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Ecogenomics / CheckM

Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes
https://ecogenomics.github.io/CheckM/
GNU General Public License v3.0
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FileNotFoundError: [Errno 2] No such file or directory: '/home/majorram/anaconda3/envs/checkm/hmms/phylo.hmm' #378

Closed ramnageena11 closed 3 months ago

ramnageena11 commented 1 year ago

Hi, I am geeting this error. Pls suggest.

checkm lineage_wf /media/majorram/Analysis_Data/singhrn/medaka_final2/s2mags_genomes/s2mags_contigs_16S/ /media/majorram/Analysis_Data/singhrn/checkM_metagenome/S2_metaAssmbly/S2mags/ --reduced_tree -x fasta -t 32 [2023-08-02 12:16:36] INFO: CheckM v1.2.0 [2023-08-02 12:16:36] INFO: checkm lineage_wf /media/majorram/Analysis_Data/singhrn/medaka_final2/s2mags_genomes/s2mags_contigs_16S/ /media/majorram/Analysis_Data/singhrn/checkM_metagenome/S2_metaAssmbly/S2mags/ --reduced_tree -x fasta -t 32 [2023-08-02 12:16:36] INFO: CheckM data: /home/majorram/anaconda3/envs/checkm [2023-08-02 12:16:36] INFO: [CheckM - tree] Placing bins in reference genome tree. [2023-08-02 12:16:36] INFO: Identifying marker genes in 49 bins with 32 threads: Process Process-10:sing 0 of 49 (0.00%) bins. Traceback (most recent call last): File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap self.run() File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/multiprocessing/process.py", line 108, in run self._target(*self._args, self._kwargs) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerGeneFinder.py", line 122, in processBin hmmModelFile = markerSetParser.createHmmModelFile(binId, markerFile) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerSets.py", line 330, in createHmmModelFile markerFileType = self.markerFileType(markerFile) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerSets.py", line 430, in markerFileType with open(markerFile, 'r') as f: FileNotFoundError: [Errno 2] No such file or directory: '/home/majorram/anaconda3/envs/checkm/hmms/phylo.hmm' Process Process-3: Traceback (most recent call last): File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap self.run() File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/multiprocessing/process.py", line 108, in run self._target(*self._args, **self._kwargs) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerGeneFinder.py", line 122, in processBin hmmModelFile = markerSetParser.createHmmModelFile(binId, markerFile) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerSets.py", line 330, in createHmmModelFile markerFileType = self.markerFileType(markerFile) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerSets.py", line 430, in markerFileType with open(markerFile, 'r') as f: FileNotFoundError: [Errno 2] No such file or directory: '/home/majorram/anaconda3/envs/checkm/hmms/phylo.hmm' Process Process-33: Traceback (most recent call last): File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap self.run() File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/multiprocessing/process.py", line 108, in run self._target(*self._args, self._kwargs) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerGeneFinder.py", line 122, in processBin hmmModelFile = markerSetParser.createHmmModelFile(binId, markerFile) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerSets.py", line 330, in createHmmModelFile markerFileType = self.markerFileType(markerFile) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerSets.py", line 430, in markerFileType with open(markerFile, 'r') as f: FileNotFoundError: [Errno 2] No such file or directory: '/home/majorram/anaconda3/envs/checkm/hmms/phylo.hmm' Process Process-27: Traceback (most recent call last): File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap self.run() File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/multiprocessing/process.py", line 108, in run self._target(*self._args, **self._kwargs) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerGeneFinder.py", line 122, in processBin hmmModelFile = markerSetParser.createHmmModelFile(binId, markerFile) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerSets.py", line 330, in createHmmModelFile markerFileType = self.markerFileType(markerFile) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerSets.py", line 430, in markerFileType with open(markerFile, 'r') as f: FileNotFoundError: [Errno 2] No such file or directory: '/home/majorram/anaconda3/envs/checkm/hmms/phylo.hmm' Process Process-6: Traceback (most recent call last): File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap self.run() File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/multiprocessing/process.py", line 108, in run self._target(*self._args, self._kwargs) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerGeneFinder.py", line 122, in processBin hmmModelFile = markerSetParser.createHmmModelFile(binId, markerFile) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerSets.py", line 330, in createHmmModelFile markerFileType = self.markerFileType(markerFile) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerSets.py", line 430, in markerFileType with open(markerFile, 'r') as f: FileNotFoundError: [Errno 2] No such file or directory: '/home/majorram/anaconda3/envs/checkm/hmms/phylo.hmm' Process Process-28: Traceback (most recent call last): File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap self.run() File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/multiprocessing/process.py", line 108, in run self._target(*self._args, **self._kwargs) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerGeneFinder.py", line 122, in processBin hmmModelFile = markerSetParser.createHmmModelFile(binId, markerFile) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerSets.py", line 330, in createHmmModelFile markerFileType = self.markerFileType(markerFile) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerSets.py", line 430, in markerFileType with open(markerFile, 'r') as f: FileNotFoundError: [Errno 2] No such file or directory: '/home/majorram/anaconda3/envs/checkm/hmms/phylo.hmm' Process Process-14: Traceback (most recent call last): File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap self.run() File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/multiprocessing/process.py", line 108, in run self._target(*self._args, self._kwargs) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerGeneFinder.py", line 122, in processBin hmmModelFile = markerSetParser.createHmmModelFile(binId, markerFile) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerSets.py", line 330, in createHmmModelFile markerFileType = self.markerFileType(markerFile) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerSets.py", line 430, in markerFileType with open(markerFile, 'r') as f: FileNotFoundError: [Errno 2] No such file or directory: '/home/majorram/anaconda3/envs/checkm/hmms/phylo.hmm' Process Process-32: Traceback (most recent call last): File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap self.run() File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/multiprocessing/process.py", line 108, in run self._target(*self._args, **self._kwargs) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerGeneFinder.py", line 122, in processBin hmmModelFile = markerSetParser.createHmmModelFile(binId, markerFile) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerSets.py", line 330, in createHmmModelFile markerFileType = self.markerFileType(markerFile) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerSets.py", line 430, in markerFileType with open(markerFile, 'r') as f: FileNotFoundError: [Errno 2] No such file or directory: '/home/majorram/anaconda3/envs/checkm/hmms/phylo.hmm' Process Process-22: Traceback (most recent call last): File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap self.run() File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/multiprocessing/process.py", line 108, in run self._target(*self._args, self._kwargs) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerGeneFinder.py", line 122, in processBin hmmModelFile = markerSetParser.createHmmModelFile(binId, markerFile) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerSets.py", line 330, in createHmmModelFile markerFileType = self.markerFileType(markerFile) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerSets.py", line 430, in markerFileType with open(markerFile, 'r') as f: FileNotFoundError: [Errno 2] No such file or directory: '/home/majorram/anaconda3/envs/checkm/hmms/phylo.hmm' Process Process-25: Traceback (most recent call last): File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap self.run() File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/multiprocessing/process.py", line 108, in run self._target(*self._args, **self._kwargs) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerGeneFinder.py", line 122, in processBin hmmModelFile = markerSetParser.createHmmModelFile(binId, markerFile) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerSets.py", line 330, in createHmmModelFile markerFileType = self.markerFileType(markerFile) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerSets.py", line 430, in markerFileType with open(markerFile, 'r') as f: FileNotFoundError: [Errno 2] No such file or directory: '/home/majorram/anaconda3/envs/checkm/hmms/phylo.hmm' Process Process-5: Traceback (most recent call last): File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap self.run() File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/multiprocessing/process.py", line 108, in run self._target(*self._args, self._kwargs) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerGeneFinder.py", line 122, in processBin hmmModelFile = markerSetParser.createHmmModelFile(binId, markerFile) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerSets.py", line 330, in createHmmModelFile markerFileType = self.markerFileType(markerFile) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerSets.py", line 430, in markerFileType with open(markerFile, 'r') as f: FileNotFoundError: [Errno 2] No such file or directory: '/home/majorram/anaconda3/envs/checkm/hmms/phylo.hmm' Process Process-11: Traceback (most recent call last): File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap self.run() File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/multiprocessing/process.py", line 108, in run self._target(*self._args, **self._kwargs) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerGeneFinder.py", line 122, in processBin hmmModelFile = markerSetParser.createHmmModelFile(binId, markerFile) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerSets.py", line 330, in createHmmModelFile markerFileType = self.markerFileType(markerFile) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerSets.py", line 430, in markerFileType with open(markerFile, 'r') as f: FileNotFoundError: [Errno 2] No such file or directory: '/home/majorram/anaconda3/envs/checkm/hmms/phylo.hmm' Process Process-16: Traceback (most recent call last): File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap self.run() File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/multiprocessing/process.py", line 108, in run self._target(*self._args, self._kwargs) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerGeneFinder.py", line 122, in processBin hmmModelFile = markerSetParser.createHmmModelFile(binId, markerFile) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerSets.py", line 330, in createHmmModelFile markerFileType = self.markerFileType(markerFile) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerSets.py", line 430, in markerFileType with open(markerFile, 'r') as f: FileNotFoundError: [Errno 2] No such file or directory: '/home/majorram/anaconda3/envs/checkm/hmms/phylo.hmm' Process Process-15: Traceback (most recent call last): File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap self.run() File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/multiprocessing/process.py", line 108, in run self._target(*self._args, **self._kwargs) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerGeneFinder.py", line 122, in processBin hmmModelFile = markerSetParser.createHmmModelFile(binId, markerFile) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerSets.py", line 330, in createHmmModelFile markerFileType = self.markerFileType(markerFile) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerSets.py", line 430, in markerFileType with open(markerFile, 'r') as f: FileNotFoundError: [Errno 2] No such file or directory: '/home/majorram/anaconda3/envs/checkm/hmms/phylo.hmm' Process Process-13: Traceback (most recent call last): File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap self.run() File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/multiprocessing/process.py", line 108, in run self._target(*self._args, self._kwargs) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerGeneFinder.py", line 122, in processBin hmmModelFile = markerSetParser.createHmmModelFile(binId, markerFile) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerSets.py", line 330, in createHmmModelFile markerFileType = self.markerFileType(markerFile) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerSets.py", line 430, in markerFileType with open(markerFile, 'r') as f: FileNotFoundError: [Errno 2] No such file or directory: '/home/majorram/anaconda3/envs/checkm/hmms/phylo.hmm' Process Process-29: Traceback (most recent call last): File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap self.run() File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/multiprocessing/process.py", line 108, in run self._target(*self._args, **self._kwargs) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerGeneFinder.py", line 122, in processBin hmmModelFile = markerSetParser.createHmmModelFile(binId, markerFile) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerSets.py", line 330, in createHmmModelFile markerFileType = self.markerFileType(markerFile) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerSets.py", line 430, in markerFileType with open(markerFile, 'r') as f: FileNotFoundError: [Errno 2] No such file or directory: '/home/majorram/anaconda3/envs/checkm/hmms/phylo.hmm' Process Process-12: Traceback (most recent call last): File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap self.run() File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/multiprocessing/process.py", line 108, in run self._target(*self._args, self._kwargs) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerGeneFinder.py", line 122, in processBin hmmModelFile = markerSetParser.createHmmModelFile(binId, markerFile) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerSets.py", line 330, in createHmmModelFile markerFileType = self.markerFileType(markerFile) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerSets.py", line 430, in markerFileType with open(markerFile, 'r') as f: FileNotFoundError: [Errno 2] No such file or directory: '/home/majorram/anaconda3/envs/checkm/hmms/phylo.hmm' Process Process-4: Traceback (most recent call last): File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap self.run() File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/multiprocessing/process.py", line 108, in run self._target(*self._args, **self._kwargs) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerGeneFinder.py", line 122, in processBin hmmModelFile = markerSetParser.createHmmModelFile(binId, markerFile) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerSets.py", line 330, in createHmmModelFile markerFileType = self.markerFileType(markerFile) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerSets.py", line 430, in markerFileType with open(markerFile, 'r') as f: FileNotFoundError: [Errno 2] No such file or directory: '/home/majorram/anaconda3/envs/checkm/hmms/phylo.hmm' Process Process-23: Traceback (most recent call last): File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap self.run() File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/multiprocessing/process.py", line 108, in run self._target(*self._args, self._kwargs) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerGeneFinder.py", line 122, in processBin hmmModelFile = markerSetParser.createHmmModelFile(binId, markerFile) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerSets.py", line 330, in createHmmModelFile markerFileType = self.markerFileType(markerFile) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerSets.py", line 430, in markerFileType with open(markerFile, 'r') as f: FileNotFoundError: [Errno 2] No such file or directory: '/home/majorram/anaconda3/envs/checkm/hmms/phylo.hmm' Process Process-7: Traceback (most recent call last): File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap self.run() File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/multiprocessing/process.py", line 108, in run self._target(*self._args, **self._kwargs) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerGeneFinder.py", line 122, in processBin hmmModelFile = markerSetParser.createHmmModelFile(binId, markerFile) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerSets.py", line 330, in createHmmModelFile markerFileType = self.markerFileType(markerFile) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerSets.py", line 430, in markerFileType with open(markerFile, 'r') as f: FileNotFoundError: [Errno 2] No such file or directory: '/home/majorram/anaconda3/envs/checkm/hmms/phylo.hmm' Process Process-8: Traceback (most recent call last): File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap self.run() File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/multiprocessing/process.py", line 108, in run self._target(*self._args, self._kwargs) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerGeneFinder.py", line 122, in processBin hmmModelFile = markerSetParser.createHmmModelFile(binId, markerFile) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerSets.py", line 330, in createHmmModelFile markerFileType = self.markerFileType(markerFile) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerSets.py", line 430, in markerFileType with open(markerFile, 'r') as f: FileNotFoundError: [Errno 2] No such file or directory: '/home/majorram/anaconda3/envs/checkm/hmms/phylo.hmm' Process Process-30: Traceback (most recent call last): File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap self.run() File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/multiprocessing/process.py", line 108, in run self._target(*self._args, **self._kwargs) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerGeneFinder.py", line 122, in processBin hmmModelFile = markerSetParser.createHmmModelFile(binId, markerFile) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerSets.py", line 330, in createHmmModelFile markerFileType = self.markerFileType(markerFile) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerSets.py", line 430, in markerFileType with open(markerFile, 'r') as f: FileNotFoundError: [Errno 2] No such file or directory: '/home/majorram/anaconda3/envs/checkm/hmms/phylo.hmm' Process Process-26: Traceback (most recent call last): File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap self.run() File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/multiprocessing/process.py", line 108, in run self._target(*self._args, self._kwargs) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerGeneFinder.py", line 122, in processBin hmmModelFile = markerSetParser.createHmmModelFile(binId, markerFile) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerSets.py", line 330, in createHmmModelFile markerFileType = self.markerFileType(markerFile) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerSets.py", line 430, in markerFileType with open(markerFile, 'r') as f: FileNotFoundError: [Errno 2] No such file or directory: '/home/majorram/anaconda3/envs/checkm/hmms/phylo.hmm' Process Process-24: Traceback (most recent call last): File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap self.run() File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/multiprocessing/process.py", line 108, in run self._target(*self._args, **self._kwargs) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerGeneFinder.py", line 122, in processBin hmmModelFile = markerSetParser.createHmmModelFile(binId, markerFile) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerSets.py", line 330, in createHmmModelFile markerFileType = self.markerFileType(markerFile) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerSets.py", line 430, in markerFileType with open(markerFile, 'r') as f: FileNotFoundError: [Errno 2] No such file or directory: '/home/majorram/anaconda3/envs/checkm/hmms/phylo.hmm' Process Process-20: Traceback (most recent call last): File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap self.run() File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/multiprocessing/process.py", line 108, in run self._target(*self._args, self._kwargs) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerGeneFinder.py", line 122, in processBin hmmModelFile = markerSetParser.createHmmModelFile(binId, markerFile) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerSets.py", line 330, in createHmmModelFile markerFileType = self.markerFileType(markerFile) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerSets.py", line 430, in markerFileType with open(markerFile, 'r') as f: FileNotFoundError: [Errno 2] No such file or directory: '/home/majorram/anaconda3/envs/checkm/hmms/phylo.hmm' Process Process-17: Traceback (most recent call last): File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap self.run() File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/multiprocessing/process.py", line 108, in run self._target(*self._args, **self._kwargs) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerGeneFinder.py", line 122, in processBin hmmModelFile = markerSetParser.createHmmModelFile(binId, markerFile) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerSets.py", line 330, in createHmmModelFile markerFileType = self.markerFileType(markerFile) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerSets.py", line 430, in markerFileType with open(markerFile, 'r') as f: FileNotFoundError: [Errno 2] No such file or directory: '/home/majorram/anaconda3/envs/checkm/hmms/phylo.hmm' Process Process-21: Traceback (most recent call last): File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap self.run() File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/multiprocessing/process.py", line 108, in run self._target(*self._args, self._kwargs) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerGeneFinder.py", line 122, in processBin hmmModelFile = markerSetParser.createHmmModelFile(binId, markerFile) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerSets.py", line 330, in createHmmModelFile markerFileType = self.markerFileType(markerFile) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerSets.py", line 430, in markerFileType with open(markerFile, 'r') as f: FileNotFoundError: [Errno 2] No such file or directory: '/home/majorram/anaconda3/envs/checkm/hmms/phylo.hmm' Process Process-18: Traceback (most recent call last): File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap self.run() File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/multiprocessing/process.py", line 108, in run self._target(*self._args, **self._kwargs) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerGeneFinder.py", line 122, in processBin hmmModelFile = markerSetParser.createHmmModelFile(binId, markerFile) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerSets.py", line 330, in createHmmModelFile markerFileType = self.markerFileType(markerFile) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerSets.py", line 430, in markerFileType with open(markerFile, 'r') as f: FileNotFoundError: [Errno 2] No such file or directory: '/home/majorram/anaconda3/envs/checkm/hmms/phylo.hmm' Process Process-19: Traceback (most recent call last): File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap self.run() File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/multiprocessing/process.py", line 108, in run self._target(*self._args, self._kwargs) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerGeneFinder.py", line 122, in processBin hmmModelFile = markerSetParser.createHmmModelFile(binId, markerFile) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerSets.py", line 330, in createHmmModelFile markerFileType = self.markerFileType(markerFile) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerSets.py", line 430, in markerFileType with open(markerFile, 'r') as f: FileNotFoundError: [Errno 2] No such file or directory: '/home/majorram/anaconda3/envs/checkm/hmms/phylo.hmm' Process Process-31: Traceback (most recent call last): File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap self.run() File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/multiprocessing/process.py", line 108, in run self._target(*self._args, **self._kwargs) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerGeneFinder.py", line 122, in processBin hmmModelFile = markerSetParser.createHmmModelFile(binId, markerFile) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerSets.py", line 330, in createHmmModelFile markerFileType = self.markerFileType(markerFile) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerSets.py", line 430, in markerFileType with open(markerFile, 'r') as f: FileNotFoundError: [Errno 2] No such file or directory: '/home/majorram/anaconda3/envs/checkm/hmms/phylo.hmm' Process Process-9: Traceback (most recent call last): File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap self.run() File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/multiprocessing/process.py", line 108, in run self._target(*self._args, self._kwargs) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerGeneFinder.py", line 122, in processBin hmmModelFile = markerSetParser.createHmmModelFile(binId, markerFile) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerSets.py", line 330, in createHmmModelFile markerFileType = self.markerFileType(markerFile) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerSets.py", line 430, in markerFileType with open(markerFile, 'r') as f: FileNotFoundError: [Errno 2] No such file or directory: '/home/majorram/anaconda3/envs/checkm/hmms/phylo.hmm' Process Process-2: Traceback (most recent call last): File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap self.run() File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/multiprocessing/process.py", line 108, in run self._target(*self._args, **self._kwargs) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerGeneFinder.py", line 122, in processBin hmmModelFile = markerSetParser.createHmmModelFile(binId, markerFile) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerSets.py", line 330, in createHmmModelFile markerFileType = self.markerFileType(markerFile) File "/home/majorram/anaconda3/envs/checkm/lib/python3.9/site-packages/checkm/markerSets.py", line 430, in markerFileType with open(markerFile, 'r') as f: FileNotFoundError: [Errno 2] No such file or directory: '/home/majorram/anaconda3/envs/checkm/hmms/phylo.hmm'

[2023-08-02 12:17:04] INFO: Saving HMM info to file. [2023-08-02 12:17:04] INFO: Calculating genome statistics for 49 bins with 32 threads: Finished processing 49 of 49 (100.00%) bins. [2023-08-02 12:17:04] INFO: Extracting marker genes to align. [2023-08-02 12:17:04] ERROR: Models must be parsed before identifying HMM hits.

Controlled exit resulting from an unrecoverable error or warning.

bheimbu commented 11 months ago

Hi @ramnageena11,

did you follow this https://github.com/Ecogenomics/CheckM/wiki/Installation#required-reference-data.

Cheers Bastian

ramnageena11 commented 11 months ago

Hi Bastin, I followed this https://github.com/bxlab/metaWRAP/blob/master/installation/database_installation.md Pls suggest.

thanks rgds Ram

Ram Singh, Postdoctoral Research Scientist

Science Communication Fellow (SD Discovery Center)

Karen M. Swindler Department of Chemical & Biological Engineering

South Dakota Mines

501 E. Saint Joseph St., Rapid City, SD 57701

605.394.1730 | @.***

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On Wed, Oct 25, 2023 at 7:22 AM bheimbu @.***> wrote:

Hi @ramnageena11 https://github.com/ramnageena11,

did you follow this https://github.com/Ecogenomics/CheckM/wiki/Installation#required-reference-data .

Cheers Bastian

— Reply to this email directly, view it on GitHub https://github.com/Ecogenomics/CheckM/issues/378#issuecomment-1779266282, or unsubscribe https://github.com/notifications/unsubscribe-auth/AK4LETW3MMCUKK4QE6L5VP3YBEHCDAVCNFSM6AAAAAA3BVDSBCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTONZZGI3DMMRYGI . You are receiving this because you were mentioned.Message ID: @.***>

donovan-h-parks commented 3 months ago

Hi. This is likely due to exceeding the memory on your machine. The system requirements for CheckM can be found here: https://github.com/Ecogenomics/CheckM/wiki/Installation#system-requirements