Entering edit mode
10.4 years ago
Biogeek
▴
470
Hi guys,
All the working files needed are in the utility folder
I am running the following script:
# This is where all your job files for this particular job are located.
myjobdir=$HOME/Trinitywork/util
cd $myjobdir
PATH=/opt/bowtie2-1.0.0/bin:/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/bin:$PATH
# Small test data
/shared/homes/11774989/Trinitywork/util/alignReads.pl -o /shared/homes/11774989/Trinitywork/util --seqType fq --left CONTROL_9_R1_001.fastq.trimmed.paired1 --right CONTROL_9_R1_001.fastq.trimmed.paired2 --SS_lib_type FR --target Trinity.fasta --aligner bowtie2
It creates a directory called left_dir
, right_dir
, a file called target.fa
and another called target.fa.fai
But I keep getting this error:
CMD: ln -s /shared/homes/11774989/Trinitywork/util/Trinity.fasta target.fa
CMD: [samtools](http://samtools.sourceforge.net/) faidx target.fa
CMD: ln -s /shared/homes/11774989/Trinitywork/util/CONTROL_9_R1_001.fastq.trimmed.paired1 left_dir/left_fa
CMD: ln -s /shared/homes/11774989/Trinitywork/util/CONTROL_9_R1_001.fastq.trimmed.paired2 right_dir/right_fa
CMD: ln -s ../target.* .
CMD: ln -s ../target.* .
CMD: /shared/homes/11774989/Trinitywork/util/../util/merge_left_right_nameSorted_SAMs.pl --left_sam left_dir/left_fa.nameSorted.sam --right_sam right_dir/right_fa.nameSorted.sam -C 20 -D 2000 > combined.nameSorted.sam
Error, cannot open file left_dir/left_fa.nameSorted.sam at /shared/homes/11774989/Trinitywork/util/../PerlLib/SAM_reader.pm line 34
SAM_reader::_init('SAM_reader=HASH(0x1490d48)') called at /shared/homes/11774989/Trinitywork/util/../PerlLib/SAM_reader.pm line 24
SAM_reader::new('SAM_reader', 'left_dir/left_fa.nameSorted.sam') called at /shared/homes/11774989/Trinitywork/util/../util/merge_left_right_nameSorted_SAMs.pl line 55
Error, cmd: /shared/homes/11774989/Trinitywork/util/../util/merge_left_right_nameSorted_SAMs.pl --left_sam left_dir/left_fa.nameSorted.sam --right_sam right_dir/right_fa.nameSorted.sam -C 20 -D 2000 > combined.nameSorted.sam died with ret 512 at /shared/homes/11774989/Trinitywork/util/alignReads.pl line 652
main::process_cmd('/shared/homes/11774989/Trinitywork/util/../util/merge_left_ri...') called at /shared/homes/11774989/Trinitywork/util/alignReads.pl line 450
Any help would greatly be appreciated.
Many thanks