--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ustacks/ustacks.log	Mon Jul 01 10:59:53 2019 -0400
@@ -0,0 +1,92 @@
+ustacks parameters selected:
+  Input file: 'stacks_inputs/PopA_01.1.fastq'
+  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.
+ustacks parameters selected:
+  Input file: 'stacks_inputs/PopA_02.1.fastq'
+  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.