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nanoporetech / wub

Tools and software library developed by the ONT Applications group
Mozilla Public License 2.0
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Installation error #3

Closed Adelaam closed 6 years ago

Adelaam commented 6 years ago

Hello,

I am trying to install wub on linux mint with: git clone https://github.com/nanoporetech/wub.git cd wub python setup.py install When I run the test I get: 34 passed, 1 skipped in 3.92 seconds But when I run make docs I get this error: /home/mwiks/wub/docs/cmd_list.rst:7: WARNING: malformed hyperlink target. None:5: WARNING: Unexpected indentation. /home/mwiks/wub/docs/cmd_list.rst:7: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/mwiks/wub/wub/simulate/seq.py:docstring of wub.simulate.seq.simulate_sequencing_errors:6: WARNING: Field list ends without a blank line; unexpected unindent. looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done writing output... [100%] wub.wrappers
generating indices... genindex py-modindex highlighting module code... [100%] wub.wrappers.dnadiff
writing additional pages... search copying static files... done copying extra files... done dumping search index in English (code: en) ... done dumping object inventory... done build succeeded, 4 warnings.

The HTML pages are in _build/html.

Build finished. The HTML pages are in _build/html. make[1]: Leaving directory '/home/mwiks/wub/docs' Do you what is the problem?

Thank you!

bsipos commented 6 years ago

Hello,

Have you tried running any of the tools? It seems to me that the installation was successful. You have one test skipped as probably you don't have a required dependency.

Best, Botond

Adelaam commented 6 years ago

Yes, I have tried and I get this error: '/home/mwiks/wub/scripts/bam_accuracy.py' '/home/mwiks/mergedbacode03.bam' Traceback (most recent call last): File "/home/mwiks/wub/scripts/bam_accuracy.py", line 116, in args.bam, region=args.c, min_aqual=args.q, with_clipps=args.e, verbose=not args.Q) File "/home/mwiks/wub/wub/bam/stats.py", line 147, in read_stats bam_reader = bam_common.pysam_open(bam, in_format='BAM') File "/home/mwiks/wub/wub/bam/common.py", line 21, in pysam_open aln_iter = pysam.AlignmentFile(alignment_file, mode) File "pysam/libcalignmentfile.pyx", line 729, in pysam.libcalignmentfile.AlignmentFile.cinit File "pysam/libcalignmentfile.pyx", line 969, in pysam.libcalignmentfile.AlignmentFile._open ValueError: file has no sequences defined (mode='rb') - is it SAM/BAM format? Consider opening with check_sq=False a pdf folder has been made but I cannot open it. Thank you!

bsipos commented 6 years ago

Looks like you might have a problem with the input file. Try running "samtools view /home/mwiks/mergedbacode03.bam" and see if it works.

Botond

Adelaam commented 6 years ago

I have tried with a different one and it is working!

Thank you for your help. Adela