AlejandroMS17
commented
7 years ago Problem 2.-
Option -T does not have any effect with the sequential or parallel MPI version.
It is used to specify the number of threads for the Pthreads-based parallelization
Warning, you specified a working directory via "-w"
Keep in mind that RAxML only accepts absolute path names, not relative ones!
RAxML can't, parse the alignment file as phylip file
it will now try to parse it as FASTA file
Fasta parsing error, RAxML expects an alignment.I am trying to get the FASTA file only, but I had problem setting a TMP directory with the script as it is. Could you please help me to get the FASTA file first and then I can try to run the RAxML step.
David ran it in steps an managed to get the FASTA file, but when he ran the RAxML step he found out this:
"there is a problem in the fasta file. It contains '.' characters (i.e. no genotype called). Something was not quite right with the filtering"
adamjorr
roblanf
Hey Adam
I am trying to run filtervcf.sh and I have two problems:
Problem 1.-
Solution: adding “--no-strict” in line 19
cat $GTAB | tr -d '/' | datamash transpose --no-strict | awk '{print ">"$1; for (i=2; i<NF; i++) printf $i; print "\n"'} > $SITESFAIn this correct? or should we be using the "strict" setting?