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VDBWRAIR / ngs_mapper

Genome Mapping Pipeline
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Syntax error in nfilter.py #190

Closed necrolyte2 closed 8 years ago

necrolyte2 commented 8 years ago

Related to #189 

 This is the error I get on the newest version:
2016-03-09 10:35:34,694 -- INFO -- runsample --- Starting 11130 ---
2016-03-09 10:35:35,793 -- ERROR -- runsample

filtering with specifications, drop Ns:False, Index Quality Min:0
from folder /media/VD_Research/NGSData/ReadsBySample/11130 to folder Projects/11130/11130MScA43runsample/filtered
Traceback (most recent call last):
File "/media/VD_Research/Admin/PBS/Software/ngs_mapper-1.3.0/.ngs_mapper/bin/ngs_filter", line 9, in
load_entry_point('ngs-mapper==1.2.4', 'console_scripts', 'ngs_filter')()
File "/media/VD_Research/Admin/PBS/Software/ngs_mapper-1.3.0/.ngs_mapper/lib/python2.7/site-packages/ngs_mapper-1.2.4-py2.7.egg/ngs_mapper/nfilter.py", line 145, in main
outpaths = write_post_filter(args[''], idxMin, dropNs, args['--outdir'], args['--parallel'])
File "/media/VD_Research/Admin/PBS/Software/ngs_mapper-1.3.0/.ngs_mapper/lib/python2.7/site-packages/ngs_mapper-1.2.4-py2.7.egg/ngs_mapper/nfilter.py", line 109, in write_post_filter
return map_to_dir(readsdir, write_filters, parallel)
File "/media/VD_Research/Admin/PBS/Software/ngs_mapper-1.3.0/.ngs_mapper/lib/python2.7/site-packages/ngs_mapper-1.2.4-py2.7.egg/ngs_mapper/nfilter.py", line 67, in map_to_dir
return map(func, files)
File "/media/VD_Research/Admin/PBS/Software/ngs_mapper-1.3.0/.ngs_mapper/lib/python2.7/site-packages/ngs_mapper-1.2.4-py2.7.egg/ngs_mapper/nfilter.py", line 96, in write_filtered
outpath = name_filtered(readpath, outdir)
File "/media/VD_Research/Admin/PBS/Software/ngs_mapper-1.3.0/.ngs_mapper/lib/python2.7/site-packages/ngs_mapper-1.2.4-py2.7.egg/ngs_mapper/nfilter.py", line 36, in name_filtered
if not renamed.ends_with('.fastq'):
AttributeError: 'str' object has no attribute 'ends_with'

Traceback (most recent call last):
File "/media/VD_Research/Admin/PBS/Software/ngs_mapper-1.3.0/.ngs_mapper/bin/graphsample", line 9, in
load_entry_point('ngs-mapper==1.2.4', 'console_scripts', 'graphsample')()
File "/media/VD_Research/Admin/PBS/Software/ngs_mapper-1.3.0/.ngs_mapper/lib/python2.7/site-packages/ngs_mapper-1.2.4-py2.7.egg/ngs_mapper/graphsample.py", line 23, in main
pngfile = make_image( jfile, args.outpath )
File "/media/VD_Research/Admin/PBS/Software/ngs_mapper-1.3.0/.ngs_mapper/lib/python2.7/site-packages/ngs_mapper-1.2.4-py2.7.egg/ngs_mapper/graphsample.py", line 41, in make_image
j = json.load( open(jfile) )
IOError: [Errno 2] No such file or directory: 'Projects/11130/11130.bam.qualdepth.json'
0.23user 0.11system 0:03.83elapsed 8%CPU (0avgtext+0avgdata 26920maxresident)k
32984inputs+16outputs (14major+8835minor)pagefaults 0swaps
Traceback (most recent call last):
File "/media/VD_Research/Admin/PBS/Software/ngs_mapper-1.3.0/.ngs_mapper/bin/graph_mapunmap", line 9, in
load_entry_point('ngs-mapper==1.2.4', 'console_scripts', 'graph_mapunmap')()
File "/media/VD_Research/Admin/PBS/Software/ngs_mapper-1.3.0/.ngs_mapper/lib/python2.7/site-packages/ngs_mapper-1.2.4-py2.7.egg/ngs_mapper/graph_mapunmap.py", line 140, in main
make_graphic( args.jsons, args.outfile )
File "/media/VD_Research/Admin/PBS/Software/ngs_mapper-1.3.0/.ngs_mapper/lib/python2.7/site-packages/ngs_mapper-1.2.4-py2.7.egg/ngs_mapper/graph_mapunmap.py", line 125, in make_graphic
smu = get_mapunmap( jsons )
File "/media/VD_Research/Admin/PBS/Software/ngs_mapper-1.3.0/.ngs_mapper/lib/python2.7/site-packages/ngs_mapper-1.2.4-py2.7.egg/ngs_mapper/graph_mapunmap.py", line 60, in get_mapunmap
samples.append( sample_from_filename( jfile ) )
File "/media/VD_Research/Admin/PBS/Software/ngs_mapper-1.3.0/.ngs_mapper/lib/python2.7/site-packages/ngs_mapper-1.2.4-py2.7.egg/ngs_mapper/graph_mapunmap.py", line 45, in sample_from_filename
raise ValueError( "Filename given({0}) does not contain .bam".format(filename) )
ValueError: Filename given(Projects//.qualdepth.json) does not contain .bam
Traceback (most recent call last):
File "/media/VD_Research/Admin/PBS/Software/ngs_mapper-1.3.0/.ngs_mapper/bin/sample_coverage", line 9, in
load_entry_point('ngs-mapper==1.2.4', 'console_scripts', 'sample_coverage')()
File "/media/VD_Research/Admin/PBS/Software/ngs_mapper-1.3.0/.ngs_mapper/lib/python2.7/site-packages/ngs_mapper-1.2.4-py2.7.egg/ngs_mapper/coverage.py", line 412, in main
fig = create_figure_for_projects(projects, includes, excludes, lineargs, regionmins)
File "/media/VD_Research/Admin/PBS/Software/ngs_mapper-1.3.0/.ngs_mapper/lib/python2.7/site-packages/ngs_mapper-1.2.4-py2.7.egg/ngs_mapper/coverage.py", line 315, in create_figure_for_projects
allrefs = get_allrefs(projects, includes, excludes)
File "/media/VD_Research/Admin/PBS/Software/ngs_mapper-1.3.0/.ngs_mapper/lib/python2.7/site-packages/ngs_mapper-1.2.4-py2.7.egg/ngs_mapper/coverage.py", line 140, in get_allrefs
allrefs.update(refs_from_project(p, includes, excludes))
File "/media/VD_Research/Admin/PBS/Software/ngs_mapper-1.3.0/.ngs_mapper/lib/python2.7/site-packages/ngs_mapper-1.2.4-py2.7.egg/ngs_mapper/coverage.py", line 125, in refs_from_project
qualdepths = load_project_qualdepth(projectpath)
File "/media/VD_Research/Admin/PBS/Software/ngs_mapper-1.3.0/.ngs_mapper/lib/python2.7/site-packages/ngs_mapper-1.2.4-py2.7.egg/ngs_mapper/coverage.py", line 150, in load_project_qualdepth
raise ValueError('{0} missing qualdepth file'.format(projpath))
ValueError: Projects/11130 missing qualdepth file
convert: unable to open image Projects/*/*.qualdepth.png': No such file or directory @ error/blob.c/OpenBlob/2588. convert: unable to open fileProjects//.qualdepth.png' @ error/png.c/ReadPNGImage/3639.
convert: missing an image filename QualDepth.pdf' @ error/convert.c/ConvertImageCommand/3015. Traceback (most recent call last): File "/media/VD_Research/Admin/PBS/Software/ngs_mapper-1.3.0/.ngs_mapper/bin/graph_times", line 9, in <module> load_entry_point('ngs-mapper==1.2.4', 'console_scripts', 'graph_times')() File "/media/VD_Research/Admin/PBS/Software/ngs_mapper-1.3.0/.ngs_mapper/lib/python2.7/site-packages/ngs_mapper-1.2.4-py2.7.egg/ngs_mapper/graph_times.py", line 15, in main ss = start_stop( 'Projects' ) File "/media/VD_Research/Admin/PBS/Software/ngs_mapper-1.3.0/.ngs_mapper/lib/python2.7/site-packages/ngs_mapper-1.2.4-py2.7.egg/ngs_mapper/graph_times.py", line 57, in start_stop diff = datediff( start_stop_for_project( p ) ) File "/media/VD_Research/Admin/PBS/Software/ngs_mapper-1.3.0/.ngs_mapper/lib/python2.7/site-packages/ngs_mapper-1.2.4-py2.7.egg/ngs_mapper/graph_times.py", line 73, in start_stop_for_project with open( log ) as fh: IOError: [Errno 2] No such file or directory: 'Projects/11130/11130.log' ln: targetvcf_consensus/*.consensus.fasta.fasta' is not a directory
averagehat commented 8 years ago

closing as this has been fixed and the bug refers to a version circa july 2015