-
Notifications
You must be signed in to change notification settings - Fork 10
/
Copy pathcheckm.out
196 lines (170 loc) · 9.37 KB
/
checkm.out
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
*******************************************************************************
[CheckM - tree] Placing bins in reference genome tree.
*******************************************************************************
Identifying marker genes in 3 bins with 30 threads:
Finished processing 0 of 3 (0.00%) bins. Finished processing 1 of 3 (33.33%) bins. Finished processing 2 of 3 (66.67%) bins. Finished processing 3 of 3 (100.00%) bins.
Saving HMM info to file.
Calculating genome statistics for 3 bins with 30 threads:
Finished processing 0 of 3 (0.00%) bins. Finished processing 1 of 3 (33.33%) bins. Finished processing 2 of 3 (66.67%) bins. Finished processing 3 of 3 (100.00%) bins.
Extracting marker genes to align.
Parsing HMM hits to marker genes:
Finished parsing hits for 1 of 3 (33.33%) bins. Finished parsing hits for 2 of 3 (66.67%) bins. Finished parsing hits for 3 of 3 (100.00%) bins.
Extracting 43 HMMs with 30 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 30 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 3 bins into the genome tree with pplacer (be patient).
{ Current stage: 0:07:51.048 || Total: 0:07:51.048 }
*******************************************************************************
[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 3 (33.33%) bins. Finished parsing hits for 2 of 3 (66.67%) bins. Finished parsing hits for 3 of 3 (100.00%) bins.
Determining marker sets for each genome bin.
Finished processing 1 of 3 (33.33%) bins (current: Bin_8). Finished processing 2 of 3 (66.67%) bins (current: Bin_2). Finished processing 3 of 3 (100.00%) bins (current: Bin_1).
Marker set written to: checkm_out/lineage.ms
{ Current stage: 0:00:02.182 || Total: 0:07:53.230 }
*******************************************************************************
[CheckM - analyze] Identifying marker genes in bins.
*******************************************************************************
Identifying marker genes in 3 bins with 30 threads:
Finished processing 0 of 3 (0.00%) bins. Finished processing 1 of 3 (33.33%) bins. Finished processing 2 of 3 (66.67%) bins. Finished processing 3 of 3 (100.00%) bins.
Saving HMM info to file.
{ Current stage: 0:01:14.718 || Total: 0:09:07.949 }
Parsing HMM hits to marker genes:
Finished parsing hits for 1 of 3 (33.33%) bins. Finished parsing hits for 2 of 3 (66.67%) bins. Finished parsing hits for 3 of 3 (100.00%) bins.
Aligning marker genes with multiple hits in a single bin:
Finished processing 0 of 3 (0.00%) bins. Finished processing 1 of 3 (33.33%) bins. Finished processing 2 of 3 (66.67%) bins. Finished processing 3 of 3 (100.00%) bins.
{ Current stage: 0:00:01.456 || Total: 0:09:09.406 }
Calculating genome statistics for 3 bins with 30 threads:
Finished processing 0 of 3 (0.00%) bins. Finished processing 1 of 3 (33.33%) bins. Finished processing 2 of 3 (66.67%) bins. Finished processing 3 of 3 (100.00%) bins.
{ Current stage: 0:00:00.290 || Total: 0:09:09.696 }
*******************************************************************************
[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 3 (33.33%) bins. Finished parsing hits for 2 of 3 (66.67%) bins. Finished parsing hits for 3 of 3 (100.00%) bins.
{ Current stage: 0:00:01.679 || Total: 0:09:11.375 }
-------------------------------------------------------------------------------------------------------------------------------------------------------------
Bin Id Marker lineage # genomes # markers # marker sets 0 1 2 3 4 5+ Completeness Contamination Strain heterogeneity
-------------------------------------------------------------------------------------------------------------------------------------------------------------
Bin_8 p__Euryarchaeota (UID3) 148 188 125 1 186 1 0 0 0 99.20 0.80 100.00
Bin_1 p__Euryarchaeota (UID3) 148 187 124 3 184 0 0 0 0 97.98 0.00 0.00
Bin_2 k__Bacteria (UID2569) 434 278 186 7 271 0 0 0 0 96.77 0.00 0.00
-------------------------------------------------------------------------------------------------------------------------------------------------------------