Setting up a portable metagenome assembly pipeline for CBIO

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 [CheckM - tree] Placing bins in reference genome tree.

*******************************************************************************

  Identifying marker genes in 96 bins with 20 threads:

    Finished processing 0 of 96 (0.00%) bins.

    Finished processing 1 of 96 (1.04%) bins.

    Finished processing 2 of 96 (2.08%) bins.

    Finished processing 3 of 96 (3.12%) bins.

    Finished processing 4 of 96 (4.17%) bins.

    Finished processing 5 of 96 (5.21%) bins.

    Finished processing 6 of 96 (6.25%) bins.

    Finished processing 7 of 96 (7.29%) bins.

    Finished processing 8 of 96 (8.33%) bins.

    Finished processing 9 of 96 (9.38%) bins.

    Finished processing 10 of 96 (10.42%) bins.

    Finished processing 11 of 96 (11.46%) bins.

    Finished processing 12 of 96 (12.50%) bins.

    Finished processing 13 of 96 (13.54%) bins.

    Finished processing 14 of 96 (14.58%) bins.

    Finished processing 15 of 96 (15.62%) bins.

    Finished processing 16 of 96 (16.67%) bins.

    Finished processing 17 of 96 (17.71%) bins.

    Finished processing 18 of 96 (18.75%) bins.

    Finished processing 19 of 96 (19.79%) bins.

    Finished processing 20 of 96 (20.83%) bins.

    Finished processing 21 of 96 (21.88%) bins.

    Finished processing 22 of 96 (22.92%) bins.

    Finished processing 23 of 96 (23.96%) bins.

    Finished processing 24 of 96 (25.00%) bins.

    Finished processing 25 of 96 (26.04%) bins.

    Finished processing 26 of 96 (27.08%) bins.

    Finished processing 27 of 96 (28.12%) bins.

    Finished processing 28 of 96 (29.17%) bins.

    Finished processing 29 of 96 (30.21%) bins.

    Finished processing 30 of 96 (31.25%) bins.

    Finished processing 31 of 96 (32.29%) bins.

    Finished processing 32 of 96 (33.33%) bins.

    Finished processing 33 of 96 (34.38%) bins.

    Finished processing 34 of 96 (35.42%) bins.

    Finished processing 35 of 96 (36.46%) bins.

    Finished processing 36 of 96 (37.50%) bins.

    Finished processing 37 of 96 (38.54%) bins.

    Finished processing 38 of 96 (39.58%) bins.

    Finished processing 39 of 96 (40.62%) bins.

    Finished processing 40 of 96 (41.67%) bins.

    Finished processing 41 of 96 (42.71%) bins.

    Finished processing 42 of 96 (43.75%) bins.

    Finished processing 43 of 96 (44.79%) bins.

    Finished processing 44 of 96 (45.83%) bins.

    Finished processing 45 of 96 (46.88%) bins.

    Finished processing 46 of 96 (47.92%) bins.

    Finished processing 47 of 96 (48.96%) bins.

    Finished processing 48 of 96 (50.00%) bins.

    Finished processing 49 of 96 (51.04%) bins.

    Finished processing 50 of 96 (52.08%) bins.

    Finished processing 51 of 96 (53.12%) bins.

    Finished processing 52 of 96 (54.17%) bins.

    Finished processing 53 of 96 (55.21%) bins.

    Finished processing 54 of 96 (56.25%) bins.

    Finished processing 55 of 96 (57.29%) bins.

    Finished processing 56 of 96 (58.33%) bins.

    Finished processing 57 of 96 (59.38%) bins.

    Finished processing 58 of 96 (60.42%) bins.

    Finished processing 59 of 96 (61.46%) bins.

    Finished processing 60 of 96 (62.50%) bins.

    Finished processing 61 of 96 (63.54%) bins.

    Finished processing 62 of 96 (64.58%) bins.

    Finished processing 63 of 96 (65.62%) bins.

    Finished processing 64 of 96 (66.67%) bins.

    Finished processing 65 of 96 (67.71%) bins.

    Finished processing 66 of 96 (68.75%) bins.

    Finished processing 67 of 96 (69.79%) bins.

    Finished processing 68 of 96 (70.83%) bins.

    Finished processing 69 of 96 (71.88%) bins.

    Finished processing 70 of 96 (72.92%) bins.

    Finished processing 71 of 96 (73.96%) bins.

    Finished processing 72 of 96 (75.00%) bins.

    Finished processing 73 of 96 (76.04%) bins.

    Finished processing 74 of 96 (77.08%) bins.

    Finished processing 75 of 96 (78.12%) bins.

    Finished processing 76 of 96 (79.17%) bins.

    Finished processing 77 of 96 (80.21%) bins.

    Finished processing 78 of 96 (81.25%) bins.

    Finished processing 79 of 96 (82.29%) bins.

    Finished processing 80 of 96 (83.33%) bins.

    Finished processing 81 of 96 (84.38%) bins.

    Finished processing 82 of 96 (85.42%) bins.

    Finished processing 83 of 96 (86.46%) bins.

    Finished processing 84 of 96 (87.50%) bins.

    Finished processing 85 of 96 (88.54%) bins.

    Finished processing 86 of 96 (89.58%) bins.

    Finished processing 87 of 96 (90.62%) bins.

    Finished processing 88 of 96 (91.67%) bins.

    Finished processing 89 of 96 (92.71%) bins.

    Finished processing 90 of 96 (93.75%) bins.

    Finished processing 91 of 96 (94.79%) bins.

    Finished processing 92 of 96 (95.83%) bins.

    Finished processing 93 of 96 (96.88%) bins.

    Finished processing 94 of 96 (97.92%) bins.

    Finished processing 95 of 96 (98.96%) bins.

    Finished processing 96 of 96 (100.00%) bins.

  Saving HMM info to file.

  Calculating genome statistics for 96 bins with 20 threads:

    Finished processing 0 of 96 (0.00%) bins.

    Finished processing 1 of 96 (1.04%) bins.

    Finished processing 2 of 96 (2.08%) bins.

    Finished processing 3 of 96 (3.12%) bins.

    Finished processing 4 of 96 (4.17%) bins.

    Finished processing 5 of 96 (5.21%) bins.

    Finished processing 6 of 96 (6.25%) bins.

    Finished processing 7 of 96 (7.29%) bins.

    Finished processing 8 of 96 (8.33%) bins.

    Finished processing 9 of 96 (9.38%) bins.

    Finished processing 10 of 96 (10.42%) bins.

    Finished processing 11 of 96 (11.46%) bins.

    Finished processing 12 of 96 (12.50%) bins.

    Finished processing 13 of 96 (13.54%) bins.

    Finished processing 14 of 96 (14.58%) bins.

    Finished processing 15 of 96 (15.62%) bins.

    Finished processing 16 of 96 (16.67%) bins.

    Finished processing 17 of 96 (17.71%) bins.

    Finished processing 18 of 96 (18.75%) bins.

    Finished processing 19 of 96 (19.79%) bins.

    Finished processing 20 of 96 (20.83%) bins.

    Finished processing 21 of 96 (21.88%) bins.

    Finished processing 22 of 96 (22.92%) bins.

    Finished processing 23 of 96 (23.96%) bins.

    Finished processing 24 of 96 (25.00%) bins.

    Finished processing 25 of 96 (26.04%) bins.

    Finished processing 26 of 96 (27.08%) bins.

    Finished processing 27 of 96 (28.12%) bins.

    Finished processing 28 of 96 (29.17%) bins.

    Finished processing 29 of 96 (30.21%) bins.

    Finished processing 30 of 96 (31.25%) bins.

    Finished processing 31 of 96 (32.29%) bins.

    Finished processing 32 of 96 (33.33%) bins.

    Finished processing 33 of 96 (34.38%) bins.

    Finished processing 34 of 96 (35.42%) bins.

    Finished processing 35 of 96 (36.46%) bins.

    Finished processing 36 of 96 (37.50%) bins.

    Finished processing 37 of 96 (38.54%) bins.

    Finished processing 38 of 96 (39.58%) bins.

    Finished processing 39 of 96 (40.62%) bins.

    Finished processing 40 of 96 (41.67%) bins.

    Finished processing 41 of 96 (42.71%) bins.

    Finished processing 42 of 96 (43.75%) bins.

    Finished processing 43 of 96 (44.79%) bins.

    Finished processing 44 of 96 (45.83%) bins.

    Finished processing 45 of 96 (46.88%) bins.

    Finished processing 46 of 96 (47.92%) bins.

    Finished processing 47 of 96 (48.96%) bins.

    Finished processing 48 of 96 (50.00%) bins.

    Finished processing 49 of 96 (51.04%) bins.

    Finished processing 50 of 96 (52.08%) bins.

    Finished processing 51 of 96 (53.12%) bins.

    Finished processing 52 of 96 (54.17%) bins.

    Finished processing 53 of 96 (55.21%) bins.

    Finished processing 54 of 96 (56.25%) bins.

    Finished processing 55 of 96 (57.29%) bins.

    Finished processing 56 of 96 (58.33%) bins.

    Finished processing 57 of 96 (59.38%) bins.

    Finished processing 58 of 96 (60.42%) bins.

    Finished processing 59 of 96 (61.46%) bins.

    Finished processing 60 of 96 (62.50%) bins.

    Finished processing 61 of 96 (63.54%) bins.

    Finished processing 62 of 96 (64.58%) bins.

    Finished processing 63 of 96 (65.62%) bins.

    Finished processing 64 of 96 (66.67%) bins.

    Finished processing 65 of 96 (67.71%) bins.

    Finished processing 66 of 96 (68.75%) bins.

    Finished processing 67 of 96 (69.79%) bins.

    Finished processing 68 of 96 (70.83%) bins.

    Finished processing 69 of 96 (71.88%) bins.

    Finished processing 70 of 96 (72.92%) bins.

    Finished processing 71 of 96 (73.96%) bins.

    Finished processing 72 of 96 (75.00%) bins.

    Finished processing 73 of 96 (76.04%) bins.

    Finished processing 74 of 96 (77.08%) bins.

    Finished processing 75 of 96 (78.12%) bins.

    Finished processing 76 of 96 (79.17%) bins.

    Finished processing 77 of 96 (80.21%) bins.

    Finished processing 78 of 96 (81.25%) bins.

    Finished processing 79 of 96 (82.29%) bins.

    Finished processing 80 of 96 (83.33%) bins.

    Finished processing 81 of 96 (84.38%) bins.

    Finished processing 82 of 96 (85.42%) bins.

    Finished processing 83 of 96 (86.46%) bins.

    Finished processing 84 of 96 (87.50%) bins.

    Finished processing 85 of 96 (88.54%) bins.

    Finished processing 86 of 96 (89.58%) bins.

    Finished processing 87 of 96 (90.62%) bins.

    Finished processing 88 of 96 (91.67%) bins.

    Finished processing 89 of 96 (92.71%) bins.

    Finished processing 90 of 96 (93.75%) bins.

    Finished processing 91 of 96 (94.79%) bins.

    Finished processing 92 of 96 (95.83%) bins.

    Finished processing 93 of 96 (96.88%) bins.

    Finished processing 94 of 96 (97.92%) bins.

    Finished processing 95 of 96 (98.96%) bins.

    Finished processing 96 of 96 (100.00%) bins.

  Extracting marker genes to align.

  Parsing HMM hits to marker genes:

    Finished parsing hits for 1 of 96 (1.04%) bins.

    Finished parsing hits for 2 of 96 (2.08%) bins.

    Finished parsing hits for 3 of 96 (3.12%) bins.

    Finished parsing hits for 4 of 96 (4.17%) bins.

    Finished parsing hits for 5 of 96 (5.21%) bins.

    Finished parsing hits for 6 of 96 (6.25%) bins.

    Finished parsing hits for 7 of 96 (7.29%) bins.

    Finished parsing hits for 8 of 96 (8.33%) bins.

    Finished parsing hits for 9 of 96 (9.38%) bins.

    Finished parsing hits for 10 of 96 (10.42%) bins.

    Finished parsing hits for 11 of 96 (11.46%) bins.

    Finished parsing hits for 12 of 96 (12.50%) bins.

    Finished parsing hits for 13 of 96 (13.54%) bins.

    Finished parsing hits for 14 of 96 (14.58%) bins.

    Finished parsing hits for 15 of 96 (15.62%) bins.

    Finished parsing hits for 16 of 96 (16.67%) bins.

    Finished parsing hits for 17 of 96 (17.71%) bins.

    Finished parsing hits for 18 of 96 (18.75%) bins.

    Finished parsing hits for 19 of 96 (19.79%) bins.

    Finished parsing hits for 20 of 96 (20.83%) bins.

    Finished parsing hits for 21 of 96 (21.88%) bins.

    Finished parsing hits for 22 of 96 (22.92%) bins.

    Finished parsing hits for 23 of 96 (23.96%) bins.

    Finished parsing hits for 24 of 96 (25.00%) bins.

    Finished parsing hits for 25 of 96 (26.04%) bins.

    Finished parsing hits for 26 of 96 (27.08%) bins.

    Finished parsing hits for 27 of 96 (28.12%) bins.

    Finished parsing hits for 28 of 96 (29.17%) bins.

    Finished parsing hits for 29 of 96 (30.21%) bins.

    Finished parsing hits for 30 of 96 (31.25%) bins.

    Finished parsing hits for 31 of 96 (32.29%) bins.

    Finished parsing hits for 32 of 96 (33.33%) bins.

    Finished parsing hits for 33 of 96 (34.38%) bins.

    Finished parsing hits for 34 of 96 (35.42%) bins.

    Finished parsing hits for 35 of 96 (36.46%) bins.

    Finished parsing hits for 36 of 96 (37.50%) bins.

    Finished parsing hits for 37 of 96 (38.54%) bins.

    Finished parsing hits for 38 of 96 (39.58%) bins.

    Finished parsing hits for 39 of 96 (40.62%) bins.

    Finished parsing hits for 40 of 96 (41.67%) bins.

    Finished parsing hits for 41 of 96 (42.71%) bins.

    Finished parsing hits for 42 of 96 (43.75%) bins.

    Finished parsing hits for 43 of 96 (44.79%) bins.

    Finished parsing hits for 44 of 96 (45.83%) bins.

    Finished parsing hits for 45 of 96 (46.88%) bins.

    Finished parsing hits for 46 of 96 (47.92%) bins.

    Finished parsing hits for 47 of 96 (48.96%) bins.

    Finished parsing hits for 48 of 96 (50.00%) bins.

    Finished parsing hits for 49 of 96 (51.04%) bins.

    Finished parsing hits for 50 of 96 (52.08%) bins.

    Finished parsing hits for 51 of 96 (53.12%) bins.

    Finished parsing hits for 52 of 96 (54.17%) bins.

    Finished parsing hits for 53 of 96 (55.21%) bins.

    Finished parsing hits for 54 of 96 (56.25%) bins.

    Finished parsing hits for 55 of 96 (57.29%) bins.

    Finished parsing hits for 56 of 96 (58.33%) bins.

    Finished parsing hits for 57 of 96 (59.38%) bins.

    Finished parsing hits for 58 of 96 (60.42%) bins.

    Finished parsing hits for 59 of 96 (61.46%) bins.

    Finished parsing hits for 60 of 96 (62.50%) bins.

    Finished parsing hits for 61 of 96 (63.54%) bins.

    Finished parsing hits for 62 of 96 (64.58%) bins.

    Finished parsing hits for 63 of 96 (65.62%) bins.

    Finished parsing hits for 64 of 96 (66.67%) bins.

    Finished parsing hits for 65 of 96 (67.71%) bins.

    Finished parsing hits for 66 of 96 (68.75%) bins.

    Finished parsing hits for 67 of 96 (69.79%) bins.

    Finished parsing hits for 68 of 96 (70.83%) bins.

    Finished parsing hits for 69 of 96 (71.88%) bins.

    Finished parsing hits for 70 of 96 (72.92%) bins.

    Finished parsing hits for 71 of 96 (73.96%) bins.

    Finished parsing hits for 72 of 96 (75.00%) bins.

    Finished parsing hits for 73 of 96 (76.04%) bins.

    Finished parsing hits for 74 of 96 (77.08%) bins.

    Finished parsing hits for 75 of 96 (78.12%) bins.

    Finished parsing hits for 76 of 96 (79.17%) bins.

    Finished parsing hits for 77 of 96 (80.21%) bins.

    Finished parsing hits for 78 of 96 (81.25%) bins.

    Finished parsing hits for 79 of 96 (82.29%) bins.

    Finished parsing hits for 80 of 96 (83.33%) bins.

    Finished parsing hits for 81 of 96 (84.38%) bins.

    Finished parsing hits for 82 of 96 (85.42%) bins.

    Finished parsing hits for 83 of 96 (86.46%) bins.

    Finished parsing hits for 84 of 96 (87.50%) bins.

    Finished parsing hits for 85 of 96 (88.54%) bins.

    Finished parsing hits for 86 of 96 (89.58%) bins.

    Finished parsing hits for 87 of 96 (90.62%) bins.

    Finished parsing hits for 88 of 96 (91.67%) bins.

    Finished parsing hits for 89 of 96 (92.71%) bins.

    Finished parsing hits for 90 of 96 (93.75%) bins.

    Finished parsing hits for 91 of 96 (94.79%) bins.

    Finished parsing hits for 92 of 96 (95.83%) bins.

    Finished parsing hits for 93 of 96 (96.88%) bins.

    Finished parsing hits for 94 of 96 (97.92%) bins.

    Finished parsing hits for 95 of 96 (98.96%) bins.

    Finished parsing hits for 96 of 96 (100.00%) bins.

  Extracting 43 HMMs with 20 threads:

    Finished extracting 0 of 43 (0.00%) HMMs.

    Finished extracting 1 of 43 (2.33%) HMMs.

    Finished extracting 2 of 43 (4.65%) HMMs.

    Finished extracting 3 of 43 (6.98%) HMMs.

    Finished extracting 4 of 43 (9.30%) HMMs.

    Finished extracting 5 of 43 (11.63%) HMMs.

    Finished extracting 6 of 43 (13.95%) HMMs.

    Finished extracting 7 of 43 (16.28%) HMMs.

    Finished extracting 8 of 43 (18.60%) HMMs.

    Finished extracting 9 of 43 (20.93%) HMMs.

    Finished extracting 10 of 43 (23.26%) HMMs.

    Finished extracting 11 of 43 (25.58%) HMMs.

    Finished extracting 12 of 43 (27.91%) HMMs.

    Finished extracting 13 of 43 (30.23%) HMMs.

    Finished extracting 14 of 43 (32.56%) HMMs.

    Finished extracting 15 of 43 (34.88%) HMMs.

    Finished extracting 16 of 43 (37.21%) HMMs.

    Finished extracting 17 of 43 (39.53%) HMMs.

    Finished extracting 18 of 43 (41.86%) HMMs.

    Finished extracting 19 of 43 (44.19%) HMMs.

    Finished extracting 20 of 43 (46.51%) HMMs.

    Finished extracting 21 of 43 (48.84%) HMMs.

    Finished extracting 22 of 43 (51.16%) HMMs.

    Finished extracting 23 of 43 (53.49%) HMMs.

    Finished extracting 24 of 43 (55.81%) HMMs.

    Finished extracting 25 of 43 (58.14%) HMMs.

    Finished extracting 26 of 43 (60.47%) HMMs.

    Finished extracting 27 of 43 (62.79%) HMMs.

    Finished extracting 28 of 43 (65.12%) HMMs.

    Finished extracting 29 of 43 (67.44%) HMMs.

    Finished extracting 30 of 43 (69.77%) HMMs.

    Finished extracting 31 of 43 (72.09%) HMMs.

    Finished extracting 32 of 43 (74.42%) HMMs.

    Finished extracting 33 of 43 (76.74%) HMMs.

    Finished extracting 34 of 43 (79.07%) HMMs.

    Finished extracting 35 of 43 (81.40%) HMMs.

    Finished extracting 36 of 43 (83.72%) HMMs.

    Finished extracting 37 of 43 (86.05%) HMMs.

    Finished extracting 38 of 43 (88.37%) HMMs.

    Finished extracting 39 of 43 (90.70%) HMMs.

    Finished extracting 40 of 43 (93.02%) HMMs.

    Finished extracting 41 of 43 (95.35%) HMMs.

    Finished extracting 42 of 43 (97.67%) HMMs.

    Finished extracting 43 of 43 (100.00%) HMMs.

  Aligning 43 marker genes with 20 threads:

    Finished aligning 0 of 43 (0.00%) marker genes.

    Finished aligning 1 of 43 (2.33%) marker genes.

    Finished aligning 2 of 43 (4.65%) marker genes.

    Finished aligning 3 of 43 (6.98%) marker genes.

    Finished aligning 4 of 43 (9.30%) marker genes.

    Finished aligning 5 of 43 (11.63%) marker genes.

    Finished aligning 6 of 43 (13.95%) marker genes.

    Finished aligning 7 of 43 (16.28%) marker genes.

    Finished aligning 8 of 43 (18.60%) marker genes.

    Finished aligning 9 of 43 (20.93%) marker genes.

    Finished aligning 10 of 43 (23.26%) marker genes.

    Finished aligning 11 of 43 (25.58%) marker genes.

    Finished aligning 12 of 43 (27.91%) marker genes.

    Finished aligning 13 of 43 (30.23%) marker genes.

    Finished aligning 14 of 43 (32.56%) marker genes.

    Finished aligning 15 of 43 (34.88%) marker genes.

    Finished aligning 16 of 43 (37.21%) marker genes.

    Finished aligning 17 of 43 (39.53%) marker genes.

    Finished aligning 18 of 43 (41.86%) marker genes.

    Finished aligning 19 of 43 (44.19%) marker genes.

    Finished aligning 20 of 43 (46.51%) marker genes.

    Finished aligning 21 of 43 (48.84%) marker genes.

    Finished aligning 22 of 43 (51.16%) marker genes.

    Finished aligning 23 of 43 (53.49%) marker genes.

    Finished aligning 24 of 43 (55.81%) marker genes.

    Finished aligning 25 of 43 (58.14%) marker genes.

    Finished aligning 26 of 43 (60.47%) marker genes.

    Finished aligning 27 of 43 (62.79%) marker genes.

    Finished aligning 28 of 43 (65.12%) marker genes.

    Finished aligning 29 of 43 (67.44%) marker genes.

    Finished aligning 30 of 43 (69.77%) marker genes.

    Finished aligning 31 of 43 (72.09%) marker genes.

    Finished aligning 32 of 43 (74.42%) marker genes.

    Finished aligning 33 of 43 (76.74%) marker genes.

    Finished aligning 34 of 43 (79.07%) marker genes.

    Finished aligning 35 of 43 (81.40%) marker genes.

    Finished aligning 36 of 43 (83.72%) marker genes.

    Finished aligning 37 of 43 (86.05%) marker genes.

    Finished aligning 38 of 43 (88.37%) marker genes.

    Finished aligning 39 of 43 (90.70%) marker genes.

    Finished aligning 40 of 43 (93.02%) marker genes.

    Finished aligning 41 of 43 (95.35%) marker genes.

    Finished aligning 42 of 43 (97.67%) marker genes.

    Finished aligning 43 of 43 (100.00%) marker genes.

  Reading marker alignment files.

  Concatenating alignments.

  Placing 96 bins into the genome tree with pplacer (be patient).

  { Current stage: 0:24:35.623 || Total: 0:24:35.623 }

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 [CheckM - lineage_set] Inferring lineage-specific marker sets.

*******************************************************************************

  Reading HMM info from file.

  Parsing HMM hits to marker genes:

    Finished parsing hits for 1 of 96 (1.04%) bins.

    Finished parsing hits for 2 of 96 (2.08%) bins.

    Finished parsing hits for 3 of 96 (3.12%) bins.

    Finished parsing hits for 4 of 96 (4.17%) bins.

    Finished parsing hits for 5 of 96 (5.21%) bins.

    Finished parsing hits for 6 of 96 (6.25%) bins.

    Finished parsing hits for 7 of 96 (7.29%) bins.

    Finished parsing hits for 8 of 96 (8.33%) bins.

    Finished parsing hits for 9 of 96 (9.38%) bins.

    Finished parsing hits for 10 of 96 (10.42%) bins.

    Finished parsing hits for 11 of 96 (11.46%) bins.

    Finished parsing hits for 12 of 96 (12.50%) bins.

    Finished parsing hits for 13 of 96 (13.54%) bins.

    Finished parsing hits for 14 of 96 (14.58%) bins.

    Finished parsing hits for 15 of 96 (15.62%) bins.

    Finished parsing hits for 16 of 96 (16.67%) bins.

    Finished parsing hits for 17 of 96 (17.71%) bins.

    Finished parsing hits for 18 of 96 (18.75%) bins.

    Finished parsing hits for 19 of 96 (19.79%) bins.

    Finished parsing hits for 20 of 96 (20.83%) bins.

    Finished parsing hits for 21 of 96 (21.88%) bins.

    Finished parsing hits for 22 of 96 (22.92%) bins.

    Finished parsing hits for 23 of 96 (23.96%) bins.

    Finished parsing hits for 24 of 96 (25.00%) bins.

    Finished parsing hits for 25 of 96 (26.04%) bins.

    Finished parsing hits for 26 of 96 (27.08%) bins.

    Finished parsing hits for 27 of 96 (28.12%) bins.

    Finished parsing hits for 28 of 96 (29.17%) bins.

    Finished parsing hits for 29 of 96 (30.21%) bins.

    Finished parsing hits for 30 of 96 (31.25%) bins.

    Finished parsing hits for 31 of 96 (32.29%) bins.

    Finished parsing hits for 32 of 96 (33.33%) bins.

    Finished parsing hits for 33 of 96 (34.38%) bins.

    Finished parsing hits for 34 of 96 (35.42%) bins.

    Finished parsing hits for 35 of 96 (36.46%) bins.

    Finished parsing hits for 36 of 96 (37.50%) bins.

    Finished parsing hits for 37 of 96 (38.54%) bins.

    Finished parsing hits for 38 of 96 (39.58%) bins.

    Finished parsing hits for 39 of 96 (40.62%) bins.

    Finished parsing hits for 40 of 96 (41.67%) bins.

    Finished parsing hits for 41 of 96 (42.71%) bins.

    Finished parsing hits for 42 of 96 (43.75%) bins.

    Finished parsing hits for 43 of 96 (44.79%) bins.

    Finished parsing hits for 44 of 96 (45.83%) bins.

    Finished parsing hits for 45 of 96 (46.88%) bins.

    Finished parsing hits for 46 of 96 (47.92%) bins.

    Finished parsing hits for 47 of 96 (48.96%) bins.

    Finished parsing hits for 48 of 96 (50.00%) bins.

    Finished parsing hits for 49 of 96 (51.04%) bins.

    Finished parsing hits for 50 of 96 (52.08%) bins.

    Finished parsing hits for 51 of 96 (53.12%) bins.

    Finished parsing hits for 52 of 96 (54.17%) bins.

    Finished parsing hits for 53 of 96 (55.21%) bins.

    Finished parsing hits for 54 of 96 (56.25%) bins.

    Finished parsing hits for 55 of 96 (57.29%) bins.

    Finished parsing hits for 56 of 96 (58.33%) bins.

    Finished parsing hits for 57 of 96 (59.38%) bins.

    Finished parsing hits for 58 of 96 (60.42%) bins.

    Finished parsing hits for 59 of 96 (61.46%) bins.

    Finished parsing hits for 60 of 96 (62.50%) bins.

    Finished parsing hits for 61 of 96 (63.54%) bins.

    Finished parsing hits for 62 of 96 (64.58%) bins.

    Finished parsing hits for 63 of 96 (65.62%) bins.

    Finished parsing hits for 64 of 96 (66.67%) bins.

    Finished parsing hits for 65 of 96 (67.71%) bins.

    Finished parsing hits for 66 of 96 (68.75%) bins.

    Finished parsing hits for 67 of 96 (69.79%) bins.

    Finished parsing hits for 68 of 96 (70.83%) bins.

    Finished parsing hits for 69 of 96 (71.88%) bins.

    Finished parsing hits for 70 of 96 (72.92%) bins.

    Finished parsing hits for 71 of 96 (73.96%) bins.

    Finished parsing hits for 72 of 96 (75.00%) bins.

    Finished parsing hits for 73 of 96 (76.04%) bins.

    Finished parsing hits for 74 of 96 (77.08%) bins.

    Finished parsing hits for 75 of 96 (78.12%) bins.

    Finished parsing hits for 76 of 96 (79.17%) bins.

    Finished parsing hits for 77 of 96 (80.21%) bins.

    Finished parsing hits for 78 of 96 (81.25%) bins.

    Finished parsing hits for 79 of 96 (82.29%) bins.

    Finished parsing hits for 80 of 96 (83.33%) bins.

    Finished parsing hits for 81 of 96 (84.38%) bins.

    Finished parsing hits for 82 of 96 (85.42%) bins.

    Finished parsing hits for 83 of 96 (86.46%) bins.

    Finished parsing hits for 84 of 96 (87.50%) bins.

    Finished parsing hits for 85 of 96 (88.54%) bins.

    Finished parsing hits for 86 of 96 (89.58%) bins.

    Finished parsing hits for 87 of 96 (90.62%) bins.

    Finished parsing hits for 88 of 96 (91.67%) bins.

    Finished parsing hits for 89 of 96 (92.71%) bins.

    Finished parsing hits for 90 of 96 (93.75%) bins.

    Finished parsing hits for 91 of 96 (94.79%) bins.

    Finished parsing hits for 92 of 96 (95.83%) bins.

    Finished parsing hits for 93 of 96 (96.88%) bins.

    Finished parsing hits for 94 of 96 (97.92%) bins.

    Finished parsing hits for 95 of 96 (98.96%) bins.

    Finished parsing hits for 96 of 96 (100.00%) bins.

  Determining marker sets for each genome bin.

    Finished processing 1 of 96 (1.04%) bins (current: b87_scaffold_IDs.matches).

    Finished processing 2 of 96 (2.08%) bins (current: b81_scaffold_IDs.matches).

    Finished processing 3 of 96 (3.12%) bins (current: b93_scaffold_IDs.matches).

    Finished processing 4 of 96 (4.17%) bins (current: b19_scaffold_IDs.matches).

    Finished processing 5 of 96 (5.21%) bins (current: b53_scaffold_IDs.matches).

    Finished processing 6 of 96 (6.25%) bins (current: b18_scaffold_IDs.matches).

    Finished processing 7 of 96 (7.29%) bins (current: b46_scaffold_IDs.matches).

    Finished processing 8 of 96 (8.33%) bins (current: b13_scaffold_IDs.matches).

    Finished processing 9 of 96 (9.38%) bins (current: b3_scaffold_IDs.matches).

    Finished processing 10 of 96 (10.42%) bins (current: b40_scaffold_IDs.matches).

    Finished processing 11 of 96 (11.46%) bins (current: b0_scaffold_IDs.matches).

    Finished processing 12 of 96 (12.50%) bins (current: b47_scaffold_IDs.matches).

    Finished processing 13 of 96 (13.54%) bins (current: b20_scaffold_IDs.matches).

    Finished processing 14 of 96 (14.58%) bins (current: b28_scaffold_IDs.matches).

    Finished processing 15 of 96 (15.62%) bins (current: b92_scaffold_IDs.matches).

    Finished processing 16 of 96 (16.67%) bins (current: b25_scaffold_IDs.matches).

    Finished processing 17 of 96 (17.71%) bins (current: b17_scaffold_IDs.matches).

    Finished processing 18 of 96 (18.75%) bins (current: b14_scaffold_IDs.matches).

    Finished processing 19 of 96 (19.79%) bins (current: b73_scaffold_IDs.matches).

    Finished processing 20 of 96 (20.83%) bins (current: b2_scaffold_IDs.matches).

    Finished processing 21 of 96 (21.88%) bins (current: b59_scaffold_IDs.matches).

    Finished processing 22 of 96 (22.92%) bins (current: b39_scaffold_IDs.matches).

    Finished processing 23 of 96 (23.96%) bins (current: b74_scaffold_IDs.matches).

    Finished processing 24 of 96 (25.00%) bins (current: b50_scaffold_IDs.matches).

    Finished processing 25 of 96 (26.04%) bins (current: b21_scaffold_IDs.matches).

    Finished processing 26 of 96 (27.08%) bins (current: b66_scaffold_IDs.matches).

    Finished processing 27 of 96 (28.12%) bins (current: b51_scaffold_IDs.matches).

    Finished processing 28 of 96 (29.17%) bins (current: b82_scaffold_IDs.matches).

    Finished processing 29 of 96 (30.21%) bins (current: b70_scaffold_IDs.matches).

    Finished processing 30 of 96 (31.25%) bins (current: b33_scaffold_IDs.matches).

    Finished processing 31 of 96 (32.29%) bins (current: b34_scaffold_IDs.matches).

    Finished processing 32 of 96 (33.33%) bins (current: b84_scaffold_IDs.matches).

    Finished processing 33 of 96 (34.38%) bins (current: b89_scaffold_IDs.matches).

    Finished processing 34 of 96 (35.42%) bins (current: b85_scaffold_IDs.matches).

    Finished processing 35 of 96 (36.46%) bins (current: b68_scaffold_IDs.matches).

    Finished processing 36 of 96 (37.50%) bins (current: b1_scaffold_IDs.matches).

    Finished processing 37 of 96 (38.54%) bins (current: b32_scaffold_IDs.matches).

    Finished processing 38 of 96 (39.58%) bins (current: b83_scaffold_IDs.matches).

    Finished processing 39 of 96 (40.62%) bins (current: b11_scaffold_IDs.matches).

    Finished processing 40 of 96 (41.67%) bins (current: b86_scaffold_IDs.matches).

    Finished processing 41 of 96 (42.71%) bins (current: b52_scaffold_IDs.matches).

    Finished processing 42 of 96 (43.75%) bins (current: b24_scaffold_IDs.matches).

    Finished processing 43 of 96 (44.79%) bins (current: b79_scaffold_IDs.matches).

    Finished processing 44 of 96 (45.83%) bins (current: b64_scaffold_IDs.matches).

    Finished processing 45 of 96 (46.88%) bins (current: b35_scaffold_IDs.matches).

    Finished processing 46 of 96 (47.92%) bins (current: b29_scaffold_IDs.matches).

    Finished processing 47 of 96 (48.96%) bins (current: b90_scaffold_IDs.matches).

    Finished processing 48 of 96 (50.00%) bins (current: b27_scaffold_IDs.matches).

    Finished processing 49 of 96 (51.04%) bins (current: b38_scaffold_IDs.matches).

    Finished processing 50 of 96 (52.08%) bins (current: b37_scaffold_IDs.matches).

    Finished processing 51 of 96 (53.12%) bins (current: b60_scaffold_IDs.matches).

    Finished processing 52 of 96 (54.17%) bins (current: b77_scaffold_IDs.matches).

    Finished processing 53 of 96 (55.21%) bins (current: b58_scaffold_IDs.matches).

    Finished processing 54 of 96 (56.25%) bins (current: b88_scaffold_IDs.matches).

    Finished processing 55 of 96 (57.29%) bins (current: b55_scaffold_IDs.matches).

    Finished processing 56 of 96 (58.33%) bins (current: b31_scaffold_IDs.matches).

    Finished processing 57 of 96 (59.38%) bins (current: b7_scaffold_IDs.matches).

    Finished processing 58 of 96 (60.42%) bins (current: b36_scaffold_IDs.matches).

    Finished processing 59 of 96 (61.46%) bins (current: b69_scaffold_IDs.matches).

    Finished processing 60 of 96 (62.50%) bins (current: b67_scaffold_IDs.matches).

    Finished processing 61 of 96 (63.54%) bins (current: b61_scaffold_IDs.matches).

    Finished processing 62 of 96 (64.58%) bins (current: b43_scaffold_IDs.matches).

    Finished processing 63 of 96 (65.62%) bins (current: b75_scaffold_IDs.matches).

    Finished processing 64 of 96 (66.67%) bins (current: b41_scaffold_IDs.matches).

    Finished processing 65 of 96 (67.71%) bins (current: b76_scaffold_IDs.matches).

    Finished processing 66 of 96 (68.75%) bins (current: b94_scaffold_IDs.matches).

    Finished processing 67 of 96 (69.79%) bins (current: b62_scaffold_IDs.matches).

    Finished processing 68 of 96 (70.83%) bins (current: b15_scaffold_IDs.matches).

    Finished processing 69 of 96 (71.88%) bins (current: b57_scaffold_IDs.matches).

    Finished processing 70 of 96 (72.92%) bins (current: b63_scaffold_IDs.matches).

    Finished processing 71 of 96 (73.96%) bins (current: b71_scaffold_IDs.matches).

    Finished processing 72 of 96 (75.00%) bins (current: b91_scaffold_IDs.matches).

    Finished processing 73 of 96 (76.04%) bins (current: b30_scaffold_IDs.matches).

    Finished processing 74 of 96 (77.08%) bins (current: b45_scaffold_IDs.matches).

    Finished processing 75 of 96 (78.12%) bins (current: b4_scaffold_IDs.matches).

    Finished processing 76 of 96 (79.17%) bins (current: b8_scaffold_IDs.matches).

    Finished processing 77 of 96 (80.21%) bins (current: b44_scaffold_IDs.matches).

    Finished processing 78 of 96 (81.25%) bins (current: b23_scaffold_IDs.matches).

    Finished processing 79 of 96 (82.29%) bins (current: b6_scaffold_IDs.matches).

    Finished processing 80 of 96 (83.33%) bins (current: b48_scaffold_IDs.matches).

    Finished processing 81 of 96 (84.38%) bins (current: b49_scaffold_IDs.matches).

    Finished processing 82 of 96 (85.42%) bins (current: b54_scaffold_IDs.matches).

    Finished processing 83 of 96 (86.46%) bins (current: b26_scaffold_IDs.matches).

    Finished processing 84 of 96 (87.50%) bins (current: b72_scaffold_IDs.matches).

    Finished processing 85 of 96 (88.54%) bins (current: b80_scaffold_IDs.matches).

    Finished processing 86 of 96 (89.58%) bins (current: b42_scaffold_IDs.matches).

    Finished processing 87 of 96 (90.62%) bins (current: b16_scaffold_IDs.matches).

    Finished processing 88 of 96 (91.67%) bins (current: b12_scaffold_IDs.matches).

    Finished processing 89 of 96 (92.71%) bins (current: b56_scaffold_IDs.matches).

    Finished processing 90 of 96 (93.75%) bins (current: b10_scaffold_IDs.matches).

    Finished processing 91 of 96 (94.79%) bins (current: b65_scaffold_IDs.matches).

    Finished processing 92 of 96 (95.83%) bins (current: b78_scaffold_IDs.matches).

    Finished processing 93 of 96 (96.88%) bins (current: b22_scaffold_IDs.matches).

    Finished processing 94 of 96 (97.92%) bins (current: b95_scaffold_IDs.matches).

    Finished processing 95 of 96 (98.96%) bins (current: b9_scaffold_IDs.matches).

    Finished processing 96 of 96 (100.00%) bins (current: b5_scaffold_IDs.matches).

  Marker set written to: /researchdata/fhgfs/cbio/cbio/project08/team/katie/metagenomics_pipeline_testing/out_dir/checkm/lineage.ms

  { Current stage: 0:00:29.385 || Total: 0:25:05.009 }

*******************************************************************************

 [CheckM - analyze] Identifying marker genes in bins.

*******************************************************************************

  Identifying marker genes in 96 bins with 20 threads:

    Finished processing 0 of 96 (0.00%) bins.

    Finished processing 1 of 96 (1.04%) bins.

    Finished processing 2 of 96 (2.08%) bins.

    Finished processing 3 of 96 (3.12%) bins.

    Finished processing 4 of 96 (4.17%) bins.

    Finished processing 5 of 96 (5.21%) bins.

    Finished processing 6 of 96 (6.25%) bins.

    Finished processing 7 of 96 (7.29%) bins.

    Finished processing 8 of 96 (8.33%) bins.

    Finished processing 9 of 96 (9.38%) bins.

    Finished processing 10 of 96 (10.42%) bins.

    Finished processing 11 of 96 (11.46%) bins.

    Finished processing 12 of 96 (12.50%) bins.

    Finished processing 13 of 96 (13.54%) bins.

    Finished processing 14 of 96 (14.58%) bins.

    Finished processing 15 of 96 (15.62%) bins.

    Finished processing 16 of 96 (16.67%) bins.

    Finished processing 17 of 96 (17.71%) bins.

    Finished processing 18 of 96 (18.75%) bins.

    Finished processing 19 of 96 (19.79%) bins.

    Finished processing 20 of 96 (20.83%) bins.

    Finished processing 21 of 96 (21.88%) bins.

    Finished processing 22 of 96 (22.92%) bins.

    Finished processing 23 of 96 (23.96%) bins.

    Finished processing 24 of 96 (25.00%) bins.

    Finished processing 25 of 96 (26.04%) bins.

    Finished processing 26 of 96 (27.08%) bins.

    Finished processing 27 of 96 (28.12%) bins.

    Finished processing 28 of 96 (29.17%) bins.

    Finished processing 29 of 96 (30.21%) bins.

    Finished processing 30 of 96 (31.25%) bins.

    Finished processing 31 of 96 (32.29%) bins.

    Finished processing 32 of 96 (33.33%) bins.

    Finished processing 33 of 96 (34.38%) bins.

    Finished processing 34 of 96 (35.42%) bins.

    Finished processing 35 of 96 (36.46%) bins.

    Finished processing 36 of 96 (37.50%) bins.

    Finished processing 37 of 96 (38.54%) bins.

    Finished processing 38 of 96 (39.58%) bins.

    Finished processing 39 of 96 (40.62%) bins.

    Finished processing 40 of 96 (41.67%) bins.

    Finished processing 41 of 96 (42.71%) bins.

    Finished processing 42 of 96 (43.75%) bins.

    Finished processing 43 of 96 (44.79%) bins.

    Finished processing 44 of 96 (45.83%) bins.

    Finished processing 45 of 96 (46.88%) bins.

    Finished processing 46 of 96 (47.92%) bins.

    Finished processing 47 of 96 (48.96%) bins.

    Finished processing 48 of 96 (50.00%) bins.

    Finished processing 49 of 96 (51.04%) bins.

    Finished processing 50 of 96 (52.08%) bins.

    Finished processing 51 of 96 (53.12%) bins.

    Finished processing 52 of 96 (54.17%) bins.

    Finished processing 53 of 96 (55.21%) bins.

    Finished processing 54 of 96 (56.25%) bins.

    Finished processing 55 of 96 (57.29%) bins.

    Finished processing 56 of 96 (58.33%) bins.

    Finished processing 57 of 96 (59.38%) bins.

    Finished processing 58 of 96 (60.42%) bins.

    Finished processing 59 of 96 (61.46%) bins.

    Finished processing 60 of 96 (62.50%) bins.

    Finished processing 61 of 96 (63.54%) bins.

    Finished processing 62 of 96 (64.58%) bins.

    Finished processing 63 of 96 (65.62%) bins.

    Finished processing 64 of 96 (66.67%) bins.

    Finished processing 65 of 96 (67.71%) bins.

    Finished processing 66 of 96 (68.75%) bins.

    Finished processing 67 of 96 (69.79%) bins.

    Finished processing 68 of 96 (70.83%) bins.

    Finished processing 69 of 96 (71.88%) bins.

    Finished processing 70 of 96 (72.92%) bins.

    Finished processing 71 of 96 (73.96%) bins.

    Finished processing 72 of 96 (75.00%) bins.

    Finished processing 73 of 96 (76.04%) bins.

    Finished processing 74 of 96 (77.08%) bins.

    Finished processing 75 of 96 (78.12%) bins.

    Finished processing 76 of 96 (79.17%) bins.

    Finished processing 77 of 96 (80.21%) bins.

    Finished processing 78 of 96 (81.25%) bins.

    Finished processing 79 of 96 (82.29%) bins.

    Finished processing 80 of 96 (83.33%) bins.

    Finished processing 81 of 96 (84.38%) bins.

    Finished processing 82 of 96 (85.42%) bins.

    Finished processing 83 of 96 (86.46%) bins.

    Finished processing 84 of 96 (87.50%) bins.

    Finished processing 85 of 96 (88.54%) bins.

    Finished processing 86 of 96 (89.58%) bins.

    Finished processing 87 of 96 (90.62%) bins.

    Finished processing 88 of 96 (91.67%) bins.

    Finished processing 89 of 96 (92.71%) bins.

    Finished processing 90 of 96 (93.75%) bins.

    Finished processing 91 of 96 (94.79%) bins.

    Finished processing 92 of 96 (95.83%) bins.

    Finished processing 93 of 96 (96.88%) bins.

    Finished processing 94 of 96 (97.92%) bins.

    Finished processing 95 of 96 (98.96%) bins.

    Finished processing 96 of 96 (100.00%) bins.

  Saving HMM info to file.

  { Current stage: 0:11:30.139 || Total: 0:36:35.149 }

  Parsing HMM hits to marker genes:

    Finished parsing hits for 1 of 96 (1.04%) bins.

    Finished parsing hits for 2 of 96 (2.08%) bins.

    Finished parsing hits for 3 of 96 (3.12%) bins.

    Finished parsing hits for 4 of 96 (4.17%) bins.

    Finished parsing hits for 5 of 96 (5.21%) bins.

    Finished parsing hits for 6 of 96 (6.25%) bins.

    Finished parsing hits for 7 of 96 (7.29%) bins.

    Finished parsing hits for 8 of 96 (8.33%) bins.

    Finished parsing hits for 9 of 96 (9.38%) bins.

    Finished parsing hits for 10 of 96 (10.42%) bins.

    Finished parsing hits for 11 of 96 (11.46%) bins.

    Finished parsing hits for 12 of 96 (12.50%) bins.

    Finished parsing hits for 13 of 96 (13.54%) bins.

    Finished parsing hits for 14 of 96 (14.58%) bins.

    Finished parsing hits for 15 of 96 (15.62%) bins.

    Finished parsing hits for 16 of 96 (16.67%) bins.

    Finished parsing hits for 17 of 96 (17.71%) bins.

    Finished parsing hits for 18 of 96 (18.75%) bins.

    Finished parsing hits for 19 of 96 (19.79%) bins.

    Finished parsing hits for 20 of 96 (20.83%) bins.

    Finished parsing hits for 21 of 96 (21.88%) bins.

    Finished parsing hits for 22 of 96 (22.92%) bins.

    Finished parsing hits for 23 of 96 (23.96%) bins.

    Finished parsing hits for 24 of 96 (25.00%) bins.

    Finished parsing hits for 25 of 96 (26.04%) bins.

    Finished parsing hits for 26 of 96 (27.08%) bins.

    Finished parsing hits for 27 of 96 (28.12%) bins.

    Finished parsing hits for 28 of 96 (29.17%) bins.

    Finished parsing hits for 29 of 96 (30.21%) bins.

    Finished parsing hits for 30 of 96 (31.25%) bins.

    Finished parsing hits for 31 of 96 (32.29%) bins.

    Finished parsing hits for 32 of 96 (33.33%) bins.

    Finished parsing hits for 33 of 96 (34.38%) bins.

    Finished parsing hits for 34 of 96 (35.42%) bins.

    Finished parsing hits for 35 of 96 (36.46%) bins.

    Finished parsing hits for 36 of 96 (37.50%) bins.

    Finished parsing hits for 37 of 96 (38.54%) bins.

    Finished parsing hits for 38 of 96 (39.58%) bins.

    Finished parsing hits for 39 of 96 (40.62%) bins.

    Finished parsing hits for 40 of 96 (41.67%) bins.

    Finished parsing hits for 41 of 96 (42.71%) bins.

    Finished parsing hits for 42 of 96 (43.75%) bins.

    Finished parsing hits for 43 of 96 (44.79%) bins.

    Finished parsing hits for 44 of 96 (45.83%) bins.

    Finished parsing hits for 45 of 96 (46.88%) bins.

    Finished parsing hits for 46 of 96 (47.92%) bins.

    Finished parsing hits for 47 of 96 (48.96%) bins.

    Finished parsing hits for 48 of 96 (50.00%) bins.

    Finished parsing hits for 49 of 96 (51.04%) bins.

    Finished parsing hits for 50 of 96 (52.08%) bins.

    Finished parsing hits for 51 of 96 (53.12%) bins.

    Finished parsing hits for 52 of 96 (54.17%) bins.

    Finished parsing hits for 53 of 96 (55.21%) bins.

    Finished parsing hits for 54 of 96 (56.25%) bins.

    Finished parsing hits for 55 of 96 (57.29%) bins.

    Finished parsing hits for 56 of 96 (58.33%) bins.

    Finished parsing hits for 57 of 96 (59.38%) bins.

    Finished parsing hits for 58 of 96 (60.42%) bins.

    Finished parsing hits for 59 of 96 (61.46%) bins.

    Finished parsing hits for 60 of 96 (62.50%) bins.

    Finished parsing hits for 61 of 96 (63.54%) bins.

    Finished parsing hits for 62 of 96 (64.58%) bins.

    Finished parsing hits for 63 of 96 (65.62%) bins.

    Finished parsing hits for 64 of 96 (66.67%) bins.

    Finished parsing hits for 65 of 96 (67.71%) bins.

    Finished parsing hits for 66 of 96 (68.75%) bins.

    Finished parsing hits for 67 of 96 (69.79%) bins.

    Finished parsing hits for 68 of 96 (70.83%) bins.

    Finished parsing hits for 69 of 96 (71.88%) bins.

    Finished parsing hits for 70 of 96 (72.92%) bins.

    Finished parsing hits for 71 of 96 (73.96%) bins.

    Finished parsing hits for 72 of 96 (75.00%) bins.

    Finished parsing hits for 73 of 96 (76.04%) bins.

    Finished parsing hits for 74 of 96 (77.08%) bins.

    Finished parsing hits for 75 of 96 (78.12%) bins.

    Finished parsing hits for 76 of 96 (79.17%) bins.

    Finished parsing hits for 77 of 96 (80.21%) bins.

    Finished parsing hits for 78 of 96 (81.25%) bins.

    Finished parsing hits for 79 of 96 (82.29%) bins.

    Finished parsing hits for 80 of 96 (83.33%) bins.

    Finished parsing hits for 81 of 96 (84.38%) bins.

    Finished parsing hits for 82 of 96 (85.42%) bins.

    Finished parsing hits for 83 of 96 (86.46%) bins.

    Finished parsing hits for 84 of 96 (87.50%) bins.

    Finished parsing hits for 85 of 96 (88.54%) bins.

    Finished parsing hits for 86 of 96 (89.58%) bins.

    Finished parsing hits for 87 of 96 (90.62%) bins.

    Finished parsing hits for 88 of 96 (91.67%) bins.

    Finished parsing hits for 89 of 96 (92.71%) bins.

    Finished parsing hits for 90 of 96 (93.75%) bins.

    Finished parsing hits for 91 of 96 (94.79%) bins.

    Finished parsing hits for 92 of 96 (95.83%) bins.

    Finished parsing hits for 93 of 96 (96.88%) bins.

    Finished parsing hits for 94 of 96 (97.92%) bins.

    Finished parsing hits for 95 of 96 (98.96%) bins.

    Finished parsing hits for 96 of 96 (100.00%) bins.

  Aligning marker genes with multiple hits in a single bin:

    Finished processing 0 of 96 (0.00%) bins.

    Finished processing 1 of 96 (1.04%) bins.

    Finished processing 2 of 96 (2.08%) bins.

    Finished processing 3 of 96 (3.12%) bins.

    Finished processing 4 of 96 (4.17%) bins.

    Finished processing 5 of 96 (5.21%) bins.

    Finished processing 6 of 96 (6.25%) bins.

    Finished processing 7 of 96 (7.29%) bins.

    Finished processing 8 of 96 (8.33%) bins.

    Finished processing 9 of 96 (9.38%) bins.

    Finished processing 10 of 96 (10.42%) bins.

    Finished processing 11 of 96 (11.46%) bins.

    Finished processing 12 of 96 (12.50%) bins.

    Finished processing 13 of 96 (13.54%) bins.

    Finished processing 14 of 96 (14.58%) bins.

    Finished processing 15 of 96 (15.62%) bins.

    Finished processing 16 of 96 (16.67%) bins.

    Finished processing 17 of 96 (17.71%) bins.

    Finished processing 18 of 96 (18.75%) bins.

    Finished processing 19 of 96 (19.79%) bins.

    Finished processing 20 of 96 (20.83%) bins.

    Finished processing 21 of 96 (21.88%) bins.

    Finished processing 22 of 96 (22.92%) bins.

    Finished processing 23 of 96 (23.96%) bins.

    Finished processing 24 of 96 (25.00%) bins.

    Finished processing 25 of 96 (26.04%) bins.

    Finished processing 26 of 96 (27.08%) bins.

    Finished processing 27 of 96 (28.12%) bins.

    Finished processing 28 of 96 (29.17%) bins.

    Finished processing 29 of 96 (30.21%) bins.

    Finished processing 30 of 96 (31.25%) bins.

    Finished processing 31 of 96 (32.29%) bins.

    Finished processing 32 of 96 (33.33%) bins.

    Finished processing 33 of 96 (34.38%) bins.

    Finished processing 34 of 96 (35.42%) bins.

    Finished processing 35 of 96 (36.46%) bins.

    Finished processing 36 of 96 (37.50%) bins.

    Finished processing 37 of 96 (38.54%) bins.

    Finished processing 38 of 96 (39.58%) bins.

    Finished processing 39 of 96 (40.62%) bins.

    Finished processing 40 of 96 (41.67%) bins.

    Finished processing 41 of 96 (42.71%) bins.

    Finished processing 42 of 96 (43.75%) bins.

    Finished processing 43 of 96 (44.79%) bins.

    Finished processing 44 of 96 (45.83%) bins.

    Finished processing 45 of 96 (46.88%) bins.

    Finished processing 46 of 96 (47.92%) bins.

    Finished processing 47 of 96 (48.96%) bins.

    Finished processing 48 of 96 (50.00%) bins.

    Finished processing 49 of 96 (51.04%) bins.

    Finished processing 50 of 96 (52.08%) bins.

    Finished processing 51 of 96 (53.12%) bins.

    Finished processing 52 of 96 (54.17%) bins.

    Finished processing 53 of 96 (55.21%) bins.

    Finished processing 54 of 96 (56.25%) bins.

    Finished processing 55 of 96 (57.29%) bins.

    Finished processing 56 of 96 (58.33%) bins.

    Finished processing 57 of 96 (59.38%) bins.

    Finished processing 58 of 96 (60.42%) bins.

    Finished processing 59 of 96 (61.46%) bins.

    Finished processing 60 of 96 (62.50%) bins.

    Finished processing 61 of 96 (63.54%) bins.

    Finished processing 62 of 96 (64.58%) bins.

    Finished processing 63 of 96 (65.62%) bins.

    Finished processing 64 of 96 (66.67%) bins.

    Finished processing 65 of 96 (67.71%) bins.

    Finished processing 66 of 96 (68.75%) bins.

    Finished processing 67 of 96 (69.79%) bins.

    Finished processing 68 of 96 (70.83%) bins.

    Finished processing 69 of 96 (71.88%) bins.

    Finished processing 70 of 96 (72.92%) bins.

    Finished processing 71 of 96 (73.96%) bins.

    Finished processing 72 of 96 (75.00%) bins.

    Finished processing 73 of 96 (76.04%) bins.

    Finished processing 74 of 96 (77.08%) bins.

    Finished processing 75 of 96 (78.12%) bins.

    Finished processing 76 of 96 (79.17%) bins.

    Finished processing 77 of 96 (80.21%) bins.

    Finished processing 78 of 96 (81.25%) bins.

    Finished processing 79 of 96 (82.29%) bins.

    Finished processing 80 of 96 (83.33%) bins.

    Finished processing 81 of 96 (84.38%) bins.

    Finished processing 82 of 96 (85.42%) bins.

    Finished processing 83 of 96 (86.46%) bins.

    Finished processing 84 of 96 (87.50%) bins.

    Finished processing 85 of 96 (88.54%) bins.

    Finished processing 86 of 96 (89.58%) bins.

    Finished processing 87 of 96 (90.62%) bins.

    Finished processing 88 of 96 (91.67%) bins.

    Finished processing 89 of 96 (92.71%) bins.

    Finished processing 90 of 96 (93.75%) bins.

    Finished processing 91 of 96 (94.79%) bins.

    Finished processing 92 of 96 (95.83%) bins.

    Finished processing 93 of 96 (96.88%) bins.

    Finished processing 94 of 96 (97.92%) bins.

    Finished processing 95 of 96 (98.96%) bins.

    Finished processing 96 of 96 (100.00%) bins.

  { Current stage: 0:01:25.486 || Total: 0:38:00.635 }

  Calculating genome statistics for 96 bins with 20 threads:

    Finished processing 0 of 96 (0.00%) bins.

    Finished processing 1 of 96 (1.04%) bins.

    Finished processing 2 of 96 (2.08%) bins.

    Finished processing 3 of 96 (3.12%) bins.

    Finished processing 4 of 96 (4.17%) bins.

    Finished processing 5 of 96 (5.21%) bins.

    Finished processing 6 of 96 (6.25%) bins.

    Finished processing 7 of 96 (7.29%) bins.

    Finished processing 8 of 96 (8.33%) bins.

    Finished processing 9 of 96 (9.38%) bins.

    Finished processing 10 of 96 (10.42%) bins.

    Finished processing 11 of 96 (11.46%) bins.

    Finished processing 12 of 96 (12.50%) bins.

    Finished processing 13 of 96 (13.54%) bins.

    Finished processing 14 of 96 (14.58%) bins.

    Finished processing 15 of 96 (15.62%) bins.

    Finished processing 16 of 96 (16.67%) bins.

    Finished processing 17 of 96 (17.71%) bins.

    Finished processing 18 of 96 (18.75%) bins.

    Finished processing 19 of 96 (19.79%) bins.

    Finished processing 20 of 96 (20.83%) bins.

    Finished processing 21 of 96 (21.88%) bins.

    Finished processing 22 of 96 (22.92%) bins.

    Finished processing 23 of 96 (23.96%) bins.

    Finished processing 24 of 96 (25.00%) bins.

    Finished processing 25 of 96 (26.04%) bins.

    Finished processing 26 of 96 (27.08%) bins.

    Finished processing 27 of 96 (28.12%) bins.

    Finished processing 28 of 96 (29.17%) bins.

    Finished processing 29 of 96 (30.21%) bins.

    Finished processing 30 of 96 (31.25%) bins.

    Finished processing 31 of 96 (32.29%) bins.

    Finished processing 32 of 96 (33.33%) bins.

    Finished processing 33 of 96 (34.38%) bins.

    Finished processing 34 of 96 (35.42%) bins.

    Finished processing 35 of 96 (36.46%) bins.

    Finished processing 36 of 96 (37.50%) bins.

    Finished processing 37 of 96 (38.54%) bins.

    Finished processing 38 of 96 (39.58%) bins.

    Finished processing 39 of 96 (40.62%) bins.

    Finished processing 40 of 96 (41.67%) bins.

    Finished processing 41 of 96 (42.71%) bins.

    Finished processing 42 of 96 (43.75%) bins.

    Finished processing 43 of 96 (44.79%) bins.

    Finished processing 44 of 96 (45.83%) bins.

    Finished processing 45 of 96 (46.88%) bins.

    Finished processing 46 of 96 (47.92%) bins.

    Finished processing 47 of 96 (48.96%) bins.

    Finished processing 48 of 96 (50.00%) bins.

    Finished processing 49 of 96 (51.04%) bins.

    Finished processing 50 of 96 (52.08%) bins.

    Finished processing 51 of 96 (53.12%) bins.

    Finished processing 52 of 96 (54.17%) bins.

    Finished processing 53 of 96 (55.21%) bins.

    Finished processing 54 of 96 (56.25%) bins.

    Finished processing 55 of 96 (57.29%) bins.

    Finished processing 56 of 96 (58.33%) bins.

    Finished processing 57 of 96 (59.38%) bins.

    Finished processing 58 of 96 (60.42%) bins.

    Finished processing 59 of 96 (61.46%) bins.

    Finished processing 60 of 96 (62.50%) bins.

    Finished processing 61 of 96 (63.54%) bins.

    Finished processing 62 of 96 (64.58%) bins.

    Finished processing 63 of 96 (65.62%) bins.

    Finished processing 64 of 96 (66.67%) bins.

    Finished processing 65 of 96 (67.71%) bins.

    Finished processing 66 of 96 (68.75%) bins.

    Finished processing 67 of 96 (69.79%) bins.

    Finished processing 68 of 96 (70.83%) bins.

    Finished processing 69 of 96 (71.88%) bins.

    Finished processing 70 of 96 (72.92%) bins.

    Finished processing 71 of 96 (73.96%) bins.

    Finished processing 72 of 96 (75.00%) bins.

    Finished processing 73 of 96 (76.04%) bins.

    Finished processing 74 of 96 (77.08%) bins.

    Finished processing 75 of 96 (78.12%) bins.

    Finished processing 76 of 96 (79.17%) bins.

    Finished processing 77 of 96 (80.21%) bins.

    Finished processing 78 of 96 (81.25%) bins.

    Finished processing 79 of 96 (82.29%) bins.

    Finished processing 80 of 96 (83.33%) bins.

    Finished processing 81 of 96 (84.38%) bins.

    Finished processing 82 of 96 (85.42%) bins.

    Finished processing 83 of 96 (86.46%) bins.

    Finished processing 84 of 96 (87.50%) bins.

    Finished processing 85 of 96 (88.54%) bins.

    Finished processing 86 of 96 (89.58%) bins.

    Finished processing 87 of 96 (90.62%) bins.

    Finished processing 88 of 96 (91.67%) bins.

    Finished processing 89 of 96 (92.71%) bins.

    Finished processing 90 of 96 (93.75%) bins.

    Finished processing 91 of 96 (94.79%) bins.

    Finished processing 92 of 96 (95.83%) bins.

    Finished processing 93 of 96 (96.88%) bins.

    Finished processing 94 of 96 (97.92%) bins.

    Finished processing 95 of 96 (98.96%) bins.

    Finished processing 96 of 96 (100.00%) bins.

  { Current stage: 0:00:02.547 || Total: 0:38:03.183 }

*******************************************************************************

 [CheckM - qa] Tabulating genome statistics.

*******************************************************************************

  Calculating AAI between multi-copy marker genes.

  Reading HMM info from file.

  Parsing HMM hits to marker genes:

    Finished parsing hits for 1 of 96 (1.04%) bins.

    Finished parsing hits for 2 of 96 (2.08%) bins.

    Finished parsing hits for 3 of 96 (3.12%) bins.

    Finished parsing hits for 4 of 96 (4.17%) bins.

    Finished parsing hits for 5 of 96 (5.21%) bins.

    Finished parsing hits for 6 of 96 (6.25%) bins.

    Finished parsing hits for 7 of 96 (7.29%) bins.

    Finished parsing hits for 8 of 96 (8.33%) bins.

    Finished parsing hits for 9 of 96 (9.38%) bins.

    Finished parsing hits for 10 of 96 (10.42%) bins.

    Finished parsing hits for 11 of 96 (11.46%) bins.

    Finished parsing hits for 12 of 96 (12.50%) bins.

    Finished parsing hits for 13 of 96 (13.54%) bins.

    Finished parsing hits for 14 of 96 (14.58%) bins.

    Finished parsing hits for 15 of 96 (15.62%) bins.

    Finished parsing hits for 16 of 96 (16.67%) bins.

    Finished parsing hits for 17 of 96 (17.71%) bins.

    Finished parsing hits for 18 of 96 (18.75%) bins.

    Finished parsing hits for 19 of 96 (19.79%) bins.

    Finished parsing hits for 20 of 96 (20.83%) bins.

    Finished parsing hits for 21 of 96 (21.88%) bins.

    Finished parsing hits for 22 of 96 (22.92%) bins.

    Finished parsing hits for 23 of 96 (23.96%) bins.

    Finished parsing hits for 24 of 96 (25.00%) bins.

    Finished parsing hits for 25 of 96 (26.04%) bins.

    Finished parsing hits for 26 of 96 (27.08%) bins.

    Finished parsing hits for 27 of 96 (28.12%) bins.

    Finished parsing hits for 28 of 96 (29.17%) bins.

    Finished parsing hits for 29 of 96 (30.21%) bins.

    Finished parsing hits for 30 of 96 (31.25%) bins.

    Finished parsing hits for 31 of 96 (32.29%) bins.

    Finished parsing hits for 32 of 96 (33.33%) bins.

    Finished parsing hits for 33 of 96 (34.38%) bins.

    Finished parsing hits for 34 of 96 (35.42%) bins.

    Finished parsing hits for 35 of 96 (36.46%) bins.

    Finished parsing hits for 36 of 96 (37.50%) bins.

    Finished parsing hits for 37 of 96 (38.54%) bins.

    Finished parsing hits for 38 of 96 (39.58%) bins.

    Finished parsing hits for 39 of 96 (40.62%) bins.

    Finished parsing hits for 40 of 96 (41.67%) bins.

    Finished parsing hits for 41 of 96 (42.71%) bins.

    Finished parsing hits for 42 of 96 (43.75%) bins.

    Finished parsing hits for 43 of 96 (44.79%) bins.

    Finished parsing hits for 44 of 96 (45.83%) bins.

    Finished parsing hits for 45 of 96 (46.88%) bins.

    Finished parsing hits for 46 of 96 (47.92%) bins.

    Finished parsing hits for 47 of 96 (48.96%) bins.

    Finished parsing hits for 48 of 96 (50.00%) bins.

    Finished parsing hits for 49 of 96 (51.04%) bins.

    Finished parsing hits for 50 of 96 (52.08%) bins.

    Finished parsing hits for 51 of 96 (53.12%) bins.

    Finished parsing hits for 52 of 96 (54.17%) bins.

    Finished parsing hits for 53 of 96 (55.21%) bins.

    Finished parsing hits for 54 of 96 (56.25%) bins.

    Finished parsing hits for 55 of 96 (57.29%) bins.

    Finished parsing hits for 56 of 96 (58.33%) bins.

    Finished parsing hits for 57 of 96 (59.38%) bins.

    Finished parsing hits for 58 of 96 (60.42%) bins.

    Finished parsing hits for 59 of 96 (61.46%) bins.

    Finished parsing hits for 60 of 96 (62.50%) bins.

    Finished parsing hits for 61 of 96 (63.54%) bins.

    Finished parsing hits for 62 of 96 (64.58%) bins.

    Finished parsing hits for 63 of 96 (65.62%) bins.

    Finished parsing hits for 64 of 96 (66.67%) bins.

    Finished parsing hits for 65 of 96 (67.71%) bins.

    Finished parsing hits for 66 of 96 (68.75%) bins.

    Finished parsing hits for 67 of 96 (69.79%) bins.

    Finished parsing hits for 68 of 96 (70.83%) bins.

    Finished parsing hits for 69 of 96 (71.88%) bins.

    Finished parsing hits for 70 of 96 (72.92%) bins.

    Finished parsing hits for 71 of 96 (73.96%) bins.

    Finished parsing hits for 72 of 96 (75.00%) bins.

    Finished parsing hits for 73 of 96 (76.04%) bins.

    Finished parsing hits for 74 of 96 (77.08%) bins.

    Finished parsing hits for 75 of 96 (78.12%) bins.

    Finished parsing hits for 76 of 96 (79.17%) bins.

    Finished parsing hits for 77 of 96 (80.21%) bins.

    Finished parsing hits for 78 of 96 (81.25%) bins.

    Finished parsing hits for 79 of 96 (82.29%) bins.

    Finished parsing hits for 80 of 96 (83.33%) bins.

    Finished parsing hits for 81 of 96 (84.38%) bins.

    Finished parsing hits for 82 of 96 (85.42%) bins.

    Finished parsing hits for 83 of 96 (86.46%) bins.

    Finished parsing hits for 84 of 96 (87.50%) bins.

    Finished parsing hits for 85 of 96 (88.54%) bins.

    Finished parsing hits for 86 of 96 (89.58%) bins.

    Finished parsing hits for 87 of 96 (90.62%) bins.

    Finished parsing hits for 88 of 96 (91.67%) bins.

    Finished parsing hits for 89 of 96 (92.71%) bins.

    Finished parsing hits for 90 of 96 (93.75%) bins.

    Finished parsing hits for 91 of 96 (94.79%) bins.

    Finished parsing hits for 92 of 96 (95.83%) bins.

    Finished parsing hits for 93 of 96 (96.88%) bins.

    Finished parsing hits for 94 of 96 (97.92%) bins.

    Finished parsing hits for 95 of 96 (98.96%) bins.

    Finished parsing hits for 96 of 96 (100.00%) bins.

  { Current stage: 0:01:10.671 || Total: 0:39:13.854 }