BLAT call fails about aligngraph HOT 1 OPEN

See FAQs 4:
Why do I get the error "BLAT CALL FAILED!" even if I have put BLAT to my $PATH?
The current version of BLAT (v35) is not compatible with AlignGraph, so you would have to use an earlier version to avoid this error.

Best,
Bao

From: sandrasan [[email protected]]
Sent: Thursday, May 19, 2016 5:42 AM
To: baoe/AlignGraph
Subject: [baoe/AlignGraph] BLAT call fails (#21)

Hi,

Every time I'm trying to run AlignGraph, I get an error saying BLAT call fails. This is my script:

#####AlignGraph to scaffold with a reference
#set machtype
MACHTYPE=x86_64
export MACHTYPE

#adding the path to bowtie
export PATH=/cm/shared/apps/bowtie/2.2.3:$PATH
#adding the path to blat
export PATH=/ernie/home/bin/aligngraph/blatSrc/bin/x86_64:$PATH
#adding the path to pblat
export PATH=/ernie/home/bin/aligngraph/pblat-1.6.0:$PATH
#adding the path to nucmer
export PATH=/ernie/home/bin/aligngraph/MUMmer3.23:$PATH
#path to AlignGraph
export PATH=/ernie/home/bin/aligngraph/AlignGraph-master/AlignGraph:$PATH

NAME=R11
KMER=k41
GENOME='/ernie/groups/quoats/contigs/combined_genomic.fasta'
READ1="${NAME}_all_R1.fasta"
READ2="${NAME}_all_R2.fasta"

AlignGraph --read1 ${READ1} --read2 ${READ2} --contig ${NAME}-${KMER}-scaf.fasta --genome ${GENOME} --distanceLow 101 --distanceHigh 1068 --extendedContig ${NAME}-${KMER}-extendedContigs.fa --remainingContig ${NAME}-${KMER}-remainingContigs.fa

When installing BLAT I did 'MACHTYPE=x86_64' and 'export MACHTYPE' too. I have it in my script since every time I log out I have to export it again, so I've got it in my script. I've also added paths to all dependencies thinking that maybe I've copied my executables to the /home/bin directory wrongly. But I'm still getting this error. Is there anything else I can try?

Thanks!

—
You are receiving this because you are subscribed to this thread.
Reply to this email directly or view it on GitHub<redir.aspx?REF=tTTA-r5HK6fGdzHdGZCytgekNSyL_UQOsv786SPYkZAUG7FU5X_TCAFodHRwczovL2dpdGh1Yi5jb20vYmFvZS9BbGlnbkdyYXBoL2lzc3Vlcy8yMQ..>

from aligngraph.