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annotate test-data/test_02.log @ 7:2042e25c495c draft default tip

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 1f26c1ff5410d5b05ad2681e003426a1b42930cb-dirty
author jdv
date Mon, 30 Jan 2017 22:18:58 -0500
parents 2569a83977f5
children
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2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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1 ----> ENTRY HEADER:@FOO:13415:1851
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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2 Threads: 1 (effective) 1 (requested)
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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3 IDX = 0: reading from 0 to 86912
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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4 Staggering at 125000 reads; processed 203 reads
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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5 IDX(0) counted 203 reads
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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6 GLOBAL READ COUNT = 203
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
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7 Trim Time: 5 ms
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
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8
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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9 PROGRAM ELAPSED TIME: 6 ms
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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10 [M::bwa_idx_load_from_disk] read 0 ALT contigs
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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11 [M::process] read 1226 sequences (40027 bp)...
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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12 [M::mem_process_seqs] Processed 1226 reads in 0.396 CPU sec, 0.201 real sec
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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13 [main] Version: 0.7.12-r1039
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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14 [main] CMD: bwa mem -k 30 -T 0 -B 100 -O 100 -E 100 -t 2 got/db/test_db.species -
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
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15 [main] Real time: 0.206 sec; CPU: 0.400 sec
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
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16
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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17 Parsing foo/test_temp/test_splitrim.stats.txt... found 203 reads (split-trimmed: 1226) and 39924 bases.
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
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18 ->Retrieving parsed DB from disk [got/db/test_db.species.parsedGOTTCHA.dmp]...done. 0 wallclock secs ( 0.00 usr + 0.00 sys = 0.00 CPU)
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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19 ->Parsing SAM file [-] done. Mapped split-trimmed reads: 30; Mapped split-trimmed reads to plasmids: 0; Unmapped split-trimmed reads: 1190; Mapped raw reads: 20; Mapped raw reads to plasmids: 0. 0 wallclock secs ( 0.00 usr + 0.00 sys = 0.00 CPU)
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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20 ->Consolidating hits...done. 0 wallclock secs ( 0.00 usr + 0.00 sys = 0.00 CPU)
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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21 ->Retrieving Genome Vitals from disk [got/db/genomeVitals.dmp]...done. 0 wallclock secs ( 0.00 usr + 0.00 sys = 0.00 CPU)
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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22 ->Storing coordinates to disk [foo/test_temp/test.replicon.contig.coords.csv]...done. 0 wallclock secs ( 0.00 usr + 0.00 sys = 0.00 CPU)
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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23 ->Storing datastructure GI coordinates to disk in BINARY format as "foo/test_temp/test.giCoords.dmp"...done. 0 wallsecs
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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24 ->Storing datastructure contig length histogram (by entry) to disk in BINARY format as "foo/test_temp/test.replicon.contig.HistoByEntry.dmp"...done. 0 wallsecs
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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25 ->Storing datastructure contig length histogram (by GI) to disk in BINARY format as "foo/test_temp/test.replicon.contig.HistoByGI.dmp"...done. 0 wallsecs
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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26 ->Storing parseable contig length histogram(s) to disk...done. 0 wallclock secs ( 0.00 usr + 0.00 sys = 0.00 CPU)
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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27 ->Calculating non-overlapping coverage from mapping results...done. 0 wallclock secs ( 0.00 usr + 0.00 sys = 0.00 CPU)
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
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28 ===== REPLICON-level Analysis =====
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
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29 ->Writing REPLICON-level results to disk [foo/test_temp/test.replicon.tsv]...done. 0 wallclock secs ( 0.00 usr + 0.00 sys = 0.00 CPU)
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
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30 ===== Extended Taxonomic Rank-level Analysis =====
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
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31 ->Pulling replicon GIs from DB entries...done. 0 wallclock secs ( 0.00 usr + 0.00 sys = 0.00 CPU)
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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32 ->Mapping replicon GIs to source organisms...done. 0 wallclock secs ( 0.00 usr + 0.00 sys = 0.00 CPU)
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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33 ->Retrieving Tax Tree from disk [got/db/speciesTreeGI.dmp]...done. 0 wallclock secs ( 0.00 usr + 0.00 sys = 0.00 CPU)
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
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34 ->Mapping source organism to its tax tree...done. 0 wallclock secs ( 0.00 usr + 0.00 sys = 0.00 CPU)
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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35 Congratulations! All organisms have been identified!
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
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36 ->Rolling up results for rank STRAIN [foo/test_temp/test.strain.tsv]...done. 0 wallclock secs ( 0.07 usr + 0.00 sys = 0.07 CPU)
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
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37 ->Rolling up results for rank SPECIES [foo/test_temp/test.species.tsv]...done. 0 wallclock secs ( 0.03 usr + 0.00 sys = 0.03 CPU)
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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38 ->Rolling up results for rank GENUS [foo/test_temp/test.genus.tsv]...done. 0 wallclock secs ( 0.02 usr + 0.00 sys = 0.02 CPU)
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
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39 ->Rolling up results for rank FAMILY [foo/test_temp/test.family.tsv]...done. 0 wallclock secs ( 0.02 usr + 0.00 sys = 0.02 CPU)
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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40 ->Rolling up results for rank ORDER [foo/test_temp/test.order.tsv]...done. 0 wallclock secs ( 0.03 usr + 0.00 sys = 0.03 CPU)
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
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41 ->Rolling up results for rank CLASS [foo/test_temp/test.class.tsv]...done. 0 wallclock secs ( 0.03 usr + 0.00 sys = 0.03 CPU)
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
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42 ->Rolling up results for rank PHYLUM [foo/test_temp/test.phylum.tsv]...done. 0 wallclock secs ( 0.02 usr + 0.00 sys = 0.02 CPU)
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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43 Saving updated table to "foo/test_temp/test.strain.tsv.ABU"...done. (2 taxonomie(s), 1 filtered)
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
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44 Saving updated table to "foo/test_temp/test.species.tsv.ABU"...done. (2 taxonomie(s), 1 filtered)
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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45 Saving updated table to "foo/test_temp/test.genus.tsv.ABU"...done. (2 taxonomie(s), 1 filtered)
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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46 Saving updated table to "foo/test_temp/test.family.tsv.ABU"...done. (2 taxonomie(s), 1 filtered)
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
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47 Saving updated table to "foo/test_temp/test.order.tsv.ABU"...done. (2 taxonomie(s), 1 filtered)
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
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48 Saving updated table to "foo/test_temp/test.class.tsv.ABU"...done. (2 taxonomie(s), 1 filtered)
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
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49 Saving updated table to "foo/test_temp/test.phylum.tsv.ABU"...done. (2 taxonomie(s), 1 filtered)
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
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50 ------------------
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
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51 TOTAL SCRIPT TIME: - 0 wallclock secs ( 0.22 usr + 0.00 sys = 0.22 CPU)
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
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52 ------------------
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
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53 Loading STRAIN Lookup file...done!
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
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54 Loading SPECIES Lookup file...done!
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
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55 Loading GENUS Lookup file...done!
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
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56 Loading FAMILY Lookup file...done!
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
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57 Loading ORDER Lookup file...done!
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
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58 Loading CLASS Lookup file...done!
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
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59 Loading PHYLUM Lookup file...done!
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
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60 Loading TAX Lookup file...done!
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
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61 Parsing table "foo/test_temp/test.strain.tsv"...Done!
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
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2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
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64 STRAIN LINEAR_LENGTH TOTAL_BP_MAPPED HIT_COUNT HIT_COUNT_PLASMID READ_COUNT LINEAR_DOC NORM_COV
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
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65 Newcastle disease virus B1 366 544 18 0 17 1.48633879781421 1
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
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66 =================================================================
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
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2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
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2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
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69 SPECIES LINEAR_LENGTH TOTAL_BP_MAPPED HIT_COUNT HIT_COUNT_PLASMID READ_COUNT LINEAR_DOC NORM_COV
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
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70 Newcastle disease virus 366 544 18 0 17 1.48633879781421 1
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
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71 =================================================================
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
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74 GENUS LINEAR_LENGTH TOTAL_BP_MAPPED HIT_COUNT HIT_COUNT_PLASMID READ_COUNT LINEAR_DOC NORM_COV
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
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75 Avulavirus 366 544 18 0 17 1.48633879781421 1
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
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76 =================================================================
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
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79 FAMILY LINEAR_LENGTH TOTAL_BP_MAPPED HIT_COUNT HIT_COUNT_PLASMID READ_COUNT LINEAR_DOC NORM_COV
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80 Paramyxoviridae 366 544 18 0 17 1.48633879781421 1
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81 =================================================================
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84 ORDER LINEAR_LENGTH TOTAL_BP_MAPPED HIT_COUNT HIT_COUNT_PLASMID READ_COUNT LINEAR_DOC NORM_COV
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85 Mononegavirales 366 544 18 0 17 1.48633879781421 1
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86 =================================================================
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89 CLASS LINEAR_LENGTH TOTAL_BP_MAPPED HIT_COUNT HIT_COUNT_PLASMID READ_COUNT LINEAR_DOC NORM_COV
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90 Unassigned class - Mononegavirales 366 544 18 0 17 1.48633879781421 1
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91 =================================================================
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94 PHYLUM LINEAR_LENGTH TOTAL_BP_MAPPED HIT_COUNT HIT_COUNT_PLASMID READ_COUNT LINEAR_DOC NORM_COV
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95 Unassigned phylum - Unassigned class - Mononegavirales 366 544 18 0 17 1.48633879781421 1
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96 =================================================================
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97 Exporting results to disk [foo/test_temp/test.species.tsv.ABUX]...Done!
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98 Done converting 1 files to list.