bs3-call_methylation gave no results

[k1197445]

I used bs3-call_methylation with alignment from test data, but got error message as follow,

 BS-Seeker3 beta

[bam_sort] Use -T PREFIX / -o FILE to specify temporary and final output files 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 -t TAG Sort by value of TAG. Uses position as secondary index (or read name if -n is set) -o FILE Write final output to FILE rather than standard output -T PREFIX Write temporary files to PREFIX.nnnn.bam --input-fmt-option OPT[=VAL] Specify a single input file format option in the form of OPTION or OPTION=VALUE -O, --output-fmt FORMAT[,OPT[=VAL]]... Specify output format (SAM, BAM, CRAM) --output-fmt-option OPT[=VAL] Specify a single output file format option in the form of OPTION or OPTION=VALUE --reference FILE Reference sequence FASTA FILE [null] -@, --threads INT Number of additional threads to use [0] [E::bgzf_flush] File write failed (wrong size) samtools view: writing to standard output failed: Broken pipe [E::bgzf_close] File write failed samtools view: error closing standard output: -1 [2019-01-31 16:53:54] indexing sorted alignments [E::hts_open_format] Failed to open file output.bam samtools index: failed to open "output.bam": No such file or directory [2019-01-31 16:53:54] calculating methylation levels [E::hts_open_format] Failed to open file output.bam Traceback (most recent call last): File "bs3-call_methylation.py", line 128, in sorted_input = pysam.Samfile('output.bam', 'rb') File "pysam/libcalignmentfile.pyx", line 736, in pysam.libcalignmentfile.AlignmentFile.cinit File "pysam/libcalignmentfile.pyx", line 935, in pysam.libcalignmentfile.AlignmentFile._open IOError: [Errno 2] could not open alignment file output.bam: No such file or directory

[anapopicsbg]

Has anybody solved this issue? Thank you!

[Bio-finder]

Hi, I get also the same issue so I think that it's quite important to try to solve this. Does someone has any clues of what is happening?