Question: HISAT problem on local galaxy
0
biowz • 0 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!
