FASTQC :: [Mon Jul 2 14:53:44 2018] Checking /mnt/Raid_Dell/RNAseq.Dietas.Dmel/smRNA/Known_miRNAs/results/ for FastQC analysis FASTQC :: [Mon Jul 2 14:53:44 2018] Executing mkdir -p /mnt/Raid_Dell/RNAseq.Dietas.Dmel/smRNA/Known_miRNAs/results//Pre_fastqc_results/ ; fastqc -f fastq -t 20 /mnt/Raid_Dell/RNAseq.Dietas.Dmel/smRNA//HF-2_S3_L001_R1_001.fastq.gz /mnt/Raid_Dell/RNAseq.Dietas.Dmel/smRNA//HS-2_S2_L001_R1_001.fastq.gz /mnt/Raid_Dell/RNAseq.Dietas.Dmel/smRNA//LS-2_S1_L001_R1_001.fastq.gz -o /mnt/Raid_Dell/RNAseq.Dietas.Dmel/smRNA/Known_miRNAs/results//Pre_fastqc_results/ >> /mnt/Raid_Dell/RNAseq.Dietas.Dmel/smRNA/Known_miRNAs/results/run_log.log 2>&1 Started analysis of HF-2_S3_L001_R1_001.fastq.gz Started analysis of HS-2_S2_L001_R1_001.fastq.gz Started analysis of LS-2_S1_L001_R1_001.fastq.gz Approx 5% complete for HF-2_S3_L001_R1_001.fastq.gz Approx 5% complete for HS-2_S2_L001_R1_001.fastq.gz Approx 5% complete for LS-2_S1_L001_R1_001.fastq.gz Approx 10% complete for HF-2_S3_L001_R1_001.fastq.gz Approx 10% complete for HS-2_S2_L001_R1_001.fastq.gz Approx 10% complete for LS-2_S1_L001_R1_001.fastq.gz Approx 15% complete for HF-2_S3_L001_R1_001.fastq.gz Approx 15% complete for HS-2_S2_L001_R1_001.fastq.gz Approx 20% complete for HF-2_S3_L001_R1_001.fastq.gz Approx 15% complete for LS-2_S1_L001_R1_001.fastq.gz Approx 25% complete for HF-2_S3_L001_R1_001.fastq.gz Approx 20% complete for HS-2_S2_L001_R1_001.fastq.gz Approx 20% complete for LS-2_S1_L001_R1_001.fastq.gz Approx 30% complete for HF-2_S3_L001_R1_001.fastq.gz Approx 25% complete for HS-2_S2_L001_R1_001.fastq.gz Approx 35% complete for HF-2_S3_L001_R1_001.fastq.gz Approx 25% complete for LS-2_S1_L001_R1_001.fastq.gz Approx 30% complete for HS-2_S2_L001_R1_001.fastq.gz Approx 40% complete for HF-2_S3_L001_R1_001.fastq.gz Approx 30% complete for LS-2_S1_L001_R1_001.fastq.gz Approx 45% complete for HF-2_S3_L001_R1_001.fastq.gz Approx 35% complete for HS-2_S2_L001_R1_001.fastq.gz Approx 50% complete for HF-2_S3_L001_R1_001.fastq.gz Approx 35% complete for LS-2_S1_L001_R1_001.fastq.gz Approx 40% complete for HS-2_S2_L001_R1_001.fastq.gz Approx 55% complete for HF-2_S3_L001_R1_001.fastq.gz Approx 40% complete for LS-2_S1_L001_R1_001.fastq.gz Approx 45% complete for HS-2_S2_L001_R1_001.fastq.gz Approx 60% complete for HF-2_S3_L001_R1_001.fastq.gz Approx 65% complete for HF-2_S3_L001_R1_001.fastq.gz Approx 45% complete for LS-2_S1_L001_R1_001.fastq.gz Approx 50% complete for HS-2_S2_L001_R1_001.fastq.gz Approx 70% complete for HF-2_S3_L001_R1_001.fastq.gz Approx 55% complete for HS-2_S2_L001_R1_001.fastq.gz Approx 50% complete for LS-2_S1_L001_R1_001.fastq.gz Approx 75% complete for HF-2_S3_L001_R1_001.fastq.gz Approx 60% complete for HS-2_S2_L001_R1_001.fastq.gz Approx 80% complete for HF-2_S3_L001_R1_001.fastq.gz Approx 55% complete for LS-2_S1_L001_R1_001.fastq.gz Approx 85% complete for HF-2_S3_L001_R1_001.fastq.gz Approx 65% complete for HS-2_S2_L001_R1_001.fastq.gz Approx 60% complete for LS-2_S1_L001_R1_001.fastq.gz Approx 90% complete for HF-2_S3_L001_R1_001.fastq.gz Approx 70% complete for HS-2_S2_L001_R1_001.fastq.gz Approx 65% complete for LS-2_S1_L001_R1_001.fastq.gz Approx 95% complete for HF-2_S3_L001_R1_001.fastq.gz Approx 75% complete for HS-2_S2_L001_R1_001.fastq.gz Analysis complete for HF-2_S3_L001_R1_001.fastq.gz Approx 70% complete for LS-2_S1_L001_R1_001.fastq.gz Approx 80% complete for HS-2_S2_L001_R1_001.fastq.gz Approx 75% complete for LS-2_S1_L001_R1_001.fastq.gz Approx 85% complete for HS-2_S2_L001_R1_001.fastq.gz Approx 80% complete for LS-2_S1_L001_R1_001.fastq.gz Approx 90% complete for HS-2_S2_L001_R1_001.fastq.gz Approx 85% complete for LS-2_S1_L001_R1_001.fastq.gz Approx 95% complete for HS-2_S2_L001_R1_001.fastq.gz Approx 90% complete for LS-2_S1_L001_R1_001.fastq.gz Analysis complete for HS-2_S2_L001_R1_001.fastq.gz Approx 95% complete for LS-2_S1_L001_R1_001.fastq.gz Analysis complete for LS-2_S1_L001_R1_001.fastq.gz CUTADAPT :: [Mon Jul 2 14:55:51 2018] Executing mkdir -p /mnt/Raid_Dell/RNAseq.Dietas.Dmel/smRNA/Known_miRNAs/results///cutadapt_results/ ; cut_adapt -b AGATCGGAAGAG -m 15 -M 35 -q 0 /mnt/Raid_Dell/RNAseq.Dietas.Dmel/smRNA///HF-2_S3_L001_R1_001.fastq.gz > /mnt/Raid_Dell/RNAseq.Dietas.Dmel/smRNA/Known_miRNAs/results///cutadapt_results/HF-2_S3_L001_R1_001_cut.fastq 2>> /mnt/Raid_Dell/RNAseq.Dietas.Dmel/smRNA/Known_miRNAs/results/miARma_stat.871.log CUTADAPT :: [Mon Jul 2 15:00:32 2018] Executing mkdir -p /mnt/Raid_Dell/RNAseq.Dietas.Dmel/smRNA/Known_miRNAs/results///cutadapt_results/ ; cut_adapt -b AGATCGGAAGAG -m 15 -M 35 -q 0 /mnt/Raid_Dell/RNAseq.Dietas.Dmel/smRNA///HS-2_S2_L001_R1_001.fastq.gz > /mnt/Raid_Dell/RNAseq.Dietas.Dmel/smRNA/Known_miRNAs/results///cutadapt_results/HS-2_S2_L001_R1_001_cut.fastq 2>> /mnt/Raid_Dell/RNAseq.Dietas.Dmel/smRNA/Known_miRNAs/results/miARma_stat.871.log CUTADAPT :: [Mon Jul 2 15:06:59 2018] Executing mkdir -p /mnt/Raid_Dell/RNAseq.Dietas.Dmel/smRNA/Known_miRNAs/results///cutadapt_results/ ; cut_adapt -b AGATCGGAAGAG -m 15 -M 35 -q 0 /mnt/Raid_Dell/RNAseq.Dietas.Dmel/smRNA///LS-2_S1_L001_R1_001.fastq.gz > /mnt/Raid_Dell/RNAseq.Dietas.Dmel/smRNA/Known_miRNAs/results///cutadapt_results/LS-2_S1_L001_R1_001_cut.fastq 2>> /mnt/Raid_Dell/RNAseq.Dietas.Dmel/smRNA/Known_miRNAs/results/miARma_stat.871.log FASTQC :: [Mon Jul 2 15:14:14 2018] Checking /mnt/Raid_Dell/RNAseq.Dietas.Dmel/smRNA/Known_miRNAs/results/ for FastQC analysis FASTQC :: [Mon Jul 2 15:14:14 2018] Executing mkdir -p /mnt/Raid_Dell/RNAseq.Dietas.Dmel/smRNA/Known_miRNAs/results//Post_fastqc_results/ ; fastqc -f fastq -t 20 /mnt/Raid_Dell/RNAseq.Dietas.Dmel/smRNA/Known_miRNAs/results///cutadapt_results/HF-2_S3_L001_R1_001_cut.fastq /mnt/Raid_Dell/RNAseq.Dietas.Dmel/smRNA/Known_miRNAs/results///cutadapt_results/HS-2_S2_L001_R1_001_cut.fastq /mnt/Raid_Dell/RNAseq.Dietas.Dmel/smRNA/Known_miRNAs/results///cutadapt_results/LS-2_S1_L001_R1_001_cut.fastq -o /mnt/Raid_Dell/RNAseq.Dietas.Dmel/smRNA/Known_miRNAs/results//Post_fastqc_results/ >> /mnt/Raid_Dell/RNAseq.Dietas.Dmel/smRNA/Known_miRNAs/results/run_log.log 2>&1 Started analysis of HF-2_S3_L001_R1_001_cut.fastq Approx 5% complete for HF-2_S3_L001_R1_001_cut.fastq Approx 10% complete for HF-2_S3_L001_R1_001_cut.fastq Approx 15% complete for HF-2_S3_L001_R1_001_cut.fastq Approx 20% complete for HF-2_S3_L001_R1_001_cut.fastq Approx 25% complete for HF-2_S3_L001_R1_001_cut.fastq Approx 30% complete for HF-2_S3_L001_R1_001_cut.fastq Approx 35% complete for HF-2_S3_L001_R1_001_cut.fastq Approx 40% complete for HF-2_S3_L001_R1_001_cut.fastq Approx 45% complete for HF-2_S3_L001_R1_001_cut.fastq Approx 50% complete for HF-2_S3_L001_R1_001_cut.fastq Approx 55% complete for HF-2_S3_L001_R1_001_cut.fastq Approx 60% complete for HF-2_S3_L001_R1_001_cut.fastq Approx 65% complete for HF-2_S3_L001_R1_001_cut.fastq Approx 70% complete for HF-2_S3_L001_R1_001_cut.fastq Approx 75% complete for HF-2_S3_L001_R1_001_cut.fastq Approx 80% complete for HF-2_S3_L001_R1_001_cut.fastq Approx 85% complete for HF-2_S3_L001_R1_001_cut.fastq Approx 90% complete for HF-2_S3_L001_R1_001_cut.fastq Approx 95% complete for HF-2_S3_L001_R1_001_cut.fastq Analysis complete for HF-2_S3_L001_R1_001_cut.fastq Started analysis of HS-2_S2_L001_R1_001_cut.fastq Approx 5% complete for HS-2_S2_L001_R1_001_cut.fastq Approx 10% complete for HS-2_S2_L001_R1_001_cut.fastq Approx 15% complete for HS-2_S2_L001_R1_001_cut.fastq Approx 20% complete for HS-2_S2_L001_R1_001_cut.fastq Approx 25% complete for HS-2_S2_L001_R1_001_cut.fastq Approx 30% complete for HS-2_S2_L001_R1_001_cut.fastq Approx 35% complete for HS-2_S2_L001_R1_001_cut.fastq Approx 40% complete for HS-2_S2_L001_R1_001_cut.fastq Approx 45% complete for HS-2_S2_L001_R1_001_cut.fastq Approx 50% complete for HS-2_S2_L001_R1_001_cut.fastq Approx 55% complete for HS-2_S2_L001_R1_001_cut.fastq Approx 60% complete for HS-2_S2_L001_R1_001_cut.fastq Approx 65% complete for HS-2_S2_L001_R1_001_cut.fastq Approx 70% complete for HS-2_S2_L001_R1_001_cut.fastq Approx 75% complete for HS-2_S2_L001_R1_001_cut.fastq Approx 80% complete for HS-2_S2_L001_R1_001_cut.fastq Approx 85% complete for HS-2_S2_L001_R1_001_cut.fastq Approx 90% complete for HS-2_S2_L001_R1_001_cut.fastq Approx 95% complete for HS-2_S2_L001_R1_001_cut.fastq Analysis complete for HS-2_S2_L001_R1_001_cut.fastq Started analysis of LS-2_S1_L001_R1_001_cut.fastq Approx 5% complete for LS-2_S1_L001_R1_001_cut.fastq Approx 10% complete for LS-2_S1_L001_R1_001_cut.fastq Approx 15% complete for LS-2_S1_L001_R1_001_cut.fastq Approx 20% complete for LS-2_S1_L001_R1_001_cut.fastq Approx 25% complete for LS-2_S1_L001_R1_001_cut.fastq Approx 30% complete for LS-2_S1_L001_R1_001_cut.fastq Approx 35% complete for LS-2_S1_L001_R1_001_cut.fastq Approx 40% complete for LS-2_S1_L001_R1_001_cut.fastq Approx 45% complete for LS-2_S1_L001_R1_001_cut.fastq Approx 50% complete for LS-2_S1_L001_R1_001_cut.fastq Approx 55% complete for LS-2_S1_L001_R1_001_cut.fastq Approx 60% complete for LS-2_S1_L001_R1_001_cut.fastq Approx 65% complete for LS-2_S1_L001_R1_001_cut.fastq Approx 70% complete for LS-2_S1_L001_R1_001_cut.fastq Approx 75% complete for LS-2_S1_L001_R1_001_cut.fastq Approx 80% complete for LS-2_S1_L001_R1_001_cut.fastq Approx 85% complete for LS-2_S1_L001_R1_001_cut.fastq Approx 90% complete for LS-2_S1_L001_R1_001_cut.fastq Approx 95% complete for LS-2_S1_L001_R1_001_cut.fastq Analysis complete for LS-2_S1_L001_R1_001_cut.fastq BOWTIE2_INDEX :: [Mon Jul 2 15:14:19 2018] Executing mkdir -p /mnt/Raid_Dell/RNAseq.Dietas.Dmel/smRNA/Known_miRNAs/results//Bowtie2_index ; bowtie2-build --threads 20 -f /mnt/Raid_Dell/Dmel.genome/fastas.flybase/dmel-all-chromosome-r6.21.fasta /mnt/Raid_Dell/RNAseq.Dietas.Dmel/smRNA/Known_miRNAs/results//Bowtie2_index/dmel.flybase >> /mnt/Raid_Dell/RNAseq.Dietas.Dmel/smRNA/Known_miRNAs/results/run_log.log 2>&1 Settings: Output files: "/mnt/Raid_Dell/RNAseq.Dietas.Dmel/smRNA/Known_miRNAs/results//Bowtie2_index/dmel.flybase.*.bt2" Line rate: 6 (line is 64 bytes) Lines per side: 1 (side is 64 bytes) Offset rate: 4 (one in 16) FTable chars: 10 Strings: unpacked Max bucket size: default Max bucket size, sqrt multiplier: default Max bucket size, len divisor: 4 Difference-cover sample period: 1024 Endianness: little Actual local endianness: little Sanity checking: disabled Assertions: disabled Random seed: 0 Sizeofs: void*:8, int:4, long:8, size_t:8 Input files DNA, FASTA: /mnt/Raid_Dell/Dmel.genome/fastas.flybase/dmel-all-chromosome-r6.21.fasta Building a SMALL index Reading reference sizes Time reading reference sizes: 00:00:02 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:01 bmax according to bmaxDivN setting: 35643256 Using parameters --bmax 26732442 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 26732442 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:02 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:00:01 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:00:01 Sanity-checking and returning Building samples Reserving space for 12 sample suffixes Generating random suffixes QSorting 12 sample offsets, eliminating duplicates QSorting sample offsets, eliminating duplicates time: 00:00:00 Multikey QSorting 12 samples (Using difference cover) Multikey QSorting samples time: 00:00:00 Calculating bucket sizes Splitting and merging Splitting and merging time: 00:00:00 Split 1, merged 4; iterating... Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 1.58414e+07 (target: 26732441) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 9 Reserving size (26732442) for bucket 1 Getting block 2 of 9 Getting block 4 of 9 Getting block 3 of 9 Reserving size (26732442) for bucket 3 Reserving size (26732442) for bucket 4 Reserving size (26732442) for bucket 2 Getting block 5 of 9 Calculating Z arrays for bucket 1 Reserving size (26732442) for bucket 5 Getting block 6 of 9 Reserving size (26732442) for bucket 6 Getting block 7 of 9 Getting block 8 of 9 Reserving size (26732442) for bucket 8 Calculating Z arrays for bucket 3 Entering block accumulator loop for bucket 1: Calculating Z arrays for bucket 4 Calculating Z arrays for bucket 2 Reserving size (26732442) for bucket 7 Entering block accumulator loop for bucket 4: Entering block accumulator loop for bucket 3: Entering block accumulator loop for bucket 2: Calculating Z arrays for bucket 8 Calculating Z arrays for bucket 5 Entering block accumulator loop for bucket 8: Entering block accumulator loop for bucket 5: Calculating Z arrays for bucket 7 Entering block accumulator loop for bucket 7: Calculating Z arrays for bucket 6 Entering block accumulator loop for bucket 6: Getting block 9 of 9 Reserving size (26732442) for bucket 9 Calculating Z arrays for bucket 9 Entering block accumulator loop for bucket 9: Could not open file for reading a reference graph: "/mnt/Raid_Dell/RNAseq.Dietas.Dmel/smRNA/Known_miRNAs/results//Bowtie2_index/dmel.flybase.0.sa" bucket 1: 10% bucket 9: 10% bucket 3: 10% bucket 2: 10% bucket 5: 10% bucket 6: 10% bucket 1: 20% bucket 4: 10% bucket 7: 10% bucket 8: 10% bucket 1: 30% bucket 9: 20% bucket 3: 20% bucket 2: 20% bucket 6: 20% bucket 5: 20% bucket 1: 40% bucket 4: 20% bucket 9: 30% bucket 8: 20% bucket 7: 20% bucket 1: 50% bucket 3: 30% bucket 2: 30% bucket 6: 30% bucket 5: 30% bucket 1: 60% bucket 9: 40% bucket 4: 30% bucket 1: 70% bucket 8: 30% bucket 3: 40% bucket 7: 30% bucket 2: 40% bucket 9: 50% bucket 5: 40% bucket 6: 40% bucket 1: 80% bucket 4: 40% bucket 3: 50% bucket 2: 50% bucket 1: 90% bucket 9: 60% bucket 8: 40% bucket 7: 40% bucket 5: 50% bucket 6: 50% bucket 1: 100% Sorting block of length 9586584 for bucket 1 (Using difference cover) bucket 3: 60% bucket 2: 60% bucket 4: 50% bucket 9: 70% bucket 5: 60% bucket 7: 50% bucket 8: 50% bucket 6: 60% bucket 3: 70% bucket 2: 70% bucket 9: 80% bucket 4: 60% bucket 5: 70% bucket 2: 80% bucket 3: 80% bucket 6: 70% bucket 9: 90% bucket 7: 60% bucket 8: 60% bucket 5: 80% bucket 4: 70% bucket 2: 90% bucket 3: 90% bucket 9: 100% Sorting block of length 14679497 for bucket 9 (Using difference cover) bucket 5: 90% bucket 6: 80% bucket 4: 80% bucket 7: 70% bucket 8: 70% bucket 2: 100% Sorting block of length 19637635 for bucket 2 (Using difference cover) bucket 3: 100% Sorting block of length 12175070 for bucket 3 (Using difference cover) bucket 5: 100% Sorting block of length 22000306 for bucket 5 (Using difference cover) bucket 6: 90% bucket 4: 90% bucket 7: 80% bucket 8: 80% bucket 4: 100% Sorting block of length 21717866 for bucket 4 (Using difference cover) bucket 6: 100% Sorting block of length 9971415 for bucket 6 (Using difference cover) bucket 8: 90% bucket 7: 90% bucket 8: 100% Sorting block of length 15575379 for bucket 8 (Using difference cover) bucket 7: 100% Sorting block of length 17229264 for bucket 7 (Using difference cover) Sorting block time: 00:00:07 Returning block of 9586585 for bucket 1 Sorting block time: 00:00:07 Returning block of 9971416 for bucket 6 Sorting block time: 00:00:09 Returning block of 12175071 for bucket 3 Sorting block time: 00:00:11 Returning block of 14679498 for bucket 9 Sorting block time: 00:00:11 Returning block of 15575380 for bucket 8 Sorting block time: 00:00:12 Returning block of 17229265 for bucket 7 Sorting block time: 00:00:14 Returning block of 19637636 for bucket 2 Sorting block time: 00:00:15 Returning block of 21717867 for bucket 4 Sorting block time: 00:00:15 Returning block of 22000307 for bucket 5 Total time for call to driver() for forward index: 00:00:29 Error: Encountered internal Bowtie 2 exception (#1) Command: bowtie2-build --wrapper basic-0 --threads 20 -f /mnt/Raid_Dell/Dmel.genome/fastas.flybase/dmel-all-chromosome-r6.21.fasta /mnt/Raid_Dell/RNAseq.Dietas.Dmel/smRNA/Known_miRNAs/results//Bowtie2_index/dmel.flybase Deleting "/mnt/Raid_Dell/RNAseq.Dietas.Dmel/smRNA/Known_miRNAs/results//Bowtie2_index/dmel.flybase.3.bt2" file written during aborted indexing attempt. Deleting "/mnt/Raid_Dell/RNAseq.Dietas.Dmel/smRNA/Known_miRNAs/results//Bowtie2_index/dmel.flybase.4.bt2" file written during aborted indexing attempt. Deleting "/mnt/Raid_Dell/RNAseq.Dietas.Dmel/smRNA/Known_miRNAs/results//Bowtie2_index/dmel.flybase.1.bt2" file written during aborted indexing attempt. Deleting "/mnt/Raid_Dell/RNAseq.Dietas.Dmel/smRNA/Known_miRNAs/results//Bowtie2_index/dmel.flybase.2.bt2" file written during aborted indexing attempt.