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?