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+++ b/test-data/denovo_map/denovo_map.log	Mon Jul 01 11:00:33 2019 -0400
@@ -0,0 +1,309 @@
+denovo_map.pl version 2.4 started at 2019-06-18 10:34:45
+/home/berntm/miniconda3/envs/mulled-v1-2b57e7596f85ebb3b321e6c9681e8fd9250523a80d97945c46ac7743359454e7/bin/denovo_map.pl --samples demultiplexed --popmap denovo_map/popmap_cstacks.tsv -o stacks_outputs --paired
+
+ustacks
+==========
+
+Sample 1 of 2 'PopA_01'
+----------
+ustacks -t fastq -f demultiplexed/PopA_01.1.fq -o stacks_outputs -i 1 --name PopA_01
+ustacks parameters selected:
+  Input file: 'demultiplexed/PopA_01.1.fq'
+  Sample ID: 1
+  Min depth of coverage to create a stack (m): 3
+  Repeat removal algorithm: enabled
+  Max distance allowed between stacks (M): 2
+  Max distance allowed to align secondary reads: 4
+  Max number of stacks allowed per de novo locus: 3
+  Deleveraging algorithm: disabled
+  Gapped assembly: enabled
+  Minimum alignment length: 0.8
+  Model type: SNP
+  Alpha significance level for model: 0.05
+
+Loading RAD-Tags...
+
+Loaded 66 reads; formed:
+  4 stacks representing 63 primary reads (95.5%)
+  3 secondary stacks representing 3 secondary reads (4.5%)
+
+Stack coverage: mean=15.75; stdev=7.46; max=27; n_reads=63(95.5%)
+Removing repetitive stacks: cov > 39 (mean+3*stdev)...
+  Blacklisted 0 stacks.
+Coverage after repeat removal: mean=15.75; stdev=7.46; max=27; n_reads=63(95.5%)
+
+Assembling stacks (max. dist. M=2)...
+  Assembled 4 stacks into 3; blacklisted 0 stacks.
+Coverage after assembling stacks: mean=21.00; stdev=4.24; max=27; n_reads=63(95.5%)
+
+Merging secondary stacks (max. dist. N=4 from consensus)...
+  Merged 3 out of 3 secondary reads (100.0%), 1 merged with gapped alignments.
+Coverage after merging secondary stacks: mean=22.00; stdev=4.32; max=28; n_reads=66(100.0%)
+
+Assembling stacks, allowing for gaps (min. match length 80.0%)...
+  Assembled 3 stacks into 3 stacks.
+Coverage after gapped assembly: mean=22.00; stdev=4.32; max=28; n_reads=66(100.0%)
+
+Merging secondary stacks, allowing for gaps (min. match length 80.0%)...
+  Merged 0 out of 0 secondary reads (-nan%).
+Coverage after merging gapped secondary stacks: mean=22.00; stdev=4.32; max=28; n_reads=66(100.0%)
+
+Final coverage: mean=22.00; stdev=4.32; max=28; n_reads=66(100.0%)
+Calling consensus sequences and haplotypes for catalog assembly...
+Writing tags, SNPs, and alleles files...
+Refetching read IDs...done.
+ustacks is done.
+
+Sample 2 of 2 'PopA_02'
+----------
+ustacks -t fastq -f demultiplexed/PopA_02.1.fq -o stacks_outputs -i 2 --name PopA_02
+ustacks parameters selected:
+  Input file: 'demultiplexed/PopA_02.1.fq'
+  Sample ID: 2
+  Min depth of coverage to create a stack (m): 3
+  Repeat removal algorithm: enabled
+  Max distance allowed between stacks (M): 2
+  Max distance allowed to align secondary reads: 4
+  Max number of stacks allowed per de novo locus: 3
+  Deleveraging algorithm: disabled
+  Gapped assembly: enabled
+  Minimum alignment length: 0.8
+  Model type: SNP
+  Alpha significance level for model: 0.05
+
+Loading RAD-Tags...
+
+Loaded 60 reads; formed:
+  4 stacks representing 55 primary reads (91.7%)
+  5 secondary stacks representing 5 secondary reads (8.3%)
+
+Stack coverage: mean=13.75; stdev=9.12; max=26; n_reads=55(91.7%)
+Removing repetitive stacks: cov > 42 (mean+3*stdev)...
+  Blacklisted 0 stacks.
+Coverage after repeat removal: mean=13.75; stdev=9.12; max=26; n_reads=55(91.7%)
+
+Assembling stacks (max. dist. M=2)...
+  Assembled 4 stacks into 3; blacklisted 0 stacks.
+Coverage after assembling stacks: mean=18.33; stdev=6.55; max=26; n_reads=55(91.7%)
+
+Merging secondary stacks (max. dist. N=4 from consensus)...
+  Merged 5 out of 5 secondary reads (100.0%), 0 merged with gapped alignments.
+Coverage after merging secondary stacks: mean=20.00; stdev=6.53; max=28; n_reads=60(100.0%)
+
+Assembling stacks, allowing for gaps (min. match length 80.0%)...
+  Assembled 3 stacks into 3 stacks.
+Coverage after gapped assembly: mean=20.00; stdev=6.53; max=28; n_reads=60(100.0%)
+
+Merging secondary stacks, allowing for gaps (min. match length 80.0%)...
+  Merged 0 out of 0 secondary reads (-nan%).
+Coverage after merging gapped secondary stacks: mean=20.00; stdev=6.53; max=28; n_reads=60(100.0%)
+
+Final coverage: mean=20.00; stdev=6.53; max=28; n_reads=60(100.0%)
+Calling consensus sequences and haplotypes for catalog assembly...
+Writing tags, SNPs, and alleles files...
+Refetching read IDs...done.
+ustacks is done.
+
+Depths of Coverage for Processed Samples:
+PopA_01: 22.00x
+PopA_02: 20.00x
+
+cstacks
+==========
+cstacks -P stacks_outputs -M denovo_map/popmap_cstacks.tsv
+
+cstacks parameters selected:
+  Loci matched based on sequence identity.
+  Number of mismatches allowed between stacks: 1
+  Gapped alignments: enabled
+Constructing catalog from 2 samples.
+
+Initializing new catalog...
+  Parsing stacks_outputs/PopA_01.tags.tsv
+  Parsing stacks_outputs/PopA_01.snps.tsv
+  Parsing stacks_outputs/PopA_01.alleles.tsv
+  3 loci were newly added to the catalog.
+
+Processing sample stacks_outputs/PopA_02 [2 of 2]
+  Parsing stacks_outputs/PopA_02.tags.tsv
+  Parsing stacks_outputs/PopA_02.snps.tsv
+  Parsing stacks_outputs/PopA_02.alleles.tsv
+Searching for sequence matches...
+  3 loci in the catalog, 184 kmers in the catalog hash.
+Searching for gapped alignments...
+Merging matches into catalog...
+  3 loci were matched to a catalog locus.
+  0 loci were matched to a catalog locus using gapped alignments.
+  0 loci were newly added to the catalog.
+  0 loci matched more than one catalog locus, linking them.
+    0 linked catalog loci were merged into 0 loci.
+
+Writing catalog in directory 'stacks_outputs/'.
+Final catalog contains 3 loci.
+cstacks is done.
+
+sstacks
+==========
+sstacks -P stacks_outputs -M denovo_map/popmap_cstacks.tsv
+
+Searching for matches by sequence identity...
+  Parsing stacks_outputs/catalog.tags.tsv
+  Parsing stacks_outputs/catalog.snps.tsv
+  Parsing stacks_outputs/catalog.alleles.tsv
+Populating kmer dictionary for exact matches...done.
+Populating kmer dictionary for gapped alignments...done.
+
+Processing sample 'stacks_outputs/PopA_01' [1 of 2]
+  Parsing stacks_outputs/PopA_01.tags.tsv
+  Parsing stacks_outputs/PopA_01.snps.tsv
+  Parsing stacks_outputs/PopA_01.alleles.tsv
+Searching for sequence matches...
+3 sample loci compared against the catalog containing 3 loci.
+  3 matching loci, 0 contained no verified haplotypes.
+  0 loci matched more than one catalog locus and were excluded.
+  0 loci contained SNPs unaccounted for in the catalog and were excluded.
+  4 total haplotypes examined from matching loci, 4 verified.
+Searching for gapped alignments...
+Out of 3 query loci, 0 gapped alignments attempted.
+  0 loci matched one catalog locus; 0 total haplotypes examined, 0 verified.
+  0 loci matched no catalog locus;
+    0 loci matched more than one catalog locus and were excluded.
+    0 loci contained SNPs unaccounted for in the catalog and were excluded.
+    0 loci had no verified haplotypes.
+    0 loci had inconsistent alignments to a catalog locus and were excluded.
+Outputing to file stacks_outputs/PopA_01.matches.tsv
+
+Processing sample 'stacks_outputs/PopA_02' [2 of 2]
+  Parsing stacks_outputs/PopA_02.tags.tsv
+  Parsing stacks_outputs/PopA_02.snps.tsv
+  Parsing stacks_outputs/PopA_02.alleles.tsv
+Searching for sequence matches...
+3 sample loci compared against the catalog containing 3 loci.
+  3 matching loci, 0 contained no verified haplotypes.
+  0 loci matched more than one catalog locus and were excluded.
+  0 loci contained SNPs unaccounted for in the catalog and were excluded.
+  4 total haplotypes examined from matching loci, 4 verified.
+Searching for gapped alignments...
+Out of 3 query loci, 0 gapped alignments attempted.
+  0 loci matched one catalog locus; 0 total haplotypes examined, 0 verified.
+  0 loci matched no catalog locus;
+    0 loci matched more than one catalog locus and were excluded.
+    0 loci contained SNPs unaccounted for in the catalog and were excluded.
+    0 loci had no verified haplotypes.
+    0 loci had inconsistent alignments to a catalog locus and were excluded.
+Outputing to file stacks_outputs/PopA_02.matches.tsv
+
+sstacks is done.
+
+tsv2bam
+==========
+tsv2bam -P stacks_outputs  -M denovo_map/popmap_cstacks.tsv -R demultiplexed/
+
+Logging to 'stacks_outputs/tsv2bam.log'.
+Configuration for this run:
+  Stacks directory: 'stacks_outputs/'
+  Population map: 'denovo_map/popmap_cstacks.tsv'
+  Num. samples: 2
+  Paired-end reads directory: 'demultiplexed/'
+
+Paired-end reads files found, e.g. 'demultiplexed/PopA_01.2.fq'.
+Loading the catalog...
+Processing sample 'PopA_01'...
+Processing sample 'PopA_02'...
+
+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.
+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.
+
+tsv2bam is done.
+
+gstacks
+==========
+gstacks -P stacks_outputs -M denovo_map/popmap_cstacks.tsv
+
+Logging to 'stacks_outputs/gstacks.log'.
+Locus/sample distributions will be written to 'stacks_outputs/gstacks.log.distribs'.
+
+Configuration for this run:
+  Input mode: denovo
+  Population map: 'denovo_map/popmap_cstacks.tsv'
+  Input files: 2, e.g. 'stacks_outputs/PopA_01.matches.bam'
+  Output to: 'stacks_outputs/'
+  Model: marukilow (var_alpha: 0.01, gt_alpha: 0.05)
+
+Reading BAM headers...
+Processing all loci...
+20%...
+50%...
+100%
+
+Attempted to assemble and align paired-end reads for 3 loci:
+  0 loci had no or almost no paired-end reads (0.0%);
+  0 loci had paired-end reads that couldn't be assembled into a contig (0.0%);
+  For the remaining 3 loci (100.0%), a paired-end contig was assembled;
+    Average contig size was 204.3 bp;
+  0 paired-end contigs overlapped the forward region (0.0%)
+    Mean overlap: -nanbp; mean size of overlapped loci after merging: -nan;
+  Out of 252 paired-end reads in these loci (mean 84.0 reads per locus),
+    252 were successfuly aligned (100.0%);
+  Mean insert length was -nan, stdev: nan (based on aligned reads in overlapped loci).
+
+Genotyped 3 loci:
+  effective per-sample coverage: mean=31.0x, stdev=1.0x, min=30.0x, max=32.0x
+  mean number of sites per locus: 194.3
+  a consistent phasing was found for 5 of out 5 (100.0%) diploid loci needing phasing
+
+gstacks is done.
+
+populations
+==========
+populations -P stacks_outputs -M denovo_map/popmap_cstacks.tsv
+
+Logging to 'stacks_outputs/populations.log'.
+Locus/sample distributions will be written to 'stacks_outputs/populations.log.distribs'.
+populations parameters selected:
+  Percent samples limit per population: 0
+  Locus Population limit: 1
+  Percent samples overall: 0
+  Minor allele frequency cutoff: 0
+  Maximum observed heterozygosity cutoff: 1
+  Applying Fst correction: none.
+  Pi/Fis kernel smoothing: off
+  Fstats kernel smoothing: off
+  Bootstrap resampling: off
+
+Parsing population map...
+The population map contained 2 samples, 1 population(s), 1 group(s).
+Working on 2 samples.
+Working on 1 population(s):
+    1: PopA_01, PopA_02
+Working on 1 group(s) of populations:
+    defaultgrp: 1
+
+Genotyping markers will be written to 'stacks_outputs/populations.markers.tsv'
+Raw Genotypes/Haplotypes will be written to 'stacks_outputs/populations.haplotypes.tsv'
+Population-level summary statistics will be written to 'stacks_outputs/populations.sumstats.tsv'
+Population-level haplotype summary statistics will be written to 'stacks_outputs/populations.hapstats.tsv'
+
+Processing data in batches:
+  * load a batch of catalog loci and apply filters
+  * compute SNP- and haplotype-wise per-population statistics
+  * write the above statistics in the output files
+  * export the genotypes/haplotypes in specified format(s)
+More details in 'stacks_outputs/populations.log.distribs'.
+Now processing...
+Batch 1 
+
+Removed 0 loci that did not pass sample/population constraints from 3 loci.
+Kept 3 loci, composed of 613 sites; 0 of those sites were filtered, 6 variant sites remained.
+Number of loci with PE contig: 3.00 (100.0%);
+  Mean length of loci: 194.33bp (stderr 0.33);
+Number of loci with SE/PE overlap: 0.00 (0.0%);
+  Mean length of overlapping loci: -nanbp (stderr -0.00); mean overlap: -nanbp (stderr -0.00);
+Mean genotyped sites per locus: 194.33bp (stderr 0.33).
+
+Population summary statistics (more detail in populations.sumstats_summary.tsv):
+  1: 2 samples per locus; pi: 0.61111; all/variant/polymorphic sites: 583/6/6; private alleles: 0
+Populations is done.
+denovo_map.pl is done.
+
+denovo_map.pl completed at 2019-06-18 10:34:45