Flair combine exiting without any error, status says completed but no output files generated #622
Description
#!/bin/bash
#Submit this script with: sbatch thefilename
#SBATCH --job-name=$jobname_Flair_combine ##name that will show up in the queue
#SBATCH --output=/scratch/%u/%x-%N-%j.out ##filename of the output
#SBATCH --error=/scratch/%u/%x-%N-%j.err ##filename of the error output
#SBATCH --nodes=1 ##number of nodes to use
#SBATCH --ntasks=1 ##number of tasks to run
#SBATCH --time=1-00:00:00 ##time for analysis (day-hour:min:sec)
#SBATCH --cpus-per-task=8 ##the number of threads the code will use
#SBATCH --mem=70GB ##memory allocation per node
#SBATCH --partition normal ##the partition to run in
#SBATCH --mail-user ##your email address
#SBATCH --mail-type BEGIN ##slurm will email you when your job starts
#SBATCH --mail-type END ##slurm will email you when your job ends
#SBATCH --mail-type FAIL ##slurm will email you when your job fails
Commands to Load Modules:
source miniforge/bin/activate nextflow
conda activate flair_env
Load modules, insert code, and run your programs here.
cd /$PATH
flair_combine
-m combine_manifest.fixed.tsv
-o $name
--threads ${SLURM_CPUS_PER_TASK}
2> allsamples.log
My manifest file looks like this:
Control_R1 isoform $path_to_Control_R1collapse.isoforms.bed $path_to_Control_R1collapse.isoforms.fa
Control_R2 isoform $path_to_Control_R2collapse.isoforms.bed $path_to_Control_R2collapse.isoforms.fa
Treated_R1 isoform $path_to_Treated_R1collapse.isoforms.bed $path_to_Treated_R1collapse.isoforms.fa
Treated_R2 isoform $path_to_Treated_R2collapse.isoforms.bed $path_to_Treated_R2collapse.isoforms.fa
The isoforms.bed and isoforms.fa are the outputs from flair collapse.
I tried running the command by using "flair_combine" and "flair combine", but it exits immediately with exit code 0, giving the status as completed but generating no outputs.