Traceback Error + Missing Temporary Fastq File

[ReginaEsinamAbotsi]

Hello,

Thank you so much for developing this awesome tool!

I am trying to simulate reads by running this script on hpc but kept getting the error below. I thought it was a resource issue so I increased the cpu and memory but still no luck. Any ideas how to resolve this?

cat << EOF > sepi1M.sh

!/usr/bin/bash

source /data/abotsire/conda/etc/profile.d/conda.sh conda activate insilicoseq_env cd /data/abotsire/insilicoseq/workingdocs/sepi1M iss generate --cpus 16 --n_reads 1000000 --draft ../ALL.draft.sepi/.fna -g ../ALL.complete/.fna --abundance_file ../abundance_file_FINALsepi.txt --model novaseq --output sepi1M conda deactivate EOF

sbatch --cpus-per-task=16 --mem=150g --time=4:00:00 sepi1M.sh

The error is

INFO:iss.app:Starting iss generate INFO:iss.generator:Using kde ErrorModel INFO:iss.util:Stitching input files together INFO:iss.generator:Using abundance file:../abundance_file_FINALsepi.txt INFO:iss.app:Using 16 cpus for read generation INFO:iss.app:Generating 1000000 reads INFO:iss.util:Stitching input files together Traceback (most recent call last): File "/gpfs/gsfs12/users/abotsire/conda/envs/insilicoseq_env/bin/iss", line 10, in sys.exit(main()) File "/gpfs/gsfs12/users/abotsire/conda/envs/insilicoseq_env/lib/python3.10/site-packages/iss/app.py", line 454, in main args.func(args) File "/gpfs/gsfs12/users/abotsire/conda/envs/insilicoseq_env/lib/python3.10/site-packages/iss/app.py", line 126, in generate_reads util.concatenate(temp_R1, args.output + "_R1.fastq") File "/gpfs/gsfs12/users/abotsire/conda/envs/insilicoseq_env/lib/python3.10/site-packages/iss/util.py", line 233, in concatenate with open(file_name, "rb") as f: FileNotFoundError: [Errno 2] No such file or directory: 'sepi1M.iss.tmp.13_R1.fastq'

Thank you so much!

[ReginaEsinamAbotsi]

Solved, thanks!