IndexError: list index out of range

[mictadlo]

> cat flnc.fofn
m54105_171201_020331.ccs-lima.Clontech_5p--NEB_Clontech_3p.flnc.bam
m54105_171201_121745.ccs-lima.Clontech_5p--NEB_Clontech_3p.flnc.bam

> cat ~/scripts/tama_degradation_pbs.sh
#!/bin/bash
# usage: bash tama_degradation_pbs.sh flnc.fofn genome.fasta

cat << EOF |qsub
#!/bin/bash -l
#PBS -N degradation
#PBS -l walltime=12:00:00
#PBS -j oe
#PBS -l mem=35G
#PBS -l ncpus=1
#PBS -M m.lorenc@qut.edu.au

cd \$PBS_O_WORKDIR

conda activate isoseq
bamtools merge -list $1 -out flnc.bam
conda deactivate

conda activate gs-tama
tama_collapse.py -b BAM -s flnc.bam -f $2 -p no_cap_flnc -x no_cap
tama_collapse.py -b BAM -s flnc.bam -f $2 -p capped_flnc -x capped

tama_degradation_signature.py -c capped_flnc_trans_read.bed -nc no_cap_flnc_trans_read.bed -o degradation-signature.txt

EOF

> head degradation.o1107695
tc_version_date_2021_11_03
Default collapse exon ends flag will be used: common_ends
Default coverage: 99
Default identity: 85
Default identity calculation method: ident_cov
Default 5 prime threshold: 10
Default exon/splice junction threshold: 10
Default 3 prime threshold: 10
Default duplicate merge flag: merge_dup
Default splice junction priority: no_priority
...

time taken since last check:	0:0:27
time taken since beginning:	0:1:20
going through groups: 0
Error, no groups found!
opening capped file
opening nocap file
Traceback (most recent call last):
  File "/work/waterhouse_team/miniconda2/envs/gs-tama/bin/tama_degradation_signature.py", line 68, in <module>
    id_line = line_split[3]
IndexError: list index out of range

What did I miss?

Thank you in advance,

Michal

[GenomeRIK]

Hi Michal,

It looks like there is something wrong with one of the input files. Did the TAMA Collapse runs both complete with the correct completion message?

Could you copy paste a few lines from each of the trans_read.bed files you are using as input for the degradation signature tool?

Cheers,
Richard

[mictadlo]

Hi Richard,
Both files are empty:

-rw-rw---- 1 lorencm default    0 Feb 18 10:45 no_cap_flnc_trans_read.bed
-rw-rw---- 1 lorencm default    0 Feb 18 10:46 capped_flnc_trans_read.bed

What did I miss?

Thank you in advance

Michal

[GenomeRIK]

Hi Michal,

It looks like the TAMA Collapse run did not finish. You will need to run it again and make sure that you see the finish message when it is done.

It might be that you ran out of memory or it could be some error so you will need to pay attention to the last output to the screen that it generates.

Cheers,
Richard