I had run the tophat script and it went through everything but in the last after "Reporting output tracks" it gave me the following error. Please help me. Thanks in Advance.
Error: [Errno 2] No such file or directory: 'SRR493360/thout/tmp/accepted_hits0_sorted.bam'
Found 46454 junctions from happy spliced reads
1 answer
Did you run out of space on the drive? That's the most common cause of this.
It depends on how big your fastq files are. Tophat has to have room for ~3x the output, since it creates an unsorted BAM file and then sorts that (requiring creation of tmp files approximately the same size as the resulting sorted BAM files). So unless your fastq files are <300 megs or so, I wouldn't expect you to have enough room.
Subset 1000 reads and see if it runs fine. This helps to check if the issue is with hard drive space.
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GouthamAtla
zcat R1.fastq.gz | head -4000 > R1_subset.fastqzcat R2.fastq.gz | head -4000 > R2_subset.fastqHi, could you show me how to do top hat on cluster, I have same problem and with huge file, so even I run "head 8000000 > 1_subset.fastq. But the remaining reads are more than 2 million, so I tried to run tail 8000000 > 2_subset.fastq. How should I deal with the middle part? And how to output the results, separately or combine together?
Thanks
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didiren87 •
Hi, could you show me how to do top hat on cluster, I have same problem and with huge file, so even I run head 8000000 > 1_subset.fastq. But the remaining reads are more than 2 million, so I tried to run tail 8000000 > 2_subset.fastq. How should I deal with the middle part? And how to output the results, separately or combine together?
Thanks
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didiren87 •
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