OrthoFinder
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ERROR: external program called by OrthoFinder returned an error code: 137
my version is 2.5.5. when i run the code , i get an error, how to solve the problem? hoping your reply.
inpath="/mnt/e/2_orthofinder/pae/base" outpath="/mnt/e/2_orthofinder/pae/out" orthofinder -f ${inpath} -o ${outpath}/1
2023-10-19 08:07:12 : Written final scores for species 540 to graph file 2023-10-19 08:12:09 : Written final scores for species 472 to graph file 2023-10-19 08:20:03 : Written final scores for species 473 to graph file 2023-10-19 08:26:34 : Written final scores for species 474 to graph file 2023-10-19 08:31:14 : Written final scores for species 475 to graph file
ERROR: external program called by OrthoFinder returned an error code: 137
Command: mcl /mnt/e/2_orthofinder/pae/out/1/Results_Oct09/WorkingDirectory/OrthoFinder_graph.txt -I 1.5 -o /mnt/e/2_orthofinder/pae/out/1/Results_Oct09/WorkingDirectory/clusters_OrthoFinder_I1.5.txt -te 2 -V all
stdout
b'' stderr
b'Killed\n'
2023-10-19 20:47:20 : Ran MCL
[Errno 2] No such file or directory: '/mnt/e/2_orthofinder/pae/out/1/Results_Oct09/WorkingDirectory/clusters_OrthoFinder_I1.5.txt'
File "/home/qin/anaconda3/bin/scripts_of/main.py", line 1787, in main
DoOrthogroups(options, speciesInfoObj, seqsInfo)
File "/home/qin/anaconda3/bin/scripts_of/main.py", line 1394, in DoOrthogroups
mcl.ConvertSingleIDsToIDPair(seqsInfo, clustersFilename, clustersFilename_pairs)
File "/home/qin/anaconda3/bin/scripts_of/mcl.py", line 78, in ConvertSingleIDsToIDPair
with open(clustersFilename, 'r') as clusterFile, open(newFilename, "w") as output:
Traceback (most recent call last):
File "/home/qin/anaconda3/bin/orthofinder", line 7, in
File "/home/qin/anaconda3/bin/scripts_of/main.py", line 1394, in DoOrthogroups
mcl.ConvertSingleIDsToIDPair(seqsInfo, clustersFilename, clustersFilename_pairs)
File "/home/qin/anaconda3/bin/scripts_of/mcl.py", line 78, in ConvertSingleIDsToIDPair
with open(clustersFilename, 'r') as clusterFile, open(newFilename, "w") as output:
FileNotFoundError: [Errno 2] No such file or directory: '/mnt/e/2_orthofinder/pae/out/1/Results_Oct09/WorkingDirectory/clusters_OrthoFinder_I1.5.txt'