[2018-09-12 13:52:07] INFO: GTDB-Tk v0.1.1
[2018-09-12 13:52:07] INFO: gtdbtk classify_wf --genome_dir ./genomeTest --out_dir gtdbtkOutput --extension .fasta
[2018-09-12 13:52:07] WARNING: Results are still being validated and taxonomic assignments may be incorrect! Use at your own risk!
[2018-09-12 13:52:07] INFO: Identifying markers in 11 genomes with 1 threads.
[2018-09-12 13:52:07] INFO: Running Prodigal to identify genes.
==> Finished processing 11 of 11 (100.0%) genomes.
[2018-09-12 13:59:58] INFO: Identifying TIGRFAM protein families.
==> Finished processing 11 of 11 (100.0%) genomes.
[2018-09-12 14:01:51] INFO: Identifying Pfam protein families.
==> Finished processing 11 of 11 (100.0%) genomes.
[2018-09-12 14:02:15] INFO: Done.
[2018-09-12 14:02:15] INFO: Aligning markers in 11 genomes with 1 threads.
[2018-09-12 14:02:15] INFO: Processing 11 genomes identified as bacterial.
[2018-09-12 14:02:30] INFO: Read concatenated alignment for 21263 GTDB genomes.
Process Process-9:
Traceback (most recent call last):
File "/nfs/vedanta/sw/packages/miniconda2/lib/python2.7/multiprocessing/process.py", line 267, in _bootstrap
self.run()
File "/nfs/vedanta/sw/packages/miniconda2/lib/python2.7/multiprocessing/process.py", line 114, in run
self._target(*self._args, **self._kwargs)
File "/nfs/vedanta/sw/packages/miniconda2/lib/python2.7/site-packages/gtdbtk/external/hmm_aligner.py", line 96, in _worker
marker_set_id)
File "/nfs/vedanta/sw/packages/miniconda2/lib/python2.7/site-packages/gtdbtk/external/hmm_aligner.py", line 192, in _run_multi_align
result_aligns.get(db_genome_id).update(self._run_align(gene_dict, db_genome_id))
File "/nfs/vedanta/sw/packages/miniconda2/lib/python2.7/site-packages/gtdbtk/external/hmm_aligner.py", line 229, in _run_align
result = self._get_aligned_marker(marker_info.get("gene"), proc.stdout)
File "/nfs/vedanta/sw/packages/miniconda2/lib/python2.7/site-packages/gtdbtk/external/hmm_aligner.py", line 268, in _get_aligned_marker
raise Exception("Unable to get mask from hmm align result file")
Exception: Unable to get mask from hmm align result file
GreatScissors
commented
6 years ago
[2018-09-12 13:52:07] INFO: GTDB-Tk v0.1.1 [2018-09-12 13:52:07] INFO: gtdbtk classify_wf --genome_dir ./genomeTest --out_dir gtdbtkOutput --extension .fasta [2018-09-12 13:52:07] WARNING: Results are still being validated and taxonomic assignments may be incorrect! Use at your own risk! [2018-09-12 13:52:07] INFO: Identifying markers in 11 genomes with 1 threads. [2018-09-12 13:52:07] INFO: Running Prodigal to identify genes. ==> Finished processing 11 of 11 (100.0%) genomes. [2018-09-12 13:59:58] INFO: Identifying TIGRFAM protein families. ==> Finished processing 11 of 11 (100.0%) genomes. [2018-09-12 14:01:51] INFO: Identifying Pfam protein families. ==> Finished processing 11 of 11 (100.0%) genomes. [2018-09-12 14:02:15] INFO: Done. [2018-09-12 14:02:15] INFO: Aligning markers in 11 genomes with 1 threads. [2018-09-12 14:02:15] INFO: Processing 11 genomes identified as bacterial. [2018-09-12 14:02:30] INFO: Read concatenated alignment for 21263 GTDB genomes. Process Process-9: Traceback (most recent call last): File "/nfs/vedanta/sw/packages/miniconda2/lib/python2.7/multiprocessing/process.py", line 267, in _bootstrap self.run() File "/nfs/vedanta/sw/packages/miniconda2/lib/python2.7/multiprocessing/process.py", line 114, in run self._target(*self._args, **self._kwargs) File "/nfs/vedanta/sw/packages/miniconda2/lib/python2.7/site-packages/gtdbtk/external/hmm_aligner.py", line 96, in _worker marker_set_id) File "/nfs/vedanta/sw/packages/miniconda2/lib/python2.7/site-packages/gtdbtk/external/hmm_aligner.py", line 192, in _run_multi_align result_aligns.get(db_genome_id).update(self._run_align(gene_dict, db_genome_id)) File "/nfs/vedanta/sw/packages/miniconda2/lib/python2.7/site-packages/gtdbtk/external/hmm_aligner.py", line 229, in _run_align result = self._get_aligned_marker(marker_info.get("gene"), proc.stdout) File "/nfs/vedanta/sw/packages/miniconda2/lib/python2.7/site-packages/gtdbtk/external/hmm_aligner.py", line 268, in _get_aligned_marker raise Exception("Unable to get mask from hmm align result file") Exception: Unable to get mask from hmm align result file