Closed cbossu closed 3 years ago
Is the number of sites correct? Which command line are you using?
I used the following code:
$NGSTOOLS/angsd/angsd -P 16 -glf $outfile.glf.gz -fai BUOW.fasta.fai -nInd 170 -doMajorMinor 1 -doPost 1 -doMaf 1 -doGeno 8 -out all_incl_SC.rmrelFinal
So I haven't even run ngsDist yet, where the nsites actually comes into play. I'm just preparing the genotype file. I used the glf 4 option. Thanks for your help.
Ch
Hello,
I'm running into an error while formatting the glf file to run ngsDist.
[glfReader.cpp:fetch():34] Error reading full chunk: bytesRead:3157 expected:13600 will exit
I don't think it is a memory issue as it stops at this point when I run in on a regular memory and large memory node. I originally thought it was a glf issue (so I ran glf in two ways --doGlf 2 and --doGlf 4), but I get the same error. There was a previous post about this that said the glf might be corrupt, however, I can use the glf in ngsLD without an error. Do you have any ideas why this error is being thrown? Thanks.
CH