From e8a4d6f12cc657059c168c3ffeadc297a5fc495f Mon Sep 17 00:00:00 2001 From: Priyanka Surana Date: Wed, 20 Dec 2023 18:03:30 +0000 Subject: [PATCH] update docker runOptions --- btk.5617705.e | 0 btk.5617705.o | 153 ++++++++++++++++++++++++++++++++++++++++++++++++ nextflow.config | 4 +- 3 files changed, 155 insertions(+), 2 deletions(-) create mode 100644 btk.5617705.e create mode 100644 btk.5617705.o diff --git a/btk.5617705.e b/btk.5617705.e new file mode 100644 index 00000000..e69de29b diff --git a/btk.5617705.o b/btk.5617705.o new file mode 100644 index 00000000..84df51e0 --- /dev/null +++ b/btk.5617705.o @@ -0,0 +1,153 @@ +N E X T F L O W ~ version 23.10.0 +Launching `./main.nf` [intergalactic_shirley] DSL2 - revision: 2b4d066371 + + +------------------------------------------------------ + _____  _______  _ + / ____| |__ __| | | + | (___ __ _ _ __ __ _ ___ _ __  ___ | | ___ | | + \___ \ / _` | '_ \ / _` |/ _ \ '__||___|| |/ _ \| | + ____) | (_| | | | | (_| | __/ | | | (_) | |____ + |_____/ \__,_|_| |_|\__, |\___|_| |_|\___/|______| + __/ | + |___/ + sanger-tol/blobtoolkit v0.2.0 +------------------------------------------------------ +Core Nextflow options + runName : intergalactic_shirley + containerEngine : singularity + launchDir : /lustre/scratch123/tol/teams/tolit/users/ps22/pipelines/blobtoolkit + workDir : /lustre/scratch123/tol/teams/tolit/users/ps22/pipelines/blobtoolkit/work + projectDir : /lustre/scratch123/tol/teams/tolit/users/ps22/pipelines/blobtoolkit + userName : ps22 + profile : test_full,singularity,sanger + configFiles :  + +Input/output options + input : /lustre/scratch123/tol/teams/tolit/users/ps22/pipelines/blobtoolkit/assets/test_full/full_samplesheet.csv + +Reference genome options + taxon : Laetiporus sulphureus + accession : GCA_927399515.1 + fasta : https://tolit.cog.sanger.ac.uk/test-data/Laetiporus_sulphureus/assembly/release/gfLaeSulp1.1/insdc/GCA_927399515.1.fasta.gz + +Databases + busco : /lustre/scratch123/tol/resources/busco/latest + blastp : /lustre/scratch123/tol/teams/tolit/users/ps22/pipelines/blobtoolkit/assets/test_full/gfLaeSulp1.1.buscogenes.dmnd + blastx : /lustre/scratch123/tol/teams/tolit/users/ps22/pipelines/blobtoolkit/assets/test_full/gfLaeSulp1.1.buscoregions.dmnd + blastn : /lustre/scratch123/tol/teams/tolit/users/ps22/pipelines/blobtoolkit/assets/test_full/nt_gfLaeSulp1.1 + taxdump : /lustre/scratch123/tol/teams/grit/geval_pipeline/btk_databases/taxdump + +Institutional config options + config_profile_name : Full test profile + config_profile_description: Full test dataset to check pipeline function + config_profile_contact : Priyanka Surana (@priyanka-surana) + config_profile_url : https://www.sanger.ac.uk + +Max job request options + max_cpus : 64 + max_memory : 1.4 TB + max_time : 24d 20h 31m 24s + +!! Only displaying parameters that differ from the pipeline defaults !! +------------------------------------------------------ +If you use sanger-tol/blobtoolkit for your analysis please cite: + +* The pipeline + https://doi.org/10.5281/zenodo.7949058 + +* The nf-core framework + https://doi.org/10.1038/s41587-020-0439-x + +* Software dependencies + https://github.com/sanger-tol/blobtoolkit/blob/master/CITATIONS.md + +WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition +WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition +WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition +WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition +[27/c1d5d0] Submitted process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:BUSCO_DIAMOND:GOAT_TAXONSEARCH (GCA_927399515.1) +[47/dca135] Submitted process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:INPUT_CHECK:SAMPLESHEET_CHECK (full_samplesheet.csv) +[de/9ddad2] Submitted process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:PREPARE_GENOME:GUNZIP (GCA_927399515.1.fasta.gz) +[7b/523254] Submitted process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:BLOBTOOLKIT_CONFIG (GCA_927399515.1) +[29/c21249] Submitted process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:COVERAGE_STATS:FASTAWINDOWS (GCA_927399515.1) +[75/3bf10e] Submitted process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:BUSCO_DIAMOND:BUSCO (GCA_927399515.1_eukaryota_odb10) +[57/759cc9] Submitted process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:BUSCO_DIAMOND:BUSCO (GCA_927399515.1_basidiomycota_odb10) +[24/74230f] Submitted process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:BUSCO_DIAMOND:BUSCO (GCA_927399515.1_agaricomycetes_odb10) +[e6/153c8c] Submitted process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:BUSCO_DIAMOND:BUSCO (GCA_927399515.1_archaea_odb10) +[6d/1a9087] Submitted process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:BUSCO_DIAMOND:BUSCO (GCA_927399515.1_polyporales_odb10) +[1f/6d42a1] Submitted process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:BUSCO_DIAMOND:BUSCO (GCA_927399515.1_fungi_odb10) +[aa/e265d0] Submitted process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:BUSCO_DIAMOND:BUSCO (GCA_927399515.1_bacteria_odb10) +[b4/187697] Submitted process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:COVERAGE_STATS:SAMTOOLS_VIEW (gfLaeSulp1_T1) +[20/746778] Submitted process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:COVERAGE_STATS:SAMTOOLS_VIEW (gfLaeSulp1_T2) +[eb/5318dd] Submitted process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:BLOBTOOLS:BLOBTOOLKIT_METADATA (GCA_927399515.1) +[8c/01e78e] Submitted process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:COVERAGE_STATS:CREATE_BED (GCA_927399515.1) +[82/45753e] Submitted process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:COVERAGE_STATS:BLOBTOOLKIT_DEPTH (gfLaeSulp1_T2) +[08/fa648c] Submitted process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTX:BLOBTOOLKIT_CHUNK (GCA_927399515.1) +[9f/dc60f1] Submitted process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTX:DIAMOND_BLASTX (GCA_927399515.1) +[48/85111b] Submitted process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTX:BLOBTOOLKIT_UNCHUNK (GCA_927399515.1) +[48/4a0f0a] Submitted process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTN:NOHIT_LIST (GCA_927399515.1) +[1e/df75fb] Submitted process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTN:SEQTK_SUBSEQ (GCA_927399515.1.fasta) +[3f/cd0e44] Submitted process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTN:GUNZIP (GCA_927399515.1.fasta.fa.gz) +[6a/f58007] Submitted process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:BUSCO_DIAMOND:BLOBTOOLKIT_EXTRACTBUSCOS (GCA_927399515.1) +[d3/3f2ff4] Submitted process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTN:BLOBTOOLKIT_CHUNK (GCA_927399515.1) +[fb/49d287] Submitted process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:COLLATE_STATS:BLOBTOOLKIT_COUNTBUSCOS (GCA_927399515.1) +[4c/09515c] Submitted process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:BUSCO_DIAMOND:DIAMOND_BLASTP (GCA_927399515.1) +[3f/21cfeb] Submitted process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTN:BLASTN_TAXON (GCA_927399515.1) +[15/b8cd2d] Submitted process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTN:BLAST_BLASTN (GCA_927399515.1) +[e7/c38390] Submitted process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTN:BLOBTOOLKIT_UNCHUNK (GCA_927399515.1) +[71/39eacd] Submitted process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:COVERAGE_STATS:BLOBTOOLKIT_DEPTH (gfLaeSulp1_T1) +[4b/400be0] Submitted process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:COLLATE_STATS:WINDOWSTATS_INPUT (GCA_927399515.1) +[60/d253c5] Submitted process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:COLLATE_STATS:BLOBTOOLKIT_WINDOWSTATS (GCA_927399515.1) +[bf/3e27ea] Submitted process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:BLOBTOOLS:BLOBTOOLKIT_CREATEBLOBDIR (GCA_927399515.1) +[a0/f38b25] Submitted process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:BLOBTOOLS:BLOBTOOLKIT_UPDATEBLOBDIR (GCA_927399515.1) +[85/f6febf] Submitted process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:VIEW:BLOBTOOLKIT_IMAGES (GCA_927399515.1_snail) +[fe/ad7967] Submitted process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:VIEW:BLOBTOOLKIT_IMAGES (GCA_927399515.1_blob) +[f6/c92dbf] Submitted process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:VIEW:BLOBTOOLKIT_IMAGES (GCA_927399515.1_cumulative) +[9f/2fa07f] Submitted process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:VIEW:BLOBTOOLKIT_SUMMARY (GCA_927399515.1) +[d8/19189e] Submitted process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:CUSTOM_DUMPSOFTWAREVERSIONS (1) +[e7/d2eedd] Submitted process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:MULTIQC +-[sanger-tol/blobtoolkit] Pipeline completed successfully- + +------------------------------------------------------------ +Sender: LSF System +Subject: Job 5617705: in cluster Done + +Job was submitted from host by user in cluster at Wed Dec 20 14:32:02 2023 +Job was executed on host(s) <2*tol-oversubscribed04>, in queue , as user in cluster at Wed Dec 20 14:32:03 2023 + was used as the home directory. + was used as the working directory. +Started at Wed Dec 20 14:32:03 2023 +Terminated at Wed Dec 20 17:07:11 2023 +Results reported at Wed Dec 20 17:07:11 2023 + +Your job looked like: + +------------------------------------------------------------ +# LSBATCH: User input +nextflow run . -profile test_full,singularity,sanger -ansi-log false +------------------------------------------------------------ + +Successfully completed. + +Resource usage summary: + + CPU time : 118.14 sec. + Max Memory : 1161 MB + Average Memory : 1131.83 MB + Total Requested Memory : 5000.00 MB + Delta Memory : 3839.00 MB + Max Swap : - + Max Processes : 9 + Max Threads : 88 + Run time : 9306 sec. + Turnaround time : 9309 sec. + +The output (if any) is above this job summary. + + + +PS: + +Read file for stderr output of this job. + diff --git a/nextflow.config b/nextflow.config index 52d9510a..98b0398c 100644 --- a/nextflow.config +++ b/nextflow.config @@ -125,10 +125,10 @@ profiles { shifter.enabled = false charliecloud.enabled = false apptainer.enabled = false - runOptions = '-u $(id -u):$(id -g)' + docker.runOptions = '-u $(id -u):$(id -g)' } arm { - docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64' + docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64' } singularity { singularity.enabled = true