rnaseqr/RNASEQR — Issue #2: IndexError: list index out of range
Author: caddymob
Created: 2012-01-04 18:15:54+00:00
State: open

Hi,

I am getting a `IndexError: list index out of range` error. This appears to be a python specific error. Here is my output:

=== Sepicified Parameters ===
RNASEQR path: /users02/jcorneveaux/bin/RNASEQR
Aligner: Bowtie [/users02/jcorneveaux/bin/bowtie]
Mismatch: 0
Segment mismatch:1
Thread number:7
Phred: Sanger
Annotation: GTF [/users02/jcorneveaux/resources/RAT_iGenome/Rattus_norvegicus/Ensembl/RGSC3.4/Annotation/Genes/Rattus_norvegicus.RGSC3.4.65.gtf,/users02/jcorneveaux/resources/RAT_iGenome/Rattus_norvegicus/Ensembl/RGSC3.4/Annotation/Genes/Rattus_norvegicus.RGSC3.4.65.transcriptome]
Genome: [/scratch/jcorneveaux/RAT_iGenome/Rattus_norvegicus/Ensembl/RGSC3.4/Sequence/BowtieIndex/genome]
Maximum number of overlapping exons in annotation: [40]
Local aligner: /users02/jcorneveaux/bin/blat
Local aligner index: /users02/jcorneveaux/resources/RAT_iGenome/Rattus_norvegicus/Ensembl/RGSC3.4/Sequence/BlatIndex/genome.2bit
Input: G2_62.R1.fq,G2_62.R2.fq
Read Length: 50
Anchor-and-Map: Enabled
Anchor Length: 16
num_of_hit_anchor_to_be_valid: 2
Colorspace: False
==============================

Starting Preporcessing: Wed, 04 Jan 2012 18:12:02 +0000
Finish Preporcessing: Wed, 04 Jan 2012 18:12:07 +0000
Start Aligning: Wed, 04 Jan 2012 18:12:07 +0000
Traceback (most recent call last):
File "/users02/jcorneveaux/bin/RNASEQR/RNASEQRp.py", line 227, in
instrcution='''%s -v %d -p %d %s -k %d -m %d --best --strata -S --sam-nohead -I %d -X %d --un phase1.pe.unmapped.fastq --max /dev/null %s %s -S --sam-nohead %s -1 %s -2 %s ''' % (aligner_path,align_mismatch,number_of_thread,mate_orientation,max_num_overlap_exon,max_num_overlap_exon,paired_end_gap[0],paired_end_gap[1],phred_type,colorspace,annotation_index_prefix,input_fastq[0],input_fastq[1])
IndexError: list index out of range