Hi everyone,
I am trying to calculate Theta for the first time using ANGSD and this tutorial . I installed it using Conda (as I am running it on a cluster and don't want bother loading C packages to make and all). The first command
angsd -i MYsorted.bam -doSaf 1 -anc ref/human_g1k_v37.fa.gz -GL 1 -out TESTOUT
run, I believe correctly, here is :
angsd version: 0.933 (htslib: 1.9) build(May 6 2020 21:25:11)
Reading fasta: ref/human_g1k_v37.fa.gz
[bammer_main] 1 samples in 1 input files
-> Parsing 1 number of samples
-> Printing at chr: GL000239.1 pos:32549 chunknumber 26300 contains 222 sites
-> Done reading data waiting for calculations to finish
-> Done waiting for threads
-> Output filenames:
->"TESTOUT.arg"
->"TESTOUT.saf.gz"
->"TESTOUT.saf.pos.gz" ->"TESTOUT.saf.idx"
-> Wed Nov 4 17:45:56 2020
-> Arguments and parameters for all analysis are located in .arg file
-> Total number of sites analyzed: 33057855
-> Number of sites retained after filtering: 33007015
[ALL done] cpu-time used = 75.00 sec
[ALL done] walltime used = 75.00 sec
However when I try to do the second command of step 1:
realSFS TESTOUT.saf.idx -P 24 -fold 1 > TESTOUT.sfs
I have the output:
-> Version of fname:TESTOUT.saf.idx is:2
Segmentation fault
Do you have an idea from where this can come from ? Thanks a lot !
