I wanted to run groopM on my old PhD work and got the following
groopm refine combined.gm
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[[GroopM 0.3.0]] Running in core refining mode...
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Loading data from: combined.gm
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*** Upgrading GM DB from version 1 to version 2 ***
please be patient...
Calculating and storing the kmer signature PCAs
Please specify fasta file containing the bam reference sequences: Error opening DB: combined.gm <type 'exceptions.IOError'>
Error loading DB: combined.gm <type 'exceptions.IOError'>
Unexpected error: <type 'exceptions.IOError'>
Traceback (most recent call last):
File "/srv/sw/GroopM/0.3.0/bin/groopm", line 381, in <module>
GM_parser.parseOptions(args)
File "/srv/sw/GroopM/0.3.0/lib/python2.7/site-packages/groopm/groopm.py", line 155, in parseOptions
loadContigNames=True)
File "/srv/sw/GroopM/0.3.0/lib/python2.7/site-packages/groopm/refine.py", line 128, in __init__
transform=transform)
File "/srv/sw/GroopM/0.3.0/lib/python2.7/site-packages/groopm/binManager.py", line 173, in loadBins
loadLinks=loadLinks
File "/srv/sw/GroopM/0.3.0/lib/python2.7/site-packages/groopm/profileManager.py", line 190, in loadData
silent=silent)
File "/srv/sw/GroopM/0.3.0/lib/python2.7/site-packages/groopm/mstore.py", line 954, in getConditionalIndices
self.checkAndUpgradeDB(dbFileName, silent=silent)
File "/srv/sw/GroopM/0.3.0/lib/python2.7/site-packages/groopm/mstore.py", line 557, in checkAndUpgradeDB
upgrade_tasks[task](dbFileName)
File "/srv/sw/GroopM/0.3.0/lib/python2.7/site-packages/groopm/mstore.py", line 648, in upgradeDB_1_to_2
with open(contigFile, "r") as f:
IOError: [Errno 2] No such file or directory: ''
I wanted to run groopM on my old PhD work and got the following