egapx:rnaseq_short_plane:star:run_star (1) [ 50%] 1 of 2, failed: 1, retries: 1

[shin0727]

Hello, I have some problems in "rnaseq_short_plane:star:run_str" step in egapx.

1. egapx command

PREFIX=PS
YAML=/home/jwshin0727/Project/240729_Polypterus/08_gene_annotation/PS.yaml

python /home/junkim/tools/egapx/ui/egapx.py \
${YAML} \
-o ./${PREFIX} \
-e singularity \
-w ./tmp_${PREFIX} \
-v > ./${PREFIX}.log 2>&1

2. YAML.file

genome: /home/jwshin0727/Project/240729_Polypterus/07_MtDNA_prep/04_exclude_MtDNA_contig/02_filter/PS_h1/PS_h1.add_title.filtered.fa
taxid: 178879
reads:
    - /home/jwshin0727/Project/240729_Polypterus/00_raw/01_shortWGS/PS_WGS_S0_L009_R1_001.fastq.gz
    - /home/jwshin0727/Project/240729_Polypterus/00_raw/01_shortWGS/PS_WGS_S0_L009_R2_001.fastq.gz

annotation_provider: GenBank submitter 

nexflow.log

The FASTA file input into the program is correctly formatted and includes sequence titles. Additionally, the input files in the YAML are all Illumina short-read sequencing data.
Is there anyone who might be able to assist?

[victzh]

So what's happening? It does not complete the process? Fails? Cam you also attach the file run.trace.txt from your output directory and the file PS.log you redirect your output to.
Thanks,
Victor.

[boukn]

There are time time limits defined in ui/assets/config/process_resources.config , specifically the 16h under long_job. The star job ran past that limit. Assuming there is not something else holding STAR back, just upping that number is the solution.

[shin0727]

@victzh
It does not complete the process, retrying over time without Fails.

run.trace.txt
PS.log

[shin0727]

@boukn

Thank you for the solution.
I will try after upping the number of the time limits.
(48 h)