cheberling
commented
6 years ago This issue was opened by my colleague, and I have already fixed it. Turns out the config file pointed to a file path that was a symlink which wasn't present on all compute nodes in the cluster setup, making the filepath invalid, so none of the external database files (e.g. masks) were able to be found.
Please see another issue I opened (#39) which is still unresolved, and should require intervention from the authors.
[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