[2022-01-19 03:49:56] INFO: CheckM v1.1.3
[2022-01-19 03:49:56] INFO: checkm lineage_wf -t 8 --pplacer_threads 8 -x fa BIN_REFINEMENT/metawrap_50_10_bins output_checkM
[2022-01-19 03:49:56] INFO: [CheckM - tree] Placing bins in reference genome tree.
[2022-01-19 03:49:56] INFO: Identifying marker genes in 14 bins with 8 threads:
[2022-01-19 03:50:43] INFO: Saving HMM info to file.
[2022-01-19 03:50:43] INFO: Calculating genome statistics for 14 bins with 8 threads:
[2022-01-19 03:50:44] INFO: Extracting marker genes to align.
[2022-01-19 03:50:44] INFO: Parsing HMM hits to marker genes:
[2022-01-19 03:50:44] INFO: Extracting 43 HMMs with 8 threads:
[2022-01-19 03:50:44] INFO: Aligning 43 marker genes with 8 threads:
[2022-01-19 03:50:45] INFO: Reading marker alignment files.
[2022-01-19 03:50:45] INFO: Concatenating alignments.
[2022-01-19 03:50:45] INFO: Placing 14 bins into the genome tree with pplacer (be patient).
[2022-01-19 03:55:23] INFO: { Current stage: 0:05:27.948 || Total: 0:05:27.948 }
[2022-01-19 03:55:23] INFO: [CheckM - lineage_set] Inferring lineage-specific marker sets.
[2022-01-19 03:55:23] INFO: Reading HMM info from file.
[2022-01-19 03:55:24] INFO: Parsing HMM hits to marker genes:
[2022-01-19 03:55:24] INFO: Determining marker sets for each genome bin.
[2022-01-19 03:55:27] INFO: Marker set written to: output_checkM/lineage.ms
[2022-01-19 03:55:27] INFO: { Current stage: 0:00:03.163 || Total: 0:05:31.112 }
[2022-01-19 03:55:27] INFO: [CheckM - analyze] Identifying marker genes in bins.
[2022-01-19 03:55:27] INFO: Identifying marker genes in 14 bins with 8 threads:
[2022-01-19 03:59:00] INFO: Saving HMM info to file.
[2022-01-19 03:59:01] INFO: { Current stage: 0:03:34.286 || Total: 0:09:05.398 }
[2022-01-19 03:59:01] INFO: Parsing HMM hits to marker genes:
[2022-01-19 03:59:04] INFO: Aligning marker genes with multiple hits in a single bin:
[2022-01-19 03:59:12] INFO: { Current stage: 0:00:11.168 || Total: 0:09:16.567 }
[2022-01-19 03:59:12] INFO: Calculating genome statistics for 14 bins with 8 threads:
[2022-01-19 03:59:12] INFO: { Current stage: 0:00:00.259 || Total: 0:09:16.826 }
[2022-01-19 03:59:12] INFO: [CheckM - qa] Tabulating genome statistics.
[2022-01-19 03:59:12] INFO: Calculating AAI between multi-copy marker genes.
[2022-01-19 03:59:12] INFO: Reading HMM info from file.
[2022-01-19 03:59:13] INFO: Parsing HMM hits to marker genes:
[2022-01-19 03:59:16] INFO: { Current stage: 0:00:03.373 || Total: 0:09:20.200 }