlapping reads : not counted || || Read orientations : fr || || || \\===================== http://subread.sourceforge.net/ ======================// //================================= Running ==================================\\ || || || Load annotation file Examples/basic_examples/miRNAs/data/miRBase_Annot ... || || Features : 2794 || || Meta-features : 2576 || || Chromosomes/contigs : 24 || || || || Process SAM file Examples/basic_examples/miRNAs/Known_miRNAs/results// ... || || Single-end reads are included. || || Assign reads to features... || || Total reads : 0 || || Successfully assigned reads : 0 || || Running time : 0.00 minutes || || || || Read assignment finished. || || || \\===================== http://subread.sourceforge.net/ ======================// SEQCOUNT :: [Sun Jul 8 19:03:10 2018] Please check the folder: Examples/basic_examples/miRNAs/Known_miRNAs/results//Readcount_results/. QC_EdgeR :: [Sun Jul 8 19:03:11 2018] Executing source("./lib/CbBio/RNASeq/R-Scripts/QC_EdgeR.R") setwd("/home/leila/apps/miARma/cbbio-miarma-42e187a7f514/Examples/basic_examples/miRNAs/Known_miRNAs/results/Readcount_results") resultsfiles<-QC_EdgeR(projectdir="/home/leila/apps/miARma/cbbio-miarma-42e187a7f514/Examples/basic_examples/miRNAs/Known_miRNAs/results",dir="/home/leila/apps/miARma/cbbio-miarma-42e187a7f514/Examples/basic_examples/miRNAs/Known_miRNAs/results/Readcount_results", file="nat_bw1-ReadCount.tab", targetfile="/home/leila/apps/miARma/cbbio-miarma-42e187a7f514/Examples/basic_examples/miRNAs/data/targets.txt", label="Hypoxia_nat_bw1", filter="yes") FASTQC :: [Sun Jul 8 20:04:42 2018] Checking Examples/basic_examples/miRNAs/Known_miRNAs/results/ for FastQC analysis FASTQC :: [Sun Jul 8 20:04:42 2018] Executing mkdir -p Examples/basic_examples/miRNAs/Known_miRNAs/results//Pre_fastqc_results/ ; fastqc -f fastq -t 4 Examples/basic_examples/miRNAs/reads//SRR873382.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873383.fq.gz Examples/basic_examples/miRNAs/reads//SRR873384.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873385.fq.gz Examples/basic_examples/miRNAs/reads//SRR873386.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873387.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873388.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873389.fastq.gz -o Examples/basic_examples/miRNAs/Known_miRNAs/results//Pre_fastqc_results/ >> Examples/basic_examples/miRNAs/Known_miRNAs/results//miARma_logfile.2498.log 2>&1 Started analysis of SRR873382.fastq.gz Approx 5% complete for SRR873382.fastq.gz Approx 10% complete for SRR873382.fastq.gz Approx 15% complete for SRR873382.fastq.gz Started analysis of SRR873383.fq.gz Approx 20% complete for SRR873382.fastq.gz Approx 5% complete for SRR873383.fq.gz Approx 25% complete for SRR873382.fastq.gz Approx 10% complete for SRR873383.fq.gz Approx 30% complete for SRR873382.fastq.gz Approx 15% complete for SRR873383.fq.gz Approx 35% complete for SRR873382.fastq.gz Approx 20% complete for SRR873383.fq.gz Approx 40% complete for SRR873382.fastq.gz Started analysis of SRR873384.fastq.gz Approx 25% complete for SRR873383.fq.gz Approx 45% complete for SRR873382.fastq.gz Approx 5% complete for SRR873384.fastq.gz Approx 30% complete for SRR873383.fq.gz Approx 50% complete for SRR873382.fastq.gz Approx 10% complete for SRR873384.fastq.gz Approx 35% complete for SRR873383.fq.gz Approx 55% complete for SRR873382.fastq.gz Approx 15% complete for SRR873384.fastq.gz Approx 40% complete for SRR873383.fq.gz Approx 60% complete for SRR873382.fastq.gz Approx 20% complete for SRR873384.fastq.gz Started analysis of SRR873385.fq.gz Approx 45% complete for SRR873383.fq.gz Approx 25% complete for SRR873384.fastq.gz Approx 65% complete for SRR873382.fastq.gz Approx 5% complete for SRR873385.fq.gz Approx 50% complete for SRR873383.fq.gz Approx 70% complete for SRR873382.fastq.gz Approx 30% complete for 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SRR873389.fastq.gz BOWTIE 1 :: [Sun Jul 8 20:04:54 2018] Executing mkdir -p Examples/basic_examples/miRNAs/Known_miRNAs/results//Bowtie1_results/ ;bowtie --sam -p 4 Genomes/Indexes/bowtie1/human/bw1_homo_sapiens19 Examples/basic_examples/miRNAs/Known_miRNAs/results//cutadapt_results/SRR873382_cut.fastq Examples/basic_examples/miRNAs/Known_miRNAs/results//Bowtie1_results/SRR873382_cut_nat_bw1.bam 2>> Examples/basic_examples/miRNAs/Known_miRNAs/results//miARma_stat.2498.log File:Examples/basic_examples/miRNAs/Known_miRNAs/results//cutadapt_results/SRR873382_cut.fastq SEQCOUNT :: [Sun Jul 8 20:05:21 2018] Reading counts from Examples/basic_examples/miRNAs/Known_miRNAs/results//Bowtie1_results/SRR873382_cut_nat_bw1.bam SEQCOUNT :: [Sun Jul 8 20:05:21 2018] Executing mkdir -p Examples/basic_examples/miRNAs/Known_miRNAs/results//nat_bw1_readcount_results/ ;featureCounts -s 1 -t miRNA -g transcript_id -T 4 -a Examples/basic_examples/miRNAs/data/miRBase_Annotation_20_for_hsa_mature_miRNA.gtf -o Examples/basic_examples/miRNAs/Known_miRNAs/results//nat_bw1_readcount_results/SRR873382_cut_nat_bw1.tab Examples/basic_examples/miRNAs/Known_miRNAs/results//Bowtie1_results/SRR873382_cut_nat_bw1.bam 2>> Examples/basic_examples/miRNAs/Known_miRNAs/results//miARma_logfile.2498.log ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.5.0-p1 //========================== featureCounts setting ===========================\\ || || || Input files : 1 SAM file || || S Examples/basic_examples/miRNAs/Known_miRNA ... || || || || Output file : Examples/basic_examples/miRNAs/Known_miRNAs/ ... || || Annotations : Examples/basic_examples/miRNAs/data/miRBase_ ... || || || || Threads : 4 || || Level : meta-feature level || || Paired-end : no || || Strand specific : yes || || Multimapping reads : not counted || || Multi-overlapping reads : not counted || || Read orientations : fr || || || \\===================== http://subread.sourceforge.net/ ======================// //================================= Running ==================================\\ || || || Load annotation file Examples/basic_examples/miRNAs/data/miRBase_Annot ... || || Features : 2794 || || Meta-features : 2576 || || Chromosomes/contigs : 24 || || || || Process SAM file Examples/basic_examples/miRNAs/Known_miRNAs/results// ... || || Single-end reads are included. || || Assign reads to features... || || Total reads : 0 || || Successfully assigned reads : 0 || || Running time : 0.00 minutes || || || || Read assignment finished. || || || \\===================== http://subread.sourceforge.net/ ======================// SEQCOUNT :: [Sun Jul 8 20:05:21 2018] Please check the folder: Examples/basic_examples/miRNAs/Known_miRNAs/results//Readcount_results/. QC_EdgeR :: [Sun Jul 8 20:05:22 2018] Executing source("./lib/CbBio/RNASeq/R-Scripts/QC_EdgeR.R") setwd("/home/leila/apps/miARma/cbbio-miarma-42e187a7f514/Examples/basic_examples/miRNAs/Known_miRNAs/results/Readcount_results") resultsfiles<-QC_EdgeR(projectdir="/home/leila/apps/miARma/cbbio-miarma-42e187a7f514/Examples/basic_examples/miRNAs/Known_miRNAs/results",dir="/home/leila/apps/miARma/cbbio-miarma-42e187a7f514/Examples/basic_examples/miRNAs/Known_miRNAs/results/Readcount_results", file="nat_bw1-ReadCount.tab", targetfile="/home/leila/apps/miARma/cbbio-miarma-42e187a7f514/Examples/basic_examples/miRNAs/data/targets.txt", label="Hypoxia_nat_bw1", filter="yes") FASTQC :: [Sun Jul 8 20:58:12 2018] Checking Examples/basic_examples/miRNAs/Known_miRNAs/results/ for FastQC analysis FASTQC :: [Sun Jul 8 20:58:12 2018] Executing mkdir -p Examples/basic_examples/miRNAs/Known_miRNAs/results//Pre_fastqc_results/ ; fastqc -f fastq -t 4 Examples/basic_examples/miRNAs/reads//SRR873382.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873383.fq.gz Examples/basic_examples/miRNAs/reads//SRR873384.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873385.fq.gz Examples/basic_examples/miRNAs/reads//SRR873386.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873387.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873388.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873389.fastq.gz -o Examples/basic_examples/miRNAs/Known_miRNAs/results//Pre_fastqc_results/ >> Examples/basic_examples/miRNAs/Known_miRNAs/results//miARma_logfile.2498.log 2>&1 Started analysis of SRR873382.fastq.gz Approx 5% complete for SRR873382.fastq.gz Approx 10% complete for SRR873382.fastq.gz Approx 15% complete for SRR873382.fastq.gz Approx 20% complete for SRR873382.fastq.gz Started analysis of SRR873383.fq.gz Approx 25% complete for SRR873382.fastq.gz Approx 5% complete for SRR873383.fq.gz Approx 30% complete for SRR873382.fastq.gz Approx 10% complete for SRR873383.fq.gz Approx 35% complete for SRR873382.fastq.gz Approx 15% complete for SRR873383.fq.gz Approx 40% complete for SRR873382.fastq.gz Approx 20% complete for SRR873383.fq.gz Started analysis of SRR873384.fastq.gz Approx 45% complete for SRR873382.fastq.gz Approx 5% complete for SRR873384.fastq.gz Approx 25% complete for SRR873383.fq.gz Approx 50% complete for SRR873382.fastq.gz Approx 10% complete for SRR873384.fastq.gz Approx 30% complete for SRR873383.fq.gz Approx 55% complete for SRR873382.fastq.gz Approx 15% complete for SRR873384.fastq.gz Approx 35% complete for SRR873383.fq.gz Approx 60% complete for SRR873382.fastq.gz Approx 40% complete for SRR873383.fq.gz Approx 20% complete for SRR873384.fastq.gz Started analysis of SRR873385.fq.gz Approx 65% complete for SRR873382.fastq.gz Approx 45% complete for SRR873383.fq.gz Approx 25% complete for SRR873384.fastq.gz Approx 5% complete for SRR873385.fq.gz Approx 70% complete for SRR873382.fastq.gz Approx 50% complete for SRR873383.fq.gz Approx 30% complete for 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SRR873384.fastq.gz Approx 85% complete for SRR873385.fq.gz Approx 90% complete for SRR873385.fq.gz Approx 95% complete for SRR873385.fq.gz Approx 100% complete for SRR873385.fq.gz Analysis complete for SRR873385.fq.gz Started analysis of SRR873386.fastq.gz Approx 5% complete for SRR873386.fastq.gz Approx 10% complete for SRR873386.fastq.gz Approx 15% complete for SRR873386.fastq.gz Approx 20% complete for SRR873386.fastq.gz Approx 25% complete for SRR873386.fastq.gz Started analysis of SRR873387.fastq.gz Approx 30% complete for SRR873386.fastq.gz Approx 5% complete for SRR873387.fastq.gz Approx 35% complete for SRR873386.fastq.gz Approx 10% complete for SRR873387.fastq.gz Approx 40% complete for SRR873386.fastq.gz Approx 15% complete for SRR873387.fastq.gz Approx 45% complete for SRR873386.fastq.gz Approx 20% complete for SRR873387.fastq.gz Approx 50% complete for SRR873386.fastq.gz Approx 25% complete for SRR873387.fastq.gz Approx 55% complete for SRR873386.fastq.gz Approx 30% complete for SRR873387.fastq.gz Started analysis of SRR873388.fastq.gz Approx 60% complete for SRR873386.fastq.gz Approx 35% complete for SRR873387.fastq.gz Approx 5% complete for SRR873388.fastq.gz Approx 40% complete for SRR873387.fastq.gz Approx 65% complete for SRR873386.fastq.gz Approx 10% complete for SRR873388.fastq.gz Approx 15% complete for SRR873388.fastq.gz Approx 45% complete for SRR873387.fastq.gz Approx 70% complete for SRR873386.fastq.gz Approx 50% complete for SRR873387.fastq.gz Approx 20% complete for SRR873388.fastq.gz Approx 75% complete for SRR873386.fastq.gz Approx 55% complete for SRR873387.fastq.gz Started analysis of SRR873389.fastq.gz Approx 25% complete for SRR873388.fastq.gz Approx 80% complete for SRR873386.fastq.gz Approx 60% complete for SRR873387.fastq.gz Approx 5% complete for SRR873389.fastq.gz Approx 30% complete for SRR873388.fastq.gz Approx 85% complete for SRR873386.fastq.gz Approx 65% complete for SRR873387.fastq.gz Approx 10% complete for 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SRR873389.fastq.gz BOWTIE 1 :: [Sun Jul 8 20:58:28 2018] Executing mkdir -p Examples/basic_examples/miRNAs/Known_miRNAs/results//Bowtie1_results/ ;bowtie --sam -p 4 Genomes/Indexes/bowtie1/human/bw1_homo_sapiens19 Examples/basic_examples/miRNAs/Known_miRNAs/results//cutadapt_results/SRR873382_cut.fastq Examples/basic_examples/miRNAs/Known_miRNAs/results//Bowtie1_results/SRR873382_cut_nat_bw1.bam 2>> Examples/basic_examples/miRNAs/Known_miRNAs/results//miARma_stat.2498.log File:Examples/basic_examples/miRNAs/Known_miRNAs/results//cutadapt_results/SRR873382_cut.fastq SEQCOUNT :: [Sun Jul 8 20:58:29 2018] Reading counts from Examples/basic_examples/miRNAs/Known_miRNAs/results//Bowtie1_results/SRR873382_cut_nat_bw1.bam SEQCOUNT :: [Sun Jul 8 20:58:29 2018] Executing mkdir -p Examples/basic_examples/miRNAs/Known_miRNAs/results//nat_bw1_readcount_results/ ;featureCounts -s 1 -t miRNA -g transcript_id -T 4 -a Examples/basic_examples/miRNAs/data/miRBase_Annotation_20_for_hsa_mature_miRNA.gtf -o Examples/basic_examples/miRNAs/Known_miRNAs/results//nat_bw1_readcount_results/SRR873382_cut_nat_bw1.tab Examples/basic_examples/miRNAs/Known_miRNAs/results//Bowtie1_results/SRR873382_cut_nat_bw1.bam 2>> Examples/basic_examples/miRNAs/Known_miRNAs/results//miARma_logfile.2498.log ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.5.0-p1 //========================== featureCounts setting ===========================\\ || || || Input files : 1 SAM file || || S Examples/basic_examples/miRNAs/Known_miRNA ... || || || || Output file : Examples/basic_examples/miRNAs/Known_miRNAs/ ... || || Annotations : Examples/basic_examples/miRNAs/data/miRBase_ ... || || || || Threads : 4 || || Level : meta-feature level || || Paired-end : no || || Strand specific : yes || || Multimapping reads : not counted || || Multi-overlapping reads : not counted || || Read orientations : fr || || || \\===================== http://subread.sourceforge.net/ ======================// //================================= Running ==================================\\ || || || Load annotation file Examples/basic_examples/miRNAs/data/miRBase_Annot ... || || Features : 2794 || || Meta-features : 2576 || || Chromosomes/contigs : 24 || || || || Process SAM file Examples/basic_examples/miRNAs/Known_miRNAs/results// ... || || Single-end reads are included. || || Assign reads to features... || || Total reads : 0 || || Successfully assigned reads : 0 || || Running time : 0.00 minutes || || || || Read assignment finished. || || || \\===================== http://subread.sourceforge.net/ ======================// SEQCOUNT :: [Sun Jul 8 20:58:29 2018] Please check the folder: Examples/basic_examples/miRNAs/Known_miRNAs/results//Readcount_results/. QC_EdgeR :: [Sun Jul 8 20:58:29 2018] Executing source("./lib/CbBio/RNASeq/R-Scripts/QC_EdgeR.R") setwd("/home/leila/apps/miARma/cbbio-miarma-42e187a7f514/Examples/basic_examples/miRNAs/Known_miRNAs/results/Readcount_results") resultsfiles<-QC_EdgeR(projectdir="/home/leila/apps/miARma/cbbio-miarma-42e187a7f514/Examples/basic_examples/miRNAs/Known_miRNAs/results",dir="/home/leila/apps/miARma/cbbio-miarma-42e187a7f514/Examples/basic_examples/miRNAs/Known_miRNAs/results/Readcount_results", file="nat_bw1-ReadCount.tab", targetfile="/home/leila/apps/miARma/cbbio-miarma-42e187a7f514/Examples/basic_examples/miRNAs/data/targets.txt", label="Hypoxia_nat_bw1", filter="yes") FASTQC :: [Sun Jul 8 21:10:28 2018] Checking Examples/basic_examples/miRNAs/Known_miRNAs/results/ for FastQC analysis FASTQC :: [Sun Jul 8 21:10:28 2018] Executing mkdir -p Examples/basic_examples/miRNAs/Known_miRNAs/results//Pre_fastqc_results/ ; fastqc -f fastq -t 4 Examples/basic_examples/miRNAs/reads//SRR873382.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873383.fq.gz Examples/basic_examples/miRNAs/reads//SRR873384.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873385.fq.gz Examples/basic_examples/miRNAs/reads//SRR873386.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873387.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873388.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873389.fastq.gz -o Examples/basic_examples/miRNAs/Known_miRNAs/results//Pre_fastqc_results/ >> Examples/basic_examples/miRNAs/Known_miRNAs/results//miARma_logfile.2498.log 2>&1 Started analysis of SRR873382.fastq.gz Approx 5% complete for SRR873382.fastq.gz Approx 10% complete for SRR873382.fastq.gz Approx 15% complete for SRR873382.fastq.gz Started analysis of SRR873383.fq.gz Approx 20% complete for SRR873382.fastq.gz Approx 5% complete for SRR873383.fq.gz Approx 25% complete for SRR873382.fastq.gz Approx 10% complete for SRR873383.fq.gz Approx 30% complete for SRR873382.fastq.gz Approx 15% complete for SRR873383.fq.gz Approx 35% complete for SRR873382.fastq.gz Approx 20% complete for SRR873383.fq.gz Started analysis of SRR873384.fastq.gz Approx 40% complete for SRR873382.fastq.gz Approx 25% complete for SRR873383.fq.gz Approx 5% complete for SRR873384.fastq.gz Approx 45% complete for SRR873382.fastq.gz Approx 30% complete for SRR873383.fq.gz Approx 10% complete for SRR873384.fastq.gz Approx 50% complete for SRR873382.fastq.gz Approx 35% complete for SRR873383.fq.gz Approx 15% complete for SRR873384.fastq.gz Approx 40% complete for SRR873383.fq.gz Approx 55% complete for SRR873382.fastq.gz Approx 45% complete for SRR873383.fq.gz Approx 20% complete for SRR873384.fastq.gz Approx 60% complete for SRR873382.fastq.gz Started analysis of SRR873385.fq.gz Approx 50% complete for SRR873383.fq.gz Approx 25% complete for SRR873384.fastq.gz Approx 5% complete for SRR873385.fq.gz Approx 65% complete for SRR873382.fastq.gz Approx 55% complete for SRR873383.fq.gz Approx 30% complete for 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SRR873388.fastq.gz Approx 30% complete for SRR873387.fastq.gz Approx 55% complete for SRR873386.fastq.gz Approx 10% complete for SRR873388.fastq.gz Approx 35% complete for SRR873387.fastq.gz Approx 15% complete for SRR873388.fastq.gz Approx 60% complete for SRR873386.fastq.gz Approx 40% complete for SRR873387.fastq.gz Approx 20% complete for SRR873388.fastq.gz Approx 65% complete for SRR873386.fastq.gz Approx 45% complete for SRR873387.fastq.gz Started analysis of SRR873389.fastq.gz Approx 25% complete for SRR873388.fastq.gz Approx 70% complete for SRR873386.fastq.gz Approx 50% complete for SRR873387.fastq.gz Approx 5% complete for SRR873389.fastq.gz Approx 30% complete for SRR873388.fastq.gz Approx 75% complete for SRR873386.fastq.gz Approx 55% complete for SRR873387.fastq.gz Approx 10% complete for SRR873389.fastq.gz Approx 35% complete for SRR873388.fastq.gz Approx 80% complete for SRR873386.fastq.gz Approx 15% complete for SRR873389.fastq.gz Approx 60% complete for 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SRR873389.fastq.gz Approx 90% complete for SRR873387.fastq.gz Approx 75% complete for SRR873388.fastq.gz Approx 50% complete for SRR873389.fastq.gz Approx 95% complete for SRR873387.fastq.gz Approx 80% complete for SRR873388.fastq.gz Approx 55% complete for SRR873389.fastq.gz Approx 100% complete for SRR873387.fastq.gz Analysis complete for SRR873387.fastq.gz Approx 85% complete for SRR873388.fastq.gz Approx 60% complete for SRR873389.fastq.gz Approx 90% complete for SRR873388.fastq.gz Approx 65% complete for SRR873389.fastq.gz Approx 95% complete for SRR873388.fastq.gz Approx 70% complete for SRR873389.fastq.gz Approx 100% complete for SRR873388.fastq.gz Analysis complete for SRR873388.fastq.gz Approx 75% complete for SRR873389.fastq.gz Approx 80% complete for SRR873389.fastq.gz Approx 85% complete for SRR873389.fastq.gz Approx 90% complete for SRR873389.fastq.gz Approx 95% complete for SRR873389.fastq.gz Approx 100% complete for SRR873389.fastq.gz Analysis complete for SRR873389.fastq.gz BOWTIE 1 :: [Sun Jul 8 21:10:40 2018] Executing mkdir -p Examples/basic_examples/miRNAs/Known_miRNAs/results//Bowtie1_results/ ;bowtie --sam -p 4 Genomes/Indexes/bowtie1/human/bw1_homo_sapiens19 Examples/basic_examples/miRNAs/Known_miRNAs/results//cutadapt_results/SRR873382_cut.fastq Examples/basic_examples/miRNAs/Known_miRNAs/results//Bowtie1_results/SRR873382_cut_nat_bw1.bam 2>> Examples/basic_examples/miRNAs/Known_miRNAs/results//miARma_stat.2498.log File:Examples/basic_examples/miRNAs/Known_miRNAs/results//cutadapt_results/SRR873382_cut.fastq SEQCOUNT :: [Sun Jul 8 21:10:48 2018] Reading counts from Examples/basic_examples/miRNAs/Known_miRNAs/results//Bowtie1_results/SRR873382_cut_nat_bw1.bam SEQCOUNT :: [Sun Jul 8 21:10:48 2018] Executing mkdir -p Examples/basic_examples/miRNAs/Known_miRNAs/results//nat_bw1_readcount_results/ ;featureCounts -s 1 -t miRNA -g transcript_id -T 4 -a Examples/basic_examples/miRNAs/data/miRBase_Annotation_20_for_hsa_mature_miRNA.gtf -o Examples/basic_examples/miRNAs/Known_miRNAs/results//nat_bw1_readcount_results/SRR873382_cut_nat_bw1.tab Examples/basic_examples/miRNAs/Known_miRNAs/results//Bowtie1_results/SRR873382_cut_nat_bw1.bam 2>> Examples/basic_examples/miRNAs/Known_miRNAs/results//miARma_logfile.2498.log ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.5.0-p1 //========================== featureCounts setting ===========================\\ || || || Input files : 1 SAM file || || S Examples/basic_examples/miRNAs/Known_miRNA ... || || || || Output file : Examples/basic_examples/miRNAs/Known_miRNAs/ ... || || Annotations : Examples/basic_examples/miRNAs/data/miRBase_ ... || || || || Threads : 4 || || Level : meta-feature level || || Paired-end : no || || Strand specific : yes || || Multimapping reads : not counted || || Multi-overlapping reads : not counted || || Read orientations : fr || || || \\===================== http://subread.sourceforge.net/ ======================// //================================= Running ==================================\\ || || || Load annotation file Examples/basic_examples/miRNAs/data/miRBase_Annot ... || || Features : 2794 || || Meta-features : 2576 || || Chromosomes/contigs : 24 || || || || Process SAM file Examples/basic_examples/miRNAs/Known_miRNAs/results// ... || || Single-end reads are included. || || Assign reads to features... || || Total reads : 0 || || Successfully assigned reads : 0 || || Running time : 0.00 minutes || || || || Read assignment finished. || || || \\===================== http://subread.sourceforge.net/ ======================// SEQCOUNT :: [Sun Jul 8 21:10:48 2018] Please check the folder: Examples/basic_examples/miRNAs/Known_miRNAs/results//Readcount_results/. QC_EdgeR :: [Sun Jul 8 21:10:48 2018] Executing source("./lib/CbBio/RNASeq/R-Scripts/QC_EdgeR.R") setwd("/home/leila/apps/miARma/cbbio-miarma-42e187a7f514/Examples/basic_examples/miRNAs/Known_miRNAs/results/Readcount_results") resultsfiles<-QC_EdgeR(projectdir="/home/leila/apps/miARma/cbbio-miarma-42e187a7f514/Examples/basic_examples/miRNAs/Known_miRNAs/results",dir="/home/leila/apps/miARma/cbbio-miarma-42e187a7f514/Examples/basic_examples/miRNAs/Known_miRNAs/results/Readcount_results", file="nat_bw1-ReadCount.tab", targetfile="/home/leila/apps/miARma/cbbio-miarma-42e187a7f514/Examples/basic_examples/miRNAs/data/targets.txt", label="Hypoxia_nat_bw1", filter="yes") FASTQC :: [Sun Jul 8 21:43:12 2018] Checking Examples/basic_examples/miRNAs/Known_miRNAs/results/ for FastQC analysis FASTQC :: [Sun Jul 8 21:43:12 2018] Executing mkdir -p Examples/basic_examples/miRNAs/Known_miRNAs/results//Pre_fastqc_results/ ; fastqc -f fastq -t 4 Examples/basic_examples/miRNAs/reads//SRR873382.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873383.fq.gz Examples/basic_examples/miRNAs/reads//SRR873384.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873385.fq.gz Examples/basic_examples/miRNAs/reads//SRR873386.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873387.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873388.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873389.fastq.gz -o Examples/basic_examples/miRNAs/Known_miRNAs/results//Pre_fastqc_results/ >> Examples/basic_examples/miRNAs/Known_miRNAs/results//miARma_logfile.2498.log 2>&1 Started analysis of SRR873382.fastq.gz Approx 5% complete for SRR873382.fastq.gz Started analysis of SRR873383.fq.gz Approx 10% complete for SRR873382.fastq.gz Approx 15% complete for SRR873382.fastq.gz Approx 5% complete for SRR873383.fq.gz Approx 20% complete for SRR873382.fastq.gz Approx 10% complete for SRR873383.fq.gz Approx 25% complete for SRR873382.fastq.gz Started analysis of SRR873384.fastq.gz Approx 15% complete for SRR873383.fq.gz 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SRR873388.fastq.gz Approx 50% complete for SRR873389.fastq.gz Approx 75% complete for SRR873388.fastq.gz Approx 95% complete for SRR873387.fastq.gz Approx 55% complete for SRR873389.fastq.gz Approx 80% complete for SRR873388.fastq.gz Approx 100% complete for SRR873387.fastq.gz Analysis complete for SRR873387.fastq.gz Approx 60% complete for SRR873389.fastq.gz Approx 85% complete for SRR873388.fastq.gz Approx 65% complete for SRR873389.fastq.gz Approx 90% complete for SRR873388.fastq.gz Approx 70% complete for SRR873389.fastq.gz Approx 95% complete for SRR873388.fastq.gz Approx 75% complete for SRR873389.fastq.gz Approx 100% complete for SRR873388.fastq.gz Analysis complete for SRR873388.fastq.gz Approx 80% complete for SRR873389.fastq.gz Approx 85% complete for SRR873389.fastq.gz Approx 90% complete for SRR873389.fastq.gz Approx 95% complete for SRR873389.fastq.gz Approx 100% complete for SRR873389.fastq.gz Analysis complete for SRR873389.fastq.gz BOWTIE 1 :: [Sun Jul 8 21:43:28 2018] Executing mkdir -p Examples/basic_examples/miRNAs/Known_miRNAs/results//Bowtie1_results/ ;bowtie --sam -p 4 Genomes/Indexes/bowtie1/human/bw1_homo_sapiens19 Examples/basic_examples/miRNAs/Known_miRNAs/results//cutadapt_results/SRR873382_cut.fastq Examples/basic_examples/miRNAs/Known_miRNAs/results//Bowtie1_results/SRR873382_cut_nat_bw1.bam 2>> Examples/basic_examples/miRNAs/Known_miRNAs/results//miARma_stat.2498.log File:Examples/basic_examples/miRNAs/Known_miRNAs/results//cutadapt_results/SRR873382_cut.fastq SEQCOUNT :: [Sun Jul 8 21:43:31 2018] Reading counts from Examples/basic_examples/miRNAs/Known_miRNAs/results//Bowtie1_results/SRR873382_cut_nat_bw1.bam SEQCOUNT :: [Sun Jul 8 21:43:31 2018] Executing mkdir -p Examples/basic_examples/miRNAs/Known_miRNAs/results//nat_bw1_readcount_results/ ;featureCounts -s 1 -t miRNA -g transcript_id -T 4 -a Examples/basic_examples/miRNAs/data/miRBase_Annotation_20_for_hsa_mature_miRNA.gtf -o Examples/basic_examples/miRNAs/Known_miRNAs/results//nat_bw1_readcount_results/SRR873382_cut_nat_bw1.tab Examples/basic_examples/miRNAs/Known_miRNAs/results//Bowtie1_results/SRR873382_cut_nat_bw1.bam 2>> Examples/basic_examples/miRNAs/Known_miRNAs/results//miARma_logfile.2498.log ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.5.0-p1 //========================== featureCounts setting ===========================\\ || || || Input files : 1 SAM file || || S Examples/basic_examples/miRNAs/Known_miRNA ... || || || || Output file : Examples/basic_examples/miRNAs/Known_miRNAs/ ... || || Annotations : Examples/basic_examples/miRNAs/data/miRBase_ ... || || || || Threads : 4 || || Level : meta-feature level || || Paired-end : no || || Strand specific : yes || || Multimapping reads : not counted || || Multi-overlapping reads : not counted || || Read orientations : fr || || || \\===================== http://subread.sourceforge.net/ ======================// //================================= Running ==================================\\ || || || Load annotation file Examples/basic_examples/miRNAs/data/miRBase_Annot ... || || Features : 2794 || || Meta-features : 2576 || || Chromosomes/contigs : 24 || || || || Process SAM file Examples/basic_examples/miRNAs/Known_miRNAs/results// ... || || Single-end reads are included. || || Assign reads to features... || || Total reads : 0 || || Successfully assigned reads : 0 || || Running time : 0.00 minutes || || || || Read assignment finished. || || || \\===================== http://subread.sourceforge.net/ ======================// SEQCOUNT :: [Sun Jul 8 21:43:31 2018] Please check the folder: Examples/basic_examples/miRNAs/Known_miRNAs/results//Readcount_results/. QC_EdgeR :: [Sun Jul 8 21:43:31 2018] Executing source("./lib/CbBio/RNASeq/R-Scripts/QC_EdgeR.R") setwd("/home/leila/apps/miARma/cbbio-miarma-42e187a7f514/Examples/basic_examples/miRNAs/Known_miRNAs/results/Readcount_results") resultsfiles<-QC_EdgeR(projectdir="/home/leila/apps/miARma/cbbio-miarma-42e187a7f514/Examples/basic_examples/miRNAs/Known_miRNAs/results",dir="/home/leila/apps/miARma/cbbio-miarma-42e187a7f514/Examples/basic_examples/miRNAs/Known_miRNAs/results/Readcount_results", file="nat_bw1-ReadCount.tab", targetfile="/home/leila/apps/miARma/cbbio-miarma-42e187a7f514/Examples/basic_examples/miRNAs/data/targets.txt", label="Hypoxia_nat_bw1", filter="yes") FASTQC :: [Sun Jul 8 21:59:46 2018] Checking Examples/basic_examples/miRNAs/Known_miRNAs/results/ for FastQC analysis FASTQC :: [Sun Jul 8 21:59:46 2018] Executing mkdir -p Examples/basic_examples/miRNAs/Known_miRNAs/results//Pre_fastqc_results/ ; fastqc -f fastq -t 4 Examples/basic_examples/miRNAs/reads//SRR873382.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873383.fq.gz Examples/basic_examples/miRNAs/reads//SRR873384.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873385.fq.gz Examples/basic_examples/miRNAs/reads//SRR873386.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873387.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873388.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873389.fastq.gz -o Examples/basic_examples/miRNAs/Known_miRNAs/results//Pre_fastqc_results/ >> Examples/basic_examples/miRNAs/Known_miRNAs/results//miARma_logfile.2498.log 2>&1 Started analysis of SRR873382.fastq.gz Approx 5% complete for SRR873382.fastq.gz Approx 10% complete for SRR873382.fastq.gz Started analysis of SRR873383.fq.gz Approx 15% complete for SRR873382.fastq.gz Approx 5% complete for SRR873383.fq.gz Approx 20% complete for SRR873382.fastq.gz Approx 10% complete for SRR873383.fq.gz Approx 25% complete for SRR873382.fastq.gz Approx 15% complete for SRR873383.fq.gz Approx 30% complete for SRR873382.fastq.gz Started analysis of SRR873384.fastq.gz Approx 35% complete for SRR873382.fastq.gz Approx 20% complete for SRR873383.fq.gz Approx 5% complete for SRR873384.fastq.gz Approx 40% complete for SRR873382.fastq.gz Approx 25% complete for SRR873383.fq.gz Approx 10% complete for SRR873384.fastq.gz Approx 45% complete for SRR873382.fastq.gz Approx 30% complete for SRR873383.fq.gz Approx 15% complete for SRR873384.fastq.gz Approx 50% complete for SRR873382.fastq.gz Started analysis of SRR873385.fq.gz Approx 35% complete for SRR873383.fq.gz Approx 20% complete for SRR873384.fastq.gz Approx 5% complete for SRR873385.fq.gz Approx 40% complete for SRR873383.fq.gz Approx 55% complete for SRR873382.fastq.gz Approx 25% complete for SRR873384.fastq.gz Approx 10% complete for SRR873385.fq.gz Approx 60% complete for SRR873382.fastq.gz Approx 45% complete for SRR873383.fq.gz Approx 15% complete for SRR873385.fq.gz Approx 30% complete for SRR873384.fastq.gz Approx 65% complete for 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SRR873382.fastq.gz Approx 50% complete for SRR873385.fq.gz Approx 80% complete for SRR873383.fq.gz Approx 65% complete for SRR873384.fastq.gz Approx 100% complete for SRR873382.fastq.gz Analysis complete for SRR873382.fastq.gz Approx 55% complete for SRR873385.fq.gz Approx 85% complete for SRR873383.fq.gz Approx 70% complete for SRR873384.fastq.gz Approx 60% complete for SRR873385.fq.gz Approx 75% complete for SRR873384.fastq.gz Approx 65% complete for SRR873385.fq.gz Approx 90% complete for SRR873383.fq.gz Approx 70% complete for SRR873385.fq.gz Approx 80% complete for SRR873384.fastq.gz Approx 75% complete for SRR873385.fq.gz Approx 95% complete for SRR873383.fq.gz Approx 80% complete for SRR873385.fq.gz Approx 85% complete for SRR873384.fastq.gz Approx 100% complete for SRR873383.fq.gz Analysis complete for SRR873383.fq.gz Approx 85% complete for SRR873385.fq.gz Approx 90% complete for SRR873384.fastq.gz Approx 90% complete for SRR873385.fq.gz Approx 95% complete for 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complete for SRR873386.fastq.gz Approx 15% complete for SRR873388.fastq.gz Approx 30% complete for SRR873387.fastq.gz Started analysis of SRR873389.fastq.gz Approx 50% complete for SRR873386.fastq.gz Approx 20% complete for SRR873388.fastq.gz Approx 35% complete for SRR873387.fastq.gz Approx 5% complete for SRR873389.fastq.gz Approx 55% complete for SRR873386.fastq.gz Approx 25% complete for SRR873388.fastq.gz Approx 40% complete for SRR873387.fastq.gz Approx 10% complete for SRR873389.fastq.gz Approx 30% complete for SRR873388.fastq.gz Approx 60% complete for SRR873386.fastq.gz Approx 45% complete for SRR873387.fastq.gz Approx 15% complete for SRR873389.fastq.gz Approx 35% complete for SRR873388.fastq.gz Approx 65% complete for SRR873386.fastq.gz Approx 50% complete for SRR873387.fastq.gz Approx 20% complete for SRR873389.fastq.gz Approx 70% complete for SRR873386.fastq.gz Approx 40% complete for SRR873388.fastq.gz Approx 55% complete for SRR873387.fastq.gz Approx 25% complete for SRR873389.fastq.gz Approx 75% complete for SRR873386.fastq.gz Approx 45% complete for SRR873388.fastq.gz Approx 60% complete for SRR873387.fastq.gz Approx 30% complete for SRR873389.fastq.gz Approx 80% complete for SRR873386.fastq.gz Approx 50% complete for SRR873388.fastq.gz Approx 65% complete for SRR873387.fastq.gz Approx 35% complete for SRR873389.fastq.gz Approx 85% complete for SRR873386.fastq.gz Approx 55% complete for SRR873388.fastq.gz Approx 40% complete for SRR873389.fastq.gz Approx 70% complete for SRR873387.fastq.gz Approx 90% complete for SRR873386.fastq.gz Approx 60% complete for SRR873388.fastq.gz Approx 45% complete for SRR873389.fastq.gz Approx 75% complete for SRR873387.fastq.gz Approx 95% complete for SRR873386.fastq.gz Approx 50% complete for SRR873389.fastq.gz Approx 65% complete for SRR873388.fastq.gz Approx 80% complete for SRR873387.fastq.gz Approx 100% complete for SRR873386.fastq.gz Analysis complete for SRR873386.fastq.gz Approx 55% complete for SRR873389.fastq.gz Approx 70% complete for SRR873388.fastq.gz Approx 60% complete for SRR873389.fastq.gz Approx 85% complete for SRR873387.fastq.gz Approx 75% complete for SRR873388.fastq.gz Approx 65% complete for SRR873389.fastq.gz Approx 90% complete for SRR873387.fastq.gz Approx 80% complete for SRR873388.fastq.gz Approx 70% complete for SRR873389.fastq.gz Approx 85% complete for SRR873388.fastq.gz Approx 95% complete for SRR873387.fastq.gz Approx 75% complete for SRR873389.fastq.gz Approx 90% complete for SRR873388.fastq.gz Approx 100% complete for SRR873387.fastq.gz Analysis complete for SRR873387.fastq.gz Approx 80% complete for SRR873389.fastq.gz Approx 95% complete for SRR873388.fastq.gz Approx 85% complete for SRR873389.fastq.gz Approx 100% complete for SRR873388.fastq.gz Analysis complete for SRR873388.fastq.gz Approx 90% complete for SRR873389.fastq.gz Approx 95% complete for SRR873389.fastq.gz Approx 100% complete for SRR873389.fastq.gz Analysis complete for SRR873389.fastq.gz CUTADAPT :: [Sun Jul 8 22:00:03 2018] Executing mkdir -p Examples/basic_examples/miRNAs/Known_miRNAs/results///cutadapt_results/ ; cut_adapt -b ATCTCGTATGCCGTCTTCTGCTTGAA -m 15 -M 35 -q 0 Examples/basic_examples/miRNAs/reads///SRR873382.fastq.gz > Examples/basic_examples/miRNAs/Known_miRNAs/results///cutadapt_results/SRR873382_cut.fastq 2>> Examples/basic_examples/miRNAs/Known_miRNAs/results//miARma_stat.2498.log FASTQC :: [Sun Jul 8 22:06:28 2018] Checking Examples/basic_examples/miRNAs/Known_miRNAs/results/ for FastQC analysis FASTQC :: [Sun Jul 8 22:06:28 2018] Executing mkdir -p Examples/basic_examples/miRNAs/Known_miRNAs/results//Pre_fastqc_results/ ; fastqc -f fastq -t 4 Examples/basic_examples/miRNAs/reads//SRR873382.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873383.fq.gz Examples/basic_examples/miRNAs/reads//SRR873384.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873385.fq.gz Examples/basic_examples/miRNAs/reads//SRR873386.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873387.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873388.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873389.fastq.gz -o Examples/basic_examples/miRNAs/Known_miRNAs/results//Pre_fastqc_results/ >> Examples/basic_examples/miRNAs/Known_miRNAs/results//miARma_logfile.2498.log 2>&1 Started analysis of SRR873382.fastq.gz Approx 5% complete for SRR873382.fastq.gz Approx 10% complete for SRR873382.fastq.gz Approx 15% complete for SRR873382.fastq.gz Approx 20% complete for SRR873382.fastq.gz Approx 25% complete for SRR873382.fastq.gz Started analysis of SRR873383.fq.gz Approx 5% complete for SRR873383.fq.gz Approx 30% complete for SRR873382.fastq.gz Approx 10% complete for SRR873383.fq.gz Approx 35% complete for SRR873382.fastq.gz Approx 15% complete for SRR873383.fq.gz Approx 40% complete for SRR873382.fastq.gz Approx 20% complete for SRR873383.fq.gz Approx 45% complete for SRR873382.fastq.gz Approx 25% complete for SRR873383.fq.gz Approx 50% complete for SRR873382.fastq.gz Started analysis of SRR873384.fastq.gz Approx 30% complete for SRR873383.fq.gz Approx 55% complete for SRR873382.fastq.gz Approx 5% complete for SRR873384.fastq.gz Approx 10% complete for SRR873384.fastq.gz Approx 35% complete for SRR873383.fq.gz Approx 60% complete for SRR873382.fastq.gz Approx 15% complete for SRR873384.fastq.gz Approx 40% complete for SRR873383.fq.gz Approx 65% complete for SRR873382.fastq.gz Approx 20% complete for SRR873384.fastq.gz Approx 45% complete for SRR873383.fq.gz Approx 70% complete for SRR873382.fastq.gz Approx 25% complete for SRR873384.fastq.gz Approx 30% complete for SRR873384.fastq.gz Approx 50% complete for SRR873383.fq.gz Approx 75% complete for SRR873382.fastq.gz Started analysis of SRR873385.fq.gz Approx 35% complete for SRR873384.fastq.gz Approx 5% complete for SRR873385.fq.gz Approx 55% complete for SRR873383.fq.gz Approx 80% complete for SRR873382.fastq.gz Approx 40% complete for SRR873384.fastq.gz Approx 10% complete for SRR873385.fq.gz Approx 60% complete for SRR873383.fq.gz Approx 85% complete for SRR873382.fastq.gz Approx 45% complete for SRR873384.fastq.gz Approx 15% complete for SRR873385.fq.gz Approx 90% complete for SRR873382.fastq.gz Approx 65% complete for SRR873383.fq.gz Approx 50% complete for SRR873384.fastq.gz Approx 95% complete for SRR873382.fastq.gz Approx 70% complete for SRR873383.fq.gz Approx 20% complete for SRR873385.fq.gz Approx 55% complete for SRR873384.fastq.gz Approx 75% complete for SRR873383.fq.gz Approx 100% complete for SRR873382.fastq.gz Approx 25% complete for SRR873385.fq.gz Analysis complete for SRR873382.fastq.gz Approx 60% complete for SRR873384.fastq.gz Approx 30% complete for SRR873385.fq.gz Approx 80% complete for SRR873383.fq.gz Approx 65% complete for SRR873384.fastq.gz Approx 35% complete for SRR873385.fq.gz Approx 85% complete for SRR873383.fq.gz Approx 70% complete for SRR873384.fastq.gz Approx 40% complete for SRR873385.fq.gz Approx 75% complete for SRR873384.fastq.gz Approx 90% complete for SRR873383.fq.gz Approx 45% complete for SRR873385.fq.gz Approx 80% complete for SRR873384.fastq.gz Approx 95% complete for SRR873383.fq.gz Approx 50% complete for SRR873385.fq.gz Approx 85% complete for SRR873384.fastq.gz Approx 55% complete for SRR873385.fq.gz Approx 100% complete for SRR873383.fq.gz Analysis complete for SRR873383.fq.gz Approx 90% complete for SRR873384.fastq.gz Approx 60% complete for SRR873385.fq.gz Approx 95% complete for SRR873384.fastq.gz Approx 65% complete for SRR873385.fq.gz Approx 100% complete for SRR873384.fastq.gz Approx 70% complete for SRR873385.fq.gz Analysis complete for SRR873384.fastq.gz Approx 75% complete for SRR873385.fq.gz Approx 80% complete for SRR873385.fq.gz Approx 85% complete for SRR873385.fq.gz Approx 90% complete for SRR873385.fq.gz Approx 95% complete for SRR873385.fq.gz Approx 100% complete for SRR873385.fq.gz Analysis complete for SRR873385.fq.gz Started analysis of SRR873386.fastq.gz Approx 5% complete for SRR873386.fastq.gz Approx 10% complete for SRR873386.fastq.gz Approx 15% complete for SRR873386.fastq.gz Approx 20% complete for SRR873386.fastq.gz Approx 25% complete for SRR873386.fastq.gz Approx 30% complete for SRR873386.fastq.gz Approx 35% complete for SRR873386.fastq.gz Started analysis of SRR873387.fastq.gz Approx 5% complete for SRR873387.fastq.gz Approx 40% complete for SRR873386.fastq.gz Approx 10% complete for SRR873387.fastq.gz Approx 45% complete for SRR873386.fastq.gz Approx 15% complete for SRR873387.fastq.gz Approx 50% complete for SRR873386.fastq.gz Approx 20% complete for SRR873387.fastq.gz Approx 55% complete for SRR873386.fastq.gz Approx 25% complete for SRR873387.fastq.gz Approx 60% complete for SRR873386.fastq.gz Approx 30% complete for SRR873387.fastq.gz Approx 65% complete for SRR873386.fastq.gz Started analysis of SRR873388.fastq.gz Approx 70% complete for SRR873386.fastq.gz Approx 35% complete for SRR873387.fastq.gz Approx 75% complete for SRR873386.fastq.gz Approx 5% complete for SRR873388.fastq.gz Approx 40% complete for SRR873387.fastq.gz Approx 80% complete for SRR873386.fastq.gz Approx 10% complete for SRR873388.fastq.gz Approx 45% complete for SRR873387.fastq.gz Approx 85% complete for SRR873386.fastq.gz Approx 15% complete for SRR873388.fastq.gz Approx 50% complete for SRR873387.fastq.gz Approx 20% complete for SRR873388.fastq.gz Approx 90% complete for SRR873386.fastq.gz Approx 55% complete for SRR873387.fastq.gz Started analysis of SRR873389.fastq.gz Approx 60% complete for SRR873387.fastq.gz Approx 95% complete for SRR873386.fastq.gz Approx 25% complete for SRR873388.fastq.gz Approx 5% complete for SRR873389.fastq.gz Approx 30% complete for SRR873388.fastq.gz Approx 65% complete for SRR873387.fastq.gz Approx 100% complete for SRR873386.fastq.gz Analysis complete for SRR873386.fastq.gz Approx 10% complete for SRR873389.fastq.gz Approx 35% complete for SRR873388.fastq.gz Approx 70% complete for SRR873387.fastq.gz Approx 15% complete for SRR873389.fastq.gz Approx 40% complete for SRR873388.fastq.gz Approx 75% complete for SRR873387.fastq.gz Approx 20% complete for SRR873389.fastq.gz Approx 45% complete for SRR873388.fastq.gz Approx 80% complete for SRR873387.fastq.gz Approx 25% complete for SRR873389.fastq.gz Approx 50% complete for SRR873388.fastq.gz Approx 85% complete for SRR873387.fastq.gz Approx 30% complete for SRR873389.fastq.gz Approx 55% complete for SRR873388.fastq.gz Approx 90% complete for SRR873387.fastq.gz Approx 35% complete for SRR873389.fastq.gz Approx 60% complete for SRR873388.fastq.gz Approx 95% complete for SRR873387.fastq.gz Approx 40% complete for SRR873389.fastq.gz Approx 100% complete for SRR873387.fastq.gz Approx 65% complete for SRR873388.fastq.gz Analysis complete for SRR873387.fastq.gz Approx 45% complete for SRR873389.fastq.gz Approx 70% complete for SRR873388.fastq.gz Approx 50% complete for SRR873389.fastq.gz Approx 75% complete for SRR873388.fastq.gz Approx 55% complete for SRR873389.fastq.gz Approx 80% complete for SRR873388.fastq.gz Approx 60% complete for SRR873389.fastq.gz Approx 85% complete for SRR873388.fastq.gz Approx 65% complete for SRR873389.fastq.gz Approx 90% complete for SRR873388.fastq.gz Approx 70% complete for SRR873389.fastq.gz Approx 95% complete for SRR873388.fastq.gz Approx 75% complete for SRR873389.fastq.gz Approx 100% complete for SRR873388.fastq.gz Analysis complete for SRR873388.fastq.gz Approx 80% complete for SRR873389.fastq.gz Approx 85% complete for SRR873389.fastq.gz Approx 90% complete for SRR873389.fastq.gz Approx 95% complete for SRR873389.fastq.gz Approx 100% complete for SRR873389.fastq.gz Analysis complete for SRR873389.fastq.gz CUTADAPT :: [Sun Jul 8 22:06:39 2018] Executing mkdir -p Examples/basic_examples/miRNAs/Known_miRNAs/results///cutadapt_results/ ; cut_adapt -b ATCTCGTATGCCGTCTTCTGCTTGAA -m 15 -M 35 -q 0 Examples/basic_examples/miRNAs/reads///SRR873382.fastq.gz > Examples/basic_examples/miRNAs/Known_miRNAs/results///cutadapt_results/SRR873382_cut.fastq 2>> Examples/basic_examples/miRNAs/Known_miRNAs/results//miARma_stat.2498.log FASTQC :: [Sun Jul 8 22:53:48 2018] Checking Examples/basic_examples/miRNAs/Known_miRNAs/results/ for FastQC analysis FASTQC :: [Sun Jul 8 22:53:48 2018] Executing mkdir -p Examples/basic_examples/miRNAs/Known_miRNAs/results//Pre_fastqc_results/ ; fastqc -f fastq -t 4 Examples/basic_examples/miRNAs/reads//SRR873382.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873383.fq.gz Examples/basic_examples/miRNAs/reads//SRR873384.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873385.fq.gz Examples/basic_examples/miRNAs/reads//SRR873386.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873387.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873388.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873389.fastq.gz -o Examples/basic_examples/miRNAs/Known_miRNAs/results//Pre_fastqc_results/ >> Examples/basic_examples/miRNAs/Known_miRNAs/results//miARma_logfile.2498.log 2>&1 Started analysis of SRR873382.fastq.gz Approx 5% complete for SRR873382.fastq.gz Approx 10% complete for SRR873382.fastq.gz Approx 15% complete for SRR873382.fastq.gz Approx 20% complete for SRR873382.fastq.gz Started analysis of SRR873383.fq.gz Approx 25% complete for SRR873382.fastq.gz Approx 5% complete for SRR873383.fq.gz Approx 30% complete for SRR873382.fastq.gz Approx 10% complete for SRR873383.fq.gz Approx 35% complete for SRR873382.fastq.gz Approx 15% complete for SRR873383.fq.gz Started analysis of SRR873384.fastq.gz Approx 40% complete for SRR873382.fastq.gz Approx 20% complete for SRR873383.fq.gz Approx 5% complete for SRR873384.fastq.gz Approx 45% complete for SRR873382.fastq.gz Approx 25% complete for SRR873383.fq.gz Approx 10% complete for SRR873384.fastq.gz Approx 50% complete for SRR873382.fastq.gz Approx 30% complete for SRR873383.fq.gz Approx 15% complete for SRR873384.fastq.gz Approx 55% complete for SRR873382.fastq.gz Approx 35% complete for SRR873383.fq.gz Approx 60% complete for SRR873382.fastq.gz Approx 20% complete for SRR873384.fastq.gz Approx 40% complete for SRR873383.fq.gz Started analysis of SRR873385.fq.gz Approx 65% complete for SRR873382.fastq.gz Approx 25% complete for SRR873384.fastq.gz Approx 5% complete for SRR873385.fq.gz Approx 45% complete for SRR873383.fq.gz Approx 70% complete for SRR873382.fastq.gz Approx 30% complete for SRR873384.fastq.gz Approx 10% complete for SRR873385.fq.gz Approx 75% complete for SRR873382.fastq.gz Approx 50% complete for SRR873383.fq.gz Approx 35% complete for SRR873384.fastq.gz Approx 15% complete for SRR873385.fq.gz Approx 80% complete for SRR873382.fastq.gz Approx 55% complete for SRR873383.fq.gz Approx 40% complete for SRR873384.fastq.gz Approx 20% complete for SRR873385.fq.gz Approx 85% complete for SRR873382.fastq.gz Approx 60% complete for SRR873383.fq.gz Approx 45% complete for SRR873384.fastq.gz Approx 25% complete for SRR873385.fq.gz Approx 90% complete for SRR873382.fastq.gz Approx 65% complete for SRR873383.fq.gz Approx 50% complete for SRR873384.fastq.gz Approx 30% complete for SRR873385.fq.gz Approx 95% complete for SRR873382.fastq.gz Approx 70% complete for SRR873383.fq.gz Approx 55% complete for SRR873384.fastq.gz Approx 35% complete for SRR873385.fq.gz Approx 100% complete for SRR873382.fastq.gz Analysis complete for SRR873382.fastq.gz Approx 75% complete for SRR873383.fq.gz Approx 60% complete for SRR873384.fastq.gz Approx 40% complete for SRR873385.fq.gz Approx 45% complete for SRR873385.fq.gz Approx 80% complete for SRR873383.fq.gz Approx 65% complete for SRR873384.fastq.gz Approx 50% complete for SRR873385.fq.gz Approx 55% complete for SRR873385.fq.gz Approx 60% complete for SRR873385.fq.gz Approx 70% complete for SRR873384.fastq.gz Approx 65% complete for SRR873385.fq.gz Approx 85% complete for SRR873383.fq.gz Approx 70% complete for SRR873385.fq.gz Approx 75% complete for SRR873385.fq.gz Approx 75% complete for SRR873384.fastq.gz Approx 80% complete for SRR873385.fq.gz Approx 90% complete for SRR873383.fq.gz Approx 85% complete for SRR873385.fq.gz Approx 90% complete for SRR873385.fq.gz Approx 80% complete for SRR873384.fastq.gz Approx 95% complete for SRR873385.fq.gz Approx 95% complete for SRR873383.fq.gz Approx 100% complete for SRR873385.fq.gz Analysis complete for SRR873385.fq.gz Approx 85% complete for SRR873384.fastq.gz Approx 100% complete for SRR873383.fq.gz Analysis complete for SRR873383.fq.gz Approx 90% complete for SRR873384.fastq.gz Approx 95% complete for SRR873384.fastq.gz Approx 100% complete for SRR873384.fastq.gz Analysis complete for SRR873384.fastq.gz Started analysis of SRR873386.fastq.gz Approx 5% complete for SRR873386.fastq.gz Approx 10% complete for SRR873386.fastq.gz Approx 15% complete for SRR873386.fastq.gz Approx 20% complete for SRR873386.fastq.gz Approx 25% complete for SRR873386.fastq.gz Approx 30% complete for SRR873386.fastq.gz Approx 35% complete for SRR873386.fastq.gz Started analysis of SRR873387.fastq.gz Approx 40% complete for SRR873386.fastq.gz Approx 5% complete for SRR873387.fastq.gz Approx 45% complete for SRR873386.fastq.gz Approx 10% complete for SRR873387.fastq.gz Approx 50% complete for SRR873386.fastq.gz Approx 15% complete for SRR873387.fastq.gz Approx 55% complete for SRR873386.fastq.gz Approx 20% complete for SRR873387.fastq.gz Approx 60% complete for SRR873386.fastq.gz Approx 25% complete for SRR873387.fastq.gz Approx 65% complete for SRR873386.fastq.gz Started analysis of SRR873388.fastq.gz Approx 30% complete for SRR873387.fastq.gz Approx 5% complete for SRR873388.fastq.gz Approx 70% complete for SRR873386.fastq.gz Approx 35% complete for SRR873387.fastq.gz Approx 10% complete for SRR873388.fastq.gz Approx 75% complete for SRR873386.fastq.gz Approx 40% complete for SRR873387.fastq.gz Approx 15% complete for SRR873388.fastq.gz Approx 80% complete for SRR873386.fastq.gz Approx 45% complete for SRR873387.fastq.gz Approx 20% complete for SRR873388.fastq.gz Approx 85% complete for SRR873386.fastq.gz Approx 50% complete for SRR873387.fastq.gz Started analysis of SRR873389.fastq.gz Approx 90% complete for SRR873386.fastq.gz Approx 25% complete for SRR873388.fastq.gz Approx 5% complete for SRR873389.fastq.gz Approx 55% complete for SRR873387.fastq.gz Approx 95% complete for SRR873386.fastq.gz Approx 30% complete for SRR873388.fastq.gz Approx 10% complete for SRR873389.fastq.gz Approx 60% complete for SRR873387.fastq.gz Approx 100% complete for SRR873386.fastq.gz Approx 35% complete for SRR873388.fastq.gz Analysis complete for SRR873386.fastq.gz Approx 15% complete for SRR873389.fastq.gz Approx 65% complete for SRR873387.fastq.gz Approx 40% complete for SRR873388.fastq.gz Approx 20% complete for SRR873389.fastq.gz Approx 70% complete for SRR873387.fastq.gz Approx 45% complete for SRR873388.fastq.gz Approx 25% complete for SRR873389.fastq.gz Approx 75% complete for SRR873387.fastq.gz Approx 50% complete for SRR873388.fastq.gz Approx 30% complete for SRR873389.fastq.gz Approx 80% complete for SRR873387.fastq.gz Approx 55% complete for SRR873388.fastq.gz Approx 35% complete for SRR873389.fastq.gz Approx 85% complete for SRR873387.fastq.gz Approx 60% complete for SRR873388.fastq.gz Approx 40% complete for SRR873389.fastq.gz Approx 90% complete for SRR873387.fastq.gz Approx 65% complete for SRR873388.fastq.gz Approx 45% complete for SRR873389.fastq.gz Approx 95% complete for SRR873387.fastq.gz Approx 70% complete for SRR873388.fastq.gz Approx 50% complete for SRR873389.fastq.gz Approx 100% complete for SRR873387.fastq.gz Analysis complete for SRR873387.fastq.gz Approx 75% complete for SRR873388.fastq.gz Approx 55% complete for SRR873389.fastq.gz Approx 80% complete for SRR873388.fastq.gz Approx 60% complete for SRR873389.fastq.gz Approx 85% complete for SRR873388.fastq.gz Approx 65% complete for SRR873389.fastq.gz Approx 90% complete for SRR873388.fastq.gz Approx 70% complete for SRR873389.fastq.gz Approx 95% complete for SRR873388.fastq.gz Approx 75% complete for SRR873389.fastq.gz Approx 100% complete for SRR873388.fastq.gz Analysis complete for SRR873388.fastq.gz Approx 80% complete for SRR873389.fastq.gz Approx 85% complete for SRR873389.fastq.gz Approx 90% complete for SRR873389.fastq.gz Approx 95% complete for SRR873389.fastq.gz Approx 100% complete for SRR873389.fastq.gz Analysis complete for SRR873389.fastq.gz CUTADAPT :: [Sun Jul 8 22:54:00 2018] Executing mkdir -p Examples/basic_examples/miRNAs/Known_miRNAs/results///cutadapt_results/ ; cut_adapt -b ATCTCGTATGCCGTCTTCTGCTTGAA -m 15 -M 35 -q 0 Examples/basic_examples/miRNAs/reads///SRR873382.fastq.gz > Examples/basic_examples/miRNAs/Known_miRNAs/results///cutadapt_results/SRR873382_cut.fastq 2>> Examples/basic_examples/miRNAs/Known_miRNAs/results//miARma_stat.2498.log FASTQC :: [Mon Jul 9 13:36:18 2018] Checking Examples/basic_examples/miRNAs/Known_miRNAs/results/ for FastQC analysis FASTQC :: [Mon Jul 9 13:36:18 2018] Executing mkdir -p Examples/basic_examples/miRNAs/Known_miRNAs/results//Pre_fastqc_results/ ; fastqc -f fastq -t 4 Examples/basic_examples/miRNAs/reads//SRR873382.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873383.fq.gz Examples/basic_examples/miRNAs/reads//SRR873384.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873385.fq.gz Examples/basic_examples/miRNAs/reads//SRR873386.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873387.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873388.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873389.fastq.gz -o Examples/basic_examples/miRNAs/Known_miRNAs/results//Pre_fastqc_results/ >> Examples/basic_examples/miRNAs/Known_miRNAs/results//miARma_logfile.2498.log 2>&1 Started analysis of SRR873382.fastq.gz Approx 5% complete for SRR873382.fastq.gz Approx 10% complete for SRR873382.fastq.gz Approx 15% complete for SRR873382.fastq.gz Approx 20% complete for SRR873382.fastq.gz Started analysis of SRR873383.fq.gz Approx 25% complete for SRR873382.fastq.gz Approx 5% complete for SRR873383.fq.gz Approx 30% complete for SRR873382.fastq.gz Approx 10% complete for SRR873383.fq.gz Approx 15% complete for SRR873383.fq.gz Approx 35% complete for SRR873382.fastq.gz Approx 20% complete for SRR873383.fq.gz Approx 40% complete for SRR873382.fastq.gz Started analysis of SRR873384.fastq.gz Approx 45% complete for SRR873382.fastq.gz Approx 25% complete for SRR873383.fq.gz Approx 5% complete for SRR873384.fastq.gz Approx 50% complete for SRR873382.fastq.gz Approx 10% complete for SRR873384.fastq.gz Approx 30% complete for SRR873383.fq.gz Approx 55% complete for SRR873382.fastq.gz Approx 15% complete for SRR873384.fastq.gz Approx 35% complete for SRR873383.fq.gz Approx 60% complete for SRR873382.fastq.gz Approx 40% complete for SRR873383.fq.gz Approx 20% complete for SRR873384.fastq.gz Approx 65% complete for SRR873382.fastq.gz Approx 45% complete for SRR873383.fq.gz Started analysis of SRR873385.fq.gz Approx 25% complete for SRR873384.fastq.gz Approx 70% complete for SRR873382.fastq.gz Approx 5% complete for SRR873385.fq.gz Approx 30% complete for SRR873384.fastq.gz Approx 50% complete for SRR873383.fq.gz Approx 75% complete for SRR873382.fastq.gz Approx 10% complete for SRR873385.fq.gz Approx 35% complete for SRR873384.fastq.gz Approx 55% complete for SRR873383.fq.gz Approx 80% complete for SRR873382.fastq.gz Approx 40% complete for SRR873384.fastq.gz Approx 15% complete for SRR873385.fq.gz Approx 60% complete for SRR873383.fq.gz Approx 85% complete for SRR873382.fastq.gz Approx 45% complete for SRR873384.fastq.gz Approx 20% complete for SRR873385.fq.gz Approx 65% complete for SRR873383.fq.gz Approx 90% complete for SRR873382.fastq.gz Approx 50% complete for SRR873384.fastq.gz Approx 25% complete for SRR873385.fq.gz Approx 70% complete for SRR873383.fq.gz Approx 95% complete for SRR873382.fastq.gz Approx 55% complete for SRR873384.fastq.gz Approx 30% complete for SRR873385.fq.gz Approx 75% complete for SRR873383.fq.gz Approx 100% complete for SRR873382.fastq.gz Analysis complete for SRR873382.fastq.gz Approx 60% complete for SRR873384.fastq.gz Approx 35% complete for SRR873385.fq.gz Approx 80% complete for SRR873383.fq.gz Approx 65% complete for SRR873384.fastq.gz Approx 40% complete for SRR873385.fq.gz Approx 85% complete for SRR873383.fq.gz Approx 70% complete for SRR873384.fastq.gz Approx 45% complete for SRR873385.fq.gz Approx 90% complete for SRR873383.fq.gz Approx 75% complete for SRR873384.fastq.gz Approx 50% complete for SRR873385.fq.gz Approx 95% complete for SRR873383.fq.gz Approx 80% complete for SRR873384.fastq.gz Approx 55% complete for SRR873385.fq.gz Approx 100% complete for SRR873383.fq.gz Analysis complete for SRR873383.fq.gz Approx 85% complete for SRR873384.fastq.gz Approx 60% complete for SRR873385.fq.gz Approx 90% complete for SRR873384.fastq.gz Approx 65% complete for SRR873385.fq.gz Approx 70% complete for SRR873385.fq.gz Approx 75% complete for SRR873385.fq.gz Approx 95% complete for SRR873384.fastq.gz Approx 80% complete for SRR873385.fq.gz Approx 85% complete for SRR873385.fq.gz Approx 100% complete for SRR873384.fastq.gz Analysis complete for SRR873384.fastq.gz Approx 90% complete for SRR873385.fq.gz Approx 95% complete for SRR873385.fq.gz Approx 100% complete for SRR873385.fq.gz Analysis complete for SRR873385.fq.gz Started analysis of SRR873386.fastq.gz Approx 5% complete for SRR873386.fastq.gz Approx 10% complete for SRR873386.fastq.gz Approx 15% complete for SRR873386.fastq.gz Approx 20% complete for SRR873386.fastq.gz Approx 25% complete for SRR873386.fastq.gz Approx 30% complete for SRR873386.fastq.gz Approx 35% complete for SRR873386.fastq.gz Started analysis of SRR873387.fastq.gz Approx 40% complete for SRR873386.fastq.gz Approx 5% complete for SRR873387.fastq.gz Approx 45% complete for SRR873386.fastq.gz Approx 10% complete for SRR873387.fastq.gz Approx 50% complete for SRR873386.fastq.gz Approx 15% complete for SRR873387.fastq.gz Approx 55% complete for SRR873386.fastq.gz Approx 20% complete for SRR873387.fastq.gz Approx 60% complete for SRR873386.fastq.gz Approx 25% complete for SRR873387.fastq.gz Approx 65% complete for SRR873386.fastq.gz Started analysis of SRR873388.fastq.gz Approx 30% complete for SRR873387.fastq.gz Approx 5% complete for SRR873388.fastq.gz Approx 70% complete for SRR873386.fastq.gz Approx 35% complete for SRR873387.fastq.gz Approx 40% complete for SRR873387.fastq.gz Approx 10% complete for SRR873388.fastq.gz Approx 75% complete for SRR873386.fastq.gz Approx 45% complete for SRR873387.fastq.gz Approx 15% complete for SRR873388.fastq.gz Approx 80% complete for SRR873386.fastq.gz Approx 50% complete for SRR873387.fastq.gz Approx 55% complete for SRR873387.fastq.gz Started analysis of SRR873389.fastq.gz Approx 20% complete for SRR873388.fastq.gz Approx 85% complete for SRR873386.fastq.gz Approx 60% complete for SRR873387.fastq.gz Approx 5% complete for SRR873389.fastq.gz Approx 25% complete for SRR873388.fastq.gz Approx 90% complete for SRR873386.fastq.gz Approx 65% complete for SRR873387.fastq.gz Approx 10% complete for SRR873389.fastq.gz Approx 30% complete for SRR873388.fastq.gz Approx 95% complete for SRR873386.fastq.gz Approx 15% complete for SRR873389.fastq.gz Approx 70% complete for SRR873387.fastq.gz Approx 35% complete for SRR873388.fastq.gz Approx 100% complete for SRR873386.fastq.gz Analysis complete for SRR873386.fastq.gz Approx 20% complete for SRR873389.fastq.gz Approx 75% complete for SRR873387.fastq.gz Approx 40% complete for SRR873388.fastq.gz Approx 25% complete for SRR873389.fastq.gz Approx 80% complete for SRR873387.fastq.gz Approx 45% complete for SRR873388.fastq.gz Approx 30% complete for SRR873389.fastq.gz Approx 85% complete for SRR873387.fastq.gz Approx 50% complete for SRR873388.fastq.gz Approx 35% complete for SRR873389.fastq.gz Approx 90% complete for SRR873387.fastq.gz Approx 55% complete for SRR873388.fastq.gz Approx 40% complete for SRR873389.fastq.gz Approx 60% complete for SRR873388.fastq.gz Approx 95% complete for SRR873387.fastq.gz Approx 45% complete for SRR873389.fastq.gz Approx 100% complete for SRR873387.fastq.gz Analysis complete for SRR873387.fastq.gz Approx 65% complete for SRR873388.fastq.gz Approx 50% complete for SRR873389.fastq.gz Approx 70% complete for SRR873388.fastq.gz Approx 55% complete for SRR873389.fastq.gz Approx 75% complete for SRR873388.fastq.gz Approx 60% complete for SRR873389.fastq.gz Approx 80% complete for SRR873388.fastq.gz Approx 65% complete for SRR873389.fastq.gz Approx 85% complete for SRR873388.fastq.gz Approx 70% complete for SRR873389.fastq.gz Approx 90% complete for SRR873388.fastq.gz Approx 75% complete for SRR873389.fastq.gz Approx 95% complete for SRR873388.fastq.gz Approx 80% complete for SRR873389.fastq.gz Approx 100% complete for SRR873388.fastq.gz Analysis complete for SRR873388.fastq.gz Approx 85% complete for SRR873389.fastq.gz Approx 90% complete for SRR873389.fastq.gz Approx 95% complete for SRR873389.fastq.gz Approx 100% complete for SRR873389.fastq.gz Analysis complete for SRR873389.fastq.gz CUTADAPT :: [Mon Jul 9 13:36:33 2018] Executing mkdir -p Examples/basic_examples/miRNAs/Known_miRNAs/results///cutadapt_results/ ; cut_adapt -b ATCTCGTATGCCGTCTTCTGCTTGAA -m 15 -M 35 -q 0 Examples/basic_examples/miRNAs/reads///SRR873382.fastq.gz > Examples/basic_examples/miRNAs/Known_miRNAs/results///cutadapt_results/SRR873382_cut.fastq 2>> Examples/basic_examples/miRNAs/Known_miRNAs/results//miARma_stat.2498.log FASTQC :: [Mon Jul 9 13:38:48 2018] Checking Examples/basic_examples/miRNAs/Known_miRNAs/results/ for FastQC analysis FASTQC :: [Mon Jul 9 13:38:48 2018] Executing mkdir -p Examples/basic_examples/miRNAs/Known_miRNAs/results//Pre_fastqc_results/ ; fastqc -f fastq -t 4 Examples/basic_examples/miRNAs/reads//SRR873382.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873383.fq.gz Examples/basic_examples/miRNAs/reads//SRR873384.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873385.fq.gz Examples/basic_examples/miRNAs/reads//SRR873386.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873387.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873388.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873389.fastq.gz -o Examples/basic_examples/miRNAs/Known_miRNAs/results//Pre_fastqc_results/ >> Examples/basic_examples/miRNAs/Known_miRNAs/results//miARma_logfile.2498.log 2>&1 Started analysis of SRR873382.fastq.gz Approx 5% complete for SRR873382.fastq.gz Approx 10% complete for SRR873382.fastq.gz Approx 15% complete for SRR873382.fastq.gz Approx 20% complete for SRR873382.fastq.gz Started analysis of SRR873383.fq.gz Approx 25% complete for SRR873382.fastq.gz Approx 5% complete for SRR873383.fq.gz Approx 30% complete for SRR873382.fastq.gz Approx 10% complete for SRR873383.fq.gz Approx 35% complete for SRR873382.fastq.gz Approx 15% complete for SRR873383.fq.gz Approx 40% complete for SRR873382.fastq.gz Approx 20% complete for SRR873383.fq.gz Started analysis of SRR873384.fastq.gz Approx 45% complete for SRR873382.fastq.gz Approx 5% complete for SRR873384.fastq.gz Approx 25% complete for SRR873383.fq.gz Approx 50% complete for SRR873382.fastq.gz Approx 30% complete for SRR873383.fq.gz Approx 10% complete for SRR873384.fastq.gz Approx 35% complete for SRR873383.fq.gz Approx 55% complete for SRR873382.fastq.gz Approx 15% complete for SRR873384.fastq.gz Approx 40% complete for SRR873383.fq.gz Approx 60% complete for SRR873382.fastq.gz Approx 20% complete for SRR873384.fastq.gz Approx 45% complete for SRR873383.fq.gz Started analysis of SRR873385.fq.gz Approx 65% complete for SRR873382.fastq.gz Approx 25% complete for SRR873384.fastq.gz Approx 50% complete for SRR873383.fq.gz Approx 5% complete for SRR873385.fq.gz Approx 70% complete for SRR873382.fastq.gz Approx 30% complete for SRR873384.fastq.gz Approx 55% complete for SRR873383.fq.gz Approx 10% complete for SRR873385.fq.gz Approx 75% complete for SRR873382.fastq.gz Approx 35% complete for SRR873384.fastq.gz Approx 60% complete for SRR873383.fq.gz Approx 15% complete for SRR873385.fq.gz Approx 80% complete for SRR873382.fastq.gz Approx 40% complete for SRR873384.fastq.gz Approx 65% complete for SRR873383.fq.gz Approx 20% complete for SRR873385.fq.gz Approx 85% complete for SRR873382.fastq.gz Approx 45% complete for SRR873384.fastq.gz Approx 70% complete for SRR873383.fq.gz Approx 25% complete for SRR873385.fq.gz Approx 90% complete for SRR873382.fastq.gz Approx 50% complete for SRR873384.fastq.gz Approx 75% complete for SRR873383.fq.gz Approx 30% complete for SRR873385.fq.gz Approx 55% complete for SRR873384.fastq.gz Approx 95% complete for SRR873382.fastq.gz Approx 80% complete for SRR873383.fq.gz Approx 35% complete for SRR873385.fq.gz Approx 60% complete for SRR873384.fastq.gz Approx 100% complete for SRR873382.fastq.gz Approx 85% complete for SRR873383.fq.gz Analysis complete for SRR873382.fastq.gz Approx 40% complete for SRR873385.fq.gz Approx 65% complete for SRR873384.fastq.gz Approx 45% complete for SRR873385.fq.gz Approx 90% complete for SRR873383.fq.gz Approx 70% complete for SRR873384.fastq.gz Approx 50% complete for SRR873385.fq.gz Approx 75% complete for SRR873384.fastq.gz Approx 55% complete for SRR873385.fq.gz Approx 80% complete for SRR873384.fastq.gz Approx 60% complete for SRR873385.fq.gz Approx 95% complete for SRR873383.fq.gz Approx 85% complete for SRR873384.fastq.gz Approx 65% complete for SRR873385.fq.gz Approx 90% complete for SRR873384.fastq.gz Approx 100% complete for SRR873383.fq.gz Approx 70% complete for SRR873385.fq.gz Analysis complete for SRR873383.fq.gz Approx 95% complete for SRR873384.fastq.gz Approx 75% complete for SRR873385.fq.gz Approx 100% complete for SRR873384.fastq.gz Analysis complete for SRR873384.fastq.gz Approx 80% complete for SRR873385.fq.gz Approx 85% complete for SRR873385.fq.gz Approx 90% complete for SRR873385.fq.gz Approx 95% complete for SRR873385.fq.gz Approx 100% complete for SRR873385.fq.gz Analysis complete for SRR873385.fq.gz Started analysis of SRR873386.fastq.gz Approx 5% complete for SRR873386.fastq.gz Approx 10% complete for SRR873386.fastq.gz Approx 15% complete for SRR873386.fastq.gz Approx 20% complete for SRR873386.fastq.gz Approx 25% complete for SRR873386.fastq.gz Started analysis of SRR873387.fastq.gz Approx 30% complete for SRR873386.fastq.gz Approx 5% complete for SRR873387.fastq.gz Approx 35% complete for SRR873386.fastq.gz Approx 10% complete for SRR873387.fastq.gz Approx 40% complete for SRR873386.fastq.gz Approx 15% complete for SRR873387.fastq.gz Approx 45% complete for SRR873386.fastq.gz Approx 20% complete for SRR873387.fastq.gz Approx 50% complete for SRR873386.fastq.gz Approx 25% complete for SRR873387.fastq.gz Started analysis of SRR873388.fastq.gz Approx 55% complete for SRR873386.fastq.gz Approx 30% complete for SRR873387.fastq.gz Approx 5% complete for SRR873388.fastq.gz Approx 60% complete for SRR873386.fastq.gz Approx 35% complete for SRR873387.fastq.gz Approx 10% complete for SRR873388.fastq.gz Approx 40% complete for SRR873387.fastq.gz Approx 65% complete for SRR873386.fastq.gz Approx 45% complete for SRR873387.fastq.gz Approx 15% complete for SRR873388.fastq.gz Approx 70% complete for SRR873386.fastq.gz Approx 20% complete for SRR873388.fastq.gz Approx 50% complete for SRR873387.fastq.gz Approx 75% complete for SRR873386.fastq.gz Approx 25% complete for SRR873388.fastq.gz Started analysis of SRR873389.fastq.gz Approx 55% complete for SRR873387.fastq.gz Approx 80% complete for SRR873386.fastq.gz Approx 30% complete for SRR873388.fastq.gz Approx 5% complete for SRR873389.fastq.gz Approx 60% complete for SRR873387.fastq.gz Approx 85% complete for SRR873386.fastq.gz Approx 35% complete for SRR873388.fastq.gz Approx 10% complete for SRR873389.fastq.gz Approx 65% complete for SRR873387.fastq.gz Approx 90% complete for SRR873386.fastq.gz Approx 40% complete for SRR873388.fastq.gz Approx 15% complete for SRR873389.fastq.gz Approx 70% complete for SRR873387.fastq.gz Approx 95% complete for SRR873386.fastq.gz Approx 20% complete for SRR873389.fastq.gz Approx 45% complete for SRR873388.fastq.gz Approx 75% complete for SRR873387.fastq.gz Approx 100% complete for SRR873386.fastq.gz Analysis complete for SRR873386.fastq.gz Approx 25% complete for SRR873389.fastq.gz Approx 50% complete for SRR873388.fastq.gz Approx 80% complete for SRR873387.fastq.gz Approx 30% complete for SRR873389.fastq.gz Approx 55% complete for SRR873388.fastq.gz Approx 85% complete for SRR873387.fastq.gz Approx 35% complete for SRR873389.fastq.gz Approx 60% complete for SRR873388.fastq.gz Approx 90% complete for SRR873387.fastq.gz Approx 40% complete for SRR873389.fastq.gz Approx 65% complete for SRR873388.fastq.gz Approx 95% complete for SRR873387.fastq.gz Approx 45% complete for SRR873389.fastq.gz Approx 70% complete for SRR873388.fastq.gz Approx 100% complete for SRR873387.fastq.gz Analysis complete for SRR873387.fastq.gz Approx 50% complete for SRR873389.fastq.gz Approx 75% complete for SRR873388.fastq.gz Approx 55% complete for SRR873389.fastq.gz Approx 80% complete for SRR873388.fastq.gz Approx 60% complete for SRR873389.fastq.gz Approx 85% complete for SRR873388.fastq.gz Approx 65% complete for SRR873389.fastq.gz Approx 90% complete for SRR873388.fastq.gz Approx 70% complete for SRR873389.fastq.gz Approx 95% complete for SRR873388.fastq.gz Approx 75% complete for SRR873389.fastq.gz Approx 100% complete for SRR873388.fastq.gz Analysis complete for SRR873388.fastq.gz Approx 80% complete for SRR873389.fastq.gz Approx 85% complete for SRR873389.fastq.gz Approx 90% complete for SRR873389.fastq.gz Approx 95% complete for SRR873389.fastq.gz Approx 100% complete for SRR873389.fastq.gz Analysis complete for SRR873389.fastq.gz BOWTIE 1 :: [Mon Jul 9 13:39:00 2018] Executing mkdir -p Examples/basic_examples/miRNAs/Known_miRNAs/results//Bowtie1_results/ ;bowtie --sam -p 4 Genomes/Indexes/bowtie1/human/bw1_homo_sapiens19 Examples/basic_examples/miRNAs/Known_miRNAs/results//cutadapt_results/SRR873382_cut.fastq Examples/basic_examples/miRNAs/Known_miRNAs/results//Bowtie1_results/SRR873382_cut_nat_bw1.bam 2>> Examples/basic_examples/miRNAs/Known_miRNAs/results//miARma_stat.2498.log File:Examples/basic_examples/miRNAs/Known_miRNAs/results//cutadapt_results/SRR873382_cut.fastq SEQCOUNT :: [Mon Jul 9 13:40:17 2018] Reading counts from Examples/basic_examples/miRNAs/Known_miRNAs/results//Bowtie1_results/SRR873382_cut_nat_bw1.bam SEQCOUNT :: [Mon Jul 9 13:40:17 2018] Executing mkdir -p Examples/basic_examples/miRNAs/Known_miRNAs/results//nat_bw1_readcount_results/ ;featureCounts -s 1 -t miRNA -g transcript_id -T 4 -a Examples/basic_examples/miRNAs/data/miRBase_Annotation_20_for_hsa_mature_miRNA.gtf -o Examples/basic_examples/miRNAs/Known_miRNAs/results//nat_bw1_readcount_results/SRR873382_cut_nat_bw1.tab Examples/basic_examples/miRNAs/Known_miRNAs/results//Bowtie1_results/SRR873382_cut_nat_bw1.bam 2>> Examples/basic_examples/miRNAs/Known_miRNAs/results//miARma_logfile.2498.log ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.5.0-p1 //========================== featureCounts setting ===========================\\ || || || Input files : 1 SAM file || || S Examples/basic_examples/miRNAs/Known_miRNA ... || || || || Output file : Examples/basic_examples/miRNAs/Known_miRNAs/ ... || || Annotations : Examples/basic_examples/miRNAs/data/miRBase_ ... || || || || Threads : 4 || || Level : meta-feature level || || Paired-end : no || || Strand specific : yes || || Multimapping reads : not counted || || Multi-overlapping reads : not counted || || Read orientations : fr || || || \\===================== http://subread.sourceforge.net/ ======================// //================================= Running ==================================\\ || || || Load annotation file Examples/basic_examples/miRNAs/data/miRBase_Annot ... || || Features : 2794 || || Meta-features : 2576 || || Chromosomes/contigs : 24 || || || || Process SAM file Examples/basic_examples/miRNAs/Known_miRNAs/results// ... || || Single-end reads are included. || || Assign reads to features... || || Total reads : 0 || || Successfully assigned reads : 0 || || Running time : 0.00 minutes || || || || Read assignment finished. || || || \\===================== http://subread.sourceforge.net/ ======================// SEQCOUNT :: [Mon Jul 9 13:40:17 2018] Please check the folder: Examples/basic_examples/miRNAs/Known_miRNAs/results//Readcount_results/. QC_EdgeR :: [Mon Jul 9 13:40:18 2018] Executing source("./lib/CbBio/RNASeq/R-Scripts/QC_EdgeR.R") setwd("/home/leila/apps/miARma/cbbio-miarma-42e187a7f514/Examples/basic_examples/miRNAs/Known_miRNAs/results/Readcount_results") resultsfiles<-QC_EdgeR(projectdir="/home/leila/apps/miARma/cbbio-miarma-42e187a7f514/Examples/basic_examples/miRNAs/Known_miRNAs/results",dir="/home/leila/apps/miARma/cbbio-miarma-42e187a7f514/Examples/basic_examples/miRNAs/Known_miRNAs/results/Readcount_results", file="nat_bw1-ReadCount.tab", targetfile="/home/leila/apps/miARma/cbbio-miarma-42e187a7f514/Examples/basic_examples/miRNAs/data/targets.txt", label="Hypoxia_nat_bw1", filter="yes") FASTQC :: [Mon Jul 9 13:48:45 2018] Checking Examples/basic_examples/miRNAs/Known_miRNAs/results/ for FastQC analysis FASTQC :: [Mon Jul 9 13:48:45 2018] Executing mkdir -p Examples/basic_examples/miRNAs/Known_miRNAs/results//Pre_fastqc_results/ ; fastqc -f fastq -t 4 Examples/basic_examples/miRNAs/reads//SRR873382.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873383.fq.gz Examples/basic_examples/miRNAs/reads//SRR873384.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873385.fq.gz Examples/basic_examples/miRNAs/reads//SRR873386.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873387.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873388.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873389.fastq.gz -o Examples/basic_examples/miRNAs/Known_miRNAs/results//Pre_fastqc_results/ >> Examples/basic_examples/miRNAs/Known_miRNAs/results//miARma_logfile.2498.log 2>&1 Started analysis of SRR873382.fastq.gz Approx 5% complete for SRR873382.fastq.gz Approx 10% complete for SRR873382.fastq.gz Approx 15% complete for SRR873382.fastq.gz Started analysis of SRR873383.fq.gz Approx 20% complete for SRR873382.fastq.gz Approx 5% complete for SRR873383.fq.gz Approx 25% complete for SRR873382.fastq.gz Approx 10% complete for SRR873383.fq.gz Approx 30% complete for SRR873382.fastq.gz Approx 15% complete for SRR873383.fq.gz Approx 35% complete for SRR873382.fastq.gz Approx 20% complete for SRR873383.fq.gz Approx 40% complete for SRR873382.fastq.gz Started analysis of SRR873384.fastq.gz Approx 25% complete for SRR873383.fq.gz Approx 45% complete for SRR873382.fastq.gz Approx 5% complete for SRR873384.fastq.gz Approx 30% complete for SRR873383.fq.gz Approx 50% complete for SRR873382.fastq.gz Approx 10% complete for SRR873384.fastq.gz Approx 35% complete for SRR873383.fq.gz Approx 55% complete for SRR873382.fastq.gz Started analysis of SRR873385.fq.gz Approx 15% complete for SRR873384.fastq.gz Approx 40% complete for SRR873383.fq.gz Approx 20% complete for SRR873384.fastq.gz Approx 60% complete for SRR873382.fastq.gz Approx 45% complete for SRR873383.fq.gz Approx 5% complete for SRR873385.fq.gz Approx 25% complete for SRR873384.fastq.gz Approx 65% complete for SRR873382.fastq.gz Approx 50% complete for SRR873383.fq.gz Approx 10% complete for SRR873385.fq.gz Approx 30% complete for 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SRR873389.fastq.gz BOWTIE 1 :: [Mon Jul 9 13:48:59 2018] Executing mkdir -p Examples/basic_examples/miRNAs/Known_miRNAs/results//Bowtie1_results/ ;bowtie --sam -p 4 Genomes/Indexes/bowtie1/human/bw1_homo_sapiens19 Examples/basic_examples/miRNAs/Known_miRNAs/results//cutadapt_results/SRR873382_cut.fastq Examples/basic_examples/miRNAs/Known_miRNAs/results//Bowtie1_results/SRR873382_cut_nat_bw1.bam 2>> Examples/basic_examples/miRNAs/Known_miRNAs/results//miARma_stat.2498.log File:Examples/basic_examples/miRNAs/Known_miRNAs/results//cutadapt_results/SRR873382_cut.fastq SEQCOUNT :: [Mon Jul 9 13:48:59 2018] Reading counts from Examples/basic_examples/miRNAs/Known_miRNAs/results//Bowtie1_results/SRR873382_cut_nat_bw1.bam SEQCOUNT :: [Mon Jul 9 13:48:59 2018] Executing mkdir -p Examples/basic_examples/miRNAs/Known_miRNAs/results//nat_bw1_readcount_results/ ;featureCounts -s 1 -t miRNA -g transcript_id -T 4 -a Examples/basic_examples/miRNAs/data/miRBase_Annotation_20_for_hsa_mature_miRNA.gtf -o Examples/basic_examples/miRNAs/Known_miRNAs/results//nat_bw1_readcount_results/SRR873382_cut_nat_bw1.tab Examples/basic_examples/miRNAs/Known_miRNAs/results//Bowtie1_results/SRR873382_cut_nat_bw1.bam 2>> Examples/basic_examples/miRNAs/Known_miRNAs/results//miARma_logfile.2498.log ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.5.0-p1 //========================== featureCounts setting ===========================\\ || || || Input files : 1 SAM file || || S Examples/basic_examples/miRNAs/Known_miRNA ... || || || || Output file : Examples/basic_examples/miRNAs/Known_miRNAs/ ... || || Annotations : Examples/basic_examples/miRNAs/data/miRBase_ ... || || || || Threads : 4 || || Level : meta-feature level || || Paired-end : no || || Strand specific : yes || || Multimapping reads : not counted || || Multi-overlapping reads : not counted || || Read orientations : fr || || || \\===================== http://subread.sourceforge.net/ ======================// //================================= Running ==================================\\ || || || Load annotation file Examples/basic_examples/miRNAs/data/miRBase_Annot ... || || Features : 2794 || || Meta-features : 2576 || || Chromosomes/contigs : 24 || || || || Process SAM file Examples/basic_examples/miRNAs/Known_miRNAs/results// ... || || Single-end reads are included. || || Assign reads to features... || || Total reads : 0 || || Successfully assigned reads : 0 || || Running time : 0.00 minutes || || || || Read assignment finished. || || || \\===================== http://subread.sourceforge.net/ ======================// SEQCOUNT :: [Mon Jul 9 13:48:59 2018] Please check the folder: Examples/basic_examples/miRNAs/Known_miRNAs/results//Readcount_results/. QC_EdgeR :: [Mon Jul 9 13:49:00 2018] Executing source("./lib/CbBio/RNASeq/R-Scripts/QC_EdgeR.R") setwd("/home/leila/apps/miARma/cbbio-miarma-42e187a7f514/Examples/basic_examples/miRNAs/Known_miRNAs/results/Readcount_results") resultsfiles<-QC_EdgeR(projectdir="/home/leila/apps/miARma/cbbio-miarma-42e187a7f514/Examples/basic_examples/miRNAs/Known_miRNAs/results",dir="/home/leila/apps/miARma/cbbio-miarma-42e187a7f514/Examples/basic_examples/miRNAs/Known_miRNAs/results/Readcount_results", file="nat_bw1-ReadCount.tab", targetfile="/home/leila/apps/miARma/cbbio-miarma-42e187a7f514/Examples/basic_examples/miRNAs/data/targets.txt", label="Hypoxia_nat_bw1", filter="yes") FASTQC :: [Mon Jul 9 14:05:26 2018] Checking Examples/basic_examples/miRNAs/Known_miRNAs/results/ for FastQC analysis FASTQC :: [Mon Jul 9 14:05:26 2018] Executing mkdir -p Examples/basic_examples/miRNAs/Known_miRNAs/results//Pre_fastqc_results/ ; fastqc -f fastq -t 4 Examples/basic_examples/miRNAs/reads//SRR873382.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873383.fq.gz Examples/basic_examples/miRNAs/reads//SRR873384.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873385.fq.gz Examples/basic_examples/miRNAs/reads//SRR873386.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873387.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873388.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873389.fastq.gz -o Examples/basic_examples/miRNAs/Known_miRNAs/results//Pre_fastqc_results/ >> Examples/basic_examples/miRNAs/Known_miRNAs/results//miARma_logfile.2498.log 2>&1 Started analysis of SRR873382.fastq.gz Approx 5% complete for SRR873382.fastq.gz Approx 10% complete for SRR873382.fastq.gz Approx 15% complete for SRR873382.fastq.gz Approx 20% complete for SRR873382.fastq.gz Started analysis of SRR873383.fq.gz Approx 25% complete for SRR873382.fastq.gz Approx 5% complete for SRR873383.fq.gz Approx 30% complete for SRR873382.fastq.gz Approx 10% complete for SRR873383.fq.gz Approx 35% complete for SRR873382.fastq.gz Approx 15% complete for SRR873383.fq.gz Approx 40% complete for SRR873382.fastq.gz Approx 20% complete for SRR873383.fq.gz Started analysis of SRR873384.fastq.gz Approx 45% complete for SRR873382.fastq.gz Approx 25% complete for SRR873383.fq.gz Approx 5% complete for SRR873384.fastq.gz Approx 50% complete for SRR873382.fastq.gz Approx 10% complete for SRR873384.fastq.gz Approx 30% complete for SRR873383.fq.gz Approx 55% complete for SRR873382.fastq.gz Approx 35% complete for SRR873383.fq.gz Approx 15% complete for SRR873384.fastq.gz Approx 40% complete for SRR873383.fq.gz Approx 60% complete for SRR873382.fastq.gz Approx 20% complete for SRR873384.fastq.gz Approx 45% complete for SRR873383.fq.gz Started analysis of SRR873385.fq.gz Approx 65% complete for SRR873382.fastq.gz Approx 25% complete for SRR873384.fastq.gz Approx 50% complete for SRR873383.fq.gz Approx 5% complete for SRR873385.fq.gz Approx 70% complete for SRR873382.fastq.gz Approx 30% complete for 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SRR873382.fastq.gz Analysis complete for SRR873382.fastq.gz Approx 40% complete for SRR873385.fq.gz Approx 65% complete for SRR873384.fastq.gz Approx 85% complete for SRR873383.fq.gz Approx 45% complete for SRR873385.fq.gz Approx 70% complete for SRR873384.fastq.gz Approx 50% complete for SRR873385.fq.gz Approx 90% complete for SRR873383.fq.gz Approx 75% complete for SRR873384.fastq.gz Approx 55% complete for SRR873385.fq.gz Approx 80% complete for SRR873384.fastq.gz Approx 60% complete for SRR873385.fq.gz Approx 95% complete for SRR873383.fq.gz Approx 85% complete for SRR873384.fastq.gz Approx 65% complete for SRR873385.fq.gz Approx 90% complete for SRR873384.fastq.gz Approx 70% complete for SRR873385.fq.gz Approx 95% complete for SRR873384.fastq.gz Approx 100% complete for SRR873383.fq.gz Analysis complete for SRR873383.fq.gz Approx 75% complete for SRR873385.fq.gz Approx 100% complete for SRR873384.fastq.gz Analysis complete for SRR873384.fastq.gz Approx 80% complete for 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SRR873388.fastq.gz Approx 90% complete for SRR873387.fastq.gz Approx 50% complete for SRR873389.fastq.gz Approx 75% complete for SRR873388.fastq.gz Approx 95% complete for SRR873387.fastq.gz Approx 55% complete for SRR873389.fastq.gz Approx 80% complete for SRR873388.fastq.gz Approx 100% complete for SRR873387.fastq.gz Analysis complete for SRR873387.fastq.gz Approx 60% complete for SRR873389.fastq.gz Approx 85% complete for SRR873388.fastq.gz Approx 65% complete for SRR873389.fastq.gz Approx 90% complete for SRR873388.fastq.gz Approx 70% complete for SRR873389.fastq.gz Approx 95% complete for SRR873388.fastq.gz Approx 75% complete for SRR873389.fastq.gz Approx 100% complete for SRR873388.fastq.gz Analysis complete for SRR873388.fastq.gz Approx 80% complete for SRR873389.fastq.gz Approx 85% complete for SRR873389.fastq.gz Approx 90% complete for SRR873389.fastq.gz Approx 95% complete for SRR873389.fastq.gz Approx 100% complete for SRR873389.fastq.gz Analysis complete for SRR873389.fastq.gz CUTADAPT :: [Mon Jul 9 14:05:37 2018] Executing mkdir -p Examples/basic_examples/miRNAs/Known_miRNAs/results///cutadapt_results/ ; cut_adapt -b ATCTCGTATGCCGTCTTCTGCTTGAA -m 15 -M 35 -q 0 Examples/basic_examples/miRNAs/reads///SRR873382.fastq.gz > Examples/basic_examples/miRNAs/Known_miRNAs/results///cutadapt_results/SRR873382_cut.fastq 2>> Examples/basic_examples/miRNAs/Known_miRNAs/results//miARma_stat.2498.log FASTQC :: [Mon Jul 9 14:40:41 2018] Checking Examples/basic_examples/miRNAs/Known_miRNAs/results/ for FastQC analysis FASTQC :: [Mon Jul 9 14:40:41 2018] Executing mkdir -p Examples/basic_examples/miRNAs/Known_miRNAs/results//Pre_fastqc_results/ ; fastqc -f fastq -t 4 Examples/basic_examples/miRNAs/reads//SRR873382.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873383.fq.gz Examples/basic_examples/miRNAs/reads//SRR873384.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873385.fq.gz Examples/basic_examples/miRNAs/reads//SRR873386.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873387.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873388.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873389.fastq.gz -o Examples/basic_examples/miRNAs/Known_miRNAs/results//Pre_fastqc_results/ >> Examples/basic_examples/miRNAs/Known_miRNAs/results//miARma_logfile.2498.log 2>&1 Started analysis of SRR873382.fastq.gz Approx 5% complete for SRR873382.fastq.gz Approx 10% complete for SRR873382.fastq.gz Approx 15% complete for SRR873382.fastq.gz Approx 20% complete for SRR873382.fastq.gz Started analysis of SRR873383.fq.gz Approx 25% complete for SRR873382.fastq.gz Approx 5% complete for SRR873383.fq.gz Approx 30% complete for SRR873382.fastq.gz Approx 10% complete for SRR873383.fq.gz Approx 35% complete for SRR873382.fastq.gz Approx 15% complete for SRR873383.fq.gz Approx 40% complete for SRR873382.fastq.gz Approx 20% complete for SRR873383.fq.gz Started analysis of SRR873384.fastq.gz Approx 45% complete for SRR873382.fastq.gz Approx 25% complete for SRR873383.fq.gz Approx 5% complete for SRR873384.fastq.gz Approx 50% complete for SRR873382.fastq.gz Approx 30% complete for SRR873383.fq.gz Approx 10% complete for SRR873384.fastq.gz Approx 55% complete for SRR873382.fastq.gz Approx 35% complete for SRR873383.fq.gz Approx 60% complete for SRR873382.fastq.gz Approx 15% complete for SRR873384.fastq.gz Approx 40% complete for SRR873383.fq.gz Approx 65% complete for SRR873382.fastq.gz Approx 20% complete for SRR873384.fastq.gz Started analysis of SRR873385.fq.gz Approx 45% complete for SRR873383.fq.gz Approx 70% complete for SRR873382.fastq.gz Approx 25% complete for SRR873384.fastq.gz Approx 5% complete for SRR873385.fq.gz Approx 50% complete for SRR873383.fq.gz Approx 10% complete for SRR873385.fq.gz Approx 30% complete for SRR873384.fastq.gz Approx 75% complete for SRR873382.fastq.gz Approx 55% complete for SRR873383.fq.gz Approx 15% complete for SRR873385.fq.gz Approx 35% complete for SRR873384.fastq.gz Approx 80% complete for SRR873382.fastq.gz Approx 60% complete for SRR873383.fq.gz Approx 20% complete for SRR873385.fq.gz Approx 40% complete for SRR873384.fastq.gz Approx 85% complete for SRR873382.fastq.gz Approx 65% complete for SRR873383.fq.gz Approx 25% complete for SRR873385.fq.gz Approx 45% complete for SRR873384.fastq.gz Approx 90% complete for SRR873382.fastq.gz Approx 70% complete for SRR873383.fq.gz Approx 30% complete for SRR873385.fq.gz Approx 50% complete for SRR873384.fastq.gz Approx 95% complete for SRR873382.fastq.gz Approx 75% complete for SRR873383.fq.gz Approx 35% complete for SRR873385.fq.gz Approx 55% complete for SRR873384.fastq.gz Approx 100% complete for SRR873382.fastq.gz Analysis complete for SRR873382.fastq.gz Approx 80% complete for SRR873383.fq.gz Approx 40% complete for SRR873385.fq.gz Approx 60% complete for SRR873384.fastq.gz Approx 85% complete for SRR873383.fq.gz Approx 45% complete for SRR873385.fq.gz Approx 65% complete for SRR873384.fastq.gz Approx 90% complete for SRR873383.fq.gz Approx 50% complete for SRR873385.fq.gz Approx 70% complete for SRR873384.fastq.gz Approx 95% complete for SRR873383.fq.gz Approx 55% complete for SRR873385.fq.gz Approx 75% complete for SRR873384.fastq.gz Approx 100% complete for SRR873383.fq.gz Analysis complete for SRR873383.fq.gz Approx 60% complete for SRR873385.fq.gz Approx 80% complete for SRR873384.fastq.gz Approx 65% complete for SRR873385.fq.gz Approx 85% complete for SRR873384.fastq.gz Approx 70% complete for SRR873385.fq.gz Approx 90% complete for SRR873384.fastq.gz Approx 75% complete for SRR873385.fq.gz Approx 95% complete for SRR873384.fastq.gz Approx 80% complete for SRR873385.fq.gz Approx 100% complete for SRR873384.fastq.gz Analysis complete for SRR873384.fastq.gz Approx 85% complete for SRR873385.fq.gz Approx 90% complete for SRR873385.fq.gz Approx 95% complete for SRR873385.fq.gz Approx 100% complete for SRR873385.fq.gz Analysis complete for SRR873385.fq.gz Started analysis of SRR873386.fastq.gz Approx 5% complete for SRR873386.fastq.gz Approx 10% complete for SRR873386.fastq.gz Approx 15% complete for SRR873386.fastq.gz Approx 20% complete for SRR873386.fastq.gz Approx 25% complete for SRR873386.fastq.gz Approx 30% complete for SRR873386.fastq.gz Started analysis of SRR873387.fastq.gz Approx 35% complete for SRR873386.fastq.gz Approx 5% complete for SRR873387.fastq.gz Approx 40% complete for SRR873386.fastq.gz Approx 10% complete for SRR873387.fastq.gz Approx 45% complete for SRR873386.fastq.gz Approx 15% complete for SRR873387.fastq.gz Approx 50% complete for SRR873386.fastq.gz Approx 20% complete for SRR873387.fastq.gz Approx 55% complete for SRR873386.fastq.gz Approx 25% complete for SRR873387.fastq.gz Approx 60% complete for SRR873386.fastq.gz Approx 30% complete for SRR873387.fastq.gz Approx 65% complete for SRR873386.fastq.gz Started analysis of SRR873388.fastq.gz Approx 35% complete for SRR873387.fastq.gz Approx 70% complete for SRR873386.fastq.gz Approx 5% complete for SRR873388.fastq.gz Approx 40% complete for SRR873387.fastq.gz Approx 75% complete for SRR873386.fastq.gz Approx 10% complete for SRR873388.fastq.gz Approx 45% complete for SRR873387.fastq.gz Approx 80% complete for SRR873386.fastq.gz Approx 15% complete for SRR873388.fastq.gz Approx 85% complete for SRR873386.fastq.gz Approx 50% complete for SRR873387.fastq.gz Approx 55% complete for SRR873387.fastq.gz Approx 20% complete for SRR873388.fastq.gz Approx 90% complete for SRR873386.fastq.gz Started analysis of SRR873389.fastq.gz Approx 95% complete for SRR873386.fastq.gz Approx 60% complete for SRR873387.fastq.gz Approx 25% complete for SRR873388.fastq.gz Approx 5% complete for SRR873389.fastq.gz Approx 100% complete for SRR873386.fastq.gz Analysis complete for SRR873386.fastq.gz Approx 30% complete for SRR873388.fastq.gz Approx 65% complete for SRR873387.fastq.gz Approx 10% complete for SRR873389.fastq.gz Approx 35% complete for SRR873388.fastq.gz Approx 15% complete for SRR873389.fastq.gz Approx 70% complete for SRR873387.fastq.gz Approx 40% complete for SRR873388.fastq.gz Approx 20% complete for SRR873389.fastq.gz Approx 75% complete for SRR873387.fastq.gz Approx 45% complete for SRR873388.fastq.gz Approx 25% complete for SRR873389.fastq.gz Approx 80% complete for SRR873387.fastq.gz Approx 50% complete for SRR873388.fastq.gz Approx 30% complete for SRR873389.fastq.gz Approx 85% complete for SRR873387.fastq.gz Approx 55% complete for SRR873388.fastq.gz Approx 35% complete for SRR873389.fastq.gz Approx 90% complete for SRR873387.fastq.gz Approx 60% complete for SRR873388.fastq.gz Approx 40% complete for SRR873389.fastq.gz Approx 95% complete for SRR873387.fastq.gz Approx 65% complete for SRR873388.fastq.gz Approx 45% complete for SRR873389.fastq.gz Approx 100% complete for SRR873387.fastq.gz Analysis complete for SRR873387.fastq.gz Approx 70% complete for SRR873388.fastq.gz Approx 50% complete for SRR873389.fastq.gz Approx 75% complete for SRR873388.fastq.gz Approx 55% complete for SRR873389.fastq.gz Approx 80% complete for SRR873388.fastq.gz Approx 60% complete for SRR873389.fastq.gz Approx 85% complete for SRR873388.fastq.gz Approx 65% complete for SRR873389.fastq.gz Approx 90% complete for SRR873388.fastq.gz Approx 70% complete for SRR873389.fastq.gz Approx 95% complete for SRR873388.fastq.gz Approx 75% complete for SRR873389.fastq.gz Approx 100% complete for SRR873388.fastq.gz Analysis complete for SRR873388.fastq.gz Approx 80% complete for SRR873389.fastq.gz Approx 85% complete for SRR873389.fastq.gz Approx 90% complete for SRR873389.fastq.gz Approx 95% complete for SRR873389.fastq.gz Approx 100% complete for SRR873389.fastq.gz Analysis complete for SRR873389.fastq.gz CUTADAPT :: [Mon Jul 9 14:40:53 2018] Executing mkdir -p Examples/basic_examples/miRNAs/Known_miRNAs/results///cutadapt_results/ ; cut_adapt -b ATCTCGTATGCCGTCTTCTGCTTGAA -m 15 -M 35 -q 0 Examples/basic_examples/miRNAs/reads///SRR873382.fastq.gz > Examples/basic_examples/miRNAs/Known_miRNAs/results///cutadapt_results/SRR873382_cut.fastq 2>> Examples/basic_examples/miRNAs/Known_miRNAs/results//miARma_stat.2498.log FASTQC :: [Mon Jul 9 15:36:07 2018] Checking Examples/basic_examples/miRNAs/Known_miRNAs/results/ for FastQC analysis FASTQC :: [Mon Jul 9 15:36:07 2018] Executing mkdir -p Examples/basic_examples/miRNAs/Known_miRNAs/results//Pre_fastqc_results/ ; fastqc -f fastq -t 4 Examples/basic_examples/miRNAs/reads//SRR873382.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873383.fq.gz Examples/basic_examples/miRNAs/reads//SRR873384.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873385.fq.gz Examples/basic_examples/miRNAs/reads//SRR873386.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873387.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873388.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873389.fastq.gz -o Examples/basic_examples/miRNAs/Known_miRNAs/results//Pre_fastqc_results/ >> Examples/basic_examples/miRNAs/Known_miRNAs/results//miARma_logfile.2498.log 2>&1 FASTQC :: [Mon Jul 9 15:37:17 2018] Checking Examples/basic_examples/miRNAs/Known_miRNAs/results/ for FastQC analysis FASTQC :: [Mon Jul 9 15:37:17 2018] Executing mkdir -p Examples/basic_examples/miRNAs/Known_miRNAs/results//Pre_fastqc_results/ ; fastqc -f fastq -t 4 Examples/basic_examples/miRNAs/reads//SRR873382.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873383.fq.gz Examples/basic_examples/miRNAs/reads//SRR873384.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873385.fq.gz Examples/basic_examples/miRNAs/reads//SRR873386.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873387.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873388.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873389.fastq.gz -o Examples/basic_examples/miRNAs/Known_miRNAs/results//Pre_fastqc_results/ >> Examples/basic_examples/miRNAs/Known_miRNAs/results//miARma_logfile.2498.log 2>&1 Started analysis of SRR873382.fastq.gz Approx 5% complete for SRR873382.fastq.gz Approx 10% complete for SRR873382.fastq.gz Approx 15% complete for SRR873382.fastq.gz Started analysis of SRR873383.fq.gz Approx 20% complete for SRR873382.fastq.gz Approx 5% complete for SRR873383.fq.gz Approx 25% complete for SRR873382.fastq.gz Approx 10% complete for SRR873383.fq.gz Approx 30% complete for SRR873382.fastq.gz Approx 15% complete for SRR873383.fq.gz Approx 35% complete for SRR873382.fastq.gz Approx 20% complete for SRR873383.fq.gz Approx 40% complete for SRR873382.fastq.gz Started analysis of SRR873384.fastq.gz Approx 5% complete for SRR873384.fastq.gz Approx 45% complete for SRR873382.fastq.gz Approx 25% complete for SRR873383.fq.gz Approx 10% complete for SRR873384.fastq.gz Approx 50% complete for SRR873382.fastq.gz Approx 30% complete for SRR873383.fq.gz Approx 55% complete for SRR873382.fastq.gz Approx 15% complete for SRR873384.fastq.gz Approx 35% complete for SRR873383.fq.gz Approx 60% complete for SRR873382.fastq.gz Approx 20% complete for SRR873384.fastq.gz Approx 40% complete for SRR873383.fq.gz Started analysis of SRR873385.fq.gz Approx 45% complete for SRR873383.fq.gz Approx 65% complete for SRR873382.fastq.gz Approx 25% complete for SRR873384.fastq.gz Approx 5% complete for SRR873385.fq.gz Approx 50% complete for SRR873383.fq.gz Approx 30% complete for SRR873384.fastq.gz Approx 70% complete for SRR873382.fastq.gz Approx 10% complete for SRR873385.fq.gz Approx 55% complete for SRR873383.fq.gz Approx 35% complete for SRR873384.fastq.gz Approx 75% complete for SRR873382.fastq.gz Approx 15% complete for SRR873385.fq.gz Approx 40% complete for SRR873384.fastq.gz Approx 60% complete for SRR873383.fq.gz Approx 80% complete for SRR873382.fastq.gz Approx 20% complete for SRR873385.fq.gz Approx 65% complete for SRR873383.fq.gz Approx 45% complete for SRR873384.fastq.gz Approx 85% complete for SRR873382.fastq.gz Approx 25% complete for SRR873385.fq.gz Approx 50% complete for SRR873384.fastq.gz Approx 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for SRR873384.fastq.gz Approx 60% complete for SRR873385.fq.gz Approx 90% complete for SRR873384.fastq.gz Approx 65% complete for SRR873385.fq.gz Approx 95% complete for SRR873384.fastq.gz Approx 70% complete for SRR873385.fq.gz Approx 100% complete for SRR873384.fastq.gz Analysis complete for SRR873384.fastq.gz Approx 75% complete for SRR873385.fq.gz Approx 80% complete for SRR873385.fq.gz Approx 85% complete for SRR873385.fq.gz Approx 90% complete for SRR873385.fq.gz Approx 95% complete for SRR873385.fq.gz Approx 100% complete for SRR873385.fq.gz Analysis complete for SRR873385.fq.gz Started analysis of SRR873386.fastq.gz Approx 5% complete for SRR873386.fastq.gz Approx 10% complete for SRR873386.fastq.gz Approx 15% complete for SRR873386.fastq.gz Approx 20% complete for SRR873386.fastq.gz Approx 25% complete for SRR873386.fastq.gz Approx 30% complete for SRR873386.fastq.gz Approx 35% complete for SRR873386.fastq.gz Started analysis of SRR873387.fastq.gz Approx 40% complete for SRR873386.fastq.gz Approx 5% complete for SRR873387.fastq.gz Approx 45% complete for SRR873386.fastq.gz Approx 10% complete for SRR873387.fastq.gz Approx 50% complete for SRR873386.fastq.gz Approx 15% complete for SRR873387.fastq.gz Approx 55% complete for SRR873386.fastq.gz Approx 20% complete for SRR873387.fastq.gz Approx 60% complete for SRR873386.fastq.gz Approx 25% complete for SRR873387.fastq.gz Approx 65% complete for SRR873386.fastq.gz Approx 30% complete for SRR873387.fastq.gz Started analysis of SRR873388.fastq.gz Approx 70% complete for SRR873386.fastq.gz Approx 35% complete for SRR873387.fastq.gz Approx 5% complete for SRR873388.fastq.gz Approx 75% complete for SRR873386.fastq.gz Approx 40% complete for SRR873387.fastq.gz Approx 80% complete for SRR873386.fastq.gz Approx 10% complete for SRR873388.fastq.gz Approx 85% complete for SRR873386.fastq.gz Approx 45% complete for SRR873387.fastq.gz Approx 15% complete for SRR873388.fastq.gz Approx 90% complete for SRR873386.fastq.gz Approx 50% complete for SRR873387.fastq.gz Approx 20% complete for SRR873388.fastq.gz Started analysis of SRR873389.fastq.gz Approx 95% complete for SRR873386.fastq.gz Approx 55% complete for SRR873387.fastq.gz Approx 25% complete for SRR873388.fastq.gz Approx 5% complete for SRR873389.fastq.gz Approx 100% complete for SRR873386.fastq.gz Analysis complete for SRR873386.fastq.gz Approx 60% complete for SRR873387.fastq.gz Approx 30% complete for SRR873388.fastq.gz Approx 10% complete for SRR873389.fastq.gz Approx 35% complete for SRR873388.fastq.gz Approx 15% complete for SRR873389.fastq.gz Approx 65% complete for SRR873387.fastq.gz Approx 20% complete for SRR873389.fastq.gz Approx 40% complete for SRR873388.fastq.gz Approx 70% complete for SRR873387.fastq.gz Approx 25% complete for SRR873389.fastq.gz Approx 45% complete for SRR873388.fastq.gz Approx 75% complete for SRR873387.fastq.gz Approx 30% complete for SRR873389.fastq.gz Approx 50% complete for SRR873388.fastq.gz Approx 80% complete for SRR873387.fastq.gz Approx 35% complete for SRR873389.fastq.gz Approx 55% complete for SRR873388.fastq.gz Approx 85% complete for SRR873387.fastq.gz Approx 40% complete for SRR873389.fastq.gz Approx 60% complete for SRR873388.fastq.gz Approx 90% complete for SRR873387.fastq.gz Approx 45% complete for SRR873389.fastq.gz Approx 65% complete for SRR873388.fastq.gz Approx 95% complete for SRR873387.fastq.gz Approx 50% complete for SRR873389.fastq.gz Approx 70% complete for SRR873388.fastq.gz Approx 100% complete for SRR873387.fastq.gz Analysis complete for SRR873387.fastq.gz Approx 75% complete for SRR873388.fastq.gz Approx 55% complete for SRR873389.fastq.gz Approx 60% complete for SRR873389.fastq.gz Approx 80% complete for SRR873388.fastq.gz Approx 85% complete for SRR873388.fastq.gz Approx 65% complete for SRR873389.fastq.gz Approx 90% complete for SRR873388.fastq.gz Approx 70% complete for SRR873389.fastq.gz Approx 95% complete for SRR873388.fastq.gz Approx 75% complete for SRR873389.fastq.gz Approx 100% complete for SRR873388.fastq.gz Approx 80% complete for SRR873389.fastq.gz Analysis complete for SRR873388.fastq.gz Approx 85% complete for SRR873389.fastq.gz Approx 90% complete for SRR873389.fastq.gz Approx 95% complete for SRR873389.fastq.gz Approx 100% complete for SRR873389.fastq.gz Analysis complete for SRR873389.fastq.gz CUTADAPT :: [Mon Jul 9 15:37:32 2018] Executing mkdir -p Examples/basic_examples/miRNAs/Known_miRNAs/results///cutadapt_results/ ; cut_adapt -b ATCTCGTATGCCGTCTTCTGCTTGAA -m 15 -M 35 -q 0 Examples/basic_examples/miRNAs/reads///SRR873382.fastq.gz > Examples/basic_examples/miRNAs/Known_miRNAs/results///cutadapt_results/SRR873382_cut.fastq 2>> Examples/basic_examples/miRNAs/Known_miRNAs/results//miARma_stat.2498.log CUTADAPT :: [Mon Jul 9 15:37:43 2018] Executing mkdir -p Examples/basic_examples/miRNAs/Known_miRNAs/results///cutadapt_results/ ; cut_adapt -b ATCTCGTATGCCGTCTTCTGCTTGAA -m 15 -M 35 -q 0 Examples/basic_examples/miRNAs/reads///SRR873383.fq.gz > Examples/basic_examples/miRNAs/Known_miRNAs/results///cutadapt_results/SRR873383_cut.fastq 2>> Examples/basic_examples/miRNAs/Known_miRNAs/results//miARma_stat.2498.log CUTADAPT :: [Mon Jul 9 15:37:52 2018] Executing mkdir -p Examples/basic_examples/miRNAs/Known_miRNAs/results///cutadapt_results/ ; cut_adapt -b ATCTCGTATGCCGTCTTCTGCTTGAA -m 15 -M 35 -q 0 Examples/basic_examples/miRNAs/reads///SRR873384.fastq.gz > Examples/basic_examples/miRNAs/Known_miRNAs/results///cutadapt_results/SRR873384_cut.fastq 2>> Examples/basic_examples/miRNAs/Known_miRNAs/results//miARma_stat.2498.log CUTADAPT :: [Mon Jul 9 15:38:02 2018] Executing mkdir -p Examples/basic_examples/miRNAs/Known_miRNAs/results///cutadapt_results/ ; cut_adapt -b ATCTCGTATGCCGTCTTCTGCTTGAA -m 15 -M 35 -q 0 Examples/basic_examples/miRNAs/reads///SRR873385.fq.gz > Examples/basic_examples/miRNAs/Known_miRNAs/results///cutadapt_results/SRR873385_cut.fastq 2>> Examples/basic_examples/miRNAs/Known_miRNAs/results//miARma_stat.2498.log CUTADAPT :: [Mon Jul 9 15:38:11 2018] Executing mkdir -p Examples/basic_examples/miRNAs/Known_miRNAs/results///cutadapt_results/ ; cut_adapt -b ATCTCGTATGCCGTCTTCTGCTTGAA -m 15 -M 35 -q 0 Examples/basic_examples/miRNAs/reads///SRR873386.fastq.gz > Examples/basic_examples/miRNAs/Known_miRNAs/results///cutadapt_results/SRR873386_cut.fastq 2>> Examples/basic_examples/miRNAs/Known_miRNAs/results//miARma_stat.2498.log CUTADAPT :: [Mon Jul 9 15:38:19 2018] Executing mkdir -p Examples/basic_examples/miRNAs/Known_miRNAs/results///cutadapt_results/ ; cut_adapt -b ATCTCGTATGCCGTCTTCTGCTTGAA -m 15 -M 35 -q 0 Examples/basic_examples/miRNAs/reads///SRR873387.fastq.gz > Examples/basic_examples/miRNAs/Known_miRNAs/results///cutadapt_results/SRR873387_cut.fastq 2>> Examples/basic_examples/miRNAs/Known_miRNAs/results//miARma_stat.2498.log CUTADAPT :: [Mon Jul 9 15:38:28 2018] Executing mkdir -p Examples/basic_examples/miRNAs/Known_miRNAs/results///cutadapt_results/ ; cut_adapt -b ATCTCGTATGCCGTCTTCTGCTTGAA -m 15 -M 35 -q 0 Examples/basic_examples/miRNAs/reads///SRR873388.fastq.gz > Examples/basic_examples/miRNAs/Known_miRNAs/results///cutadapt_results/SRR873388_cut.fastq 2>> Examples/basic_examples/miRNAs/Known_miRNAs/results//miARma_stat.2498.log CUTADAPT :: [Mon Jul 9 15:38:37 2018] Executing mkdir -p Examples/basic_examples/miRNAs/Known_miRNAs/results///cutadapt_results/ ; cut_adapt -b ATCTCGTATGCCGTCTTCTGCTTGAA -m 15 -M 35 -q 0 Examples/basic_examples/miRNAs/reads///SRR873389.fastq.gz > Examples/basic_examples/miRNAs/Known_miRNAs/results///cutadapt_results/SRR873389_cut.fastq 2>> Examples/basic_examples/miRNAs/Known_miRNAs/results//miARma_stat.2498.log FASTQC :: [Mon Jul 9 15:38:46 2018] Checking Examples/basic_examples/miRNAs/Known_miRNAs/results/ for FastQC analysis FASTQC :: [Mon Jul 9 15:38:46 2018] Executing mkdir -p Examples/basic_examples/miRNAs/Known_miRNAs/results//Post_fastqc_results/ ; fastqc -f fastq -t 4 Examples/basic_examples/miRNAs/Known_miRNAs/results///cutadapt_results/SRR873382_cut.fastq Examples/basic_examples/miRNAs/Known_miRNAs/results///cutadapt_results/SRR873383_cut.fastq Examples/basic_examples/miRNAs/Known_miRNAs/results///cutadapt_results/SRR873384_cut.fastq Examples/basic_examples/miRNAs/Known_miRNAs/results///cutadapt_results/SRR873385_cut.fastq Examples/basic_examples/miRNAs/Known_miRNAs/results///cutadapt_results/SRR873386_cut.fastq Examples/basic_examples/miRNAs/Known_miRNAs/results///cutadapt_results/SRR873387_cut.fastq Examples/basic_examples/miRNAs/Known_miRNAs/results///cutadapt_results/SRR873388_cut.fastq Examples/basic_examples/miRNAs/Known_miRNAs/results///cutadapt_results/SRR873389_cut.fastq -o Examples/basic_examples/miRNAs/Known_miRNAs/results//Post_fastqc_results/ >> Examples/basic_examples/miRNAs/Known_miRNAs/results//miARma_logfile.2498.log 2>&1 Started analysis of SRR873382_cut.fastq Approx 5% complete for SRR873382_cut.fastq Approx 10% complete for SRR873382_cut.fastq Approx 15% complete for SRR873382_cut.fastq Approx 20% complete for SRR873382_cut.fastq Approx 25% complete for SRR873382_cut.fastq Approx 30% complete for SRR873382_cut.fastq Started analysis of SRR873383_cut.fastq Approx 35% complete for SRR873382_cut.fastq Approx 5% complete for SRR873383_cut.fastq Approx 10% complete for SRR873383_cut.fastq Approx 40% complete for SRR873382_cut.fastq Approx 15% complete for SRR873383_cut.fastq Approx 45% complete for SRR873382_cut.fastq Approx 20% complete for SRR873383_cut.fastq Approx 50% complete for SRR873382_cut.fastq Approx 25% complete for SRR873383_cut.fastq Approx 55% complete for SRR873382_cut.fastq Approx 30% complete for SRR873383_cut.fastq Approx 60% complete for SRR873382_cut.fastq Approx 35% complete for SRR873383_cut.fastq Approx 65% complete for SRR873382_cut.fastq Started analysis of SRR873384_cut.fastq Approx 70% complete for SRR873382_cut.fastq Approx 40% complete for SRR873383_cut.fastq Approx 5% complete for SRR873384_cut.fastq Approx 75% complete for SRR873382_cut.fastq Approx 45% complete for SRR873383_cut.fastq Approx 10% complete for SRR873384_cut.fastq Approx 80% complete for SRR873382_cut.fastq Approx 15% complete for SRR873384_cut.fastq Approx 50% complete for SRR873383_cut.fastq Approx 85% complete for SRR873382_cut.fastq Approx 90% complete for SRR873382_cut.fastq Approx 20% complete for SRR873384_cut.fastq Approx 55% complete for SRR873383_cut.fastq Approx 95% complete for SRR873382_cut.fastq Approx 25% complete for SRR873384_cut.fastq Approx 60% complete for SRR873383_cut.fastq Analysis complete for SRR873382_cut.fastq Approx 30% complete for SRR873384_cut.fastq Approx 65% complete for SRR873383_cut.fastq Approx 35% complete for SRR873384_cut.fastq Started analysis of SRR873385_cut.fastq Approx 70% complete for SRR873383_cut.fastq Approx 40% complete for SRR873384_cut.fastq Approx 5% complete for SRR873385_cut.fastq Approx 75% complete for SRR873383_cut.fastq Approx 45% complete for SRR873384_cut.fastq Approx 10% complete for SRR873385_cut.fastq Approx 80% complete for SRR873383_cut.fastq Approx 50% complete for SRR873384_cut.fastq Approx 15% complete for SRR873385_cut.fastq Approx 85% complete for SRR873383_cut.fastq Approx 55% complete for SRR873384_cut.fastq Approx 20% complete for SRR873385_cut.fastq Approx 60% complete for SRR873384_cut.fastq Approx 25% complete for SRR873385_cut.fastq Approx 90% complete for SRR873383_cut.fastq Approx 65% complete for SRR873384_cut.fastq Approx 95% complete for SRR873383_cut.fastq Approx 30% complete for SRR873385_cut.fastq Approx 70% complete for SRR873384_cut.fastq Analysis complete for SRR873383_cut.fastq Approx 35% complete for SRR873385_cut.fastq Approx 75% complete for SRR873384_cut.fastq Approx 40% complete for SRR873385_cut.fastq Approx 80% complete for SRR873384_cut.fastq Approx 85% complete for SRR873384_cut.fastq Approx 45% complete for SRR873385_cut.fastq Approx 90% complete for SRR873384_cut.fastq Approx 50% complete for SRR873385_cut.fastq Approx 95% complete for SRR873384_cut.fastq Approx 55% complete for SRR873385_cut.fastq Approx 60% complete for SRR873385_cut.fastq Analysis complete for SRR873384_cut.fastq Approx 65% complete for SRR873385_cut.fastq Approx 70% complete for SRR873385_cut.fastq Approx 75% complete for SRR873385_cut.fastq Approx 80% complete for SRR873385_cut.fastq Approx 85% complete for SRR873385_cut.fastq Approx 90% complete for SRR873385_cut.fastq Approx 95% complete for SRR873385_cut.fastq Analysis complete for SRR873385_cut.fastq Started analysis of SRR873386_cut.fastq Approx 5% complete for SRR873386_cut.fastq Approx 10% complete for SRR873386_cut.fastq Approx 15% complete for SRR873386_cut.fastq Approx 20% complete for SRR873386_cut.fastq Approx 25% complete for SRR873386_cut.fastq Approx 30% complete for SRR873386_cut.fastq Approx 35% complete for SRR873386_cut.fastq Approx 40% complete for SRR873386_cut.fastq Approx 45% complete for SRR873386_cut.fastq Approx 50% complete for SRR873386_cut.fastq Started analysis of SRR873387_cut.fastq Approx 55% complete for SRR873386_cut.fastq Approx 5% complete for SRR873387_cut.fastq Approx 60% complete for SRR873386_cut.fastq Approx 10% complete for SRR873387_cut.fastq Approx 65% complete for SRR873386_cut.fastq Approx 15% complete for SRR873387_cut.fastq Approx 70% complete for SRR873386_cut.fastq Approx 20% complete for SRR873387_cut.fastq Approx 75% complete for SRR873386_cut.fastq Approx 25% complete for SRR873387_cut.fastq Approx 80% complete for SRR873386_cut.fastq Approx 30% complete for SRR873387_cut.fastq Approx 85% complete for SRR873386_cut.fastq Approx 35% complete for SRR873387_cut.fastq Approx 90% complete for SRR873386_cut.fastq Approx 40% complete for SRR873387_cut.fastq Approx 95% complete for SRR873386_cut.fastq Approx 45% complete for SRR873387_cut.fastq Analysis complete for SRR873386_cut.fastq Approx 50% complete for SRR873387_cut.fastq Started analysis of SRR873388_cut.fastq Approx 55% complete for SRR873387_cut.fastq Approx 5% complete for SRR873388_cut.fastq Approx 60% complete for SRR873387_cut.fastq Approx 10% complete for SRR873388_cut.fastq Approx 65% complete for SRR873387_cut.fastq Approx 15% complete for SRR873388_cut.fastq Approx 70% complete for SRR873387_cut.fastq Approx 20% complete for SRR873388_cut.fastq Approx 75% complete for SRR873387_cut.fastq Approx 25% complete for SRR873388_cut.fastq Approx 80% complete for SRR873387_cut.fastq Approx 30% complete for SRR873388_cut.fastq Approx 85% complete for SRR873387_cut.fastq Approx 35% complete for SRR873388_cut.fastq Approx 40% complete for SRR873388_cut.fastq Approx 90% complete for SRR873387_cut.fastq Started analysis of SRR873389_cut.fastq Approx 45% complete for SRR873388_cut.fastq Approx 95% complete for SRR873387_cut.fastq Approx 5% complete for SRR873389_cut.fastq Approx 50% complete for SRR873388_cut.fastq Analysis complete for SRR873387_cut.fastq Approx 10% complete for SRR873389_cut.fastq Approx 55% complete for SRR873388_cut.fastq Approx 15% complete for SRR873389_cut.fastq Approx 60% complete for SRR873388_cut.fastq Approx 20% complete for SRR873389_cut.fastq Approx 65% complete for SRR873388_cut.fastq Approx 25% complete for SRR873389_cut.fastq Approx 70% complete for SRR873388_cut.fastq Approx 30% complete for SRR873389_cut.fastq Approx 75% complete for SRR873388_cut.fastq Approx 35% complete for SRR873389_cut.fastq Approx 80% complete for SRR873388_cut.fastq Approx 40% complete for SRR873389_cut.fastq Approx 85% complete for SRR873388_cut.fastq Approx 45% complete for SRR873389_cut.fastq Approx 90% complete for SRR873388_cut.fastq Approx 50% complete for SRR873389_cut.fastq Approx 95% complete for SRR873388_cut.fastq Approx 55% complete for SRR873389_cut.fastq Analysis complete for SRR873388_cut.fastq Approx 60% complete for SRR873389_cut.fastq Approx 65% complete for SRR873389_cut.fastq Approx 70% complete for SRR873389_cut.fastq Approx 75% complete for SRR873389_cut.fastq Approx 80% complete for SRR873389_cut.fastq Approx 85% complete for SRR873389_cut.fastq Approx 90% complete for SRR873389_cut.fastq Approx 95% complete for SRR873389_cut.fastq Analysis complete for SRR873389_cut.fastq BOWTIE 1 :: [Mon Jul 9 15:38:55 2018] Executing mkdir -p Examples/basic_examples/miRNAs/Known_miRNAs/results//Bowtie1_results/ ;bowtie --sam -p 4 Genomes/Indexes/bowtie1/human/bw1_homo_sapiens19 Examples/basic_examples/miRNAs/Known_miRNAs/results//cutadapt_results/SRR873382_cut.fastq Examples/basic_examples/miRNAs/Known_miRNAs/results//Bowtie1_results/SRR873382_cut_bw1.bam 2>> Examples/basic_examples/miRNAs/Known_miRNAs/results//miARma_stat.2498.log File:Examples/basic_examples/miRNAs/Known_miRNAs/results//cutadapt_results/SRR873382_cut.fastq BOWTIE 1 :: [Mon Jul 9 15:40:14 2018] Executing mkdir -p Examples/basic_examples/miRNAs/Known_miRNAs/results//Bowtie1_results/ ;bowtie --sam -p 4 Genomes/Indexes/bowtie1/human/bw1_homo_sapiens19 Examples/basic_examples/miRNAs/Known_miRNAs/results//cutadapt_results/SRR873383_cut.fastq Examples/basic_examples/miRNAs/Known_miRNAs/results//Bowtie1_results/SRR873383_cut_bw1.bam 2>> Examples/basic_examples/miRNAs/Known_miRNAs/results//miARma_stat.2498.log File:Examples/basic_examples/miRNAs/Known_miRNAs/results//cutadapt_results/SRR873383_cut.fastq BOWTIE 1 :: [Mon Jul 9 15:40:17 2018] Executing mkdir -p Examples/basic_examples/miRNAs/Known_miRNAs/results//Bowtie1_results/ ;bowtie --sam -p 4 Genomes/Indexes/bowtie1/human/bw1_homo_sapiens19 Examples/basic_examples/miRNAs/Known_miRNAs/results//cutadapt_results/SRR873384_cut.fastq Examples/basic_examples/miRNAs/Known_miRNAs/results//Bowtie1_results/SRR873384_cut_bw1.bam 2>> Examples/basic_examples/miRNAs/Known_miRNAs/results//miARma_stat.2498.log File:Examples/basic_examples/miRNAs/Known_miRNAs/results//cutadapt_results/SRR873384_cut.fastq BOWTIE 1 :: [Mon Jul 9 15:40:20 2018] Executing mkdir -p Examples/basic_examples/miRNAs/Known_miRNAs/results//Bowtie1_results/ ;bowtie --sam -p 4 Genomes/Indexes/bowtie1/human/bw1_homo_sapiens19 Examples/basic_examples/miRNAs/Known_miRNAs/results//cutadapt_results/SRR873385_cut.fastq Examples/basic_examples/miRNAs/Known_miRNAs/results//Bowtie1_results/SRR873385_cut_bw1.bam 2>> Examples/basic_examples/miRNAs/Known_miRNAs/results//miARma_stat.2498.log File:Examples/basic_examples/miRNAs/Known_miRNAs/results//cutadapt_results/SRR873385_cut.fastq BOWTIE 1 :: [Mon Jul 9 15:40:23 2018] Executing mkdir -p Examples/basic_examples/miRNAs/Known_miRNAs/results//Bowtie1_results/ ;bowtie --sam -p 4 Genomes/Indexes/bowtie1/human/bw1_homo_sapiens19 Examples/basic_examples/miRNAs/Known_miRNAs/results//cutadapt_results/SRR873386_cut.fastq Examples/basic_examples/miRNAs/Known_miRNAs/results//Bowtie1_results/SRR873386_cut_bw1.bam 2>> Examples/basic_examples/miRNAs/Known_miRNAs/results//miARma_stat.2498.log File:Examples/basic_examples/miRNAs/Known_miRNAs/results//cutadapt_results/SRR873386_cut.fastq BOWTIE 1 :: [Mon Jul 9 15:40:26 2018] Executing mkdir -p Examples/basic_examples/miRNAs/Known_miRNAs/results//Bowtie1_results/ ;bowtie --sam -p 4 Genomes/Indexes/bowtie1/human/bw1_homo_sapiens19 Examples/basic_examples/miRNAs/Known_miRNAs/results//cutadapt_results/SRR873387_cut.fastq Examples/basic_examples/miRNAs/Known_miRNAs/results//Bowtie1_results/SRR873387_cut_bw1.bam 2>> Examples/basic_examples/miRNAs/Known_miRNAs/results//miARma_stat.2498.log File:Examples/basic_examples/miRNAs/Known_miRNAs/results//cutadapt_results/SRR873387_cut.fastq BOWTIE 1 :: [Mon Jul 9 15:40:29 2018] Executing mkdir -p Examples/basic_examples/miRNAs/Known_miRNAs/results//Bowtie1_results/ ;bowtie --sam -p 4 Genomes/Indexes/bowtie1/human/bw1_homo_sapiens19 Examples/basic_examples/miRNAs/Known_miRNAs/results//cutadapt_results/SRR873388_cut.fastq Examples/basic_examples/miRNAs/Known_miRNAs/results//Bowtie1_results/SRR873388_cut_bw1.bam 2>> Examples/basic_examples/miRNAs/Known_miRNAs/results//miARma_stat.2498.log File:Examples/basic_examples/miRNAs/Known_miRNAs/results//cutadapt_results/SRR873388_cut.fastq BOWTIE 1 :: [Mon Jul 9 15:40:33 2018] Executing mkdir -p Examples/basic_examples/miRNAs/Known_miRNAs/results//Bowtie1_results/ ;bowtie --sam -p 4 Genomes/Indexes/bowtie1/human/bw1_homo_sapiens19 Examples/basic_examples/miRNAs/Known_miRNAs/results//cutadapt_results/SRR873389_cut.fastq Examples/basic_examples/miRNAs/Known_miRNAs/results//Bowtie1_results/SRR873389_cut_bw1.bam 2>> Examples/basic_examples/miRNAs/Known_miRNAs/results//miARma_stat.2498.log File:Examples/basic_examples/miRNAs/Known_miRNAs/results//cutadapt_results/SRR873389_cut.fastq SEQCOUNT :: [Mon Jul 9 15:40:37 2018] Reading counts from Examples/basic_examples/miRNAs/Known_miRNAs/results//Bowtie1_results/SRR873386_cut_bw1.bam SEQCOUNT :: [Mon Jul 9 15:40:37 2018] Executing mkdir -p Examples/basic_examples/miRNAs/Known_miRNAs/results//cut_bw1_readcount_results/ ;featureCounts -s 1 -t miRNA -g transcript_id -T 4 -a Examples/basic_examples/miRNAs/data/miRBase_Annotation_20_for_hsa_mature_miRNA.gtf -o Examples/basic_examples/miRNAs/Known_miRNAs/results//cut_bw1_readcount_results/SRR873386_cut_bw1.tab Examples/basic_examples/miRNAs/Known_miRNAs/results//Bowtie1_results/SRR873386_cut_bw1.bam 2>> Examples/basic_examples/miRNAs/Known_miRNAs/results//miARma_logfile.2498.log ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.5.0-p1 //========================== featureCounts setting ===========================\\ || || || Input files : 1 SAM file || || S Examples/basic_examples/miRNAs/Known_miRNA ... || || || || Output file : Examples/basic_examples/miRNAs/Known_miRNAs/ ... || || Annotations : Examples/basic_examples/miRNAs/data/miRBase_ ... || || || || Threads : 4 || || Level : meta-feature level || || Paired-end : no || || Strand specific : yes || || Multimapping reads : not counted || || Multi-overlapping reads : not counted || || Read orientations : fr || || || \\===================== http://subread.sourceforge.net/ ======================// //================================= Running ==================================\\ || || || Load annotation file Examples/basic_examples/miRNAs/data/miRBase_Annot ... || || Features : 2794 || || Meta-features : 2576 || || Chromosomes/contigs : 24 || || || || Process SAM file Examples/basic_examples/miRNAs/Known_miRNAs/results// ... || || Single-end reads are included. || || Assign reads to features... || || Total reads : 450742 || || Successfully assigned reads : 397443 (88.2%) || || Running time : 0.01 minutes || || || || Read assignment finished. || || || \\===================== http://subread.sourceforge.net/ ======================// SEQCOUNT :: [Mon Jul 9 15:40:46 2018] Reading counts from Examples/basic_examples/miRNAs/Known_miRNAs/results//Bowtie1_results/SRR873382_cut_nat_bw1.bam SEQCOUNT :: [Mon Jul 9 15:40:46 2018] Executing mkdir -p Examples/basic_examples/miRNAs/Known_miRNAs/results//nat_bw1_readcount_results/ ;featureCounts -s 1 -t miRNA -g transcript_id -T 4 -a Examples/basic_examples/miRNAs/data/miRBase_Annotation_20_for_hsa_mature_miRNA.gtf -o Examples/basic_examples/miRNAs/Known_miRNAs/results//nat_bw1_readcount_results/SRR873382_cut_nat_bw1.tab Examples/basic_examples/miRNAs/Known_miRNAs/results//Bowtie1_results/SRR873382_cut_nat_bw1.bam 2>> Examples/basic_examples/miRNAs/Known_miRNAs/results//miARma_logfile.2498.log ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.5.0-p1 //========================== featureCounts setting ===========================\\ || || || Input files : 1 SAM file || || S Examples/basic_examples/miRNAs/Known_miRNA ... || || || || Output file : Examples/basic_examples/miRNAs/Known_miRNAs/ ... || || Annotations : Examples/basic_examples/miRNAs/data/miRBase_ ... || || || || Threads : 4 || || Level : meta-feature level || || Paired-end : no || || Strand specific : yes || || Multimapping reads : not counted || || Multi-overlapping reads : not counted || || Read orientations : fr || || || \\===================== http://subread.sourceforge.net/ ======================// //================================= Running ==================================\\ || || || Load annotation file Examples/basic_examples/miRNAs/data/miRBase_Annot ... || || Features : 2794 || || Meta-features : 2576 || || Chromosomes/contigs : 24 || || || || Process SAM file Examples/basic_examples/miRNAs/Known_miRNAs/results// ... || || Single-end reads are included. || || Assign reads to features... || || Total reads : 0 || || Successfully assigned reads : 0 || || Running time : 0.00 minutes || || || || Read assignment finished. || || || \\===================== http://subread.sourceforge.net/ ======================// SEQCOUNT :: [Mon Jul 9 15:40:46 2018] Reading counts from Examples/basic_examples/miRNAs/Known_miRNAs/results//Bowtie1_results/SRR873389_cut_bw1.bam SEQCOUNT :: [Mon Jul 9 15:40:46 2018] Executing mkdir -p Examples/basic_examples/miRNAs/Known_miRNAs/results//cut_bw1_readcount_results/ ;featureCounts -s 1 -t miRNA -g transcript_id -T 4 -a Examples/basic_examples/miRNAs/data/miRBase_Annotation_20_for_hsa_mature_miRNA.gtf -o Examples/basic_examples/miRNAs/Known_miRNAs/results//cut_bw1_readcount_results/SRR873389_cut_bw1.tab Examples/basic_examples/miRNAs/Known_miRNAs/results//Bowtie1_results/SRR873389_cut_bw1.bam 2>> Examples/basic_examples/miRNAs/Known_miRNAs/results//miARma_logfile.2498.log ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.5.0-p1 //========================== featureCounts setting ===========================\\ || || || Input files : 1 SAM file || || S Examples/basic_examples/miRNAs/Known_miRNA ... || || || || Output file : Examples/basic_examples/miRNAs/Known_miRNAs/ ... || || Annotations : Examples/basic_examples/miRNAs/data/miRBase_ ... || || || || Threads : 4 || || Level : meta-feature level || || Paired-end : no || || Strand specific : yes || || Multimapping reads : not counted || || Multi-overlapping reads : not counted || || Read orientations : fr || || || \\===================== http://subread.sourceforge.net/ ======================// //================================= Running ==================================\\ || || || Load annotation file Examples/basic_examples/miRNAs/data/miRBase_Annot ... || || Features : 2794 || || Meta-features : 2576 || || Chromosomes/contigs : 24 || || || || Process SAM file Examples/basic_examples/miRNAs/Known_miRNAs/results// ... || || Single-end reads are included. || || Assign reads to features... || || Total reads : 455626 || || Successfully assigned reads : 406908 (89.3%) || || Running time : 0.01 minutes || || || || Read assignment finished. || || || \\===================== http://subread.sourceforge.net/ ======================// SEQCOUNT :: [Mon Jul 9 15:40:46 2018] Reading counts from Examples/basic_examples/miRNAs/Known_miRNAs/results//Bowtie1_results/SRR873385_cut_bw1.bam SEQCOUNT :: [Mon Jul 9 15:40:46 2018] Executing mkdir -p Examples/basic_examples/miRNAs/Known_miRNAs/results//cut_bw1_readcount_results/ ;featureCounts -s 1 -t miRNA -g transcript_id -T 4 -a Examples/basic_examples/miRNAs/data/miRBase_Annotation_20_for_hsa_mature_miRNA.gtf -o Examples/basic_examples/miRNAs/Known_miRNAs/results//cut_bw1_readcount_results/SRR873385_cut_bw1.tab Examples/basic_examples/miRNAs/Known_miRNAs/results//Bowtie1_results/SRR873385_cut_bw1.bam 2>> Examples/basic_examples/miRNAs/Known_miRNAs/results//miARma_logfile.2498.log ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.5.0-p1 //========================== featureCounts setting ===========================\\ || || || Input files : 1 SAM file || || S Examples/basic_examples/miRNAs/Known_miRNA ... || || || || Output file : Examples/basic_examples/miRNAs/Known_miRNAs/ ... || || Annotations : Examples/basic_examples/miRNAs/data/miRBase_ ... || || || || Threads : 4 || || Level : meta-feature level || || Paired-end : no || || Strand specific : yes || || Multimapping reads : not counted || || Multi-overlapping reads : not counted || || Read orientations : fr || || || \\===================== http://subread.sourceforge.net/ ======================// //================================= Running ==================================\\ || || || Load annotation file Examples/basic_examples/miRNAs/data/miRBase_Annot ... || || Features : 2794 || || Meta-features : 2576 || || Chromosomes/contigs : 24 || || || || Process SAM file Examples/basic_examples/miRNAs/Known_miRNAs/results// ... || || Single-end reads are included. || || Assign reads to features... || || Total reads : 403684 || || Successfully assigned reads : 348082 (86.2%) || || Running time : 0.00 minutes || || || || Read assignment finished. || || || \\===================== http://subread.sourceforge.net/ ======================// SEQCOUNT :: [Mon Jul 9 15:40:46 2018] Reading counts from Examples/basic_examples/miRNAs/Known_miRNAs/results//Bowtie1_results/SRR873388_cut_bw1.bam SEQCOUNT :: [Mon Jul 9 15:40:46 2018] Executing mkdir -p Examples/basic_examples/miRNAs/Known_miRNAs/results//cut_bw1_readcount_results/ ;featureCounts -s 1 -t miRNA -g transcript_id -T 4 -a Examples/basic_examples/miRNAs/data/miRBase_Annotation_20_for_hsa_mature_miRNA.gtf -o Examples/basic_examples/miRNAs/Known_miRNAs/results//cut_bw1_readcount_results/SRR873388_cut_bw1.tab Examples/basic_examples/miRNAs/Known_miRNAs/results//Bowtie1_results/SRR873388_cut_bw1.bam 2>> Examples/basic_examples/miRNAs/Known_miRNAs/results//miARma_logfile.2498.log ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.5.0-p1 //========================== featureCounts setting ===========================\\ || || || Input files : 1 SAM file || || S Examples/basic_examples/miRNAs/Known_miRNA ... || || || || Output file : Examples/basic_examples/miRNAs/Known_miRNAs/ ... || || Annotations : Examples/basic_examples/miRNAs/data/miRBase_ ... || || || || Threads : 4 || || Level : meta-feature level || || Paired-end : no || || Strand specific : yes || || Multimapping reads : not counted || || Multi-overlapping reads : not counted || || Read orientations : fr || || || \\===================== http://subread.sourceforge.net/ ======================// //================================= Running ==================================\\ || || || Load annotation file Examples/basic_examples/miRNAs/data/miRBase_Annot ... || || Features : 2794 || || Meta-features : 2576 || || Chromosomes/contigs : 24 || || || || Process SAM file Examples/basic_examples/miRNAs/Known_miRNAs/results// ... || || Single-end reads are included. || || Assign reads to features... || || Total reads : 438489 || || Successfully assigned reads : 392926 (89.6%) || || Running time : 0.00 minutes || || || || Read assignment finished. || || || \\===================== http://subread.sourceforge.net/ ======================// SEQCOUNT :: [Mon Jul 9 15:40:47 2018] Reading counts from Examples/basic_examples/miRNAs/Known_miRNAs/results//Bowtie1_results/SRR873384_cut_bw1.bam SEQCOUNT :: [Mon Jul 9 15:40:47 2018] Executing mkdir -p Examples/basic_examples/miRNAs/Known_miRNAs/results//cut_bw1_readcount_results/ ;featureCounts -s 1 -t miRNA -g transcript_id -T 4 -a Examples/basic_examples/miRNAs/data/miRBase_Annotation_20_for_hsa_mature_miRNA.gtf -o Examples/basic_examples/miRNAs/Known_miRNAs/results//cut_bw1_readcount_results/SRR873384_cut_bw1.tab Examples/basic_examples/miRNAs/Known_miRNAs/results//Bowtie1_results/SRR873384_cut_bw1.bam 2>> Examples/basic_examples/miRNAs/Known_miRNAs/results//miARma_logfile.2498.log ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.5.0-p1 //========================== featureCounts setting ===========================\\ || || || Input files : 1 SAM file || || S Examples/basic_examples/miRNAs/Known_miRNA ... || || || || Output file : Examples/basic_examples/miRNAs/Known_miRNAs/ ... || || Annotations : Examples/basic_examples/miRNAs/data/miRBase_ ... || || || || Threads : 4 || || Level : meta-feature level || || Paired-end : no || || Strand specific : yes || || Multimapping reads : not counted || || Multi-overlapping reads : not counted || || Read orientations : fr || || || \\===================== http://subread.sourceforge.net/ ======================// //================================= Running ==================================\\ || || || Load annotation file Examples/basic_examples/miRNAs/data/miRBase_Annot ... || || Features : 2794 || || Meta-features : 2576 || || Chromosomes/contigs : 24 || || || || Process SAM file Examples/basic_examples/miRNAs/Known_miRNAs/results// ... || || Single-end reads are included. || || Assign reads to features... || || Total reads : 403176 || || Successfully assigned reads : 367790 (91.2%) || || Running time : 0.00 minutes || || || || Read assignment finished. || || || \\===================== http://subread.sourceforge.net/ ======================// SEQCOUNT :: [Mon Jul 9 15:40:47 2018] Reading counts from Examples/basic_examples/miRNAs/Known_miRNAs/results//Bowtie1_results/SRR873382_cut_bw1.bam SEQCOUNT :: [Mon Jul 9 15:40:47 2018] Executing mkdir -p Examples/basic_examples/miRNAs/Known_miRNAs/results//cut_bw1_readcount_results/ ;featureCounts -s 1 -t miRNA -g transcript_id -T 4 -a Examples/basic_examples/miRNAs/data/miRBase_Annotation_20_for_hsa_mature_miRNA.gtf -o Examples/basic_examples/miRNAs/Known_miRNAs/results//cut_bw1_readcount_results/SRR873382_cut_bw1.tab Examples/basic_examples/miRNAs/Known_miRNAs/results//Bowtie1_results/SRR873382_cut_bw1.bam 2>> Examples/basic_examples/miRNAs/Known_miRNAs/results//miARma_logfile.2498.log ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.5.0-p1 //========================== featureCounts setting ===========================\\ || || || Input files : 1 SAM file || || S Examples/basic_examples/miRNAs/Known_miRNA ... || || || || Output file : Examples/basic_examples/miRNAs/Known_miRNAs/ ... || || Annotations : Examples/basic_examples/miRNAs/data/miRBase_ ... || || || || Threads : 4 || || Level : meta-feature level || || Paired-end : no || || Strand specific : yes || || Multimapping reads : not counted || || Multi-overlapping reads : not counted || || Read orientations : fr || || || \\===================== http://subread.sourceforge.net/ ======================// //================================= Running ==================================\\ || || || Load annotation file Examples/basic_examples/miRNAs/data/miRBase_Annot ... || || Features : 2794 || || Meta-features : 2576 || || Chromosomes/contigs : 24 || || || || Process SAM file Examples/basic_examples/miRNAs/Known_miRNAs/results// ... || || Single-end reads are included. || || Assign reads to features... || || Total reads : 442541 || || Successfully assigned reads : 392038 (88.6%) || || Running time : 0.01 minutes || || || || Read assignment finished. || || || \\===================== http://subread.sourceforge.net/ ======================// SEQCOUNT :: [Mon Jul 9 15:40:47 2018] Reading counts from Examples/basic_examples/miRNAs/Known_miRNAs/results//Bowtie1_results/SRR873383_cut_bw1.bam SEQCOUNT :: [Mon Jul 9 15:40:47 2018] Executing mkdir -p Examples/basic_examples/miRNAs/Known_miRNAs/results//cut_bw1_readcount_results/ ;featureCounts -s 1 -t miRNA -g transcript_id -T 4 -a Examples/basic_examples/miRNAs/data/miRBase_Annotation_20_for_hsa_mature_miRNA.gtf -o Examples/basic_examples/miRNAs/Known_miRNAs/results//cut_bw1_readcount_results/SRR873383_cut_bw1.tab Examples/basic_examples/miRNAs/Known_miRNAs/results//Bowtie1_results/SRR873383_cut_bw1.bam 2>> Examples/basic_examples/miRNAs/Known_miRNAs/results//miARma_logfile.2498.log ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.5.0-p1 //========================== featureCounts setting ===========================\\ || || || Input files : 1 SAM file || || S Examples/basic_examples/miRNAs/Known_miRNA ... || || || || Output file : Examples/basic_examples/miRNAs/Known_miRNAs/ ... || || Annotations : Examples/basic_examples/miRNAs/data/miRBase_ ... || || || || Threads : 4 || || Level : meta-feature level || || Paired-end : no || || Strand specific : yes || || Multimapping reads : not counted || || Multi-overlapping reads : not counted || || Read orientations : fr || || || \\===================== http://subread.sourceforge.net/ ======================// //================================= Running ==================================\\ || || || Load annotation file Examples/basic_examples/miRNAs/data/miRBase_Annot ... || || Features : 2794 || || Meta-features : 2576 || || Chromosomes/contigs : 24 || || || || Process SAM file Examples/basic_examples/miRNAs/Known_miRNAs/results// ... || || Single-end reads are included. || || Assign reads to features... || || Total reads : 434156 || || Successfully assigned reads : 387241 (89.2%) || || Running time : 0.00 minutes || || || || Read assignment finished. || || || \\===================== http://subread.sourceforge.net/ ======================// SEQCOUNT :: [Mon Jul 9 15:40:47 2018] Reading counts from Examples/basic_examples/miRNAs/Known_miRNAs/results//Bowtie1_results/SRR873387_cut_bw1.bam SEQCOUNT :: [Mon Jul 9 15:40:47 2018] Executing mkdir -p Examples/basic_examples/miRNAs/Known_miRNAs/results//cut_bw1_readcount_results/ ;featureCounts -s 1 -t miRNA -g transcript_id -T 4 -a Examples/basic_examples/miRNAs/data/miRBase_Annotation_20_for_hsa_mature_miRNA.gtf -o Examples/basic_examples/miRNAs/Known_miRNAs/results//cut_bw1_readcount_results/SRR873387_cut_bw1.tab Examples/basic_examples/miRNAs/Known_miRNAs/results//Bowtie1_results/SRR873387_cut_bw1.bam 2>> Examples/basic_examples/miRNAs/Known_miRNAs/results//miARma_logfile.2498.log ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.5.0-p1 //========================== featureCounts setting ===========================\\ || || || Input files : 1 SAM file || || S Examples/basic_examples/miRNAs/Known_miRNA ... || || || || Output file : Examples/basic_examples/miRNAs/Known_miRNAs/ ... || || Annotations : Examples/basic_examples/miRNAs/data/miRBase_ ... || || || || Threads : 4 || || Level : meta-feature level || || Paired-end : no || || Strand specific : yes || || Multimapping reads : not counted || || Multi-overlapping reads : not counted || || Read orientations : fr || || || \\===================== http://subread.sourceforge.net/ ======================// //================================= Running ==================================\\ || || || Load annotation file Examples/basic_examples/miRNAs/data/miRBase_Annot ... || || Features : 2794 || || Meta-features : 2576 || || Chromosomes/contigs : 24 || || || || Process SAM file Examples/basic_examples/miRNAs/Known_miRNAs/results// ... || || Single-end reads are included. || || Assign reads to features... || || Total reads : 445004 || || Successfully assigned reads : 392979 (88.3%) || || Running time : 0.01 minutes || || || || Read assignment finished. || || || \\===================== http://subread.sourceforge.net/ ======================// SEQCOUNT :: [Mon Jul 9 15:40:48 2018] Please check the folder: Examples/basic_examples/miRNAs/Known_miRNAs/results//Readcount_results/. QC_EdgeR :: [Mon Jul 9 15:40:48 2018] Executing source("./lib/CbBio/RNASeq/R-Scripts/QC_EdgeR.R") setwd("/home/leila/apps/miARma/cbbio-miarma-42e187a7f514/Examples/basic_examples/miRNAs/Known_miRNAs/results/Readcount_results") resultsfiles<-QC_EdgeR(projectdir="/home/leila/apps/miARma/cbbio-miarma-42e187a7f514/Examples/basic_examples/miRNAs/Known_miRNAs/results",dir="/home/leila/apps/miARma/cbbio-miarma-42e187a7f514/Examples/basic_examples/miRNAs/Known_miRNAs/results/Readcount_results", file="cut_bw1-ReadCount.tab", targetfile="/home/leila/apps/miARma/cbbio-miarma-42e187a7f514/Examples/basic_examples/miRNAs/data/targets.txt", label="Hypoxia_cut_bw1", filter="yes")