Question: HISAT problem on local galaxy
0
gravatar for biowz
2.8 years ago by
biowz0
United States
biowz0 wrote:
Dataset 33: HISAT on data 3Tool execution generated the following error message:
Fatal error: Exit code 1 ()
Usage: samtools sort [options...] [in.bam]
Options:
  -l INT     Set compression level, from 0 (uncompressed) to 9 (best)
  -m INT     Set maximum memory per thread; suffix K/M/G recognized [768M]
  -n         Sort by read name
  -o FILE    Write final output to FILE rather than standard output
  -O FORMAT  Write output as FORMAT ('sam'/'bam'/'cram')   (either -O or
  -T PREFIX  Write temporary files to PREFIX.nnnn.bam       -T is required)
  -@ INT     Set number of sorting and compression threads [1]

Legacy usage: samtools sort [options...] <in.bam> <out.prefix>
Options:
  -f         Use <out.prefix> as full final filename rather than prefix
  -o         Write final output to stdout rather than <out.prefix>.bam
  -l,m,n,@   Similar to corresponding options above
samtools: writing to standard output failed: Broken pipe
samtools: error closing standard output: -1
Error while flushing and closing output
libc++abi.dylib: terminating with uncaught exception of type int
(ERR): hisat-align died with signal 6 (ABRT) 
[bam_header_read] bgzf_check_EOF: Invalid argument
Galaxy attempted to build the BAM index with samtools 1.0+ but failed: [Errno 2] No such file or directory: '/Users/biowzmailustceducn/galaxy/database/job_working_directory/000/40/__dataset_43_metadata_temp_file_b5rEcP.bai'

When I used  HISAT tool in my local galaxy, I met this problem. Would you like to give some suggestion to solve this? Thank you very much in advance!

 

 

 

software error alignment • 1.3k views
ADD COMMENTlink modified 2.8 years ago • written 2.8 years ago by biowz0
0
gravatar for Jennifer Hillman Jackson
2.8 years ago by
United States
Jennifer Hillman Jackson24k wrote:

Hello,

I am wondering if the tool is compatible with the current Galaxy build and/or SAMtools version. I suggest contacting the tool author through the tool shed to see if this is a known. And if a known, what the upgrade plans are.

I didn't notice anything in here that looks like a Galaxy problem, but if someone else does, please add to this thread!

Thanks, Jen, Galaxy team

ADD COMMENTlink written 2.8 years ago by Jennifer Hillman Jackson24k

This owner is devteam (Galaxy team), How I can contact with the author in your team? Thank you 

ADD REPLYlink written 2.8 years ago by biowz0
0
gravatar for biowz
2.8 years ago by
biowz0
United States
biowz0 wrote:

Thank you very much for your reply. I will contact with the tool author through the tool shed.Have a good day!

ADD COMMENTlink written 2.8 years ago by biowz0
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