How can I run the ERDS quickly? #7
Description
I want to get outputs quickly using ERDS since it took 15 hours (when using the default option), so I used -c option.
However, the following error occured.
How do I resolve this issue? Or is there a way to get outputs quickly using ERDS?
perl $erds_path/erds_pipeline.pl -b $2 -v $vcf_path/$1/strelkaGermlineWorkflow/results/variants/variants.vcf.gz -o $output/$1 -r $reference -name $1 -c 16
error
############################ERDS1.1############################
Your input command line is
perl /home/phswin92/CNV/erds_test/erds_pipeline.pl -b /lustre/NGS/WGS/Alignment_node4/Sort/GARDWGSN02674_BWA_sort.bam -v /lustre/NGS/WGS/VariantCall_node4/Strelka2/GARDWGSN02674/strelkaGermlineWorkflow/results/variants/variants.vcf.gz -o /lustre/NGS/HS/CNV/ERDS/GARDWGSN02674 -r /lustre/NGS/WGS/need_data/hg38_v0_Homo_sapiens_assembly38.fasta -name GARDWGSN02674 -c 16
There was an error running the Slurm sbatch command.
The command was:
'/usr/bin/sbatch -e rd_bam_cluster.pl.e%A -o rd_bam_cluster.pl.o%A /lustre/NGS/HS/CNV/ERDS/GARDWGSN02674/script/rd_bam_cluster.pl /lustre/NGS/HS/CNV/ERDS/GARDWGSN02674/parameter-ame.pl /lustre/NGS/HS/CNV/ERDS/GARDWGSN02674/script/functions.pl 2>&1'
and the output was:
'sbatch: error: This does not look like a batch script. The first
sbatch: error: line must start with #! followed by the path to an interpreter.
sbatch: error: For instance: #!/bin/sh
'
There was an error running the Slurm sbatch command.
The command was:
'/usr/bin/sbatch -e pre_hmm_cluster.pl.e%A -o pre_hmm_cluster.pl.o%A /lustre/NGS/HS/CNV/ERDS/GARDWGSN02674/script/pre_hmm_cluster.pl pre_hmm.pl /lustre/NGS/HS/CNV/ERDS/GARDWGSN02674/parameter-ame.pl /lustre/NGS/HS/CNV/ERDS/GARDWGSN02674/script/functions.pl 2>&1'
and the output was:
'sbatch: error: This does not look like a batch script. The first
sbatch: error: line must start with #! followed by the path to an interpreter.
sbatch: error: For instance: #!/bin/sh
'
There was an error running the Slurm sbatch command.
The command was:
'/usr/bin/sbatch -e em_cluster.pl.e%A -o em_cluster.pl.o%A /lustre/NGS/HS/CNV/ERDS/GARDWGSN02674/script/em_cluster.pl /lustre/NGS/HS/CNV/ERDS/GARDWGSN02674/parameter-ame.pl /lustre/NGS/HS/CNV/ERDS/GARDWGSN02674/script/functions.pl 2>&1'
and the output was:
'sbatch: error: This does not look like a batch script. The first
sbatch: error: line must start with #! followed by the path to an interpreter.
sbatch: error: For instance: #!/bin/sh
'
There was an error running the Slurm sbatch command.
The command was:
'/usr/bin/sbatch -e hmm_cluster.pl.e%A -o hmm_cluster.pl.o%A /lustre/NGS/HS/CNV/ERDS/GARDWGSN02674/script/hmm_cluster.pl /lustre/NGS/HS/CNV/ERDS/GARDWGSN02674/parameter-ame.pl /lustre/NGS/HS/CNV/ERDS/GARDWGSN02674/script/functions.pl 2>&1'
and the output was:
'sbatch: error: This does not look like a batch script. The first
sbatch: error: line must start with #! followed by the path to an interpreter.
sbatch: error: For instance: #!/bin/sh
'
There was an error running the Slurm sbatch command.
The command was:
'/usr/bin/sbatch -e events_cluster.pl.e%A -o events_cluster.pl.o%A /lustre/NGS/HS/CNV/ERDS/GARDWGSN02674/script/events_cluster.pl /lustre/NGS/HS/CNV/ERDS/GARDWGSN02674/parameter-ame.pl /lustre/NGS/HS/CNV/ERDS/GARDWGSN02674/script/functions.pl 2>&1'
and the output was:
'sbatch: error: This does not look like a batch script. The first
sbatch: error: line must start with #! followed by the path to an interpreter.
sbatch: error: For instance: #!/bin/sh
'
There was an error running the Slurm sbatch command.
The command was:
'/usr/bin/sbatch -e post_events_cluster.pl.e%A -o post_events_cluster.pl.o%A /lustre/NGS/HS/CNV/ERDS/GARDWGSN02674/script/post_events_cluster.pl post_events.pl /lustre/NGS/HS/CNV/ERDS/GARDWGSN02674/parameter-ame.pl /lustre/NGS/HS/CNV/ERDS/GARDWGSN02674/script/functions.pl 2>&1'
and the output was:
'sbatch: error: This does not look like a batch script. The first
sbatch: error: line must start with #! followed by the path to an interpreter.
sbatch: error: For instance: #!/bin/sh
'
There was an error running the Slurm sbatch command.
The command was:
'/usr/bin/sbatch -e pre_hmm_dup_cluster.pl.e%A -o pre_hmm_dup_cluster.pl.o%A /lustre/NGS/HS/CNV/ERDS/GARDWGSN02674/script/pre_hmm_dup_cluster.pl pre_hmm_dup.pl /lustre/NGS/HS/CNV/ERDS/GARDWGSN02674/parameter-ame.pl /lustre/NGS/HS/CNV/ERDS/GARDWGSN02674/script/functions.pl 2>&1'
and the output was:
'sbatch: error: This does not look like a batch script. The first
sbatch: error: line must start with #! followed by the path to an interpreter.
sbatch: error: For instance: #!/bin/sh
'
There was an error running the Slurm sbatch command.
The command was:
'/usr/bin/sbatch -e hmm_dup_cluster.pl.e%A -o hmm_dup_cluster.pl.o%A /lustre/NGS/HS/CNV/ERDS/GARDWGSN02674/script/hmm_dup_cluster.pl hmm_dup.pl /lustre/NGS/HS/CNV/ERDS/GARDWGSN02674/parameter-ame.pl /lustre/NGS/HS/CNV/ERDS/GARDWGSN02674/script/functions.pl 2>&1'
and the output was:
'sbatch: error: This does not look like a batch script. The first
sbatch: error: line must start with #! followed by the path to an interpreter.
sbatch: error: For instance: #!/bin/sh
'
There was an error running the Slurm sbatch command.
The command was:
'/usr/bin/sbatch -e events_dup_cluster.pl.e%A -o events_dup_cluster.pl.o%A /lustre/NGS/HS/CNV/ERDS/GARDWGSN02674/script/events_dup_cluster.pl events_dup.pl /lustre/NGS/HS/CNV/ERDS/GARDWGSN02674/parameter-ame.pl /lustre/NGS/HS/CNV/ERDS/GARDWGSN02674/script/functions.pl 2>&1'
and the output was:
'sbatch: error: This does not look like a batch script. The first
sbatch: error: line must start with #! followed by the path to an interpreter.
sbatch: error: For instance: #!/bin/sh
'
There was an error running the Slurm sbatch command.
The command was:
'/usr/bin/sbatch -e post_events_dup_cluster.pl.e%A -o post_events_dup_cluster.pl.o%A /lustre/NGS/HS/CNV/ERDS/GARDWGSN02674/script/post_events_dup_cluster.pl post_events_dup.pl /lustre/NGS/HS/CNV/ERDS/GARDWGSN02674/parameter-ame.pl /lustre/NGS/HS/CNV/ERDS/GARDWGSN02674/script/functions.pl 2>&1'
and the output was:
'sbatch: error: This does not look like a batch script. The first
sbatch: error: line must start with #! followed by the path to an interpreter.
sbatch: error: For instance: #!/bin/sh
'
There was an error running the Slurm sbatch command.
The command was:
'/usr/bin/sbatch -e merge_cluster.pl.e%A -o merge_cluster.pl.o%A /lustre/NGS/HS/CNV/ERDS/GARDWGSN02674/script/merge_cluster.pl merge.pl /lustre/NGS/HS/CNV/ERDS/GARDWGSN02674/parameter-ame.pl /lustre/NGS/HS/CNV/ERDS/GARDWGSN02674/script/functions.pl 2>&1'
and the output was:
'sbatch: error: This does not look like a batch script. The first
sbatch: error: line must start with #! followed by the path to an interpreter.
sbatch: error: For instance: #!/bin/sh
'
############################ERDS1.1############################