Mercurial > repos > iuc > groot
comparison test-data/groot.log @ 0:7af6f7dafd22 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
| author | iuc |
|---|---|
| date | Fri, 18 Oct 2024 08:19:42 +0000 |
| parents | |
| children |
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| -1:000000000000 | 0:7af6f7dafd22 |
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| 1 2024/10/15 11:32:06 i am groot (version 1.1.2) | |
| 2 2024/10/15 11:32:06 starting the index subcommand | |
| 3 2024/10/15 11:32:06 checking parameters... | |
| 4 2024/10/15 11:32:06 directory containing MSA files: arg-annot.90 | |
| 5 2024/10/15 11:32:06 number of MSA files: 12 | |
| 6 2024/10/15 11:32:06 processors: 1 | |
| 7 2024/10/15 11:32:06 k-mer size: 41 | |
| 8 2024/10/15 11:32:06 sketch size: 21 | |
| 9 2024/10/15 11:32:06 graph window size: 150 | |
| 10 2024/10/15 11:32:06 num. partitions: 8 | |
| 11 2024/10/15 11:32:06 max. K: 4 | |
| 12 2024/10/15 11:32:06 max. sketch span: 30 | |
| 13 2024/10/15 11:32:06 initialising indexing pipeline... | |
| 14 2024/10/15 11:32:06 initialising the processes | |
| 15 2024/10/15 11:32:06 connecting data streams | |
| 16 2024/10/15 11:32:06 number of processes added to the indexing pipeline: 3 | |
| 17 2024/10/15 11:32:06 creating graphs, sketching traversals and indexing... | |
| 18 2024/10/15 11:32:07 number of groot graphs built: 12 | |
| 19 2024/10/15 11:32:07 graphs sketched: 12 | |
| 20 2024/10/15 11:32:07 graph windows processed: 35387 | |
| 21 2024/10/15 11:32:07 mean approximate distinct sketches per graph: 29.20% | |
| 22 2024/10/15 11:32:07 number of sketches added to the LSH Ensemble index: 5155 | |
| 23 2024/10/15 11:32:07 writing index files in "grootIndex"... | |
| 24 2024/10/15 11:32:07 finished in 685.70958ms | |
| 25 2024/10/15 11:32:39 i am groot (version 1.1.2) | |
| 26 2024/10/15 11:32:39 starting the sketch subcommand | |
| 27 2024/10/15 11:32:39 checking parameters... | |
| 28 2024/10/15 11:32:39 terminated | |
| 29 | |
| 30 ERROR --> file does not exist: argannot-150bp-10000-reads.fq.gz | |
| 31 | |
| 32 2024/10/15 11:33:04 i am groot (version 1.1.2) | |
| 33 2024/10/15 11:33:04 starting the sketch subcommand | |
| 34 2024/10/15 11:33:04 checking parameters... | |
| 35 2024/10/15 11:33:04 minimum k-mer coverage: 1 | |
| 36 2024/10/15 11:33:04 processors: 1 | |
| 37 2024/10/15 11:33:04 input file: argannot_light-150bp-10000-reads.fq.gz | |
| 38 2024/10/15 11:33:04 loading the index information... | |
| 39 2024/10/15 11:33:04 k-mer size: 41 | |
| 40 2024/10/15 11:33:04 sketch size: 21 | |
| 41 2024/10/15 11:33:04 window size used in indexing: 150 | |
| 42 2024/10/15 11:33:04 loading the graphs... | |
| 43 2024/10/15 11:33:04 number of variation graphs: 12 | |
| 44 2024/10/15 11:33:04 rebuilding the LSH Ensemble... | |
| 45 2024/10/15 11:33:04 containment threshold: 0.99 | |
| 46 2024/10/15 11:33:04 initialising alignment pipeline... | |
| 47 2024/10/15 11:33:04 initialising the processes | |
| 48 2024/10/15 11:33:04 connecting data streams | |
| 49 2024/10/15 11:33:04 number of processes added to the alignment pipeline: 5 | |
| 50 2024/10/15 11:33:04 now streaming reads... | |
| 51 2024/10/15 11:33:04 number of reads received from input: 5000 | |
| 52 2024/10/15 11:33:04 mean read length: 150 | |
| 53 2024/10/15 11:33:04 number of reads sketched: 5000 | |
| 54 2024/10/15 11:33:04 total number of unmapped reads: 4873 | |
| 55 2024/10/15 11:33:04 total number of mapped reads: 127 | |
| 56 2024/10/15 11:33:04 mapped to one graph: 127 | |
| 57 2024/10/15 11:33:04 mapped to multiple graphs: 0 | |
| 58 2024/10/15 11:33:04 total number of exact alignments: 954 | |
| 59 2024/10/15 11:33:04 processing graphs... | |
| 60 2024/10/15 11:33:04 total number of k-mers projected onto graphs: 10890 | |
| 61 2024/10/15 11:33:04 graph 7 has 4 remaining paths after weighting and pruning | |
| 62 2024/10/15 11:33:04 - [*argannot~~~(Bla)cfxA2~~~AF504910:1-966] | |
| 63 2024/10/15 11:33:04 - [argannot~~~(Bla)cfxA4~~~AY769933:1-966] | |
| 64 2024/10/15 11:33:04 - [argannot~~~(Bla)cfxA5~~~AY769934:28-993] | |
| 65 2024/10/15 11:33:04 - [argannot~~~(Bla)cfxA~~~U38243:150-1115] | |
| 66 2024/10/15 11:33:04 total number of graphs pruned: 12 | |
| 67 2024/10/15 11:33:04 total number of graphs remaining: 1 | |
| 68 2024/10/15 11:33:04 total number of possible haplotypes found: 4 | |
| 69 2024/10/15 11:33:04 saving graphs... | |
| 70 2024/10/15 11:33:04 finished in 223.277576ms | |
| 71 2024/10/15 11:33:15 i am groot (version 1.1.2) | |
| 72 2024/10/15 11:33:15 starting the report subcommand | |
| 73 2024/10/15 11:33:15 checking parameters... | |
| 74 2024/10/15 11:33:15 BAM file: groot.bam | |
| 75 2024/10/15 11:33:15 coverage cutoff: 0.97 | |
| 76 2024/10/15 11:33:15 processors: 1 | |
| 77 2024/10/15 11:33:15 finished |