Readcount, SEQCOUNT error in example run.

[Vasu Saini]

I am getting this error for the example file.

sh: line 1:  6532 Abort trap: 6           featureCounts -s 0 -t exon -g transcript_id -T 4 -Q 10 -a Examples/basic_examples/mRNAs/data/Homo_sapiens_GRCh37.74_chr.gtf -o Examples/basic_examples/mRNAs/results//top_bw1_readcount_results/SRR488566_top_bw1.tab Examples/basic_examples/mRNAs/results//Bowtie1_results/SRR488566_top_bw1.bam 2>> Examples/basic_examples/mRNAs/results//miARma_logfile.5806.log

SEQCOUNT ERROR :: system args failed: 34304 (mkdir -p Examples/basic_examples/mRNAs/results//top_bw1_readcount_results/ ;featureCounts  -s 0 -t exon -g transcript_id -T 4 -Q 10 -a Examples/basic_examples/mRNAs/data/Homo_sapiens_GRCh37.74_chr.gtf -o Examples/basic_examples/mRNAs/results//top_bw1_readcount_results/SRR488566_top_bw1.tab Examples/basic_examples/mRNAs/results//Bowtie1_results/SRR488566_top_bw1.bam 2>> Examples/basic_examples/mRNAs/results//miARma_logfile.5806.log) at lib/CbBio/RNASeq/Readcount.pm line 200, <RESULTS> line 30.

[Vasu Saini]

Some more information which may be required to address this problem.

I downloaded all the required files from the provided links/ steps provided.

I observed one strange thing. the log file size is almost 60 GB after the end, and the run is ending with the above mentioned error.

Any help would be much appreciated. I am unable to figure out the problem.

[Vasu Saini]

Load annotation file Examples/basic_examples/mRNAs/data/Homo_sapiens_G ... ||
|| Features : 1306656 ||
|| Meta-features : 215170 ||
|| Chromosomes/contigs : 265 ||
|| ||
|| Process BAM file Examples/basic_examples/mRNAs/results//Bowtie2_result ... ||
|| Single-end reads are included. ||
|| Assign reads to features... ||
GZIP ERROR:-2

[Vasu Saini]

GZIP ERROR: -2 is repeated n number of times

[Vasu Saini]

 Input files : 1 BAM file                                       ||

	S Examples/basic_examples/mRNAs/results//Bow ...
	Output file : Examples/basic_examples/mRNAs/results//top_b ...
	Annotations : Examples/basic_examples/mRNAs/data/Homo_sapi ...
	Threads : 4
	Level : meta-feature level
	Paired-end : no
	Strand specific : no
	Multimapping reads : not counted
	Multi-overlapping reads : not counted
	Read orientations : fr