[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: ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Bin Id Marker lineage # genomes # markers # marker sets 0 1 2 3 4 5+ Completeness Contamination Strain heterogeneity ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- bin.12 c__Gammaproteobacteria (UID4444) 263 505 231 2 500 3 0 0 0 99.71 0.70 0.00 bin.2 f__Rhodobacteraceae (UID3340) 84 568 330 11 555 2 0 0 0 97.73 0.20 0.00 bin.4 o__Actinomycetales (UID1593) 69 400 198 21 377 2 0 0 0 94.22 0.61 50.00 bin.7 f__Rhodobacteraceae (UID3356) 67 615 329 42 552 21 0 0 0 93.25 3.57 76.19 bin.9 s__algicola (UID2846) 47 571 303 64 489 18 0 0 0 87.34 2.98 61.11 bin.5 c__Gammaproteobacteria (UID4443) 356 451 270 82 358 11 0 0 0 87.04 1.96 81.82 bin.1 s__algicola (UID2847) 33 496 263 102 366 26 2 0 0 75.80 4.00 46.88 bin.8 p__Proteobacteria (UID3880) 1495 242 151 72 165 5 0 0 0 70.56 2.98 40.00 bin.10 c__Gammaproteobacteria (UID4443) 356 451 270 131 314 6 0 0 0 67.96 0.92 33.33 bin.13 c__Gammaproteobacteria (UID4443) 356 451 270 149 289 13 0 0 0 60.64 2.61 61.54 bin.15 f__Rhodobacteraceae (UID3356) 67 615 329 241 300 68 6 0 0 59.50 9.53 1.16 bin.6 k__Archaea (UID2) 207 145 103 63 77 4 1 0 0 54.88 4.37 85.71 bin.14 k__Bacteria (UID2569) 434 278 186 116 147 15 0 0 0 52.91 1.72 20.00 bin.3 c__Gammaproteobacteria (UID4443) 356 451 270 198 229 24 0 0 0 50.35 5.90 37.50 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- [2022-01-19 03:59:16] INFO: { Current stage: 0:00:03.373 || Total: 0:09:20.200 }