update docker runOptions

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 <lsfadmin@tol-oversubscribed04>
+Subject: Job 5617705: <btk_test> in cluster <tol> Done
+
+Job <btk_test> was submitted from host <tol-1-8-3> by user <ps22> in cluster <tol> at Wed Dec 20 14:32:02 2023
+Job was executed on host(s) <2*tol-oversubscribed04>, in queue <oversubscribed>, as user <ps22> in cluster <tol> at Wed Dec 20 14:32:03 2023
+</nfs/users/nfs_p/ps22> was used as the home directory.
+</lustre/scratch123/tol/teams/tolit/users/ps22/pipelines/blobtoolkit> 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 <btk.5617705.e> for stderr output of this job.
+

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