Question: Error With Trinity + Alignreader.Pl
0
gravatar for Biogeek
5.5 years ago by
Biogeek350
Biogeek350 wrote:

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 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 ~
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Any help would greatly be appreciated.

Many thanks.

trinity unix bioinformatics • 1.5k views
ADD COMMENTlink modified 5.5 years ago by JC7.9k • written 5.5 years ago by Biogeek350
0
gravatar for JC
5.5 years ago by
JC7.9k
Mexico
JC7.9k wrote:

You need to install Samtools http://samtools.sourceforge.net/

ADD COMMENTlink written 5.5 years ago by JC7.9k
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