Hi! I have been attempting to analyse my bins from my metagenomic data using CheckM. I was successful in doing so yesterday and generating graphs; however, I am facing the below error today, despite going through other issues here on github and trying to reinstall CheckM using both pip and conda.
checkm lineage_wf -t 8 -x fa final.contigs.fa.metabat-bins1500-20240315_100754/ checkmoutput
[2024-03-20 12:55:02] INFO: CheckM v1.2.2
[2024-03-20 12:55:02] INFO: checkm lineage_wf -t 8 -x fa final.contigs.fa.metabat-bins1500-20240315_100754/ checkmoutput
[2024-03-20 12:55:02] INFO: CheckM data: /home/entomolab/.checkm
[2024-03-20 12:55:02] INFO: [CheckM - tree] Placing bins in reference genome tree.
[2024-03-20 12:55:03] INFO: Identifying marker genes in 3 bins with 8 threads:
Process Process-4:ssing 0 of 3 (0.00%) bins.
Traceback (most recent call last):
File "/home/entomolab/miniconda3/lib/python3.12/multiprocessing/process.py", line 314, in _bootstrap
self.run()
File "/home/entomolab/miniconda3/lib/python3.12/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/home/entomolab/miniconda3/lib/python3.12/site-packages/checkm/markerGeneFinder.py", line 130, in _processBin
hmmModelFile = markerSetParser.createHmmModelFile(binId, markerFile)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/entomolab/miniconda3/lib/python3.12/site-packages/checkm/markerSets.py", line 330, in createHmmModelFile
markerFileType = self.markerFileType(markerFile)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/entomolab/miniconda3/lib/python3.12/site-packages/checkm/markerSets.py", line 430, in markerFileType
with open(markerFile, 'r') as f:
^^^^^^^^^^^^^^^^^^^^^
FileNotFoundError: [Errno 2] No such file or directory: '/home/entomolab/.checkm/hmms/phylo.hmm'
Process Process-3:
Traceback (most recent call last):
File "/home/entomolab/miniconda3/lib/python3.12/multiprocessing/process.py", line 314, in _bootstrap
self.run()
File "/home/entomolab/miniconda3/lib/python3.12/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/home/entomolab/miniconda3/lib/python3.12/site-packages/checkm/markerGeneFinder.py", line 130, in _processBin
hmmModelFile = markerSetParser.createHmmModelFile(binId, markerFile)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/entomolab/miniconda3/lib/python3.12/site-packages/checkm/markerSets.py", line 330, in createHmmModelFile
markerFileType = self.markerFileType(markerFile)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/entomolab/miniconda3/lib/python3.12/site-packages/checkm/markerSets.py", line 430, in markerFileType
with open(markerFile, 'r') as f:
^^^^^^^^^^^^^^^^^^^^^
FileNotFoundError: [Errno 2] No such file or directory: '/home/entomolab/.checkm/hmms/phylo.hmm'
Process Process-2:
Traceback (most recent call last):
File "/home/entomolab/miniconda3/lib/python3.12/multiprocessing/process.py", line 314, in _bootstrap
self.run()
File "/home/entomolab/miniconda3/lib/python3.12/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/home/entomolab/miniconda3/lib/python3.12/site-packages/checkm/markerGeneFinder.py", line 130, in _processBin
hmmModelFile = markerSetParser.createHmmModelFile(binId, markerFile)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/entomolab/miniconda3/lib/python3.12/site-packages/checkm/markerSets.py", line 330, in createHmmModelFile
markerFileType = self.markerFileType(markerFile)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/entomolab/miniconda3/lib/python3.12/site-packages/checkm/markerSets.py", line 430, in markerFileType
with open(markerFile, 'r') as f:
^^^^^^^^^^^^^^^^^^^^^
FileNotFoundError: [Errno 2] No such file or directory: '/home/entomolab/.checkm/hmms/phylo.hmm'
[2024-03-20 12:55:25] INFO: Saving HMM info to file.
[2024-03-20 12:55:25] INFO: Calculating genome statistics for 3 bins with 8 threads:
Finished processing 3 of 3 (100.00%) bins.
[2024-03-20 12:55:25] INFO: Extracting marker genes to align.
[2024-03-20 12:55:25] ERROR: Models must be parsed before identifying HMM hits.
Controlled exit resulting from an unrecoverable error or warning.
Hi! I have been attempting to analyse my bins from my metagenomic data using CheckM. I was successful in doing so yesterday and generating graphs; however, I am facing the below error today, despite going through other issues here on github and trying to reinstall CheckM using both pip and conda.
Can you please look into it? Thanks!