MrOlm
commented
4 months ago Hi @CujoChenFuyoh -
It seems that checkM doesn't have access to it's data. After installing checkM, you have to set the data location. See the checkM documentation for instructions. Here's the specific command that should be working:
/ubda/home/23124109r/miniconda3/envs/drep_old/bin/checkm qa /ubda/home/23124109r/genedata/6thfloor/temp/drep95/data/checkM/checkM_outdir/lineage.ms /ubda/home/23124109r/genedata/6thfloor/temp/drep95/data/checkM/checkM_outdir/ -f /ubda/home/23124109r/genedata/6thfloor/temp/drep95/data/checkM/checkM_outdir/Chdb.tsv -t 16 --tab_table -o 2
I ran my data on dRep of v 2.6.2 on centos server and threw like this in debug log. CheckM seems fail to finish the first step assigned by dRep and follow a file not found error in another log.
dRep dereplicate temp/drep_95/ \ -g temp/drep_in/*.fa \ --debug -sa 0.95 -nc 0.30 -comp 50 -con 10 -p 8
[2024-06-25 19:32:48] INFO: CheckM v1.2.2 [2024-06-25 19:32:48] INFO: checkm lineage_wf /ubda/home/23124109r/genedata/6thfloor/temp/drep95/data/prodigal/ /ubda/home/23124109r/genedata/6thfloor/temp/drep95/data/checkM/checkM_outdir/ -f /ubda/home/23124109r/genedata/6thfloor/temp/drep95/data/checkM/checkM_outdir//results.tsv --tab_table -t 16 --pplacer_threads 16 -g -x faa [2024-06-25 19:32:48] INFO: CheckM data: /ubda/home/23124109r/db/checkm [2024-06-25 19:32:48] INFO: [CheckM - tree] Placing bins in reference genome tree. [2024-06-25 19:32:48] INFO: Identifying marker genes in 3 bins with 16 threads: [2024-06-25 19:32:49] INFO: Saving HMM info to file. [2024-06-25 19:32:49] INFO: Calculating genome statistics for 3 bins with 16 threads: [2024-06-25 19:32:49] INFO: Extracting marker genes to align. [2024-06-25 19:32:49] INFO: Parsing HMM hits to marker genes: [2024-06-25 19:32:49] INFO: Extracting 43 HMMs with 16 threads: [2024-06-25 19:32:50] INFO: Aligning 43 marker genes with 16 threads: [2024-06-25 19:32:51] INFO: Reading marker alignment files. [2024-06-25 19:32:51] INFO: Concatenating alignments. [2024-06-25 19:32:51] INFO: Placing 3 bins into the genome tree with pplacer (be patient). [2024-06-25 19:36:43] INFO: { Current stage: 0:03:55.733 || Total: 0:03:55.733 } [2024-06-25 19:36:43] INFO: [CheckM - lineage_set] Inferring lineage-specific marker sets. [2024-06-25 19:36:43] INFO: Reading HMM info from file.
Unexpected error: <class 'ValueError'>
I further checked that HMMER is installed, thanks for helping debug this.
cmd_log.zip