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neurogenomics / CUT_n_TAG

Preprocessing pipeline for CUT&TAG data.
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Can't run nf-core/atacseq test example #7

Closed bschilder closed 2 years ago

bschilder commented 3 years ago

Test still fails despite being able to run our own CUT&TAG data...

nextflow run nf-core/atacseq -r 1.2.1 -profile test,singularity

Same exact issue even when I specify the config and local singularity container:

nextflow run nf-core/atacseq -r 1.2.1 -profile test,singularity -with-singularity $HOME/atacseq_latest.sif -c hpc_config
``` N E X T F L O W ~ version 20.01.0 Launching `nf-core/atacseq` [ecstatic_khorana] - revision: 1b3a832db5 [1.2.1] ---------------------------------------------------- ,--./,-. ___ __ __ __ ___ /,-._.--~' |\ | |__ __ / ` / \ |__) |__ } { | \| | \__, \__/ | \ |___ \`-._,-`-, `._,._,' nf-core/atacseq v1.2.1 ---------------------------------------------------- Run Name : ecstatic_khorana Data Type : Paired-End Design File : https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/design.csv Genome : Not supplied Fasta File : https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/reference/genome.fa GTF File : https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/reference/genes.gtf Mitochondrial Contig : MT MACS2 Genome Size : 1.2E+7 Min Consensus Reps : 1 MACS2 Narrow Peaks : No MACS2 Broad Cutoff : 0.1 Trim R1 : 0 bp Trim R2 : 0 bp Trim 3' R1 : 0 bp Trim 3' R2 : 0 bp NextSeq Trim : 0 bp Fingerprint Bins : 100 Save Genome Index : No Max Resources : 6 GB memory, 2 cpus, 12h time per job Container : singularity - /rds/general/user/bms20/home/atacseq_latest.sif Output Dir : ./results Launch Dir : /rds/general/project/neurogenomics-lab/live/GitRepos/CUT_n_TAG Working Dir : /rds/general/user/bms20/ephemeral/tmp Script Dir : /rds/general/user/bms20/home/.nextflow/assets/nf-core/atacseq User : bms20 Config Profile : test,singularity Config Description : Minimal test dataset to check pipeline function ---------------------------------------------------- [9e/7c8147] process > CHECK_DESIGN [100%] 1 of 1, failed: 1 [9e/7c8147] process > CHECK_DESIGN [100%] 1 of 1, failed: 1 [9e/7c8147] process > CHECK_DESIGN [100%] 1 of 1, failed: 1 [- ] process > BWA_INDEX [ 0%] 0 of 1 [- ] process > MAKE_GENE_BED [ 0%] 0 of 1 [- ] process > MAKE_TSS_BED - [9e/7c8147] process > CHECK_DESIGN [100%] 1 of 1, failed: 1 [- ] process > BWA_INDEX [ 0%] 0 of 1 [- ] process > MAKE_GENE_BED [ 0%] 0 of 1 [- ] process > MAKE_TSS_BED - [- ] process > MAKE_GENOME_FILTER [ 0%] 0 of 1 [- ] process > FASTQC - [- ] process > TRIMGALORE - [9e/7c8147] process > CHECK_DESIGN [100%] 1 of 1, failed: 1 [- ] process > BWA_INDEX [ 0%] 0 of 1 [- ] process > MAKE_GENE_BED [ 0%] 0 of 1 [- ] process > MAKE_TSS_BED - [- ] process > MAKE_GENOME_FILTER [ 0%] 0 of 1 [- ] process > FASTQC - [- ] process > TRIMGALORE - [- ] process > BWA_MEM - [- ] process > SORT_BAM - [9e/7c8147] process > CHECK_DESIGN [100%] 1 of 1, failed: 1 [- ] process > BWA_INDEX [ 0%] 0 of 1 [- ] process > MAKE_GENE_BED [ 0%] 0 of 1 [- ] process > MAKE_TSS_BED - [- ] process > MAKE_GENOME_FILTER [ 0%] 0 of 1 [- ] process > FASTQC - [- ] process > TRIMGALORE - [- ] process > BWA_MEM - [- ] process > SORT_BAM - [- ] process > MERGED_LIB_BAM - [- ] process > MERGED_LIB_BAM_FILTER - [- ] process > MERGED_LIB_BAM_REMOVE_ORPHAN - [9e/7c8147] process > CHECK_DESIGN [100%] 1 of 1, failed: 1 [- ] process > BWA_INDEX [ 0%] 0 of 1 [- ] process > MAKE_GENE_BED [ 0%] 0 of 1 [- ] process > MAKE_TSS_BED - [- ] process > MAKE_GENOME_FILTER [ 0%] 0 of 1 [- ] process > FASTQC - [- ] process > TRIMGALORE - [- ] process > BWA_MEM - [- ] process > SORT_BAM - [- ] process > MERGED_LIB_BAM - [- ] process > MERGED_LIB_BAM_FILTER - [- ] process > MERGED_LIB_BAM_REMOVE_ORPHAN - [- ] process > MERGED_LIB_PRESEQ - [- ] process > MERGED_LIB_PICARD_METRICS - [9e/7c8147] process > CHECK_DESIGN [100%] 1 of 1, failed: 1 [- ] process > BWA_INDEX [ 0%] 0 of 1 [- ] process > MAKE_GENE_BED [ 0%] 0 of 1 [- ] process > MAKE_TSS_BED - [- ] process > MAKE_GENOME_FILTER [ 0%] 0 of 1 [- ] process > FASTQC - [- ] process > TRIMGALORE - [- ] process > BWA_MEM - [- ] process > SORT_BAM - [- ] process > MERGED_LIB_BAM - [- ] process > MERGED_LIB_BAM_FILTER - [- ] process > MERGED_LIB_BAM_REMOVE_ORPHAN - [- ] process > MERGED_LIB_PRESEQ - [- ] process > MERGED_LIB_PICARD_METRICS - [9e/7c8147] process > CHECK_DESIGN [100%] 1 of 1, failed: 1 [- ] process > BWA_INDEX [ 0%] 0 of 1 [- ] process > MAKE_GENE_BED [ 0%] 0 of 1 [- ] process > MAKE_TSS_BED - [- ] process > MAKE_GENOME_FILTER [ 0%] 0 of 1 [- ] process > FASTQC - [- ] process > TRIMGALORE - [- ] process > BWA_MEM - [- ] process > SORT_BAM - [- ] process > MERGED_LIB_BAM - [- ] process > MERGED_LIB_BAM_FILTER - [- ] process > MERGED_LIB_BAM_REMOVE_ORPHAN - [- ] process > MERGED_LIB_PRESEQ - [- ] process > MERGED_LIB_PICARD_METRICS - [- ] process > MERGED_LIB_BIGWIG - [9e/7c8147] process > CHECK_DESIGN [100%] 1 of 1, failed: 1 [- ] process > BWA_INDEX [ 0%] 0 of 1 [- ] process > MAKE_GENE_BED [ 0%] 0 of 1 [- ] process > MAKE_TSS_BED - [- ] process > MAKE_GENOME_FILTER [ 0%] 0 of 1 [- ] process > FASTQC - [- ] process > TRIMGALORE - [- ] process > BWA_MEM - [- ] process > SORT_BAM - [- ] process > MERGED_LIB_BAM - [- ] process > MERGED_LIB_BAM_FILTER - [- ] process > MERGED_LIB_BAM_REMOVE_ORPHAN - [- ] process > MERGED_LIB_PRESEQ - [- ] process > MERGED_LIB_PICARD_METRICS - [- ] process > MERGED_LIB_BIGWIG - [- ] process > MERGED_LIB_PLOTPROFILE - [9e/7c8147] process > CHECK_DESIGN [100%] 1 of 1, failed: 1 [- ] process > BWA_INDEX [ 0%] 0 of 1 [- ] process > MAKE_GENE_BED [ 0%] 0 of 1 [- ] process > MAKE_TSS_BED - [- ] process > MAKE_GENOME_FILTER [ 0%] 0 of 1 [- ] process > FASTQC - [- ] process > TRIMGALORE - [- ] process > BWA_MEM - [- ] process > SORT_BAM - [- ] process > MERGED_LIB_BAM - [- ] process > MERGED_LIB_BAM_FILTER - [- ] process > MERGED_LIB_BAM_REMOVE_ORPHAN - [- ] process > MERGED_LIB_PRESEQ - [- ] process > MERGED_LIB_PICARD_METRICS - [- ] process > MERGED_LIB_BIGWIG - [- ] process > MERGED_LIB_PLOTPROFILE - [9e/7c8147] process > CHECK_DESIGN [100%] 1 of 1, failed: 1 [- ] process > BWA_INDEX [ 0%] 0 of 1 [- ] process > MAKE_GENE_BED [ 0%] 0 of 1 [- ] process > MAKE_TSS_BED - [- ] process > MAKE_GENOME_FILTER [ 0%] 0 of 1 [- ] process > FASTQC - [- ] process > TRIMGALORE - [- ] process > BWA_MEM - [- ] process > SORT_BAM - [- ] process > MERGED_LIB_BAM - [- ] process > MERGED_LIB_BAM_FILTER - [- ] process > MERGED_LIB_BAM_REMOVE_ORPHAN - [- ] process > MERGED_LIB_PRESEQ - [- ] process > MERGED_LIB_PICARD_METRICS - [- ] process > MERGED_LIB_BIGWIG - [- ] process > MERGED_LIB_PLOTPROFILE - [- ] process > MERGED_LIB_PLOTFINGERPRINT - [9e/7c8147] process > CHECK_DESIGN [100%] 1 of 1, failed: 1 [- ] process > BWA_INDEX [ 0%] 0 of 1 [- ] process > MAKE_GENE_BED [ 0%] 0 of 1 [- ] process > MAKE_TSS_BED - [- ] process > MAKE_GENOME_FILTER [ 0%] 0 of 1 [- ] process > FASTQC - [- ] process > TRIMGALORE - [- ] process > BWA_MEM - [- ] process > SORT_BAM - [- ] process > MERGED_LIB_BAM - [- ] process > MERGED_LIB_BAM_FILTER - [- ] process > MERGED_LIB_BAM_REMOVE_ORPHAN - [- ] process > MERGED_LIB_PRESEQ - [- ] process > MERGED_LIB_PICARD_METRICS - [- ] process > MERGED_LIB_BIGWIG - [- ] process > MERGED_LIB_PLOTPROFILE - [- ] process > MERGED_LIB_PLOTFINGERPRINT - [- ] process > MERGED_LIB_MACS2 - [- ] process > MERGED_LIB_MACS2_ANNOTATE - [- ] process > MERGED_LIB_MACS2_QC - [- ] process > MERGED_LIB_CONSENSUS - [- ] process > MERGED_LIB_CONSENSUS_ANNOTATE - [- ] process > MERGED_LIB_CONSENSUS_COUNTS - [- ] process > MERGED_LIB_CONSENSUS_DESEQ2 - [- ] process > MERGED_LIB_ATAQV - [- ] process > MERGED_LIB_ATAQV_MKARV - [- ] process > MERGED_REP_BAM - [- ] process > MERGED_REP_BIGWIG - [- ] process > MERGED_REP_MACS2 - [- ] process > MERGED_REP_MACS2_ANNOTATE - [- ] process > MERGED_REP_MACS2_QC - [- ] process > MERGED_REP_CONSENSUS - [- ] process > MERGED_REP_CONSENSUS_ANNOTATE - [- ] process > MERGED_REP_CONSENSUS_COUNTS - [- ] process > MERGED_REP_CONSENSUS_DESEQ2 - [- ] process > IGV - [- ] process > get_software_versions [ 0%] 0 of 1 [- ] process > MULTIQC - [- ] process > output_documentation [ 0%] 0 of 1 -[nf-core/atacseq] Pipeline completed with errors- Error executing process > 'CHECK_DESIGN (design.csv)' Caused by: Failed to submit process to grid scheduler for execution Command executed: qsub -N nf-CHECK_DESIGN .command.run Command exit status: 32 Command output: qsub: [ncpus] must be in the -lselect Work dir: /rds/general/user/bms20/ephemeral/tmp/9e/7c81474eb7833b3a99f3a7a8d97baf Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line ```
NathanSkene commented 3 years ago

Looks like a config issue, right? The "qsub: [ncpus] must be in the -lselect"

I guess it's not stating how many CPUs in the the command... qsub should be structured like:

qsub -X -I -l select=1:ncpus=36:mpiprocs=36 -l walltime=01:00:00 -q regular -A project_code

On Thu, 21 Jan 2021 at 10:47, Brian M. Schilder notifications@github.com wrote:

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Test still fails despite being able to run our own CUT&TAG data...

nextflow run nf-core/atacseq -r 1.2.1 -profile test,singularity

Same exact issue even when I specify the config and local singularity container:

nextflow run nf-core/atacseq -r 1.2.1 -profile test,singularity -with-singularity $HOME/atacseq_latest.sif -c hpc_config

N E X T F L O W ~ version 20.01.0 Launching nf-core/atacseq [ecstatic_khorana] - revision: 1b3a832db5 [1.2.1]

                                ,--./,-.
___     __   __   __   ___     /,-._.--~'

|\ | | / / \ |) | } { | | | _, _/ | \ |__ -.,--, .,.,' nf-core/atacseq v1.2.1 Run Name : ecstatic_khorana Data Type : Paired-End Design File : https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/design.csv Genome : Not supplied Fasta File : https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/reference/genome.fa GTF File : https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/reference/genes.gtf Mitochondrial Contig : MT MACS2 Genome Size : 1.2E+7 Min Consensus Reps : 1 MACS2 Narrow Peaks : No MACS2 Broad Cutoff : 0.1 Trim R1 : 0 bp Trim R2 : 0 bp Trim 3' R1 : 0 bp Trim 3' R2 : 0 bp NextSeq Trim : 0 bp Fingerprint Bins : 100 Save Genome Index : No Max Resources : 6 GB memory, 2 cpus, 12h time per job Container : singularity - /rds/general/user/bms20/home/atacseq_latest.sif Output Dir : ./results Launch Dir : /rds/general/project/neurogenomics-lab/live/GitRepos/CUT_n_TAG Working Dir : /rds/general/user/bms20/ephemeral/tmp Script Dir : /rds/general/user/bms20/home/.nextflow/assets/nf-core/atacseq User : bms20 Config Profile : test,singularity Config Description : Minimal test dataset to check pipeline function

[9e/7c8147] process > CHECK_DESIGN [100%] 1 of 1, failed: 1 [9e/7c8147] process > CHECK_DESIGN [100%] 1 of 1, failed: 1 [9e/7c8147] process > CHECK_DESIGN [100%] 1 of 1, failed: 1 [- ] process > BWA_INDEX [ 0%] 0 of 1 [- ] process > MAKE_GENE_BED [ 0%] 0 of 1 [- ] process > MAKE_TSS_BED - [9e/7c8147] process > CHECK_DESIGN [100%] 1 of 1, failed: 1 [- ] process > BWA_INDEX [ 0%] 0 of 1 [- ] process > MAKE_GENE_BED [ 0%] 0 of 1 [- ] process > MAKE_TSS_BED - [- ] process > MAKE_GENOME_FILTER [ 0%] 0 of 1 [- ] process > FASTQC - [- ] process > TRIMGALORE - [9e/7c8147] process > CHECK_DESIGN [100%] 1 of 1, failed: 1 [- ] process > BWA_INDEX [ 0%] 0 of 1 [- ] process > MAKE_GENE_BED [ 0%] 0 of 1 [- ] process > MAKE_TSS_BED - [- ] process > MAKE_GENOME_FILTER [ 0%] 0 of 1 [- ] process > FASTQC - [- ] process > TRIMGALORE - [- ] process > BWA_MEM - [- ] process > SORT_BAM - [9e/7c8147] process > CHECK_DESIGN [100%] 1 of 1, failed: 1 [- ] process > BWA_INDEX [ 0%] 0 of 1 [- ] process > MAKE_GENE_BED [ 0%] 0 of 1 [- ] process > MAKE_TSS_BED - [- ] process > MAKE_GENOME_FILTER [ 0%] 0 of 1 [- ] process > FASTQC - [- ] process > TRIMGALORE - [- ] process > BWA_MEM - [- ] process > SORT_BAM - [- ] process > MERGED_LIB_BAM - [- ] process > MERGED_LIB_BAM_FILTER - [- ] process > MERGED_LIB_BAM_REMOVE_ORPHAN - [9e/7c8147] process > CHECK_DESIGN [100%] 1 of 1, failed: 1 [- ] process > BWA_INDEX [ 0%] 0 of 1 [- ] process > MAKE_GENE_BED [ 0%] 0 of 1 [- ] process > MAKE_TSS_BED - [- ] process > MAKE_GENOME_FILTER [ 0%] 0 of 1 [- ] process > FASTQC - [- ] process > TRIMGALORE - [- ] process > BWA_MEM - [- ] process > SORT_BAM - [- ] process > MERGED_LIB_BAM - [- ] process > MERGED_LIB_BAM_FILTER - [- ] process > MERGED_LIB_BAM_REMOVE_ORPHAN - [- ] process > MERGED_LIB_PRESEQ - [- ] process > MERGED_LIB_PICARD_METRICS - [9e/7c8147] process > CHECK_DESIGN [100%] 1 of 1, failed: 1 [- ] process > BWA_INDEX [ 0%] 0 of 1 [- ] process > MAKE_GENE_BED [ 0%] 0 of 1 [- ] process > MAKE_TSS_BED - [- ] process > MAKE_GENOME_FILTER [ 0%] 0 of 1 [- ] process > FASTQC - [- ] process > TRIMGALORE - [- ] process > BWA_MEM - [- ] process > SORT_BAM - [- ] process > MERGED_LIB_BAM - [- ] process > MERGED_LIB_BAM_FILTER - [- ] process > MERGED_LIB_BAM_REMOVE_ORPHAN - [- ] process > MERGED_LIB_PRESEQ - [- ] process > MERGED_LIB_PICARD_METRICS - [9e/7c8147] process > CHECK_DESIGN [100%] 1 of 1, failed: 1 [- ] process > BWA_INDEX [ 0%] 0 of 1 [- ] process > MAKE_GENE_BED [ 0%] 0 of 1 [- ] process > MAKE_TSS_BED - [- ] process > MAKE_GENOME_FILTER [ 0%] 0 of 1 [- ] process > FASTQC - [- ] process > TRIMGALORE - [- ] process > BWA_MEM - [- ] process > SORT_BAM - [- ] process > MERGED_LIB_BAM - [- ] process > MERGED_LIB_BAM_FILTER - [- ] process > MERGED_LIB_BAM_REMOVE_ORPHAN - [- ] process > MERGED_LIB_PRESEQ - [- ] process > MERGED_LIB_PICARD_METRICS - [- ] process > MERGED_LIB_BIGWIG - [9e/7c8147] process > CHECK_DESIGN [100%] 1 of 1, failed: 1 [- ] process > BWA_INDEX [ 0%] 0 of 1 [- ] process > MAKE_GENE_BED [ 0%] 0 of 1 [- ] process > MAKE_TSS_BED - [- ] process > MAKE_GENOME_FILTER [ 0%] 0 of 1 [- ] process > FASTQC - [- ] process > TRIMGALORE - [- ] process > BWA_MEM - [- ] process > SORT_BAM - [- ] process > MERGED_LIB_BAM - [- ] process > MERGED_LIB_BAM_FILTER - [- ] process > MERGED_LIB_BAM_REMOVE_ORPHAN - [- ] process > MERGED_LIB_PRESEQ - [- ] process > MERGED_LIB_PICARD_METRICS - [- ] process > MERGED_LIB_BIGWIG - [- ] process > MERGED_LIB_PLOTPROFILE - [9e/7c8147] process > CHECK_DESIGN [100%] 1 of 1, failed: 1 [- ] process > BWA_INDEX [ 0%] 0 of 1 [- ] process > MAKE_GENE_BED [ 0%] 0 of 1 [- ] process > MAKE_TSS_BED - [- ] process > MAKE_GENOME_FILTER [ 0%] 0 of 1 [- ] process > FASTQC - [- ] process > TRIMGALORE - [- ] process > BWA_MEM - [- ] process > SORT_BAM - [- ] process > MERGED_LIB_BAM - [- ] process > MERGED_LIB_BAM_FILTER - [- ] process > MERGED_LIB_BAM_REMOVE_ORPHAN - [- ] process > MERGED_LIB_PRESEQ - [- ] process > MERGED_LIB_PICARD_METRICS - [- ] process > MERGED_LIB_BIGWIG - [- ] process > MERGED_LIB_PLOTPROFILE - [9e/7c8147] process > CHECK_DESIGN [100%] 1 of 1, failed: 1 [- ] process > BWA_INDEX [ 0%] 0 of 1 [- ] process > MAKE_GENE_BED [ 0%] 0 of 1 [- ] process > MAKE_TSS_BED - [- ] process > MAKE_GENOME_FILTER [ 0%] 0 of 1 [- ] process > FASTQC - [- ] process > TRIMGALORE - [- ] process > BWA_MEM - [- ] process > SORT_BAM - [- ] process > MERGED_LIB_BAM - [- ] process > MERGED_LIB_BAM_FILTER - [- ] process > MERGED_LIB_BAM_REMOVE_ORPHAN - [- ] process > MERGED_LIB_PRESEQ - [- ] process > MERGED_LIB_PICARD_METRICS - [- ] process > MERGED_LIB_BIGWIG - [- ] process > MERGED_LIB_PLOTPROFILE - [- ] process > MERGED_LIB_PLOTFINGERPRINT - [9e/7c8147] process > CHECK_DESIGN [100%] 1 of 1, failed: 1 [- ] process > BWA_INDEX [ 0%] 0 of 1 [- ] process > MAKE_GENE_BED [ 0%] 0 of 1 [- ] process > MAKE_TSS_BED - [- ] process > MAKE_GENOME_FILTER [ 0%] 0 of 1 [- ] process > FASTQC - [- ] process > TRIMGALORE - [- ] process > BWA_MEM - [- ] process > SORT_BAM - [- ] process > MERGED_LIB_BAM - [- ] process > MERGED_LIB_BAM_FILTER - [- ] process > MERGED_LIB_BAM_REMOVE_ORPHAN - [- ] process > MERGED_LIB_PRESEQ - [- ] process > MERGED_LIB_PICARD_METRICS - [- ] process > MERGED_LIB_BIGWIG - [- ] process > MERGED_LIB_PLOTPROFILE - [- ] process > MERGED_LIB_PLOTFINGERPRINT - [- ] process > MERGED_LIB_MACS2 - [- ] process > MERGED_LIB_MACS2_ANNOTATE - [- ] process > MERGED_LIB_MACS2_QC - [- ] process > MERGED_LIB_CONSENSUS - [- ] process > MERGED_LIB_CONSENSUS_ANNOTATE - [- ] process > MERGED_LIB_CONSENSUS_COUNTS - [- ] process > MERGED_LIB_CONSENSUS_DESEQ2 - [- ] process > MERGED_LIB_ATAQV - [- ] process > MERGED_LIB_ATAQV_MKARV - [- ] process > MERGED_REP_BAM - [- ] process > MERGED_REP_BIGWIG - [- ] process > MERGED_REP_MACS2 - [- ] process > MERGED_REP_MACS2_ANNOTATE - [- ] process > MERGED_REP_MACS2_QC - [- ] process > MERGED_REP_CONSENSUS - [- ] process > MERGED_REP_CONSENSUS_ANNOTATE - [- ] process > MERGED_REP_CONSENSUS_COUNTS - [- ] process > MERGED_REP_CONSENSUS_DESEQ2 - [- ] process > IGV - [- ] process > get_software_versions [ 0%] 0 of 1 [- ] process > MULTIQC - [- ] process > output_documentation [ 0%] 0 of 1 -[nf-core/atacseq] Pipeline completed with errors- Error executing process > 'CHECK_DESIGN (design.csv)'

Caused by: Failed to submit process to grid scheduler for execution

Command executed:

qsub -N nf-CHECK_DESIGN .command.run

Command exit status: 32

Command output: qsub: [ncpus] must be in the -lselect

Work dir: /rds/general/user/bms20/ephemeral/tmp/9e/7c81474eb7833b3a99f3a7a8d97baf

Tip: when you have fixed the problem you can continue the execution adding the option -resume to the run command line```

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bschilder commented 3 years ago

That would appear to be the case, but I'm able to run this nf-core/atacseq pipeline fine with our CUT&TAG data. Here' the config I'm currently using (modified from Combiz's).

-bash-4.2$ cat ~/.nextflow/config 

//Profile config names for nf-core/configs

params {
  // Config Params
  config_profile_description = 'Imperial College London - DRI - HPC Profile -- provided by nf-core/configs.'
  config_profile_contact = 'Combiz Khozoie (c.khozoie@imperial.ac.uk)'
  config_profile_url = 'http://www.github.com/combiz/scFlow'

  // Resources
  max_memory = 640.GB
  max_cpus = 32
  max_time = 168.h

  // Analysis Resource Params
  ctd_folder = "/rds/general/user/$USER/projects/ukdrmultiomicsproject/live/Analyses/scFlowResources/refs/ctd"
  ensembl_mappings = "/rds/general/user/$USER/projects/ukdrmultiomicsproject/live/Analyses/scFlowResources/src/ensembl-ids/ensembl_mappings.tsv"

}

executor {
    $pbspro {
        queueSize = 50
    }

    $local {
          cpus = 2
        queueSize = 1
        memory = '32 GB'
    }
}

singularity {
  enabled = true
  autoMounts = true
  cacheDir = "/rds/general/user/$USER/projects/neurogenomics-lab/live/.singularity-cache"
  runOptions = "-B /rds/,/rdsgpfs/,/rds/general/user/$USER/ephemeral/tmp/:/tmp,/rds/general/user/$USER/ephemeral/tmp/:/var/tmp"

}

process {
  // NOTE: queue lines are commented out bc you first need to request access to these special queues from RCS.
  // beforeScript = 'module load singularity'
  executor = 'pbspro'
  queue = 'pqmedbio-tput'

  //queue = 'med-bio' !! this is an alias and shouldn't be used

  withLabel:process_large {
    queue = 'pqmedbio-large'
   }
  //withLabel:process_high {
  //  cpus = { check_max( 32 * task.attempt, 'cpus' ) }
  //  memory = { check_max( 62.GB * task.attempt, 'memory' ) }
  //  time = { check_max( 24.h * task.attempt, 'time' ) }
  //}

}

workDir = "/rds/general/user/$USER/ephemeral/tmp"
NathanSkene commented 3 years ago

I'd suggest asking in the nf-core #help channel

On Thu, 21 Jan 2021 at 11:40, Brian M. Schilder notifications@github.com wrote:

This email from notifications@github.com originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders list https://spam.ic.ac.uk/SpamConsole/Senders.aspx to disable email stamping for this address.

That would appear to be the case, but I'm able to run this nf-core/atacseq pipeline fine with our CUT&TAG data. Here' the config I'm currently using (modified from Combiz's).

-bash-4.2$ cat ~/.nextflow/config

//Profile config names for nf-core/configs

params { // Config Params config_profile_description = 'Imperial College London - DRI - HPC Profile -- provided by nf-core/configs.' config_profile_contact = 'Combiz Khozoie (c.khozoie@imperial.ac.uk)' config_profile_url = 'http://www.github.com/combiz/scFlow'

// Resources max_memory = 640.GB max_cpus = 32 max_time = 168.h

// Analysis Resource Params ctd_folder = "/rds/general/user/$USER/projects/ukdrmultiomicsproject/live/Analyses/scFlowResources/refs/ctd" ensembl_mappings = "/rds/general/user/$USER/projects/ukdrmultiomicsproject/live/Analyses/scFlowResources/src/ensembl-ids/ensembl_mappings.tsv"

}

executor { $pbspro { queueSize = 50 }

$local {
      cpus = 2
    queueSize = 1
    memory = '32 GB'
}

}

singularity { enabled = true autoMounts = true cacheDir = "/rds/general/user/$USER/projects/neurogenomics-lab/live/.singularity-cache" runOptions = "-B /rds/,/rdsgpfs/,/rds/general/user/$USER/ephemeral/tmp/:/tmp,/rds/general/user/$USER/ephemeral/tmp/:/var/tmp"

}

process { // NOTE: queue lines are commented out bc you first need to request access to these special queues from RCS. // beforeScript = 'module load singularity' executor = 'pbspro' queue = 'pqmedbio-tput'

//queue = 'med-bio' !! this is an alias and shouldn't be used

withLabel:process_large { queue = 'pqmedbio-large' } //withLabel:process_high { // cpus = { check_max( 32 task.attempt, 'cpus' ) } // memory = { check_max( 62.GB task.attempt, 'memory' ) } // time = { check_max( 24.h * task.attempt, 'time' ) } //}

}

workDir = "/rds/general/user/$USER/ephemeral/tmp"

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bschilder commented 3 years ago

Now posted here: https://nfcore.slack.com/archives/CE6SDBX2A/p1611230712007200