Mercurial > repos > iuc > stacks2_shortreads
annotate test-data/denovo_map/denovo_map.log @ 2:43e3eeb2e0ec draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
author | iuc |
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date | Wed, 15 Jul 2020 17:42:30 -0400 |
parents | ad7a60726fc3 |
children | 17d39bf0a63a |
rev | line source |
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2
43e3eeb2e0ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
0
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changeset
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1 denovo_map.pl version 2.52 started at 2020-03-16 15:39:40 |
43e3eeb2e0ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
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2 /home/berntm/miniconda3/envs/__stacks@2.52/bin/denovo_map.pl --samples demultiplexed --popmap denovo_map/popmap_cstacks.tsv -o stacks_outputs --paired |
0
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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3 |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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4 ustacks |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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5 ========== |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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6 |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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7 Sample 1 of 2 'PopA_01' |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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8 ---------- |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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9 ustacks -t fastq -f demultiplexed/PopA_01.1.fq -o stacks_outputs -i 1 --name PopA_01 |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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10 ustacks parameters selected: |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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11 Input file: 'demultiplexed/PopA_01.1.fq' |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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12 Sample ID: 1 |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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13 Min depth of coverage to create a stack (m): 3 |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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14 Repeat removal algorithm: enabled |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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15 Max distance allowed between stacks (M): 2 |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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16 Max distance allowed to align secondary reads: 4 |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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17 Max number of stacks allowed per de novo locus: 3 |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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18 Deleveraging algorithm: disabled |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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19 Gapped assembly: enabled |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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20 Minimum alignment length: 0.8 |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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21 Model type: SNP |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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22 Alpha significance level for model: 0.05 |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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23 |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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changeset
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24 Loading RAD-Tags... |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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25 |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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26 Loaded 66 reads; formed: |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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27 4 stacks representing 63 primary reads (95.5%) |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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changeset
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28 3 secondary stacks representing 3 secondary reads (4.5%) |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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29 |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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30 Stack coverage: mean=15.75; stdev=7.46; max=27; n_reads=63(95.5%) |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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31 Removing repetitive stacks: cov > 39 (mean+3*stdev)... |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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32 Blacklisted 0 stacks. |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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33 Coverage after repeat removal: mean=15.75; stdev=7.46; max=27; n_reads=63(95.5%) |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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34 |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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35 Assembling stacks (max. dist. M=2)... |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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36 Assembled 4 stacks into 3; blacklisted 0 stacks. |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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changeset
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37 Coverage after assembling stacks: mean=21.00; stdev=4.24; max=27; n_reads=63(95.5%) |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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38 |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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changeset
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39 Merging secondary stacks (max. dist. N=4 from consensus)... |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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changeset
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40 Merged 3 out of 3 secondary reads (100.0%), 1 merged with gapped alignments. |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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41 Coverage after merging secondary stacks: mean=22.00; stdev=4.32; max=28; n_reads=66(100.0%) |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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42 |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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43 Assembling stacks, allowing for gaps (min. match length 80.0%)... |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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44 Assembled 3 stacks into 3 stacks. |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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45 Coverage after gapped assembly: mean=22.00; stdev=4.32; max=28; n_reads=66(100.0%) |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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46 |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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47 Merging secondary stacks, allowing for gaps (min. match length 80.0%)... |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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48 Merged 0 out of 0 secondary reads (-nan%). |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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49 Coverage after merging gapped secondary stacks: mean=22.00; stdev=4.32; max=28; n_reads=66(100.0%) |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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50 |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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51 Final coverage: mean=22.00; stdev=4.32; max=28; n_reads=66(100.0%) |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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52 Calling consensus sequences and haplotypes for catalog assembly... |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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53 Writing tags, SNPs, and alleles files... |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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54 Refetching read IDs...done. |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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55 ustacks is done. |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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56 |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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57 Sample 2 of 2 'PopA_02' |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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changeset
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58 ---------- |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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changeset
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59 ustacks -t fastq -f demultiplexed/PopA_02.1.fq -o stacks_outputs -i 2 --name PopA_02 |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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60 ustacks parameters selected: |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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61 Input file: 'demultiplexed/PopA_02.1.fq' |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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62 Sample ID: 2 |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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63 Min depth of coverage to create a stack (m): 3 |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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changeset
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64 Repeat removal algorithm: enabled |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
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65 Max distance allowed between stacks (M): 2 |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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66 Max distance allowed to align secondary reads: 4 |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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changeset
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67 Max number of stacks allowed per de novo locus: 3 |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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68 Deleveraging algorithm: disabled |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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69 Gapped assembly: enabled |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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70 Minimum alignment length: 0.8 |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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71 Model type: SNP |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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72 Alpha significance level for model: 0.05 |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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73 |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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74 Loading RAD-Tags... |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
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75 |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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76 Loaded 60 reads; formed: |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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77 4 stacks representing 55 primary reads (91.7%) |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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78 5 secondary stacks representing 5 secondary reads (8.3%) |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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79 |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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80 Stack coverage: mean=13.75; stdev=9.12; max=26; n_reads=55(91.7%) |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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changeset
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81 Removing repetitive stacks: cov > 42 (mean+3*stdev)... |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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82 Blacklisted 0 stacks. |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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changeset
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83 Coverage after repeat removal: mean=13.75; stdev=9.12; max=26; n_reads=55(91.7%) |
ad7a60726fc3
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84 |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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85 Assembling stacks (max. dist. M=2)... |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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86 Assembled 4 stacks into 3; blacklisted 0 stacks. |
ad7a60726fc3
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87 Coverage after assembling stacks: mean=18.33; stdev=6.55; max=26; n_reads=55(91.7%) |
ad7a60726fc3
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88 |
ad7a60726fc3
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89 Merging secondary stacks (max. dist. N=4 from consensus)... |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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90 Merged 5 out of 5 secondary reads (100.0%), 0 merged with gapped alignments. |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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91 Coverage after merging secondary stacks: mean=20.00; stdev=6.53; max=28; n_reads=60(100.0%) |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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92 |
ad7a60726fc3
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93 Assembling stacks, allowing for gaps (min. match length 80.0%)... |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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94 Assembled 3 stacks into 3 stacks. |
ad7a60726fc3
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95 Coverage after gapped assembly: mean=20.00; stdev=6.53; max=28; n_reads=60(100.0%) |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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96 |
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97 Merging secondary stacks, allowing for gaps (min. match length 80.0%)... |
ad7a60726fc3
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98 Merged 0 out of 0 secondary reads (-nan%). |
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99 Coverage after merging gapped secondary stacks: mean=20.00; stdev=6.53; max=28; n_reads=60(100.0%) |
ad7a60726fc3
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100 |
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101 Final coverage: mean=20.00; stdev=6.53; max=28; n_reads=60(100.0%) |
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102 Calling consensus sequences and haplotypes for catalog assembly... |
ad7a60726fc3
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103 Writing tags, SNPs, and alleles files... |
ad7a60726fc3
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104 Refetching read IDs...done. |
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105 ustacks is done. |
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106 |
ad7a60726fc3
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107 Depths of Coverage for Processed Samples: |
ad7a60726fc3
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108 PopA_01: 22.00x |
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109 PopA_02: 20.00x |
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110 |
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111 cstacks |
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112 ========== |
2
43e3eeb2e0ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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113 cstacks -M denovo_map/popmap_cstacks.tsv -P stacks_outputs |
0
ad7a60726fc3
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114 |
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115 cstacks parameters selected: |
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116 Loci matched based on sequence identity. |
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117 Number of mismatches allowed between stacks: 1 |
ad7a60726fc3
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118 Gapped alignments: enabled |
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119 Constructing catalog from 2 samples. |
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120 |
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121 Initializing new catalog... |
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122 Parsing stacks_outputs/PopA_01.tags.tsv |
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123 Parsing stacks_outputs/PopA_01.snps.tsv |
ad7a60726fc3
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124 Parsing stacks_outputs/PopA_01.alleles.tsv |
ad7a60726fc3
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125 3 loci were newly added to the catalog. |
ad7a60726fc3
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126 |
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127 Processing sample stacks_outputs/PopA_02 [2 of 2] |
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128 Parsing stacks_outputs/PopA_02.tags.tsv |
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129 Parsing stacks_outputs/PopA_02.snps.tsv |
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130 Parsing stacks_outputs/PopA_02.alleles.tsv |
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131 Searching for sequence matches... |
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132 3 loci in the catalog, 184 kmers in the catalog hash. |
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133 Searching for gapped alignments... |
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134 Merging matches into catalog... |
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135 3 loci were matched to a catalog locus. |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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136 0 loci were matched to a catalog locus using gapped alignments. |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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137 0 loci were newly added to the catalog. |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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138 0 loci matched more than one catalog locus, linking them. |
ad7a60726fc3
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139 0 linked catalog loci were merged into 0 loci. |
ad7a60726fc3
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140 |
ad7a60726fc3
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141 Writing catalog in directory 'stacks_outputs/'. |
ad7a60726fc3
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142 Final catalog contains 3 loci. |
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143 cstacks is done. |
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144 |
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145 sstacks |
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146 ========== |
ad7a60726fc3
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147 sstacks -P stacks_outputs -M denovo_map/popmap_cstacks.tsv |
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148 |
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149 Searching for matches by sequence identity... |
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150 Parsing stacks_outputs/catalog.tags.tsv |
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151 Parsing stacks_outputs/catalog.snps.tsv |
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152 Parsing stacks_outputs/catalog.alleles.tsv |
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153 Populating kmer dictionary for exact matches...done. |
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154 Populating kmer dictionary for gapped alignments...done. |
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155 |
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156 Processing sample 'stacks_outputs/PopA_01' [1 of 2] |
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157 Parsing stacks_outputs/PopA_01.tags.tsv |
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158 Parsing stacks_outputs/PopA_01.snps.tsv |
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159 Parsing stacks_outputs/PopA_01.alleles.tsv |
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160 Searching for sequence matches... |
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161 3 sample loci compared against the catalog containing 3 loci. |
ad7a60726fc3
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162 3 matching loci, 0 contained no verified haplotypes. |
ad7a60726fc3
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163 0 loci matched more than one catalog locus and were excluded. |
ad7a60726fc3
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164 0 loci contained SNPs unaccounted for in the catalog and were excluded. |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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165 4 total haplotypes examined from matching loci, 4 verified. |
ad7a60726fc3
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166 Searching for gapped alignments... |
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167 Out of 3 query loci, 0 gapped alignments attempted. |
ad7a60726fc3
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168 0 loci matched one catalog locus; 0 total haplotypes examined, 0 verified. |
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169 0 loci matched no catalog locus; |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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170 0 loci matched more than one catalog locus and were excluded. |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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171 0 loci contained SNPs unaccounted for in the catalog and were excluded. |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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172 0 loci had no verified haplotypes. |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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173 0 loci had inconsistent alignments to a catalog locus and were excluded. |
ad7a60726fc3
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174 Outputing to file stacks_outputs/PopA_01.matches.tsv |
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175 |
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176 Processing sample 'stacks_outputs/PopA_02' [2 of 2] |
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177 Parsing stacks_outputs/PopA_02.tags.tsv |
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178 Parsing stacks_outputs/PopA_02.snps.tsv |
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179 Parsing stacks_outputs/PopA_02.alleles.tsv |
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180 Searching for sequence matches... |
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181 3 sample loci compared against the catalog containing 3 loci. |
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182 3 matching loci, 0 contained no verified haplotypes. |
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183 0 loci matched more than one catalog locus and were excluded. |
ad7a60726fc3
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184 0 loci contained SNPs unaccounted for in the catalog and were excluded. |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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185 4 total haplotypes examined from matching loci, 4 verified. |
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186 Searching for gapped alignments... |
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187 Out of 3 query loci, 0 gapped alignments attempted. |
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188 0 loci matched one catalog locus; 0 total haplotypes examined, 0 verified. |
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189 0 loci matched no catalog locus; |
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190 0 loci matched more than one catalog locus and were excluded. |
ad7a60726fc3
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191 0 loci contained SNPs unaccounted for in the catalog and were excluded. |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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192 0 loci had no verified haplotypes. |
ad7a60726fc3
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193 0 loci had inconsistent alignments to a catalog locus and were excluded. |
ad7a60726fc3
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194 Outputing to file stacks_outputs/PopA_02.matches.tsv |
ad7a60726fc3
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195 |
ad7a60726fc3
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196 sstacks is done. |
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197 |
ad7a60726fc3
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198 tsv2bam |
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199 ========== |
ad7a60726fc3
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200 tsv2bam -P stacks_outputs -M denovo_map/popmap_cstacks.tsv -R demultiplexed/ |
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201 |
ad7a60726fc3
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202 Logging to 'stacks_outputs/tsv2bam.log'. |
ad7a60726fc3
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203 Configuration for this run: |
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204 Stacks directory: 'stacks_outputs/' |
ad7a60726fc3
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205 Population map: 'denovo_map/popmap_cstacks.tsv' |
ad7a60726fc3
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206 Num. samples: 2 |
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207 Paired-end reads directory: 'demultiplexed/' |
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208 |
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209 Paired-end reads files found, e.g. 'demultiplexed/PopA_01.2.fq'. |
ad7a60726fc3
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210 Loading the catalog... |
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211 Processing sample 'PopA_01'... |
ad7a60726fc3
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212 Processing sample 'PopA_02'... |
ad7a60726fc3
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213 |
ad7a60726fc3
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214 Sample 'PopA_01': matched 3 sample loci to 3 catalog loci; found a paired-end read for 66 (100.0%) of the assembled forward reads; wrote 132 records. |
ad7a60726fc3
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215 Sample 'PopA_02': matched 3 sample loci to 3 catalog loci; found a paired-end read for 60 (100.0%) of the assembled forward reads; wrote 120 records. |
ad7a60726fc3
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216 |
ad7a60726fc3
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217 tsv2bam is done. |
ad7a60726fc3
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218 |
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219 gstacks |
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220 ========== |
ad7a60726fc3
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221 gstacks -P stacks_outputs -M denovo_map/popmap_cstacks.tsv |
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222 |
ad7a60726fc3
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223 Logging to 'stacks_outputs/gstacks.log'. |
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224 Locus/sample distributions will be written to 'stacks_outputs/gstacks.log.distribs'. |
ad7a60726fc3
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225 |
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226 Configuration for this run: |
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227 Input mode: denovo |
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228 Population map: 'denovo_map/popmap_cstacks.tsv' |
ad7a60726fc3
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229 Input files: 2, e.g. 'stacks_outputs/PopA_01.matches.bam' |
ad7a60726fc3
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230 Output to: 'stacks_outputs/' |
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231 Model: marukilow (var_alpha: 0.01, gt_alpha: 0.05) |
ad7a60726fc3
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232 |
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233 Reading BAM headers... |
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234 Processing all loci... |
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235 20%... |
ad7a60726fc3
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236 50%... |
ad7a60726fc3
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237 100% |
ad7a60726fc3
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238 |
ad7a60726fc3
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239 Attempted to assemble and align paired-end reads for 3 loci: |
ad7a60726fc3
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240 0 loci had no or almost no paired-end reads (0.0%); |
ad7a60726fc3
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241 0 loci had paired-end reads that couldn't be assembled into a contig (0.0%); |
ad7a60726fc3
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242 For the remaining 3 loci (100.0%), a paired-end contig was assembled; |
ad7a60726fc3
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243 Average contig size was 204.3 bp; |
ad7a60726fc3
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244 0 paired-end contigs overlapped the forward region (0.0%) |
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245 Mean overlap: -nanbp; mean size of overlapped loci after merging: -nan; |
ad7a60726fc3
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246 Out of 252 paired-end reads in these loci (mean 84.0 reads per locus), |
ad7a60726fc3
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247 252 were successfuly aligned (100.0%); |
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248 Mean insert length was -nan, stdev: nan (based on aligned reads in overlapped loci). |
ad7a60726fc3
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249 |
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250 Genotyped 3 loci: |
ad7a60726fc3
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251 effective per-sample coverage: mean=31.0x, stdev=1.0x, min=30.0x, max=32.0x |
ad7a60726fc3
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252 mean number of sites per locus: 194.3 |
ad7a60726fc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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253 a consistent phasing was found for 5 of out 5 (100.0%) diploid loci needing phasing |
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254 |
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parents:
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255 gstacks is done. |
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256 |
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257 populations |
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258 ========== |
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259 populations -P stacks_outputs -M denovo_map/popmap_cstacks.tsv |
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260 |
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261 Logging to 'stacks_outputs/populations.log'. |
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262 Locus/sample distributions will be written to 'stacks_outputs/populations.log.distribs'. |
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263 populations parameters selected: |
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264 Percent samples limit per population: 0 |
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265 Locus Population limit: 1 |
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266 Percent samples overall: 0 |
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267 Minor allele frequency cutoff: 0 |
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268 Maximum observed heterozygosity cutoff: 1 |
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269 Applying Fst correction: none. |
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270 Pi/Fis kernel smoothing: off |
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271 Fstats kernel smoothing: off |
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272 Bootstrap resampling: off |
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273 |
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274 Parsing population map... |
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275 The population map contained 2 samples, 1 population(s), 1 group(s). |
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276 Working on 2 samples. |
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277 Working on 1 population(s): |
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278 1: PopA_01, PopA_02 |
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279 Working on 1 group(s) of populations: |
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280 defaultgrp: 1 |
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281 |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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282 Raw haplotypes will be written to 'stacks_outputs/populations.haplotypes.tsv' |
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283 Population-level summary statistics will be written to 'stacks_outputs/populations.sumstats.tsv' |
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284 Population-level haplotype summary statistics will be written to 'stacks_outputs/populations.hapstats.tsv' |
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285 |
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286 Processing data in batches: |
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287 * load a batch of catalog loci and apply filters |
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288 * compute SNP- and haplotype-wise per-population statistics |
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289 * write the above statistics in the output files |
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290 * export the genotypes/haplotypes in specified format(s) |
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291 More details in 'stacks_outputs/populations.log.distribs'. |
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292 Now processing... |
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293 Batch 1 |
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294 |
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295 Removed 0 loci that did not pass sample/population constraints from 3 loci. |
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296 Kept 3 loci, composed of 613 sites; 0 of those sites were filtered, 6 variant sites remained. |
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297 Number of loci with PE contig: 3.00 (100.0%); |
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298 Mean length of loci: 194.33bp (stderr 0.33); |
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299 Number of loci with SE/PE overlap: 0.00 (0.0%); |
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300 Mean length of overlapping loci: -nanbp (stderr -0.00); mean overlap: -nanbp (stderr -0.00); |
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301 Mean genotyped sites per locus: 194.33bp (stderr 0.33). |
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302 |
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303 Population summary statistics (more detail in populations.sumstats_summary.tsv): |
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304 1: 2 samples per locus; pi: 0.61111; all/variant/polymorphic sites: 583/6/6; private alleles: 0 |
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305 Populations is done. |
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306 denovo_map.pl is done. |
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307 |
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308 denovo_map.pl completed at 2020-03-16 15:39:40 |