I am trying to launch GitHub - nf-core/denovotranscript: A pipeline for de novo transcriptome assembly of paired-end short reads from bulk RNA-seq pipeline via the slurm cloud executer but faced issue related to spades “Cannot allocate memory” Seqera Cloud
so i tried to manually increase the resources to spades which did manage to finish the spades job it seems
notes.txt (170.2 KB)
but when i tried to resume the pipeline via the cloud it again created spades job and failed Seqera Cloud
with same error
The changes made were
diff /cluster/work/users/ash022/work/fe/d95a0e1229b80f0e9f505293f800f8/.command.sh /cluster/work/users/ash022/work/cd/0398682dc60dafb772a1e2a2988011/.command.sh
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< --threads 32 \
< --memory 1000 \
---
> --threads 12 \
> --memory 72 \
diff /cluster/work/users/ash022/work/fe/d95a0e1229b80f0e9f505293f800f8/.command.run /cluster/work/users/ash022/work/cd/0398682dc60dafb772a1e2a2988011/.command.run
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< #SBATCH -o /cluster/work/users/ash022/work/fe/d95a0e1229b80f0e9f505293f800f8/.command.log
---
> #SBATCH -o /cluster/work/users/ash022/work/cd/0398682dc60dafb772a1e2a2988011/.command.log
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< #SBATCH -c 30
< #SBATCH -t 256:00:00
< #SBATCH --mem 1000G
< #SBATCH --account=nn9036k --time=256:00:00 --partition=bigmem
< NXF_CHDIR=/cluster/work/users/ash022/work/fe/d95a0e1229b80f0e9f505293f800f8
---
> #SBATCH -c 12
> #SBATCH -t 16:00:00
> #SBATCH --mem 73728M
> #SBATCH --account=nn9036k --mem=512G --time=256:00:00 --partition=bigmem
> NXF_CHDIR=/cluster/work/users/ash022/work/cd/0398682dc60dafb772a1e2a2988011
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< /bin/bash -euo pipefail /cluster/work/users/ash022/work/fe/d95a0e1229b80f0e9f505293f800f8/.command.sh
---
> /bin/bash -euo pipefail /cluster/work/users/ash022/work/cd/0398682dc60dafb772a1e2a2988011/.command.sh
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< /bin/bash -euo pipefail /cluster/work/users/ash022/work/fe/d95a0e1229b80f0e9f505293f800f8/.command.sh &
---
> /bin/bash -euo pipefail /cluster/work/users/ash022/work/cd/0398682dc60dafb772a1e2a2988011/.command.sh &
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< printf -- $exit_status > /cluster/work/users/ash022/work/fe/d95a0e1229b80f0e9f505293f800f8/.exitcode
---
> printf -- $exit_status > /cluster/work/users/ash022/work/cd/0398682dc60dafb772a1e2a2988011/.exitcode
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< set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} ${NXF_TASK_WORKDIR:+SINGULARITYENV_NXF_TASK_WORKDIR="$NXF_TASK_WORKDIR"} SINGULARITYENV_NXF_DEBUG="${NXF_DEBUG:=0}" singularity exec --no-home --pid -B /cluster/work/users/ash022/work /cluster/work/users/ash022/work/singularity/depot.galaxyproject.org-singularity-spades-4.0.0--h5fb382e_1.img /bin/bash -c "cd $PWD; eval $(nxf_container_env); /bin/bash /cluster/work/users/ash022/work/fe/d95a0e1229b80f0e9f505293f800f8/.command.run nxf_trace"
---
> set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} ${NXF_TASK_WORKDIR:+SINGULARITYENV_NXF_TASK_WORKDIR="$NXF_TASK_WORKDIR"} SINGULARITYENV_NXF_DEBUG="${NXF_DEBUG:=0}" singularity exec --no-home --pid -B /cluster/work/users/ash022/work /cluster/work/users/ash022/work/singularity/depot.galaxyproject.org-singularity-spades-4.0.0--h5fb382e_1.img /bin/bash -c "cd $PWD; eval $(nxf_container_env); /bin/bash /cluster/work/users/ash022/work/cd/0398682dc60dafb772a1e2a2988011/.command.run nxf_trace"
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< touch /cluster/work/users/ash022/work/fe/d95a0e1229b80f0e9f505293f800f8/.command.begin
---
> touch /cluster/work/users/ash022/work/cd/0398682dc60dafb772a1e2a2988011/.command.begin
I am wondering how to get past this problem, any help will be appreciated 
