Hello, after 1 week of alignments (100bp paired reads, 176mil of them, 6 cores was all I had...) tophat2.0 failed after the last step of alignments (I believe):
[2012-05-22 11:16:12] Joining segment hits
[2012-05-22 14:23:48] Reporting output tracks
Traceback (most recent call last):
File "/home/data/rnaseq/bin/tophat", line 3778, in <module>
sys.exit(main())
File "/home/data/rnaseq/bin/tophat", line 3750, in main
params.gff_annotation)
File "/home/data/rnaseq/bin/tophat", line 2526, in compile_reports
os.rename(sorted_bam_parts[0], output_dir + "accepted_hits.bam")
IndexError: list index out of range
make: *** [S1.th] Error 1
I'm going to investigate if in the /tmp dir I will find all the needed files to go on with my analysis but I wanted to know if this is a known issue and if it is possible to fix it in some way...
The command line was:
tophat -p 5 -G /rogue/bioinfotree/prj/ewing-rnaseq/local/share/data/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf --transcriptome-index=transcriptome -o S1.th ../alignment/expanded_genome2 <(zcat /rogue/bioinfotree/R1_001.fastq.gz),list of 11 fastq <(zcat /rogue/bioinfotree/R2_001.fastq.gz),list of 11 fastq
[2012-05-22 11:16:12] Joining segment hits
[2012-05-22 14:23:48] Reporting output tracks
Traceback (most recent call last):
File "/home/data/rnaseq/bin/tophat", line 3778, in <module>
sys.exit(main())
File "/home/data/rnaseq/bin/tophat", line 3750, in main
params.gff_annotation)
File "/home/data/rnaseq/bin/tophat", line 2526, in compile_reports
os.rename(sorted_bam_parts[0], output_dir + "accepted_hits.bam")
IndexError: list index out of range
make: *** [S1.th] Error 1
I'm going to investigate if in the /tmp dir I will find all the needed files to go on with my analysis but I wanted to know if this is a known issue and if it is possible to fix it in some way...
The command line was:
tophat -p 5 -G /rogue/bioinfotree/prj/ewing-rnaseq/local/share/data/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf --transcriptome-index=transcriptome -o S1.th ../alignment/expanded_genome2 <(zcat /rogue/bioinfotree/R1_001.fastq.gz),list of 11 fastq <(zcat /rogue/bioinfotree/R2_001.fastq.gz),list of 11 fastq
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