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Old 07-30-2012, 01:55 PM   #1
lj907
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Default sh: samtools: command not found (Tophat)

Dear all,

I have been using tophat for my RNA-seq data. The command line I'm using is the standard: ./tophat -p 8 -G /path_to_genes.gtf/ -o <output_folder> /path_to_genome_index/ XXX.fastq

Tophat runs happily, finds bowtie and samtools, checks for bowtie index, Fasta reference, generates SAM header... all goes well and I have 4 outputs: accepted_hits.bam deletions.bam insertions.bam and junctions.bam... However, when the sam version of accepted_hits.bam is going to be written, samtools fails and I get a message saying sh:samtools: command not found...
Having gone through with the bam files till the very end (cufflinks then cuffdiff and R), I seem to get the analysis running but I don't understand why samtools fails during the mapping.... Tophat clearly recognises it at first.. and ./samtools <options> work nicely for other applications.
Just to add I have used samtools-0.1.17.tar.bz2 (I'm on a iMac) untar ed it and cp ed it into my working path (I haven't got permission for /usr/bin), I have also cp ed libbam.a into my working directory...
Can anyone help me
Cheers
lj907
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Old 07-30-2012, 07:19 PM   #2
krobison
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If you try the command

which samtools

what do you get as output?
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Old 07-31-2012, 05:19 AM   #3
lj907
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I have tried which samtools...the command line renews... no answer... is it not installed properly? but how come tophat initially recognizes it? Thanks very much

Last edited by lj907; 07-31-2012 at 05:23 AM.
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Old 07-31-2012, 05:48 AM   #4
krobison
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I don't know how tophat originally found samtools -- indeed, my guess is that it didn't and what you saw relied on linked in libraries.

Getting no output suggests that samtools is not in your PATH environment variable. Your notes above suggest you may not have compiled it. Check that there is a samtools executable in the directory you specified & that the directory appears in the output for

echo $PATH
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Old 07-31-2012, 09:44 AM   #5
lj907
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Thanks Krobison... I had originally used make to compile... I'm going to try to export the executables to $HOME/bin... and check with which samtools and echo $PATH.. hopefully this will work
cheers
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