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Gaius-Augustus / Augustus

Genome annotation with AUGUSTUS
http://bioinf.uni-greifswald.de/webaugustus/
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bamToWig.py error #179

Open PeiwenLi opened 4 years ago

PeiwenLi commented 4 years ago

Hi! I was running script bamToWig.py using this following command:

~/Augustus/scripts/bamToWig.py -b merged.bam -g ../../GCF_002910315.2_ASM291031v2_genomic.fna -o merged.wig

but returned this error:

Error in file /home/peiwen/projects/rrg-lough/peiwen/software/Augustus/scripts/bamToWig.py at line 173: Return code of subprocess was -9['/cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/intel2016.4/samtools/1.10/bin/samtools', 'mpileup', '-o', 'pileup_pwceqelrzj', 'merged.bam']

I am new to the program. Could you please give some hints on what this error message indicates and how should I solve it? Thanks!

MarioStanke commented 4 years ago

You could alternatively use the C version in Augustus/auxprogs/bam2wig.

KatharinaHoff commented 4 years ago

@PeiwenLi , this looks like an samtools problem. Try on the command line whether the call

/cvmfs/ soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/intel2016.4/samtools/1.10/bin/samtools mpileup -o pileup_pwceqelrzj merged.bam

fails. If yes, I suggest you get in touch with the samtools developers. (Of course you can try bam2wig as well.. )

Best,

Katharina

On Thu, Aug 13, 2020 at 12:59 PM Mario Stanke notifications@github.com wrote:

You could alternatively use the C version in Augustus/auxprogs/bam2wig.

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PeiwenLi commented 4 years ago

Thank you to Mario and Katharina! I tried bam2wig instead and it worked!

Sincerely, Peiwen