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use resource for possible open number of files #616

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use resource for possible open number of files #616

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39 changes: 6 additions & 33 deletions scripts_of/__main__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1675,46 +1675,19 @@ def CheckOptions(options, speciesToUse):
print("ERROR: Must use '-M msa' option to generate sequence files and infer multiple sequence alignments for orthogroups")
util.Fail()

# check can open enough files
n_extra = 50
# check can open enough files
import resource
n_extra = 100 # as used in util.number_open_files_exception_advice instead of 50
q_do_orthologs = not any((options.qStopAfterPrepare, options.qStopAfterGroups, options.qStopAfterSeqs, options.qStopAfterAlignments, options.qStopAfterTrees))
if q_do_orthologs and not options.qStartFromTrees:
n_sp = len(speciesToUse)
wd = files.FileHandler.GetWorkingDirectory_Write()
wd_files_test = wd + "Files_test/"
fh = []
try:
if not os.path.exists(wd_files_test):
os.mkdir(wd_files_test)
for i_sp in range(n_sp):
di = wd_files_test + "Sp%d/" % i_sp
if not os.path.exists(di):
os.mkdir(di)
for j_sp in range(n_sp):
fnij = di + "Sp%d.txt" % j_sp
fh.append(open(fnij, 'w'))
# create a few extra files to be safe
for i_extra in range(n_extra):
fh.append(open(wd_files_test + "Extra%d.txt" % i_extra, 'w'))
# close the files again and delete
for fhh in fh:
fhh.close()
DeleteDirectoryTree(wd_files_test)
except IOError as e:
if str(e).startswith("[Errno 24] Too many open files"):
u_nfile, sys_nfile = resource.getrlimit(resource.RLIMIT_OFILE)
if (n_sp*n_sp)+n_extra >= u_nfile :
util.number_open_files_exception_advice(len(speciesToUse), False)
for fhh in fh:
fhh.close()
DeleteDirectoryTree(wd_files_test)
util.Fail()
else:
for fhh in fh:
fhh.close()
DeleteDirectoryTree(wd_files_test)
print("ERROR: Attempted to open required files for OrthoFinder run but an unexpected error occurred. \n\nStacktrace:")
raise
return options


def main(args=None):
try:
if args is None:
Expand Down