Edge not found error #5
Description
** I can upload the fastg, fastq, mgf and par file to a datashare, can't share on github.
We are running on a Linux 5.3.18-150300.59.60-default x86_64 server, and we are submitting jobs using slurm 21.08.8-2 with the following parameters:
#SBATCH --nodes=1
#SBATCH --tasks-per-node=1
#SBATCH --cpus-per-task=20
#SBATCH --time=48:00:00
#SBATCH --mem=500
We are submitting the jobs with the following command: srun ~/software/graph2pro-var/graph2pro-var.sh ~/file.par
GCC version is 10.3.0 (GCC).
When running the the graph2pro-var.sh script while trying to running "Graph2Pep "we encounter the following error in the step "read edges from file ...":
edgeseqfile /fs/pool/pool-mann-projects/Peter_Florian_Max_Capscan/fastg/k39_all/k39_all/1249_k39.fastg
514112 edges input
Edge not found: NODE_101623_length_2622_cov_11.6744_ID_203245
And this stops the Graph2Pep pipeline from completing and the '1743.1_k39.graph2pep.fasta' is never created. Which results in another error message, ultimately leading to an absence of input for the rest of the pipeline making it complete incorrectly.
Traceback (most recent call last):
File "/fs/gpfs41/lv07/fileset03/home/b_mann/maedler/Software/graph2pro-var/pyscript/createFixedReverseKR.py", line 26, in
inf = open(argv[1], "r")
FileNotFoundError: [Errno 2] No such file or directory: '1743.1_k39.graph2pep.fasta'
output.log
error.log