Mercurial > repos > iuc > polypolish
annotate test-data/logfile_test_1.log @ 0:aaa868913641 draft
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
| author | iuc |
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| date | Thu, 22 Sep 2022 07:51:48 +0000 |
| parents | |
| children |
| rev | line source |
|---|---|
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0
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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1 |
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aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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2 [1;4;93mStarting Polypolish[0m [2m(2022-09-14 14:05:31)[0m |
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aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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3 [2m Polypolish is a tool for polishing genome assemblies with short reads. |
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aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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4 Unlike other tools in this category, Polypolish uses SAM files where each read |
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aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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5 has been aligned to all possible locations (not just a single best location). |
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aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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6 This allows it to repair errors in repeat regions that other alignment-based |
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aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
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7 polishers cannot fix.[0m |
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aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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8 |
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aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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9 Polypolish version: 0.5.0 |
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aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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10 |
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aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
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changeset
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11 Input assembly: |
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aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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12 input_data |
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aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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13 |
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aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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14 Input short-read alignments: |
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aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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15 /tmp/tmpacfaqf7s/files/0/e/6/dataset_0e63b923-512f-4f9b-b6fa-8c6ead4a29db.dat |
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aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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16 |
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aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
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17 Settings: |
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aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
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18 --fraction_invalid 0.2 |
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aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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19 --fraction_valid 0.5 |
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aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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20 --max_errors 10 |
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aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
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21 --min_depth 5 |
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aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
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22 --debug /tmp/tmpacfaqf7s/job_working_directory/000/3/outputs/galaxy_dataset_0fff3b6a-ddab-4999-b6a2-78a6dff1a4bc.dat |
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aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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23 |
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aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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24 |
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aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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25 [1;4;93mLoading assembly[0m [2m(2022-09-14 14:05:31)[0m |
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aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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26 contig00001 (5,513 bp) |
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aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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27 contig00002 (3,532 bp) |
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aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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28 contig00003 (3,227 bp) |
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aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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29 contig00004 (3,138 bp) |
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aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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30 |
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aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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31 |
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aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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32 [1;4;93mLoading alignments[0m [2m(2022-09-14 14:05:31)[0m |
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aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
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33 /tmp/tmpacfaqf7s/files/0/e/6/dataset_0e63b923-512f-4f9b-b6fa-8c6ead4a29db.dat: 75 alignments from 72 reads |
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aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
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changeset
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34 |
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aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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35 Filtering for high-quality end-to-end alignments: |
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aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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36 25 alignments kept |
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aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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37 50 alignments discarded |
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aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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38 |
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aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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39 |
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aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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40 [1;4;93mPolishing assembly sequences[0m [2m(2022-09-14 14:05:31)[0m |
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aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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41 [2m For each position in the assembly, Polypolish determines the read depth |
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aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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42 at that position and collects all aligned bases. It then polishes the assembly |
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aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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43 by looking for positions where the pileup unambiguously supports a different |
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aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
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44 sequence than the assembly.[0m |
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aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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45 |
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aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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46 Polishing contig00001 (5,513 bp): |
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aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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47 mean read depth: 1.0x |
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aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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48 2,496 bp have a depth of zero (54.7252% coverage) |
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aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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49 0 positions changed (0.0000% of total positions) |
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aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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50 estimated pre-polishing sequence accuracy: 100.0000% |
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aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
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51 |
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aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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52 Polishing contig00002 (3,532 bp): |
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aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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53 mean read depth: 0.3x |
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aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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54 2,629 bp have a depth of zero (25.5663% coverage) |
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aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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55 0 positions changed (0.0000% of total positions) |
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aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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56 estimated pre-polishing sequence accuracy: 100.0000% |
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aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
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57 |
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aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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58 Polishing contig00003 (3,227 bp): |
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aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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59 mean read depth: 0.2x |
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aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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60 2,818 bp have a depth of zero (12.6743% coverage) |
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aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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61 0 positions changed (0.0000% of total positions) |
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aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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62 estimated pre-polishing sequence accuracy: 100.0000% |
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aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
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63 |
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aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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64 Polishing contig00004 (3,138 bp): |
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aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
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changeset
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65 mean read depth: 0.1x |
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aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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66 2,842 bp have a depth of zero (9.4328% coverage) |
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aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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67 0 positions changed (0.0000% of total positions) |
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aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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68 estimated pre-polishing sequence accuracy: 100.0000% |
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aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
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69 |
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aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
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70 |
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aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
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71 [1;4;93mFinished![0m [2m(2022-09-14 14:05:31)[0m |
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aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
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72 Polished sequence (to stdout): |
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aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
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73 contig00001_polypolish (5,513 bp) |
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aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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74 contig00002_polypolish (3,532 bp) |
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aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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75 contig00003_polypolish (3,227 bp) |
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aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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76 contig00004_polypolish (3,138 bp) |
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aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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77 |
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aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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78 Per-base debugging info written to /tmp/tmpacfaqf7s/job_working_directory/000/3/outputs/galaxy_dataset_0fff3b6a-ddab-4999-b6a2-78a6dff1a4bc.dat |
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aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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79 Time to run: 0:00:00.029839 |
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aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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80 |