populations.log and popmap.tsv are generated after a denovo analysis
E Ra
Hi everyone,
After running a denovo analysis using one value of M, I could not find populations.log and popmap.tsv files in the output directory. Is it normal or should I only get them after running a loop iterating over some M values? I am following steps described in this paper.
Thanks
E Ra
I just noticed that denovo_map.pl failed to run at a certain step. Below is an excerpt of the error message from the log file. Any idea how to fix this issue?
Thank you
…
tsv2bam is done.
gstacks
==========
/usr/local/bin/gstacks -P /home/00_test/03_denovo_M2 -M /home/00_test/02_trimmed/popmap_test.txt --rm-pcr-duplicates
Logging to '/home/00_test/03_denovo_M2/gstacks.log'.
Locus/sample distributions will be written to '/home/00_test/03_denovo_M2/gstacks.log.distribs'.
Configuration for this run:
Input mode: denovo
Population map: '/home/00_test/02_trimmed/popmap_test.txt'
Input files: 20, e.g. '/home/00_test/03_denovo_M2/F1_24.matches.bam'
Output to: '/home/00_test/03_denovo_M2/'
Model: marukilow (var_alpha: 0.01, gt_alpha: 0.05)
Discarding unpaired reads.
Removing PCR duplicates.
Reading BAM headers...
Processing all loci...
1%...
2%...
5%...
10%...
20%...
50%...
100%
Input appears to be single-end (no paired-end reads were seen).
Removed 36245987 unpaired (forward) reads (100.0%); kept 0 read pairs in 0 loci.
Removed 0 read pairs whose insert length had already been seen in the same sample as putative PCR duplicates (-nan%); kept 0 read pairs.
Genotyped 0 loci:
Error: There wasn't any locus to genotype; check input/arguments.
Aborted.
denovo_map.pl: Aborted because the last command failed (1).
Last command executed by denovo_map.pl was:
/usr/local/bin/gstacks -P /home/00_test/03_denovo_M2 -M /home/00_test/02_trimmed/popmap_test.txt --rm-pcr-duplicates
