error after running tophat

Question

[Vasu]

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

Answer 1

[Devon Ryan]

Did you run out of space on the drive? That's the most common cause of this.

[Vasu]

Is it ? I'm not sure about that. Anyways thanks for the reply. I'l check once.

[Vasu]

I had checked now. Still it has some 3G left. Is that free space enough for that?

[Devon Ryan]

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.

[Vasu]

ok. Thankyou for the reply.

[GouthamAtla]

Subset 1000 reads and see if it runs fine. This helps to check if the issue is with hard drive space.

[Vasu]

hw I need to run for 1000 reads ? Can you please help me?

[GouthamAtla]

zcat R1.fastq.gz | head -4000 > R1_subset.fastq

zcat R2.fastq.gz | head -4000 > R2_subset.fastq

[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

[Vasu]

You are right! The error is due to less space in the drive. Today I did it on cluster, it worked! Thank you

[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