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radsex map not working #18
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Hi Brendan, This looks like it could be a tough problem to solve; it could be a dataset-related issue or an environment-related one. To help pinpoint what went wrong, it'd be helpful to know:
Best, |
Hi Romain, Some more information that could be relevant, I am running radsex in its own conda environment with only radsex and bwa installed.
Best, |
Hi Brendan, Thanks for the precision, my guess is that it's likely tied to the genome you're using. The easiest is probably to share the genome + the markers table from process for one dataset and I can investigate what's going on more easily. I will contact you with a way to do that safely. Thanks! |
I think this should be fixed in release 1.1.2 (and in the latest repo version). |
Hi Romain, (cd ./include/bwa && make CC=gcc -j 1)
make[1]: Entering directory '~/radsex/include/bwa'
gcc -g -Wall -Wno-unused-function -Wno-unused-but-set-variable -Wno-unused-result -O2 -c -o bntseq.o bntseq.c
bntseq.c:31:10: fatal error: zlib.h: No such file or directory
#include <zlib.h>
^~~~~~~~
compilation terminated.
<builtin>: recipe for target 'bntseq.o' failed
make[1]: *** [bntseq.o] Error 1
make[1]: Leaving directory '~/radsex/include/bwa'
Makefile:50: recipe for target 'include/bwa/libbwa.a' failed
make: *** [include/bwa/libbwa.a] Error 2 Do you have any ideas? I've tried a few things including installing a zlib folder within the radsex folder, but to no avail. |
Hi Brendan, I have two suggestions:
Let me know if either solution works! |
Brilliant! Installing the zlib1g-dev package fixed it. and it appears to be running! [M::bwa_idx_load_from_disk] read 0 ALT contigs
[2020-04-29 09:33:51]::INFO Progress: [#.................................................] - 2% (353770 markers) Thanks Romain! You've perhaps saved my dissertation! <3 |
Cool! Best of luck with the dissertation ;) |
Hi Romain,
Great job on this software, can't stress enough how great it is!
I'm having issues with version 1.0, I can't seem to get the map function to work, although I had it working a few months ago with the same data (albeit different reference genome), I'm currently working in a Ubuntu 18.04 virtual environment via Windows 10.
My command is comparable to your example:
$ radsex map --markers-file coverage_table.tsv --output-file alignment_results.tsv --popmap popmap.txt --genome-file LG.fasta --min-quality 20 --min-frequency 0.1 --min-depth 5 --groups M,F
and the error is always some variation of "Segmentation fault (core dumped)", e.g.
'''
[2020-04-26 10:16:12]::INFO Loaded popmap ("M": 7, "F": 9)
[2020-04-26 10:16:12]::INFO RADSex started
[2020-04-26 10:16:12]::INFO Comparing groups "M" and "F" [M::bwa_idx_load_from_disk] read 0 ALT contigs
terminate called after throwing an instance of 'std::out_of_range'
what(): _Map_base::at
Aborted (core dumped)
'''
Thanks again, hope this isn't too widespread!
Best,
bjp
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