alleyoop uttrates error

[mmaslon]

Hi there, I am trying to test utrrates tool on my data.

I used alleyoop rates OK, and it produced boxplot as expected. The code for your reference was:

#!/bin/bash
module load miniconda3/23.5.2-0
eval "$(conda shell.bash hook)"
conda activate slamdunk
reference="/net/pr2/projects/plgrid/plggkinetics/genome/Homo_sapiens.GRCh38.dna.primary_assembly.fa"
bed="/net/pr2/projects/plgrid/plggkinetics/genome/utrs"
bam="/net/ascratch/people/plgmmaslon/slurm_jobdir/slamseq_data/slamdunk/filter"
output_dir="/net/ascratch/people/plgmmaslon/slurm_jobdir/slamseq_data/alleyoop_rates"
alleyoop rates -o $output_dir -r $reference $bam/Unknown_A52BMK240408-BY775-ZX01-010001-01_good_1_trimmed.fq_slamdunk_mapped_filtered.bam

However, when I tried to run the uttrates on the same file using the following code:

#!/bin/bash
module load miniconda3/23.5.2-0
eval "$(conda shell.bash hook)"
conda activate slamdunk
reference="/net/pr2/projects/plgrid/plggkinetics/genome/Homo_sapiens.GRCh38.dna.primary_assembly.fa"
bed="/net/pr2/projects/plgrid/plggkinetics/genome/utrs"
bam="/net/ascratch/people/plgmmaslon/slurm_jobdir/slamseq_data/slamdunk/filter"
output_dir="/net/ascratch/people/plgmmaslon/slurm_jobdir/slamseq_data/alleyoop"
alleyoop utrrates -o $output_dir -r $reference -t 1 -b $bed -l 151 $bam/Unknown_A52BMK240408-BY775-ZX01-010001-01_good_1_trimmed.fq_slamdunk_mapped_filtered.bam

I encountered the problem. Please see the error file for the script and log produced by the tool. Unknown_A52BMK240408-BY775-ZX01-010001-01_good_1_trimmed.fq_slamdunk_mapped_filtered_mutationrates_utr.log alleyloop_err.txt

Could you please advise what the issue could be?

[t-neumann]

Can you also send the content of this file? /net/ascratch/people/plgmmaslon/slurm_jobdir/11143159/tmp/tmph3r81hoa

[mmaslon]

Sure. NF3 /net/ascratch/people/plgmmaslon/slurm_jobdir/slamseq_data/alleyoop/Unknown_A52BMK240408-BY775-ZX01-010001-01_good_1_trimmed.fq_slamdunk_mapped_filtered_mutationrates_utr.csv (sorry the file does not want to upload, so I pasted the content)

[t-neumann]

OK, then I would still need this file sorry /net/ascratch/people/plgmmaslon/slurm_jobdir/slamseq_data/alleyoop/Unknown_A52BMK240408-BY775-ZX01-010001-01_good_1_trimmed.fq_slamdunk_mapped_filtered_mutationrates_utr.csv

[mmaslon]

sure. Unknown_A52BMK240408-BY775-ZX01-010001-01_good_1_trimmed.fq_slamdunk_mapped_filtered_mutationrates_utr.csv

[mmaslon]

I see that this file has only 0 values - this must be it, but the conversions seem to be working, i.e. I do see the epxected rates for this sample Unknown_A52BMK240408-BY775-ZX01-010001-01_good_1_trimmed.fq_slamdunk_mapped_filtered_overallrates.pdf

[t-neumann]

Hm is the bed file having different chr prefixes than the reference fa?

[mmaslon]

just started looking at it,primary assembly just numbers, bed chr1 etc.

[t-neumann]

Yes then this disconnect is the problem

[t-neumann]

You should then also have 0 counts in the tcount output files

[mmaslon]

Hi again, I re-run slamdunk all with corrected UTR file. This created map, filter, snp folders and files allright, but I encountered a new problem now with the counts - all empty files. Attached error file, the script is essentially the same, the UTR file changed, but it worked fine for the upstream steps.. slamerr_280824.txt I would be grateful for any pointers..

[t-neumann]

Hm which command are you using? And are all files in the count folder empty? Because at least some processes finished