Issue with running the script: IndexError: list index out of range
j-miko opened this issue · 2 comments
Hello,
I have encountered an issue while trying to design oligos for my experiment. The script threw an IndexError, as shown in the output below.
The fasta file is the same I used for aligning, the bam file also works fine for other applications but I'm not ruling out my files being the cause.
I'd be deeply grateful for any help, thanks!
Command:
src/Ribo-ODDR.py -r my-data/Saccharomyces_cerevisiae.R64-1-1.ncrna.fa -o ./ -ap ./my-data/ -as .bam -s ncrna_mapped_sorted --RIsearch2_exe /home/janm/.conda/pkgs/risearch-2.1-h9bf148f_0/bin/RIsearch2
Output and error message (some parts omitted for brevity):
#### Ribo-ODDR: Ribo-seq Oligo Design for Depleting rRNAs ####
#### PIPELINE STARTED ####
#### These are the given args ####
# rRNA_seqs my-data/Saccharomyces_cerevisiae.R64-1-1.ncrna.fa
# output output
# RIsearch2_exe /home/janm/.conda/pkgs/risearch-2.1-h9bf148f_0/bin/RIsearch2
# bowtie2_build_exe None
# tophat_exe None
# samtools_exe None
# RNAfold_exe None
# OFFtargets None
# OFFtargetsSUF None
# samples ['ncrna_mapped_sorted']
# fastq_prefix None
# fastq_suffix None
# alignment_prefix ./my-data/
# alignment_suffix .bam
# range 25-30
# force_design 20
# oligos2optimize None
# rrna_perc_threshold 5.0
# score_threshold 0.25
#### END of the given args ####
#### RUN started ####
#### WORKING IN /home/janm/Ribo-ODDR/output directory ####
#rRNA sequence read: snR7-L_snRNA 214 nts
#rRNA sequence read: snR14_snRNA 160 nts
#rRNA sequence read: snR6_snRNA 112 nts
...
#Allowed lengths for oligo designs: range(25, 31) nts
### Reading ncrna_mapped_sorted alignment file and getting depth profile.
# 12 primary-aligned reads on snR7-L_snRNA for sample ./my-data/ncrna_mapped_sorted.bam
# 5 primary-aligned reads on snR14_snRNA for sample ./my-data/ncrna_mapped_sorted.bam
# 0 primary-aligned reads on snR6_snRNA for sample ./my-data/ncrna_mapped_sorted.bam
# 30 primary-aligned reads on LSR1_snRNA for sample ./my-data/ncrna_mapped_sorted.bam
# 15 primary-aligned reads on snR19_snRNA for sample ./my-data/ncrna_mapped_sorted.bam
# 1 primary-aligned reads on snR7-S_snRNA for sample ./my-data/ncrna_mapped_sorted.bam
...
# 3 primary-aligned reads on snR41_snoRNA for sample ./my-data/ncrna_mapped_sorted.bam
# 2 primary-aligned reads on snR69_snoRNA for sample ./my-data/ncrna_mapped_sorted.bam
# 0 primary-aligned reads on snR53_snoRNA for sample ./my-data/ncrna_mapped_sorted.bam
# 13 primary-aligned reads on snR8_snoRNA for sample ./my-data/ncrna_mapped_sorted.bam
794106 rRNA mapping reads
# Oligo design starts now
# First locating suboptimal binding regions
# WARNING: /home/janm/Ribo-ODDR/RIsearch2_suboptimal_oligobind_results already exists
# Running RIsearch2 for length=25 oligos
# Running RIsearch2 for length=26 oligos
# Running RIsearch2 for length=27 oligos
# Running RIsearch2 for length=28 oligos
# Running RIsearch2 for length=29 oligos
# Running RIsearch2 for length=30 oligos
# Calculating oligo potentials
## Designing for size 25
## Designing for TX snR7-L_snRNA
## Designing for TX snR14_snRNA
## Designing for TX snR6_snRNA
## Designing for TX LSR1_snRNA
Traceback (most recent call last): finished)
File "src/Ribo-ODDR.py", line 609, in <module>
main()
File "src/Ribo-ODDR.py", line 476, in main
risearch=risearch_exe, rRNAs_suf=rRNAs_suf, working_dir=output_path)
File "src/Ribo-ODDR.py", line 267, in get_oligos_with_reads_start_end
read_basin = ALL_READS_START_END[sample][rt_tarTX][r]
IndexError: list index out of range
Hi there. Thanks for contacting us for the error. Do you know what is the length of LSR1_snRNA?
It's 1175 nt. I can attach both fasta and bam files if that would help.