Closed markmcdowall closed 7 years ago
Dear Mark,
Thanks for writing me this comment.
May I know which system you were working on? Linux or Mac?
Could you also paste the reported message to me? Thanks a lot.
I'll keep tracking of it.
Best, Weilong
Hi Weilong,
I'm using Linux RHEL 7 and the output is:
$ time python bs_seeker2-call_methylation.py --input=datasets/PRJNA257496/GSM1465024/tmp/SRR1536575_1.filtered.matching_1.fastq_bspe.bam --output-prefix=output --db=bs_utils/reference_genomes/GCA_000001405.22.fa_bowtie2/
BS-Seeker2 v2.0.10 - Nov 5, 2015
[2016-08-03 08:09:01] sorting BS-Seeker alignments
Traceback (most recent call last):
File "bs_seeker2-call_methylation.py", line 106, in <module>
pysam.sort(options.infilename, sorted_input_filename)
File "env/lib/python2.7/site-packages/pysam/utils.py", line 75, in __call__
stderr))
pysam.utils.SamtoolsError: 'samtools returned with error 1: stdout=, stderr=[bam_sort] Use -T PREFIX / -o FILE to specify temporary and final output files\nUsage: samtools sort [options...] [in.bam]\nOptions:\n -l INT Set compression level, from 0 (uncompressed) to 9 (best)\n -m INT Set maximum memory per thread; suffix K/M/G recognized [768M]\n -n Sort by read name\n -o FILE Write final output to FILE rather than standard output\n -T PREFIX Write temporary files to PREFIX.nnnn.bam\n -@, --threads INT\n Set number of sorting and compression threads [1]\n --input-fmt-option OPT[=VAL]\n Specify a single input file format option in the form\n of OPTION or OPTION=VALUE\n -O, --output-fmt FORMAT[,OPT[=VAL]]...\n Specify output format (SAM, BAM, CRAM)\n --output-fmt-option OPT[=VAL]\n Specify a single output file format option in the form\n of OPTION or OPTION=VALUE\n --reference FILE\n Reference sequence FASTA FILE [null]\n'
real 0m0.196s
user 0m0.041s
sys 0m0.022s
Cheers,
Mark
@markmcdowall Just notice not finished this conversation.
This problem should have been finished in the latest version.
Best, Weilong
Hi,
When running the bs_seeker2-call_methylation.py script I was finding that it failed to correctly pass the input and output bam files to the pysam.sort() function.
I found that by changing line 106 from:
to
fixed the issue that I was having.
I am using python 2.7.5 and I am on the master branch of BS-Seeker2 which was checked out on the 28th July.
Hope that this helps,
Mark