Mercurial > repos > matthias > stacks2_refmap

annotate test-data/tmp/stacks_outputs/denovo_map.log @ 1:a8d93e132d3b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
author matthias
date Thu, 29 Nov 2018 12:16:18 -0500
parents bd0bf17caa4d
children
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bd0bf17caa4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
matthias
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1 denovo_map.pl version 2.2 started at 2018-11-28 13:45:54
bd0bf17caa4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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2 /home/berntm/miniconda3/envs/__stacks@2.2/bin/denovo_map.pl --samples stacks_inputs --popmap /tmp/tmpSlCHrR/files/000/dataset_3.dat -o stacks_outputs -T 1 -M 2 -n 1 --var-alpha 0.05 --gt-alpha 0.05 --paired
bd0bf17caa4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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3
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4 ustacks
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5 ==========
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6
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7 Sample 1 of 2 'PopA_01'
bd0bf17caa4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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8 ----------
bd0bf17caa4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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9 /home/berntm/miniconda3/envs/__stacks@2.2/bin/ustacks -t fastq -f stacks_inputs/PopA_01.1.fq -o stacks_outputs -i 1 --name PopA_01 -p 1 -M 2
bd0bf17caa4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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10 ustacks parameters selected:
bd0bf17caa4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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11 Input file: 'stacks_inputs/PopA_01.1.fq'
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12 Sample ID: 1
bd0bf17caa4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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13 Min depth of coverage to create a stack (m): 3
bd0bf17caa4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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14 Repeat removal algorithm: enabled
bd0bf17caa4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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15 Max distance allowed between stacks (M): 2
bd0bf17caa4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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16 Max distance allowed to align secondary reads: 4
bd0bf17caa4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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17 Max number of stacks allowed per de novo locus: 3
bd0bf17caa4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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18 Deleveraging algorithm: disabled
bd0bf17caa4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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19 Gapped assembly: enabled
bd0bf17caa4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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20 Minimum alignment length: 0.8
bd0bf17caa4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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21 Model type: SNP
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22 Alpha significance level for model: 0.05
bd0bf17caa4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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23
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24 Loading RAD-Tags...
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26 Loaded 66 reads; formed:
bd0bf17caa4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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27 4 stacks representing 63 primary reads (95.5%)
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28 3 secondary stacks representing 3 secondary reads (4.5%)
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29
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30 Stack coverage: mean=15.75; stdev=7.46; max=27; n_reads=63(95.5%)
bd0bf17caa4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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31 Removing repetitive stacks: cov > 39 (mean+3*stdev)...
bd0bf17caa4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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32 Blacklisted 0 stacks.
bd0bf17caa4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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33 Coverage after repeat removal: mean=15.75; stdev=7.46; max=27; n_reads=63(95.5%)
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34
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35 Assembling stacks (max. dist. M=2)...
bd0bf17caa4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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36 Assembled 4 stacks into 3; blacklisted 0 stacks.
bd0bf17caa4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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37 Coverage after assembling stacks: mean=21.00; stdev=4.24; max=27; n_reads=63(95.5%)
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38
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39 Merging secondary stacks (max. dist. N=4 from consensus)...
bd0bf17caa4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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40 Merged 3 out of 3 secondary reads (100.0%), 1 merged with gapped alignments.
bd0bf17caa4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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41 Coverage after merging secondary stacks: mean=22.00; stdev=4.32; max=28; n_reads=66(100.0%)
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42
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43 Assembling stacks, allowing for gaps (min. match length 80.0%)...
bd0bf17caa4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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44 Assembled 3 stacks into 3 stacks.
bd0bf17caa4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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45 Coverage after gapped assembly: mean=22.00; stdev=4.32; max=28; n_reads=66(100.0%)
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46
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47 Merging secondary stacks, allowing for gaps (min. match length 80.0%)...
bd0bf17caa4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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48 Merged 0 out of 0 secondary reads (-nan%).
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49 Coverage after merging gapped secondary stacks: mean=22.00; stdev=4.32; max=28; n_reads=66(100.0%)
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50
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51 Final coverage: mean=22.00; stdev=4.32; max=28; n_reads=66(100.0%)
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52 Calling consensus sequences and haplotypes for catalog assembly...
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53 Writing tags, SNPs, and alleles files...
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54 Refetching read IDs...done.
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55 ustacks is done.
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56
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57 Sample 2 of 2 'PopA_02'
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58 ----------
bd0bf17caa4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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59 /home/berntm/miniconda3/envs/__stacks@2.2/bin/ustacks -t fastq -f stacks_inputs/PopA_02.1.fq -o stacks_outputs -i 2 --name PopA_02 -p 1 -M 2
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60 ustacks parameters selected:
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61 Input file: 'stacks_inputs/PopA_02.1.fq'
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62 Sample ID: 2
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63 Min depth of coverage to create a stack (m): 3
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64 Repeat removal algorithm: enabled
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65 Max distance allowed between stacks (M): 2
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66 Max distance allowed to align secondary reads: 4
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67 Max number of stacks allowed per de novo locus: 3
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68 Deleveraging algorithm: disabled
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69 Gapped assembly: enabled
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70 Minimum alignment length: 0.8
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71 Model type: SNP
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72 Alpha significance level for model: 0.05
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73
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74 Loading RAD-Tags...
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75
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76 Loaded 60 reads; formed:
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77 4 stacks representing 55 primary reads (91.7%)
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78 5 secondary stacks representing 5 secondary reads (8.3%)
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79
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80 Stack coverage: mean=13.75; stdev=9.12; max=26; n_reads=55(91.7%)
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81 Removing repetitive stacks: cov > 42 (mean+3*stdev)...
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82 Blacklisted 0 stacks.
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83 Coverage after repeat removal: mean=13.75; stdev=9.12; max=26; n_reads=55(91.7%)
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84
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85 Assembling stacks (max. dist. M=2)...
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86 Assembled 4 stacks into 3; blacklisted 0 stacks.
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87 Coverage after assembling stacks: mean=18.33; stdev=6.55; max=26; n_reads=55(91.7%)
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88
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89 Merging secondary stacks (max. dist. N=4 from consensus)...
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90 Merged 5 out of 5 secondary reads (100.0%), 0 merged with gapped alignments.
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91 Coverage after merging secondary stacks: mean=20.00; stdev=6.53; max=28; n_reads=60(100.0%)
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92
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93 Assembling stacks, allowing for gaps (min. match length 80.0%)...
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94 Assembled 3 stacks into 3 stacks.
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95 Coverage after gapped assembly: mean=20.00; stdev=6.53; max=28; n_reads=60(100.0%)
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96
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97 Merging secondary stacks, allowing for gaps (min. match length 80.0%)...
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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%)
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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...
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103 Writing tags, SNPs, and alleles files...
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104 Refetching read IDs...done.
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105 ustacks is done.
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106
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107 Depths of Coverage for Processed Samples:
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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 ==========
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113 /home/berntm/miniconda3/envs/__stacks@2.2/bin/cstacks -P stacks_outputs -M /tmp/tmpSlCHrR/files/000/dataset_3.dat -p 1 -n 1
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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
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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
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124 Parsing stacks_outputs/PopA_01.alleles.tsv
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125 3 loci were newly added to the catalog.
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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.
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136 0 loci were matched to a catalog locus using gapped alignments.
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137 0 loci were newly added to the catalog.
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138 0 loci matched more than one catalog locus, linking them.
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139 0 linked catalog loci were merged into 0 loci.
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140
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141 Writing catalog in directory 'stacks_outputs/'.
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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 ==========
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147 /home/berntm/miniconda3/envs/__stacks@2.2/bin/sstacks -P stacks_outputs -M /tmp/tmpSlCHrR/files/000/dataset_3.dat -p 1
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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.
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162 3 matching loci, 0 contained no verified haplotypes.
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163 0 loci matched more than one catalog locus and were excluded.
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164 0 loci contained SNPs unaccounted for in the catalog and were excluded.
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165 4 total haplotypes examined from matching loci, 4 verified.
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166 Searching for gapped alignments...
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167 Out of 3 query loci, 0 gapped alignments attempted.
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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;
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170 0 loci matched more than one catalog locus and were excluded.
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171 0 loci contained SNPs unaccounted for in the catalog and were excluded.
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172 0 loci had no verified haplotypes.
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173 0 loci had inconsistent alignments to a catalog locus and were excluded.
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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.
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184 0 loci contained SNPs unaccounted for in the catalog and were excluded.
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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.
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191 0 loci contained SNPs unaccounted for in the catalog and were excluded.
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192 0 loci had no verified haplotypes.
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193 0 loci had inconsistent alignments to a catalog locus and were excluded.
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194 Outputing to file stacks_outputs/PopA_02.matches.tsv
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195
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196 sstacks is done.
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197
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198 tsv2bam
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199 ==========
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200 /home/berntm/miniconda3/envs/__stacks@2.2/bin/tsv2bam -P stacks_outputs -M /tmp/tmpSlCHrR/files/000/dataset_3.dat -t 1 -R stacks_inputs/
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201
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202 Logging to 'stacks_outputs/tsv2bam.log'.
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203 Configuration for this run:
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204 Stacks directory: 'stacks_outputs/'
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205 Population map: '/tmp/tmpSlCHrR/files/000/dataset_3.dat'
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206 Num. samples: 2
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207 Paired-end reads directory: 'stacks_inputs/'
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208
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209 Paired-end reads files found, e.g. 'stacks_inputs/PopA_01.2.fq'.
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210 Loading the catalog...
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211 Processing sample 'PopA_01'...
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212 Processing sample 'PopA_02'...
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213
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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.
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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.
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216
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217 tsv2bam is done.
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218
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219 gstacks
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220 ==========
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221 /home/berntm/miniconda3/envs/__stacks@2.2/bin/gstacks -P stacks_outputs -M /tmp/tmpSlCHrR/files/000/dataset_3.dat -t 1 --var-alpha 0.05 --gt-alpha 0.05
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222
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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'.
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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: '/tmp/tmpSlCHrR/files/000/dataset_3.dat'
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229 Input files: 2, e.g. 'stacks_outputs/PopA_01.matches.bam'
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230 Output to: 'stacks_outputs/'
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231 Model: marukilow (var_alpha: 0.05, gt_alpha: 0.05)
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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%...
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236 50%...
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237 100%
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238
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239 Attempted to assemble and align paired-end reads for 3 loci:
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240 0 loci had no or almost no paired-end reads (0.0%);
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241 0 loci had paired-end reads that couldn't be assembled into a contig (0.0%);
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242 For the remaining 3 loci (100.0%), a paired-end contig was assembled;
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243 Average contig size was 100.3 bp;
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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;
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246 Out of 126 paired-end reads in these loci (mean 42.0 reads per locus),
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247 126 were successfuly aligned (100.0%);
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248 Mean insert length was -nan, stdev: nan (based on aligned reads in overlapped loci).
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249
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250 Genotyped 3 loci:
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251 effective per-sample coverage: mean=31.0x, stdev=1.0x, min=30.0x, max=32.0x
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252 mean number of sites per locus: 194.3
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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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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 /home/berntm/miniconda3/envs/__stacks@2.2/bin/populations -P stacks_outputs -M /tmp/tmpSlCHrR/files/000/dataset_3.dat -t 1
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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 Log liklihood filtering: off; threshold: 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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282 Genotyping markers will be written to 'stacks_outputs/populations.markers.tsv'
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283 Raw Genotypes/Haplotypes will be written to 'stacks_outputs/populations.haplotypes.tsv'
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284 Population-level summary statistics will be written to 'stacks_outputs/populations.sumstats.tsv'
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285 Population-level haplotype summary statistics will be written to 'stacks_outputs/populations.hapstats.tsv'
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286
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287 Processing data in batches:
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288 * load a batch of catalog loci and apply filters
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289 * compute SNP- and haplotype-wise per-population statistics
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290 * write the above statistics in the output files
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291 * export the genotypes/haplotypes in specified format(s)
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292 More details in 'stacks_outputs/populations.log.distribs'.
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293 Now processing...
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294 Batch 1
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295
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296 Removed 0 loci that did not pass sample/population constraints from 3 loci.
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297 Kept 3 loci, composed of 613 sites; 0 of those sites were filtered, 6 variant sites remained.
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298 Number of loci with PE contig: 3.00 (100.0%);
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299 Mean length of loci: 194.33bp (stderr 0.33);
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300 Number of loci with SE/PE overlap: 0.00 (0.0%);
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301 Mean length of overlapping loci: -nanbp (stderr -0.00); mean overlap: -nanbp (stderr -0.00);
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302 Mean genotyped sites per locus: 194.33bp (stderr 0.33).
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303
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304 Population summary statistics (more detail in populations.sumstats_summary.tsv):
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305 1: 2 samples per locus; pi: 0.61111; all/variant/polymorphic sites: 583/6/6; private alleles: 0
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306 Populations is done.
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307 denovo_map.pl is done.
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308
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309 denovo_map.pl completed at 2018-11-28 13:45:54