I am having some problems running the command given to test PEPPAN: PEPPAN -p examples/ST131 -P examples/GCF_000010485.combined.gff.gz examples/*.gff.gz
I get an error message:
2021-06-25 15:52:46.357579 COMMAND: /home/idowuol/anaconda3/bin/PEPPAN -p examples/ST131 -P examples/GCF_000010485.combined.gff.gz examples/GCF_000010485.combined.gff.gz examples/GCF_000214765.combined.gff.gz examples/GCF_001566635.combined.gff.gz examples/GCF_001577325.combined.gff.gz
2021-06-25 15:52:48.493142 Run MMSeqs linclust to get exemplar sequences. Params: 0.9 identities and 0.8 align ratio
2021-06-25 15:53:15.976301 Iterative clustering. 8399 exemplars left with identity = 1.0
2021-06-25 15:53:46.618473 Iterative clustering. 6902 exemplars left with identity = 0.99
2021-06-25 15:54:01.761707 Iterative clustering. 6562 exemplars left with identity = 0.98
2021-06-25 15:54:26.676935 Iterative clustering. 6358 exemplars left with identity = 0.97
2021-06-25 15:54:55.481045 Iterative clustering. 6217 exemplars left with identity = 0.96
2021-06-25 15:55:14.961419 Iterative clustering. 6142 exemplars left with identity = 0.95
2021-06-25 15:55:36.852134 Iterative clustering. 6097 exemplars left with identity = 0.94
2021-06-25 15:55:47.590999 Iterative clustering. 6069 exemplars left with identity = 0.93
2021-06-25 15:55:56.188706 Iterative clustering. 6040 exemplars left with identity = 0.92
2021-06-25 15:56:09.833715 Iterative clustering. 6016 exemplars left with identity = 0.91
2021-06-25 15:56:20.936632 Iterative clustering. 5995 exemplars left with identity = 0.9
2021-06-25 15:56:20.988668 Run BLASTn starts
/home/idowuol/anaconda3/bin/blastn: error while loading shared libraries: libnsl.so.1: cannot open shared object file: No such file or directory
/home/idowuol/anaconda3/bin/blastn: error while loading shared libraries: libnsl.so.1: cannot open shared object file: No such file or directory
/home/idowuol/anaconda3/bin/blastn: error while loading shared libraries: libnsl.so.1: cannot open shared object file: No such file or directory
/home/idowuol/anaconda3/bin/blastn: error while loading shared libraries: libnsl.so.1: cannot open shared object file: No such file or directory
/home/idowuol/anaconda3/bin/blastn: error while loading shared libraries: libnsl.so.1: cannot open shared object file: No such file or directory
/home/idowuol/anaconda3/bin/blastn: error while loading shared libraries: libnsl.so.1: cannot open shared object file: No such file or directory
/home/idowuol/anaconda3/bin/blastn: error while loading shared libraries: libnsl.so.1: cannot open shared object file: No such file or directory
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/home/idowuol/anaconda3/lib/python3.8/multiprocessing/pool.py", line 125, in worker
result = (True, func(*args, **kwds))
File "/home/idowuol/anaconda3/lib/python3.8/site-packages/PEPPAN/modules/uberBlast.py", line 297, in poolBlast
if os.path.getsize(outfile) > 0 :
File "/home/idowuol/anaconda3/lib/python3.8/genericpath.py", line 50, in getsize
return os.stat(filename).st_size
FileNotFoundError: [Errno 2] No such file or directory: './NS_hhnlxmnm/qryNA.1.bsn'
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/home/idowuol/anaconda3/lib/python3.8/site-packages/PEPPAN/modules/uberBlast.py", line 345, in run
blastab.append(tools[method.lower()](ref, qry))
File "/home/idowuol/anaconda3/lib/python3.8/site-packages/PEPPAN/modules/uberBlast.py", line 500, in runBlast
for r in self.pool.imap_unordered(poolBlast, [ [blastn, refDb, q, self.min_id, self.min_cov, self.min_ratio] for q in qrys ]) :
File "/home/idowuol/anaconda3/lib/python3.8/multiprocessing/pool.py", line 868, in next
raise value
FileNotFoundError: [Errno 2] No such file or directory: './NS_hhnlxmnm/qryNA.1.bsn'
None
/home/idowuol/anaconda3/bin/blastn: error while loading shared libraries: libnsl.so.1: cannot open shared object file: No such file or directory
2021-06-25 15:56:22.771273 Obtained 0 exemplar gene sequences from examples/ST131.clust.exemplar
Traceback (most recent call last):
File "/home/idowuol/anaconda3/bin/PEPPAN", line 8, in
sys.exit(ortho())
File "/home/idowuol/anaconda3/lib/python3.8/site-packages/PEPPAN/PEPPAN.py", line 1897, in ortho
get_global_difference(get_gene_group(params['clust'], params['self_bsn']), \
File "/home/idowuol/anaconda3/lib/python3.8/site-packages/PEPPAN/PEPPAN.py", line 1593, in get_gene_group
bsn = bsn[bsn.T[2] > 0]
IndexError: index 2 is out of bounds for axis 0 with size 0
[idowuol@siprapp01p-mean idowuol]$ cmake
-bash: cmake: command not found
[idowuol@siprapp01p-mean idowuol]$ cd /home/idowuol/anaconda3/bin/blastn
-bash: cd: /home/idowuol/anaconda3/bin/blastn: Not a directory
I am having some problems running the command given to test PEPPAN:
PEPPAN -p examples/ST131 -P examples/GCF_000010485.combined.gff.gz examples/*.gff.gz
I get an error message:The above exception was the direct cause of the following exception:
Traceback (most recent call last): File "/home/idowuol/anaconda3/lib/python3.8/site-packages/PEPPAN/modules/uberBlast.py", line 345, in run blastab.append(tools[method.lower()](ref, qry)) File "/home/idowuol/anaconda3/lib/python3.8/site-packages/PEPPAN/modules/uberBlast.py", line 500, in runBlast for r in self.pool.imap_unordered(poolBlast, [ [blastn, refDb, q, self.min_id, self.min_cov, self.min_ratio] for q in qrys ]) : File "/home/idowuol/anaconda3/lib/python3.8/multiprocessing/pool.py", line 868, in next raise value FileNotFoundError: [Errno 2] No such file or directory: './NS_hhnlxmnm/qryNA.1.bsn' None /home/idowuol/anaconda3/bin/blastn: error while loading shared libraries: libnsl.so.1: cannot open shared object file: No such file or directory 2021-06-25 15:56:22.771273 Obtained 0 exemplar gene sequences from examples/ST131.clust.exemplar Traceback (most recent call last): File "/home/idowuol/anaconda3/bin/PEPPAN", line 8, in
sys.exit(ortho())
File "/home/idowuol/anaconda3/lib/python3.8/site-packages/PEPPAN/PEPPAN.py", line 1897, in ortho
get_global_difference(get_gene_group(params['clust'], params['self_bsn']), \
File "/home/idowuol/anaconda3/lib/python3.8/site-packages/PEPPAN/PEPPAN.py", line 1593, in get_gene_group
bsn = bsn[bsn.T[2] > 0]
IndexError: index 2 is out of bounds for axis 0 with size 0
[idowuol@siprapp01p-mean idowuol]$ cmake
-bash: cmake: command not found
[idowuol@siprapp01p-mean idowuol]$ cd /home/idowuol/anaconda3/bin/blastn
-bash: cd: /home/idowuol/anaconda3/bin/blastn: Not a directory