Error With Trinity + Alignreader.Pl

Question

[Biogeek]

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

Answer 1

[JC]

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