populations --phylip-var-all output is not aligned

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Marius Wenzel

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Jul 13, 2020, 10:40:38 AM7/13/20

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Hi Julian,

I'm having some trouble with a reference-aligned dataset (BWA > GSTACKS > POPULATIONS); the output I'm getting from --phylip-var-all is not aligned correctly and cannot be used for phylogenetic analysis:

Excerpt from beginning of phylip file (sample names redacted):

Lxxxxxxxxx TGCAGGATAACTGNAGNCNGANTGCNTGGAGNTAAACATACNTGTGGAGAGGGCANCANGAGTTAAAAGCANCANNGCTGTTGGNNGGACTCAAGGACGAGTCCAGTGC

Cxxxxxxxxx TGCAGGATAACTGGAGCCTGAATGCTTGGAGTTAAACATACATGTGGAGAGGGCAGCAAGAGTTAAAAGCAACAGCGCTGTTGGTTGGACTCAAGGACGAGTCCAGTGC

Cxxxxxxxx TGCAGGATAACTGGAGCCTGAATGCTTGGAGTTAAACATACATGTGGAGAGGGCAGCAAGAGTTAAAAGCAACAGCGCTGTTGGTTGGACTCAAGGACGAGTCCAGTGCA

Pxxxxxxxxx TGCAGGATAACTGNAGNCNGANTGCNTGGAGNTAAACATACNTGTGGAGAGGGCANCANGAGTTAAAAGCANCANNGCTGTTGGNNGGACTCAAGGACGAGTCCAGTGC

Cxxxxxxxxx TGCAGGATAACTGNAGNCNGANTGCNTGGAGNTAAACATACNTGTGGAGAGGGCANCANGAGTTAAAAGCANCANNGCTGTTGGNNGGACTCAAGGACGAGTCCAGTGC

Nxxxxxxxxx TGCAGGATAACTGNAGNCNGANTGCNTGGAGNTAAACATACNTGTGGAGAGGGCANCANGAGTTAAAAGCANCANNGCTGTTGGNNGGACTCAAGGACGAGTCCAGTGC

Lxxxxxxxxx TGCAGGATAACTGNAGNCNGANTGCNTGGAGNTAAACATACNTGTGGAGAGGGCANCANGAGTTAAAAGCANCANNGCTGTTGGNNGGACTCAAGGACGAGTCCAGTGC

Pxxxxxxxxx TGCAGGATAACTGGAGGCTGAATGCTTGGAGTTAAACATACATGTGGAGAGGGCAGCAAGAGTTAAAAGCAACAGCGCTGTTGGTTGGACTCAAGGACGAGTCCAGTGC

Cxxxxxxxxx TGCAGGATAACTGGAGCCTGAATGCTTGGAGATAAACATACMTGTGGAGAGGGCAGCAAGAGTTAAAAGCAACAGCGCTGTTGGTTGGACTCAAGGACGAGTCCAGTGC

Exxxxxxxx TGCAGGATAACTGNAGNCNGANTGCNTGGAGNTAAACATACNTGTGGAGAGGGCANCANGAGTTAAAAGCANCANNGCTGTTGGNNGGACTCAAGGACGAGTCCAGTGCA

Lxxxxxxxxx TGCAGGATAACTGGAGGCTGAGTGCCTGGAGTTAAACATACATGTGGAGAGGGCAGCAGGAGTTAAAAGCAGCAGCGCTGTTGGCTGGACTCAAGGACGAGTCCAGTGC

Exxxxxxxxx TGCAGGATAACTGGAGGCTGAATGCTTGGAGTTAAACATACATGTGGAGAGGGCAGCAAGAGTTAAAAGCAACATCGCTGTTGGTTGGACTCAAGGACGAGTCCAGTGC

Pxxxxxxxx TGCAGGATAACTGNAGNCNGANTGCNTGGAGNTAAACATACNTGTGGAGAGGGCANCANGAGTTAAAAGCANCANNGCTGTTGGNNGGACTCAAGGACGAGTCCAGTGCA

Pxxxxxxxx TGCAGGATAACTGGAGGCTGAATGCTTGGAGATAAACATACATGTGGAGAGGGCAGCAAGAGTTAAAAGCAACAGCGCTGTTGGTTGGACTCAAGGACGAGTCCAGTGCA

Cxxxxxxxx TGCAGGATAACTGGAGSCYGAATGCYTGGAGTTAAACATACATGTGGAGAGGGCAGCAAGAGTTAAAAGCAACAGCGCTGTTGGTTGGACTCAAGGACGAGTCCAGTGCA

Cxxxxxxxx TGCAGGATAACTGGAGGCTGAATGCCTGGAGTTAAACATACATGTGGAGAGGGCAGCAAGAGTTAAAAGCAACAGCGCTGTTGGTTGGACTCAAGGACGAGTCCAGTGCA

Cxxxxxxxx TGCAGGATAACTGSAGCCTGAATGCTTGGAGTTAAACATACATGTGGAGAGGGCAGCAAGAGTTAAAAGCAACAGCGCTGTTGGTTGGACTCAAGGACGAGTCCAGTGCA

Cxxxxxxxxx TGCAGGATAACTGGAGCCTGAATGCTTGGAGTTAAACATACATGTGGAGAGGGCAGCAAGAGTTAAAAGCAACAGCGCTGTTGGTTGGACTCAAGGACGAGTCCAGTGC

Lxxxxxxxxx TGCAGGATAACTGNAGNCNGANTGCNTGGAGNTAAACATACNTGTGGAGAGGGCANCANGAGTTAAAAGCANCANNGCTGTTGGNNGGACTCAAGGACGAGTCCAGTGC

Axxxxxxxx TGCAGGATAACTGGAGCCTGAATGCTTGGAGTTAAACATACATGTGGAGAGGGCAGCAAGAGTTAAAAGCAACAGCGCTGTTGGTTGGACTCAAGGACGAGTCCAGTGCA

Cxxxxxxxxx TGCAGGATAACTGGAGCCTGAATGCTTGGAGTTAAACATACATGTGGAGAGGGCAGCAAGAGTTAAAAGCAACAGCGCTGTTGGTTGGACTCAAGGACGAGTCCAGTGC

Exxxxxxxxx TGCAGGATAACTGGAGGCTGAATGCTTGGAGTTAAACATACATGTGGAGAGGGCAGCAAGAGTTAAAAGCAACATCGCTGTTGGTTGGACTCAAGGACGAGTCCAGTGC

Cxxxxxxxx TGCAGGATAACTGGAGGCTGAATGCCTGGAGTTAAACATACATGTGGAGAGGGCAGCAAGAGTTAAAAGCAACAGCGCTGTTGGTTGGACTCAAGGACGAGTCCAGTGCA

Cxxxxxxxxx TGCAGGATAACTGNAGNCNGANTGCNTGGAGNTAAACATACNTGTGGAGAGGGCANCANGAGTTAAAAGCANCANNGCTGTTGGNNGGACTCAAGGACGAGTCCAGTGC

Cxxxxxxxxx TGCAGGATAACTGGAGCCTGAATGCTTGGAGATAAACATACATGTGGAGAGGGCAGCAAGAGTTAAAAGCAACAGCGCTGTTGGTTGGACTCAAGGACGAGTCCAGTGC

Rxxxxxxxxx TGCAGGATAACTGNAGNCNGANTGCNTGGAGNTAAACATACNTGTGGAGAGGGCANCANGAGTTAAAAGCANCANNGCTGTTGGNNGGACTCAAGGACGAGTCCAGTGC

Exxxxxxxx TGCAGGATAACTGNAGNCNGANTGCNTGGAGNTAAACATACNTGTGGAGAGGGCANCANGAGTTAAAAGCANCANNGCTGTTGGNNGGACTCAAGGACGAGTCCAGTGCA

Exxxxxxxx TGCAGGATAACTGGAGGCTGAATGCTTGGAGTTAAACATACATGTGGAGAGGGCAGCAAGAGTTAAAAGCAACATCGCTGTTGGTTGGACTCAAGGACGAGTCCAGTGCA

Lxxxxxxxxx TGCAGGATAACTGGAGCCTGAATGCTTGGAGATAAACATACNTGTGGAGAGGGCAGCAAGAGTTAAAAGCAACAGCGCTGTTGGTTGGACTCAAGGACGAGTCCAGTGC

Exxxxxxxxx TGCAGGATAACTGGAGGCTGAATGCTTGGAGTTAAACATACATGTGGAGAGGGCAGCAAGAGTTAAAAGCAACATCGCTGTTGGTTGGACTCAAGGACGAGTCCAGTGC

Axxxxxxxxx TGCAGGATAACTGGAGCCTGAATGCTTGGAGTTAAACATACATGTGGAGAGGGCAGCAAGAGTTAAAAGCAACAGCGCTGTTGGTTGGACTCAAGGACGAGTCCAGTGC

Cxxxxxxxxx TGCAGGATAACTGGAGGCTGAATGCCTGGAGTTAAACATACATGTGGAGAGGGCAGCAAGAGTTAAAAGCAACAGTGCTGTTGGTTGGACTCAAGGACGAGTCCAGTGC

Exxxxxxxxx TGCAGGATAACTGGAGGCTGAATGCTTGGAGTTAAACATACATGTGGAGAGGGCAGCAAGAGTTAAAAGCAACATCGCTGTTGGTTGGACTCAAGGACGAGTCCAGTGC

Exxxxxxxx TGCAGGATAACTGNAGNCNGANTGCNTGGAGNTAAACATACNTGTGGAGAGGGCANCANGAGTTAAAAGCANCANNGCTGTTGGNNGGACTCAAGGACGAGTCCAGTGCA

Lxxxxxxxxx TGCAGGATAACTGGAGCCTGAATGCCTGGAGTTAAACATACATGTGGAGAGGGCAGCAAGAGTTAAAAGCAACAGCGCTGTTGGTTGGACTCAAGGACGAGTCCAGTGC

Pxxxxxxxxx TGCAGGATAACTGNAGNCNGANTGCNTGGAGNTAAACATACNTGTGGAGAGGGCANCANGAGTTAAAAGCANCANNGCTGTTGGNNGGACTCAAGGACGAGTCCAGTGC

Axxxxxxxxx TGCAGGATAACTGGAGCCTGAATGCTTGGAGTTAAACATACATGTGGAGAGGGCASCAAGAGTTAAAAGCAACAGCGCTGTTGGTTGGACTCAAGGACGAGTCCAGTGC

Cxxxxxxxx TGCAGGATAACTGGAGCCTGAATGCTTGGAGATAAACATACATGTGGAGAGGGCAGCAAGAGTTAAAAGCAACAGCGCTGTTGGTTGGACTCAAGGACGAGTCCAGTGCA

AGGACAANCCNNNNNCACTNNCTNTACCNNANACTNNTGNTGNTGCAGCCNGNTGGCACTGGNGTGGANGNAGTTTGGAGTNNANANCATTTNTTTTGCGTGTTGCAGGTGTTTGGTGAT

AGGACAACCCACGACCACTGCCTTTACCCCACACTCTTGTTGTTGCAGCCTGGTGGCACTGGAGTGGATGCAGTTTGGAGTCTAAAGCATTTATTTTGCGTGTTGCAGGTTTTTGGTGAT

GGACAANCCNNNNNCACTNNCTNTACCNNANACTNNTGNTGNTGCAGCCNGNTGGCACTGGNGTGGANGNAGTTTGGAGTNNANANCATTTNTTTTGCGTGTTGCAGGTTTTTGGTGATT

AGGACAACCCASTAMCACTGCCTTTACCCCACACTATTGTTGTTGCAGCCTGGTGGCACTGGAGTGGATGCAGTTTGGAGTCTAAAGCATTTMTTTTGCGTGTTGCAGGTTTTTGGTGAT

AGGACAACCCACTTCCACTGCCTTTACCCCACACTCTTGTTGTTGCAGCCTGGTGGCACTGGAGTGGATGCAGTTTGGAGTNNANANCATTTNTTTTGCGTGTTGCAGGTTTTTGGTGAT

AGGACAACCCACTTCCACTGCCTTTACCCCACACTCTTGTTGTTGCAGCCTGGTGGCACTGGAGTGGATGCAGTTTGGAGTCTAAAGCATTTNTTTTGCGTGTTGCAGGTTTTTGGTGAT

AGGACAACCCTCGACCACTACCTTTACCCCAAACTCNTGTTGTTGCAGCCYGATGGCACTGGAGTGGATGCAGTTTGGAGTSTAAAGCATTTCTTTTGCGTGTTGCAGGTGTTTGGTGAT

AGGACAANCCNNNNNCACTNNCTNTACCNNANACTNNTGNTGNTGCAGCCNGNTGGCACTGGNGTGGANGNAGTTTGGAGTNNANANCATTTNTTTTGCGTGTTGCAGGTGTTTGGTGAT

AGGACAACCCACTACCACTGCCTTTACCCYACACTCTTGTTGGTGCAGCCTGGTGGCACTGGAGTGGATGCAGTTTGGAGTCTAAAGCATTTCTTTTGCGTGTTGCAGGTTTTTGGTGAT

AGGACAACCCACGACCACTGCCTTTACCCCACACTCKTGTTGTTGCAGCCTGGTGGCACTGGAGTGGATGCAGTTTGGAGTCTAAAGCATTTCTTTTGCGTGTTGCAGGTTTTTGGTGAT

GGACAANCCNNNNNCACTNNCTNTACCNNANACTNNTGNTGNTGCAGCCNGNTGGCACTGGNGTGGANGNAGTTTGGAGTNNANANCATTTNTTTTGCGTGTTGCAGGTGTTTTGTGATT

AGGACAACCCACTNNCACTGCCTCTACCCCACACTCTTGTTGTTGCAGCCTGATGGCACTGGAGTGGAGGCAGTTTGGAGTCGAGAGCATTTCTTTTGCGTGTTGCAGGTGTTTGGTGAT

AGGACAACCCACTACCACTGCCTTTACCCCACACTCTTGTTGTTGCAGCCTGGTGGCACTGGAGTGGATGCAGTTTGGAGTCTAAAGCATTTCTTTTGCGTGTTGCAGGTTTTTGGTAAG

GGACAANCCNNNNNCACTNNCTNTACCNNANACTNNTGNTGNTGCAGCCNGNTGGCACTGGNGTGGANGNAGTTTGGAGTNNANANCATTTNTTTTGCGTGTTGCAGGTNTTTNGTNANT

GGACAACCCACGACCACTAACTTTACCCCACACTCTTGTTGTTGCAGCCTGGTGGCACTGGAGTGGATGCAGTTTGGAGTCTAAAGCATTTATTTTGCGTGTTGCAGGTNTTTNGTNANT

GGACAACCCACGACCACTGCCTTTACCCCACACTCTTGTTGTTGCAGCCTGGTGGCACTGGGGTGGATGCAGTTTGGAGTCTAAAGCATTTMTTTTGCGTGTTGCAGGTNTTTNGTNANT

GGACAACCCACGACCACTGCCTTTACCCCACACTCTTGTTGTTGCAGCCTGGTGGCACTGGRGTGGATGCAGTTTGGAGTCTAAAGCATTTMTTTTGCGTGTTGCAGGTNTTTNGTNANT

GGACAACCCACGACCACTGCCTTTACCCCACACTCTTGTTGTTGCAGCCTGGTGGCACTGGAGTGGATGCAGTTTGGAGTCTAAAGCATTTCTTTTGCGTGTTGCAGGTTTTTGGTRAKT

AGGACAACCCACGACCACTGCCTTTACCCCACACTCTTGTTGTTGCAGCCTGGTGGCACTGGAGTGGATGCAGTTTGGAGTCTAAAGCATTTATTTTGCGTGTTGCAGGTKTTTGGTGAT

AGGACAANCCNNNNNCACTNNCTNTACCNNANACTNNTGNTGNTGCAGCCNGNTGGCACTGGNGTGGANGNAGTTTGGAGTNNANANCATTTNTTTTGCGTGTTGCAGGTTTTTGGTGAT

GGACAACCCACGACCACTGCCTTTACCYCACACTCGTGTTGTTGCAGCCTGGTGGCACTGGAGTGGATGCAGTTTGGAGTCTAAAGCATTTCTTTTGCGTGTTGCAGGTTTTTGGTGATT

AGGACAACCCACGACCACTGCCTTTACCCCACACTCTTGTTGTTGCAGCCTGGTGGCACTGGAGTGGATGCAGTTTGGAGTCTAAAGCATTTNTTTTGCGTGTTGCAGGTTTTTGGTGAT

AGGACAANCCNNNNNCACTNNCTNTACCNNANACTNNTGNTGNTGCAGCCNGNTGGCACTGGNGTGGANGNAGTTTGGAGTNNANANCATTTNTTTTGCGTGTTGCAGGTTTTTGGTAAG

GGACAAGCCACKACCACTGCCTTTACCCCACACTCTTGTTGTTGCAGCCTGGTGGCACTGGGGTGGATGCAGTTTGGAGTCTAAAGCATTTMTTTTGCGTGTTGCAGGTNTTTNGTNANT

AGGACAANCCNNNNNCACTNNCTNTACCNNANACTNNTGNTGNTGCAGCCNGNTGGCACTGGNGTGGANGNAGTTTGGAGTNNANANCATTTNTTTTGCGTGTTGCAGGTNTTTNGTNAN

AGGACAACCCACTTCCACTGCCTTTACCCCACACTCTTGTTGTTGCAGCCTGGTGGCACTGGAGTGGATGCAGTTTGGAGTCTAAAGCATTTNTTTTGCGTGTTGCAGGTTTTTGGTGAT

AGGACAACCCACGACCACTGCCTTTACCCCACACTCTTGTTGTTGCAGCCTGGTGGCACTGGAGTGGATGCAGTTTGGAGTCTAAAGCATTTATTTTGCGTGTTGCAGGTTTTTGGTGAT

AGGACAACCCACTACCACTGCCTTTACCCCACACTCGTGTTGTTGCAGCCTGGTGGCACTGGAGTGGATGCAGTTTGGAGTCTAAAGCATTTCTTTTGCGTGTTGCAGGTTTTTGGTGAT

GGACAANCCNNNNNCACTNNCTNTACCNNANACTNNTGNTGNTGCAGCCNGNTGGCACTGGNGTGGANGNAGTTTGGAGTNNANANCATTTNTTTTGCGTGTTGCAGGTNTTTNGTNANT

GGACAANCCNNNNNCACTNNCTNTACCNNANACTNNTGNTGNTGCAGCCNGNTGGCACTGGNGTGGANGNAGTTTGGAGTNNANANCATTTNTTTTGCGTGTTGCAGGTGTTTTGTGATT

AGGACAANCCNNNNNCACTNNCTNTACCNNANACTNNTGNTGNTGCAGCCNGNTGGCACTGGNGTGGANGNAGTTTGGAGTNNANANCATTTNTTTTGCGTGTTGCAGGTGTTTGGTGAT

AGGACAANCCNNNNNCACTNNCTNTACCNNANACTNNTGNTGNTGCAGCCNGNTGGCACTGGNGTGGANGNAGTTTGGAGTNNANANCATTTNTTTTGCGTGTTGCAGGTTTTTGGTAAG

You can see that many samples have an extra "A" at the end of the first block, and their sequences remain out of phase by one bp from then onwards. The sequence lengths of all following blocks are all the same length, however; it's only the first block where the sequences are not the same length.

This problem occurs with all my datasets in stacks 2.52 and 2.53, but not in 2.41. I note that in 2.41 the phylip format was slightly different (10 characters for sample names; see this issue) and you're changed underscores to hyphens in all option names for populations, which breaks backwards compatibility.

These files cannot be read by IQTREE, for example, so I'm reverting to 2.41 for now. Do you think there is an easy fix?

Thanks and best wishes,

Marius

marius...@abdn.ac.uk

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Jun 27, 2021, 5:03:12 AM6/27/21

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Hi Julian,

I've just noticed that the issue above is still present in stacks 2.58. I am sure the bug is caused by different lengths of sequence names; those sequence names that are shorter by 1 bp have 1 bp extra on the first line of the sequence. This bug is absent from version 2.41.

Example from stacks 2.58:

203.M9.P8 TGCAGCCAAAAGCCTAGTCATTTAATCAATCATTTAGCCTACCTAGCTGTCTGCCCTTACTCACAAATTGTGGGGACTTGGACTCTACCTATATCTTCCTTACCATTGTA

204.M9.P8 TGCAGCCAAAAGCCTAGTCATTTAATCAATCATTTAGCCTACCTAGCTGTCTGCCCTTACTCACAAATTGTGGGGACTTGGACTCTACCTATATCTTCCTTACCATTGTA

205.M9.P8 TGCAGCCAAAAGCCTAGTCATTTAATCAATCATTTAGCCTACCTAGCTGTCTGCCCTTACTCACAAATTGTGGGGACTTGGACTCTACCTATATCTTCCTTACCATTGTA

206.M9.P8 TGCAGCCAAAAGCCTAGTCATTTAATCAATCATTTAGCCTACCTAGCTGTCTGCCCTTACTCACAAATTGTGGGGACTTGGACTCTACCTATATCTTCCTTACCATTGTA

53.M3.P5 TGCAGCCAAAAGCCTAGTCATTTAATCAATCATTTAGCCTACCTAGCTGTCTGCCCTTACTCACAAATTGTGGGGACTTGGACTCTACCTATATCTTCCTTACCATTGTAG

54.M3.P5 TGCAGCCAAAAGCCTAGTCATTTAATCAATCATTTAGCCTACCTAGCTGTCTGCCCTTACTCACAAATTGTGGGGACTTGGACTCTACCTATATCTTCCTTACCATTGTAG

55.M3.P5 TGCAGCCAAAAGCCTAGTCATTTAATCAATCATTTAGCCTACCTAGCTGTCTGCCCTTACTCACAAATTGTGGGGACTTGGACTCTACCTATATMTTCCTTACCATTGTAG

57.M3.P5 TGCAGCCAAAAGCCTAGTCATTTAATCAATCATTTAGCCTACCTAGCTGTCTGCCCTTACTCACAAATTGTGGGGACTTGGACTCTACCTATATCTTCCTTACCATTGTAG

GCTATTAGTGGGTCACTTGAAATCTACCTATATCTTCCTTAAAAATGTAGTCATAACTTACCCAACTGCTGTTGGTCGTTGGTACAATGRTGGAAGGTTCTTCAAGTTTTGTCTAAGCTT

GCTATTAGTGGGTCACTTGAAATCTACCTATATCTTCCTTAAAAATNTAGTCATAACTTACCCAACTGCTGTTGGTCGTTGGTACAATGNTGGAAGGTTCTTCAAGTTTTGTCTAAGCTT

GCTATTAGTGGGTCACTTGAAATCTACCTATATCTTCCTTAAAAATGTAGTCATAACTTACCCAACTGCTGTTGGTCGTTGGTACAATGRTGGAAGGTTCTTCAAGTTTTGTCTAAGCTT

CTATTAGTGGGTCACTTGAAATCTACCTATATCTTCCTTAAAAATGTAGTCATAACTTACCCAACTGCTGTTGGTCGTTGGTACAATGRTGGAAGGTTCTTCAAGTTTTGTCTAAGCTTT

…

GANGAGTGTTTTTGTGGTCACCCTGTATATTGNAAACGGGAGCCTTTGCAGTATACGTGAAAATGGGAAGTTTACTTTAGAATGAATT

GANGAGTGTTTTTNTGGTCACCCTGTATATTNNAAACGGGAGCCTTTGCAGTATACGTGAAAATGGGAAGTTTACTTTAGAATGAATT

GANGAGTGTTTTTGTGGTCACCCTGTATATTNCAAACGGGANCCTTTGCAGTATACGTGAAAATGGGAAGTTTACTTTAGAATGAATT

GANGAGTGTTTTTGTGGTCACCCTGTATATNGNAAACGGGANCCTTTGCAGTATACGTGAAAATGGGAAGTTTACTTTAGAATGAATT

ANGAGTGTTTTTNTGGTCACCCTGTATATTNNAAACGGGAGCCTTTGCAGTATACGTGAAAATGGGAAGTTTACTTTAGAATGAATT

ANGAGTGTTTTTNTGGTCACCCTGTATATNNNAAACGGGANCCTTTGCAGTATACGTGAAAATGGGAAGTTTACTTTAGAATGAATT

ANGAGTGTTTTTNTGGTCACCCTGTATATNNNAAACGNGANCCTTTGCAGTATACGTGAAAATGGGAAGTTTACTTTAGAATGAATT

ANGAGTGTTTTTNTGGTCACCCTGTATATNNNAAACGGGANCCTTTGCAGTATACGTGAAAATGGGAAGTTTACTTTAGAATGAATT

In stacks 2.41 everything is in sync:

203.M9.P8 TGCAGCCAAAAGCCTAGTCATTTAATCAATCATTTAGCCTACCTAGCTGTCTGCCCTTACTCACAAATTGTGGGGACTTGGACTCTACCTATATCTTCCTTACCATTGTA

204.M9.P8 TGCAGCCAAAAGCCTAGTCATTTAATCAATCATTTAGCCTACCTAGCTGTCTGCCCTTACTCACAAATTGTGGGGACTTGGACTCTACCTATATCTTCCTTACCATTGTA

205.M9.P8 TGCAGCCAAAAGCCTAGTCATTTAATCAATCATTTAGCCTACCTAGCTGTCTGCCCTTACTCACAAATTGTGGGGACTTGGACTCTACCTATATCTTCCTTACCATTGTA

206.M9.P8 TGCAGCCAAAAGCCTAGTCATTTAATCAATCATTTAGCCTACCTAGCTGTCTGCCCTTACTCACAAATTGTGGGGACTTGGACTCTACCTATATCTTCCTTACCATTGTA

53.M3.P5 TGCAGCCAAAAGCCTAGTCATTTAATCAATCATTTAGCCTACCTAGCTGTCTGCCCTTACTCACAAATTGTGGGGACTTGGACTCTACCTATATCTTCCTTACCATTGTA

54.M3.P5 TGCAGCCAAAAGCCTAGTCATTTAATCAATCATTTAGCCTACCTAGCTGTCTGCCCTTACTCACAAATTGTGGGGACTTGGACTCTACCTATATCTTCCTTACCATTGTA

55.M3.P5 TGCAGCCAAAAGCCTAGTCATTTAATCAATCATTTAGCCTACCTAGCTGTCTGCCCTTACTCACAAATTGTGGGGACTTGGACTCTACCTATATMTTCCTTACCATTGTA

57.M3.P5 TGCAGCCAAAAGCCTAGTCATTTAATCAATCATTTAGCCTACCTAGCTGTCTGCCCTTACTCACAAATTGTGGGGACTTGGACTCTACCTATATCTTCCTTACCATTGTA

...

I hope this will help you find the bug. As a workaround, it's probably best to keep all population names the same lengths?

Many thanks and best wishes,

Marius

Julian Catchen

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Jun 30, 2021, 5:38:35 PM6/30/21

to 'marius...@abdn.ac.uk' via Stacks

Hi Marius,

Thank you for the report and example, sorry I missed your first report.
I have corrected this and it will be in the next release (coming out in
the next couple days).

Best,

julian

'marius...@abdn.ac.uk' via Stacks wrote on 6/27/21 4:03 AM:

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