baoe
commented
8 years ago See FAQs 4: Why do I get the error "BLAT CALL FAILED!" even if I have put BLAT to my $PATH? The current version of BLAT (v35) is not compatible with AlignGraph, so you would have to use an earlier version to avoid this error.
Best, Bao
From: sandrasan [notifications@github.com] Sent: Thursday, May 19, 2016 5:42 AM To: baoe/AlignGraph Subject: [baoe/AlignGraph] BLAT call fails (#21)
Hi,
Every time I'm trying to run AlignGraph, I get an error saying BLAT call fails. This is my script:
AlignGraph to scaffold with a reference
set machtype
MACHTYPE=x86_64 export MACHTYPE
adding the path to bowtie
export PATH=/cm/shared/apps/bowtie/2.2.3:$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!
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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!