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katholt / srst2

Short Read Sequence Typing for Bacterial Pathogens
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Error with bowtie #57

Closed edgarom closed 7 years ago

edgarom commented 8 years ago

Hi...

I have problem when try to run the command srst2

Input files DNA, FASTA: salmonella.fasta Error: could not open salmonella.fasta Total time for call to driver() for forward index: 00:00:00 Error: Encountered internal Bowtie 2 exception (#1) Command: bowtie2-build --wrapper basic-0 salmonella.fasta salmonella.fasta Traceback (most recent call last): File "/usr/local/bin/srst2", line 9, in load_entry_point('srst2==0.1.7', 'console_scripts', 'srst2')() File "/usr/local/lib/python2.7/dist-packages/srst2/srst2.py", line 1604, in main bowtie_index(args.mlst_db) # index the MLST database File "/usr/local/lib/python2.7/dist-packages/srst2/srst2.py", line 154, in bowtie_index run_command([bowtie_build_exec, fasta, fasta]) File "/usr/local/lib/python2.7/dist-packages/srst2/srst2.py", line 134, in run_command raise CommandError({"message": message}) srst2.srst2.CommandError: {'message': "Command 'bowtie2-build salmonella.fasta salmonella.fasta' failed with non-zero exit status: 1"}

as I can resolve this error?....

I have a second question, if I have four files form miseq and nexseq ( 2file_R1 and 2file_R2 ) belonging to the same sample as I can gather the reads for the same result?

rrwick commented 7 years ago

I know it's been a while, but I thought I'd chime in in case you (or anybody else) are still dealing with these issues.

The first error seems to be with the bowtie2-build command bowtie2-build salmonella.fasta salmonella.fasta. It would seem that salmonella.fasta either doesn't exist or you don't have permission to read it. You could try running that same command manually to see if bowtie2-build works outside of SRST2. Failing that, reinstalling/upgrading Bowtie and SRST2 is worth a shot, as there have been releases of both since you posted this issue.

Regarding your second question, it is possible to have multiple read sets for one strain by using --merge_paired. This option makes SRST2 assume that all reads in the run are from the same sample. So it's not possible to run SRST2 on your four-file set and others at the same time - you'd have to run them separately and then merge the results after they're all done.

TreeT2 commented 6 years ago

Hi All, Ive recently encountered this error when using slurm srst2. I never had an issue when using srst2 alone. Im using samtools/0.1.18 and bowtie2/2.2.9 and python/2.7.5. Not sure what the issue is. Any suggestions?