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Hello,
I installed CheckM and all the dependencies in Conda environment (with Python 3.8).
It seems like pplacer is not working. I am trying to do launch CheckM with this command checkm lineage_wf -t 16 --tab_tabl Genomes/ CheckM_Output/
Here's the output:
[2025-03-19 23:39:18] INFO: CheckM v1.2.3
[2025-03-19 23:39:18] INFO: checkm lineage_wf -t 16 --tab_tabl Genomes/ CheckM_Output/
[2025-03-19 23:39:18] INFO: CheckM data: /home/user/Documents/CheckM_reference_data
[2025-03-19 23:39:18] INFO: [CheckM - tree] Placing bins in reference genome tree.
[2025-03-19 23:39:18] INFO: Identifying marker genes in 34 bins with 16 threads:
Finished processing 34 of 34 (100.00%) bins.
[2025-03-19 23:39:20] INFO: Saving HMM info to file.
[2025-03-19 23:39:20] INFO: Calculating genome statistics for 34 bins with 16 threads:
Finished processing 34 of 34 (100.00%) bins.
[2025-03-19 23:39:20] INFO: Extracting marker genes to align.
[2025-03-19 23:39:20] INFO: Parsing HMM hits to marker genes:
Finished parsing hits for 34 of 34 (100.00%) bins.
[2025-03-19 23:39:21] INFO: Extracting 43 HMMs with 16 threads:
Finished extracting 43 of 43 (100.00%) HMMs.
[2025-03-19 23:39:21] INFO: Aligning 43 marker genes with 16 threads:
Finished aligning 43 of 43 (100.00%) marker genes.
[2025-03-19 23:39:22] INFO: Reading marker alignment files.
[2025-03-19 23:39:22] INFO: Concatenating alignments.
[2025-03-19 23:39:22] INFO: Placing 34 bins into the genome tree with pplacer (be patient).
Killed
[2025-03-19 23:45:48] ERROR: pplacer exited with code: 35072
Controlled exit resulting from an unrecoverable error or warning.
The text was updated successfully, but these errors were encountered:
Hello,
I installed CheckM and all the dependencies in Conda environment (with Python 3.8).
It seems like pplacer is not working. I am trying to do launch CheckM with this command
checkm lineage_wf -t 16 --tab_tabl Genomes/ CheckM_Output/
Here's the output:
The text was updated successfully, but these errors were encountered: