hi everyone, I have a question: I run the following command in the samtools sorted and failed to created the output file:
$Samtools sort -n $Temp/$i.out/accepted_hits.bam -o $oDirectory/$i.out/accepted_hits_sorted.bam
and the error it's:
[sort_blocks] fail to create file /home/lgts/workspace/rnaseq/Output/KG-1_DM4h-6_6.out/accepted_hits_sorted.bam.0000.bam.
thanks you for your answers
3 answers
You are using samtools 0.1.18, which was released almost seven years ago.
If you use any of the last seven released versions of samtools, this error message will explain why it was unable to create this temporary file.
hi everybody,
I wanted to comment how finished my history with "samtools sort"
my mistake was, the syntax of the command
I used this command: $Samtools sort -n $Temp/$i.out/accepted_hits.bam -o $oDirectory/$i.out/accepted_hits_sorted.bam
and the correct command it's
samtools sort -n input.bam output.bam
Thanks to all for the help...
It's not merely “likely using” — that error message with that exact wording does not exist past 0.1.18. And, for the record, since leaving Sanger I continue to have some interest in samtools but am not “the maintainer” of samtools.
If ancient samtools is still required by particular other tools, IMHO those other tools should be named, shamed, and fixed.
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In addition to the question of genomax, can you check your hard disk isn't full and the directory you are writing to does exist?
thank you for reply genomax and Wouterdecoster. I was checking my menory capacity and apparentely that's the problem. when I solve this, I tell them if I solved the problem.
thanks again
That does not sound correct. Memory should have no effect on your ability to write to a specific directory.