question and IndexError: list index out of range

[Ivanbh214]

Hello,

I would like to use the pipeline for analysys very short amplicons (from 250 to 500 bp) . Do you think that could be possible with this pipeline?

I've tried to used, I installed all the requeriments and I'm using Python(3.6) and Numphy in a enviroment. For the rest of the softwares I've installed with setup.py(the last version), go ( the install process was ok) and blat, I had some problems whit the path for it but finally I made it.
When I run this command line for the preprocessing:

(phy3)python C3POa_preprocessing.py -i BC26.fastq -o /home/ivan/C3POa -q 7 -l 160 -s Adapters_1d2.fasta -c configf.txt

I obtained:
raceback (most recent call last):
File "C3POa_preprocessing.py", line 63, in
progs = configReader(args['config'])
File "C3POa_preprocessing.py", line 41, in configReader
progs[line[0]] = line[1]
IndexError: list index out of range

the configf.file(I've copied your example)

Order doesn't matter

If you use the config file, you should provide paths to all of the programs

You need to include all of the example programs

Use tabs to separate the program name from the path

poa /home/ivan/C3POa/bio-pipeline/poaV2/poa
racon /home/ivan/C3POa/racon/bin/racon
water /home/ivan/C3POa/EMBOSS-6.6.0/emboss/water
minimap2 /home/ivan/C3POa/minimap2/minimap2
consensus /home/ivan/C3POa/consensus.py
racon /home/ivan/C3POa/racon/bin/racon
blat /home/ivan/blatSrc

I changed /home/ivan/blatSrc for blat but the result is the same.
What do you think that could be the problem?the blat installation?

Thank you very much

[rvolden]

It looks like your config file isn't tab delimited, but is delimited with a space instead. I think changing the spaces to tabs will fix your issue.

[Ivanbh214]

Thank you very much for your answer, I changed the configf.txt file.
configf.txt that I've used.
configf.txt

#configf
poa/home/ivan/C3POa/bio-pipeline/poaV2/poa
racon/home/ivan/C3POa/racon/bin/racon
water/home/ivan/C3POa/EMBOSS-6.6.0/emboss/water
minimap2/home/ivan/C3POa/minimap2/minimap2
consensus/home/ivan/C3POa/consensus.py
racon/home/ivan/C3POa/racon/bin/racon
blat/home/ivan/blatSrc

The same result:
~/C3POa$ python C3POa_preprocessing.py -i BC26.fastq -o /home/ivan/C3POa -q 7 -l 160 -s Adapters_1d2.fasta -c configf.txt

Traceback (most recent call last):
File "C3POa_preprocessing.py", line 63, in
progs = configReader(args['config'])
File "C3POa_preprocessing.py", line 41, in configReader
progs[line[0]] = line[1]
IndexError: list index out of range

Thank you

[rvolden]

configf.txt
I have added tabs to your file, this should work

[Ivanbh214]

Thank you very much for the file.
I checked the file and worked, but I think that I have problems with the blat installation.

~/C3POa$ python C3POa_preprocessing.py -i BC26.fastq -o /home/ivan/C3POa -q 7 -l 160 -s Adapters_1d2.fasta -c configf.txt
Reading and filtering fastq file
Running BLAT to find splint locations (This can take hours)
sh: 1: /home/ivan/blatSrc: Permission denied
Parsing BLAT output
Traceback (most recent call last):
File "C3POa_preprocessing.py", line 214, in
main()
File "C3POa_preprocessing.py", line 209, in main
adapter_dict = parse_blat(output_path)
File "C3POa_preprocessing.py", line 135, in parse_blat
for line in open(alignment_file):
FileNotFoundError: [Errno 2] No such file or directory: '/home/ivan/C3POa//Splint_to_read_alignments.psl'

It could be a problem with the installation, I think,I'll try to solve it and after that I closed the issue.

Thank you very much

[rvolden]

Check your blat file to make sure it's executable