talon says my files dont exist

[abrantesas]

Hi, thanks for making this software available! Any help is appreciated!

I call Talon like this:

talon --f ./03analysis/talon/TALONconfig.csv
--db ./03analysis/talon/lr2020talon.db
--build hg38 -t 8
--o lr2020

and I immediately get this error:

Traceback (most recent call last): File "/nas/longleaf/home/abrantes/modules/anaconda2/envs/longread2020/bin/talon", line 8, in sys.exit(main()) File "/nas/longleaf/home/abrantes/modules/anaconda2/envs/longread2020/lib/python3.7/site-packages/talon/talon.py", line 2400, in main sam_files, dset_metadata = check_inputs(options) File "/nas/longleaf/home/abrantes/modules/anaconda2/envs/longread2020/lib/python3.7/site-packages/talon/talon.py", line 1414, in check_inputs raise ValueError("SAM file '%s' does not exist!" % curr_sam) ValueError: SAM file '"/nas/depts/007/sullilab/shared/longread_2020/03analysis/talon/labeled/pt_043_001/pt_043_001_labeled.sam"' does not exist!

It isn't just a typo. I can copy directly from the error output and paste into the console to view the file it claims is missing.

TranscriptClean, talon label_reads, and talon initialize_database appear to have worked fine so far in the pipeline.

Anthony

[fairliereese]

Hi, is it possible that your sam files are symlinked?

[abrantesas]

I don't think so. The files were created by talon_label_reads according to the tutorial here.

[fairliereese]

Did you try to ls the file that TALON allegedly can't find in your bash terminal? It's certainly worth double checking.

[abrantesas]

I have never worked with symbolic links so I am not sure what I am looking for. If I run ls -hs in the folder I see the labeled.sam file and the read_labels.tsv and that they are 9.4G and 113M in size.

[fairliereese]

Can you use the absolute path that's in your config file instead of just relying on relative paths? It would help if you send me your config file.

[abrantesas]

TALONconfig.csv

Thanks for the help. What do you mean by that? If I type "ls /nas/depts/007/sullilab/shared/longread_2020/03analysis/talon/labeled/pt_043_001/pt_043_001_labeled.sam" the console just echoes /nas/depts/007/sullilab/shared/longread_2020/03analysis/talon/labeled/pt_043_001/pt_043_001_labeled.sam

[fairliereese]

What you mention in that post is exactly what I meant. I just wanted to make sure you had absolute paths listed in your config file.

Now that I'm confident that your file indeed exists, I'm wondering if you're trying to run TALON on a cluster as a job where perhaps the compute nodes do not have access to where you've stored the file. This has happened to me in the past and is really the only explanation I can think of at this time.