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When running graftM graft on some bins (--search_method hmmsearch+diamond, mcra package), I get the output below. Geronimp suggested that the DIAMOND search has filtered out all reads but the pipeline still marches on.
05/05/2017 10:15:00 AM INFO: Working on oscar_grouch_bin
05/05/2017 10:15:00 AM INFO: 1 read(s) detected
Error: Unexpected end of file.
Traceback (most recent call last):
File "/gnu/store/wmqyh831hzcxfsmsxq1mizdi1jcjz0ad-graftm-0.10.1/bin/..graftM-real-real", line 444, in
Run(args).main()
File "/gnu/store/wmqyh831hzcxfsmsxq1mizdi1jcjz0ad-graftm-0.10.1/lib/python2.7/site-packages/graftm/run.py", line 588, in main
self.graft()
File "/gnu/store/wmqyh831hzcxfsmsxq1mizdi1jcjz0ad-graftm-0.10.1/lib/python2.7/site-packages/graftm/run.py", line 417, in graft
tmpname)
File "/gnu/store/wmqyh831hzcxfsmsxq1mizdi1jcjz0ad-graftm-0.10.1/lib/python2.7/site-packages/graftm/decoy_filter.py", line 44, in filter
UnpackRawReads.PROTEIN_SEQUENCE_TYPE)
File "/gnu/store/wmqyh831hzcxfsmsxq1mizdi1jcjz0ad-graftm-0.10.1/lib/python2.7/site-packages/graftm/diamond.py", line 62, in run
res = DiamondSearchResult.import_from_daa_file(daa_name)
File "/gnu/store/wmqyh831hzcxfsmsxq1mizdi1jcjz0ad-graftm-0.10.1/lib/python2.7/site-packages/graftm/sequence_search_results.py", line 90, in import_from_daa_file
"stderr was %s" % (cmd, stderr))
Exception: Problem running diamond view with cmd: 'diamond view -a '/tmp/graftm_diamond4jOMpN.daa'',stderr was None
Thanks!
Louis.
The text was updated successfully, but these errors were encountered:
Hey guys,
Great tool, thanks for sharing.
When running graftM graft on some bins (--search_method hmmsearch+diamond, mcra package), I get the output below. Geronimp suggested that the DIAMOND search has filtered out all reads but the pipeline still marches on.
05/05/2017 10:15:00 AM INFO: Working on oscar_grouch_bin
05/05/2017 10:15:00 AM INFO: 1 read(s) detected
Error: Unexpected end of file.
Traceback (most recent call last):
File "/gnu/store/wmqyh831hzcxfsmsxq1mizdi1jcjz0ad-graftm-0.10.1/bin/..graftM-real-real", line 444, in
Run(args).main()
File "/gnu/store/wmqyh831hzcxfsmsxq1mizdi1jcjz0ad-graftm-0.10.1/lib/python2.7/site-packages/graftm/run.py", line 588, in main
self.graft()
File "/gnu/store/wmqyh831hzcxfsmsxq1mizdi1jcjz0ad-graftm-0.10.1/lib/python2.7/site-packages/graftm/run.py", line 417, in graft
tmpname)
File "/gnu/store/wmqyh831hzcxfsmsxq1mizdi1jcjz0ad-graftm-0.10.1/lib/python2.7/site-packages/graftm/decoy_filter.py", line 44, in filter
UnpackRawReads.PROTEIN_SEQUENCE_TYPE)
File "/gnu/store/wmqyh831hzcxfsmsxq1mizdi1jcjz0ad-graftm-0.10.1/lib/python2.7/site-packages/graftm/diamond.py", line 62, in run
res = DiamondSearchResult.import_from_daa_file(daa_name)
File "/gnu/store/wmqyh831hzcxfsmsxq1mizdi1jcjz0ad-graftm-0.10.1/lib/python2.7/site-packages/graftm/sequence_search_results.py", line 90, in import_from_daa_file
"stderr was %s" % (cmd, stderr))
Exception: Problem running diamond view with cmd: 'diamond view -a '/tmp/graftm_diamond4jOMpN.daa'',stderr was None
Thanks!
Louis.
The text was updated successfully, but these errors were encountered: