The output (if any) follows: N E X T F L O W ~ version 23.04.1 Launching `https://github.com/nf-core/crisprseq` [hopeful_sinoussi] DSL2 - revision: 0f7bd02b40 [dev] WARN: Access to undefined parameter `monochromeLogs` -- Initialise it to a default value eg. `params.monochromeLogs = some_value` ------------------------------------------------------ ,--./,-. ___ __ __ __ ___ /,-._.--~' |\ | |__ __ / ` / \ |__) |__ } { | \| | \__, \__/ | \ |___ \`-._,-`-, `._,._,' nf-core/crisprseq v2.3.0dev-g0f7bd02 ------------------------------------------------------ Core Nextflow options revision : dev runName : hopeful_sinoussi containerEngine: singularity launchDir : /jsimonlab/projects/Deshmukh workDir : /jsimonlab/scratch/jsimon/nextflow/work projectDir : /homes8/jsimon/.nextflow/assets/nf-core/crisprseq userName : jsimon profile : standard configFiles : Input/output options input : crisprseq_samplesheet.csv outdir : Deshmukh_CRISPRscreen_etoposide_nextflow analysis : screening Screening parameters library : gRNA_annotated_geneSymbol_withID.tsv contrasts : crisprseq_contrasts.csv Reference genome options reference_fasta: /jsimonlab/genomes/hg38/GRCh38.primary_assembly.genome.fa !! Only displaying parameters that differ from the pipeline defaults !! ------------------------------------------------------ If you use nf-core/crisprseq for your analysis please cite: * The pipeline https://doi.org/10.5281/zenodo.7598496 * The nf-core framework https://doi.org/10.1038/s41587-020-0439-x * Software dependencies https://github.com/nf-core/crisprseq/blob/master/CITATIONS.md ------------------------------------------------------ [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... 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[100%] 1 of 1 ✔ [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [92/d268b6] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [ 0%] 0 of 2 [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - executor > slurm (13) [76/fb3df4] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 9 of 9 ✔ [57/f7c2cd] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 1 of 1 ✔ [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [ 0%] 0 of 2 [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [92/d268b6] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [81/f8f771] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [ 0%] 0 of 2 [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - executor > slurm (14) [76/fb3df4] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 9 of 9 ✔ [57/f7c2cd] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 1 of 1 ✔ [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [ 0%] 0 of 2 [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [92/d268b6] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [54/d3c636] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [ 0%] 0 of 2 [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - executor > slurm (15) [76/fb3df4] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 9 of 9 ✔ [57/f7c2cd] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 1 of 1 ✔ [53/126a78] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [ 0%] 0 of 2 [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [92/d268b6] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [54/d3c636] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [ 0%] 0 of 2 [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - executor > slurm (16) [76/fb3df4] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 9 of 9 ✔ [57/f7c2cd] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 1 of 1 ✔ [c9/a864f4] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [ 0%] 0 of 2 [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [92/d268b6] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [54/d3c636] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [ 0%] 0 of 2 [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - executor > slurm (16) [76/fb3df4] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 9 of 9 ✔ [57/f7c2cd] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 1 of 1 ✔ [c9/a864f4] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [ 0%] 0 of 2 [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [92/d268b6] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [54/d3c636] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [ 0%] 0 of 2 [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - executor > slurm (16) [76/fb3df4] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 9 of 9 ✔ [57/f7c2cd] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 1 of 1 ✔ [c9/a864f4] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [ 0%] 0 of 2 [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [92/d268b6] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [54/d3c636] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [ 0%] 0 of 2 [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - executor > slurm (16) [76/fb3df4] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 9 of 9 ✔ [57/f7c2cd] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 1 of 1 ✔ [c9/a864f4] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [92/d268b6] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [54/d3c636] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [ 0%] 0 of 2 [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - executor > slurm (16) [76/fb3df4] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 9 of 9 ✔ [57/f7c2cd] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 1 of 1 ✔ [c9/a864f4] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [ 0%] 0 of 2 [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [92/d268b6] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [54/d3c636] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [ 0%] 0 of 2 [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - executor > slurm (17) [76/fb3df4] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 9 of 9 ✔ [57/f7c2cd] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 1 of 1 ✔ [c9/a864f4] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [14/ec3d19] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [ 0%] 0 of 2 [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [92/d268b6] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [54/d3c636] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [ 0%] 0 of 2 [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - executor > slurm (18) [76/fb3df4] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 9 of 9 ✔ [57/f7c2cd] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 1 of 1 ✔ [c9/a864f4] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [0b/a038f8] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [ 0%] 0 of 2 [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [92/d268b6] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [54/d3c636] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [ 0%] 0 of 2 [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - executor > slurm (18) [76/fb3df4] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 9 of 9 ✔ [57/f7c2cd] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 1 of 1 ✔ [c9/a864f4] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [0b/a038f8] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [ 0%] 0 of 2 [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [92/d268b6] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [54/d3c636] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [ 0%] 0 of 2 [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - executor > slurm (18) [76/fb3df4] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 9 of 9 ✔ [57/f7c2cd] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 1 of 1 ✔ [c9/a864f4] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [0b/a038f8] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [92/d268b6] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [54/d3c636] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [ 0%] 0 of 2 [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - executor > slurm (19) [76/fb3df4] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 9 of 9 ✔ [57/f7c2cd] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 1 of 1 ✔ [c9/a864f4] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [0b/a038f8] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [e6/36035f] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [ 0%] 0 of 2 [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [92/d268b6] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [54/d3c636] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [ 0%] 0 of 2 [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - executor > slurm (20) [76/fb3df4] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 9 of 9 ✔ [57/f7c2cd] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 1 of 1 ✔ [c9/a864f4] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [0b/a038f8] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [d1/27ea4b] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [ 0%] 0 of 2 [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [92/d268b6] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [54/d3c636] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [ 0%] 0 of 2 [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - executor > slurm (20) [76/fb3df4] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 9 of 9 ✔ [57/f7c2cd] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 1 of 1 ✔ [c9/a864f4] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [0b/a038f8] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [d1/27ea4b] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [ 0%] 0 of 2 [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [92/d268b6] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [54/d3c636] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [ 0%] 0 of 2 [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - executor > slurm (20) [76/fb3df4] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 9 of 9 ✔ [57/f7c2cd] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 1 of 1 ✔ [c9/a864f4] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [0b/a038f8] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [e6/36035f] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [ 50%] 1 of 2 [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [92/d268b6] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [54/d3c636] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [ 0%] 0 of 2 [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - executor > slurm (20) [76/fb3df4] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 9 of 9 ✔ [57/f7c2cd] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 1 of 1 ✔ [c9/a864f4] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [0b/a038f8] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [d1/27ea4b] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [ 0%] 0 of 2 [92/d268b6] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [54/d3c636] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [ 0%] 0 of 2 [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - executor > slurm (21) [76/fb3df4] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 9 of 9 ✔ [57/f7c2cd] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 1 of 1 ✔ [c9/a864f4] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [0b/a038f8] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [d1/27ea4b] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [15/d566a2] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [ 0%] 0 of 2 [92/d268b6] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [54/d3c636] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [ 0%] 0 of 2 [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - executor > slurm (22) [76/fb3df4] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 9 of 9 ✔ [57/f7c2cd] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 1 of 1 ✔ [c9/a864f4] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [0b/a038f8] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [d1/27ea4b] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [58/cab0b1] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [ 0%] 0 of 2 [92/d268b6] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [54/d3c636] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [ 0%] 0 of 2 [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - executor > slurm (22) [76/fb3df4] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 9 of 9 ✔ [57/f7c2cd] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 1 of 1 ✔ [c9/a864f4] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [0b/a038f8] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [d1/27ea4b] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [58/cab0b1] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [ 0%] 0 of 2 [92/d268b6] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [54/d3c636] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [ 0%] 0 of 2 [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - executor > slurm (22) [76/fb3df4] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 9 of 9 ✔ [57/f7c2cd] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 1 of 1 ✔ [c9/a864f4] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [0b/a038f8] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [d1/27ea4b] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [58/cab0b1] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [92/d268b6] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [54/d3c636] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [ 0%] 0 of 2 [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - executor > slurm (22) [76/fb3df4] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 9 of 9 ✔ [57/f7c2cd] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 1 of 1 ✔ [c9/a864f4] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [0b/a038f8] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [d1/27ea4b] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [58/cab0b1] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [92/d268b6] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [81/f8f771] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [ 50%] 1 of 2 [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [ 0%] 0 of 1 [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [ 0%] 0 of 1 [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - executor > slurm (23) [76/fb3df4] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 9 of 9 ✔ [57/f7c2cd] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 1 of 1 ✔ [c9/a864f4] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [0b/a038f8] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [d1/27ea4b] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [58/cab0b1] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [92/d268b6] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [81/f8f771] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [ 50%] 1 of 2 [20/2cd6d9] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [ 0%] 0 of 1 [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [ 0%] 0 of 1 [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - executor > slurm (24) [76/fb3df4] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 9 of 9 ✔ [57/f7c2cd] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 1 of 1 ✔ [c9/a864f4] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [0b/a038f8] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [d1/27ea4b] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [58/cab0b1] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [92/d268b6] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [81/f8f771] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [ 50%] 1 of 2 [20/2cd6d9] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [ 0%] 0 of 1 [af/dbf9ef] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [ 0%] 0 of 1 [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - executor > slurm (24) [76/fb3df4] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 9 of 9 ✔ [57/f7c2cd] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 1 of 1 ✔ [c9/a864f4] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [0b/a038f8] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [d1/27ea4b] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [58/cab0b1] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [92/d268b6] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [81/f8f771] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [ 50%] 1 of 2 [20/2cd6d9] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [ 0%] 0 of 1 [af/dbf9ef] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [ 0%] 0 of 1 [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - executor > slurm (24) [76/fb3df4] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 9 of 9 ✔ [57/f7c2cd] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 1 of 1 ✔ [c9/a864f4] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [0b/a038f8] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [d1/27ea4b] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [58/cab0b1] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [92/d268b6] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [54/d3c636] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [20/2cd6d9] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [ 0%] 0 of 2 [af/dbf9ef] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [ 0%] 0 of 2 [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - executor > slurm (24) [76/fb3df4] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 9 of 9 ✔ [57/f7c2cd] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 1 of 1 ✔ [c9/a864f4] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [0b/a038f8] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [d1/27ea4b] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [58/cab0b1] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [92/d268b6] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [54/d3c636] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [20/2cd6d9] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [ 0%] 0 of 2 [af/dbf9ef] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [ 50%] 1 of 2 [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - executor > slurm (25) [76/fb3df4] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 9 of 9 ✔ [57/f7c2cd] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 1 of 1 ✔ [c9/a864f4] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [0b/a038f8] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [d1/27ea4b] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [58/cab0b1] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [92/d268b6] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [54/d3c636] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [20/2cd6d9] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [ 0%] 0 of 2 [2e/7bad33] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [ 50%] 1 of 2 [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - executor > slurm (26) [76/fb3df4] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 9 of 9 ✔ [57/f7c2cd] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 1 of 1 ✔ [c9/a864f4] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [0b/a038f8] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [d1/27ea4b] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [58/cab0b1] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [92/d268b6] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [54/d3c636] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [5b/f8c309] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [ 0%] 0 of 2 [2e/7bad33] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [ 50%] 1 of 2 [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - executor > slurm (26) [76/fb3df4] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 9 of 9 ✔ [57/f7c2cd] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 1 of 1 ✔ [c9/a864f4] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [0b/a038f8] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [d1/27ea4b] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [58/cab0b1] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [92/d268b6] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [54/d3c636] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [5b/f8c309] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [ 0%] 0 of 2 [2e/7bad33] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [ 50%] 1 of 2 [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - executor > slurm (26) [76/fb3df4] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 9 of 9 ✔ [57/f7c2cd] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 1 of 1 ✔ [c9/a864f4] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [0b/a038f8] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [d1/27ea4b] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [58/cab0b1] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [92/d268b6] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [54/d3c636] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [5b/f8c309] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [ 0%] 0 of 2 [2e/7bad33] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - executor > slurm (26) [76/fb3df4] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 9 of 9 ✔ [57/f7c2cd] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 1 of 1 ✔ [c9/a864f4] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [0b/a038f8] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [d1/27ea4b] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [58/cab0b1] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [92/d268b6] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [54/d3c636] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [5b/f8c309] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [ 0%] 0 of 2 [2e/7bad33] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - ERROR ~ Error executing process > 'NFCORE_CRISPRSEQ:CRISPRSEQ_SCREENING:MAGECK_FLUTEMLE_CONTRASTS (treated_5hr_vs_control)' Caused by: Process `NFCORE_CRISPRSEQ:CRISPRSEQ_SCREENING:MAGECK_FLUTEMLE_CONTRASTS (treated_5hr_vs_control)` terminated with an error exit status (1) Command executed [/homes8/jsimon/.nextflow/assets/nf-core/crisprseq/templates/template_fluteMLE.R]: #!/usr/bin/env Rscript #### author: Laurence Kuhlburger #### Released under the MIT license. See git repository (https://github.com/nf-core/crisprseq) for full license text. #### #### graphs mageck MLE library(MAGeCKFlute) library(clusterProfiler) library(ggplot2) library(pathview) options(ggrepel.max.overlaps = Inf) mle <- read.table("treated_5hr_vs_control.gene_summary.txt", header = TRUE, sep = " ", stringsAsFactors = FALSE) if("treated_5hr_vs_control" == "day0") { beta_strings <- grep("\\.beta", colnames(mle), value = TRUE) before_beta <- sub("\\.beta.*", "", beta_strings) unique_strings <- unique(before_beta) for(i in unique_strings) { FluteMLE(mle, treatname= i, proj=i, pathview.top=5) } } else { beta_strings <- grep("\\.beta", colnames(mle), value = TRUE) before_beta <- sub("\\.beta.*", "", beta_strings) unique_strings <- unique(before_beta) for(i in unique_strings) { FluteMLE(mle, treatname= i, proj=i, , pathview.top=5) } } version_file_path <- "versions.yml" version_flute <- paste(unlist(packageVersion("MAGeCKFlute")), collapse = ".") version_ggplot <- paste(unlist(packageVersion("ggplot2")), collapse = ".") version_clusterprofiler <- paste(unlist(packageVersion("clusterProfiler")), collapse = ".") version_pathview <- paste(unlist(packageVersion("pathview")), collapse = ".") f <- file(version_file_path, "w") writeLines('"NFCORE_CRISPRSEQ:CRISPRSEQ_SCREENING:MAGECK_FLUTEMLE_CONTRASTS":', f) writeLines(" MAGeCKFlute: ", f, sep = "") writeLines(version_flute, f) writeLines(" ggplot2: ", f, sep = "") writeLines(version_ggplot, f) writeLines(" clusterProfiler: ", f, sep = "") writeLines(version_clusterprofiler, f) writeLines(" pathview: ", f, sep = "") writeLines(version_pathview, f) close(f) Command exit status: 1 Command output: (empty) Command error: 36 genes have duplicate Entrez IDs: HIST1H2BC, HIST1H2BG, HIST1H2BF, PLEKHG7, DEC1, HIST1H2BI, MUM1, KIAA1107, AKAP2, NEBL, HN1L, SLC35E2, WWTR1, NOV, DCDC1, C10orf12, ZASP, HYAL1, MICALCL, QARS, LOXL2, CC2D2B, GIF, RAB34, C16orf47, TMEM257, C17orf47, ARHGAP42, MARS, TXNRD3, RRM2, HIST1H2BE, SEPT6, SEM1, C9orf47, DUPD1 snapshotDate(): 2022-10-31 see ?depmap and browseVignettes('depmap') for documentation loading from cache snapshotDate(): 2022-10-31 see ?depmap and browseVignettes('depmap') for documentation loading from cache snapshotDate(): 2022-10-31 see ?depmap and browseVignettes('depmap') for documentation loading from cache snapshotDate(): 2022-10-31 see ?depmap and browseVignettes('depmap') for documentation loading from cache 2024-07-03 19:14:43 # Enrichment analysis of Positive and Negative selected genes ... 2024-07-03 19:14:43 # Running KEGG+REACTOME+GOBP+Complex enrichment analysis 446 genes are mapped ... 2024-07-03 19:14:52 # Running KEGG+REACTOME+GOBP+Complex enrichment analysis 330 genes are mapped ... 2024-07-03 19:15:07 # Starting plot kegg pathways for Group A Info: Downloading xml files for hsa04115, 1/1 pathways.. Info: Downloading png files for hsa04115, 1/1 pathways.. 'select()' returned 1:1 mapping between keys and columns Info: Working in directory /jsimonlab/scratch/jsimon/nextflow/work/20/2cd6d926916e086179100326a47cbe Info: Writing image file hsa04115.pathview.multi.png Info: Downloading xml files for hsa04215, 1/1 pathways.. Info: Downloading png files for hsa04215, 1/1 pathways.. 'select()' returned 1:1 mapping between keys and columns Info: Working in directory /jsimonlab/scratch/jsimon/nextflow/work/20/2cd6d926916e086179100326a47cbe Info: Writing image file hsa04215.pathview.multi.png Info: some node width is different from others, and hence adjusted! pathview failed for hsa04215 Info: Downloading xml files for hsa05222, 1/1 pathways.. Info: Downloading png files for hsa05222, 1/1 pathways.. 'select()' returned 1:1 mapping between keys and columns Info: Working in directory /jsimonlab/scratch/jsimon/nextflow/work/20/2cd6d926916e086179100326a47cbe Info: Writing image file hsa05222.pathview.multi.png Info: Downloading xml files for hsa04210, 1/1 pathways.. Info: Downloading png files for hsa04210, 1/1 pathways.. 'select()' returned 1:1 mapping between keys and columns Info: Working in directory /jsimonlab/scratch/jsimon/nextflow/work/20/2cd6d926916e086179100326a47cbe Info: Writing image file hsa04210.pathview.multi.png Info: Downloading xml files for hsa01524, 1/1 pathways.. Info: Downloading png files for hsa01524, 1/1 pathways.. 'select()' returned 1:1 mapping between keys and columns Info: Working in directory /jsimonlab/scratch/jsimon/nextflow/work/20/2cd6d926916e086179100326a47cbe Info: Writing image file hsa01524.pathview.multi.png Error in png::readPNG(figure, native = FALSE) : file is not in PNG format Calls: FluteMLE ... arrangePathview -> lapply -> FUN -> -> In addition: There were 12 warnings (use warnings() to see them) Execution halted Work dir: /jsimonlab/scratch/jsimon/nextflow/work/20/2cd6d926916e086179100326a47cbe Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out` -- Check '.nextflow.log' file for details executor > slurm (26) [76/fb3df4] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 9 of 9 ✔ [57/f7c2cd] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 1 of 1 ✔ [c9/a864f4] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [0b/a038f8] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [d1/27ea4b] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [58/cab0b1] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [92/d268b6] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [54/d3c636] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [20/2cd6d9] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [ 50%] 1 of 2, failed: 1 [2e/7bad33] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - Execution cancelled -- Finishing pending tasks before exit ERROR ~ Error executing process > 'NFCORE_CRISPRSEQ:CRISPRSEQ_SCREENING:MAGECK_FLUTEMLE_CONTRASTS (treated_5hr_vs_control)' Caused by: Process `NFCORE_CRISPRSEQ:CRISPRSEQ_SCREENING:MAGECK_FLUTEMLE_CONTRASTS (treated_5hr_vs_control)` terminated with an error exit status (1) Command executed [/homes8/jsimon/.nextflow/assets/nf-core/crisprseq/templates/template_fluteMLE.R]: #!/usr/bin/env Rscript #### author: Laurence Kuhlburger #### Released under the MIT license. See git repository (https://github.com/nf-core/crisprseq) for full license text. #### #### graphs mageck MLE library(MAGeCKFlute) library(clusterProfiler) library(ggplot2) library(pathview) options(ggrepel.max.overlaps = Inf) mle <- read.table("treated_5hr_vs_control.gene_summary.txt", header = TRUE, sep = " ", stringsAsFactors = FALSE) if("treated_5hr_vs_control" == "day0") { beta_strings <- grep("\\.beta", colnames(mle), value = TRUE) before_beta <- sub("\\.beta.*", "", beta_strings) unique_strings <- unique(before_beta) for(i in unique_strings) { FluteMLE(mle, treatname= i, proj=i, pathview.top=5) } } else { beta_strings <- grep("\\.beta", colnames(mle), value = TRUE) before_beta <- sub("\\.beta.*", "", beta_strings) unique_strings <- unique(before_beta) for(i in unique_strings) { FluteMLE(mle, treatname= i, proj=i, , pathview.top=5) } } version_file_path <- "versions.yml" version_flute <- paste(unlist(packageVersion("MAGeCKFlute")), collapse = ".") version_ggplot <- paste(unlist(packageVersion("ggplot2")), collapse = ".") version_clusterprofiler <- paste(unlist(packageVersion("clusterProfiler")), collapse = ".") version_pathview <- paste(unlist(packageVersion("pathview")), collapse = ".") f <- file(version_file_path, "w") writeLines('"NFCORE_CRISPRSEQ:CRISPRSEQ_SCREENING:MAGECK_FLUTEMLE_CONTRASTS":', f) writeLines(" MAGeCKFlute: ", f, sep = "") writeLines(version_flute, f) writeLines(" ggplot2: ", f, sep = "") writeLines(version_ggplot, f) writeLines(" clusterProfiler: ", f, sep = "") writeLines(version_clusterprofiler, f) writeLines(" pathview: ", f, sep = "") writeLines(version_pathview, f) close(f) Command exit status: 1 Command output: (empty) Command error: 36 genes have duplicate Entrez IDs: HIST1H2BC, HIST1H2BG, HIST1H2BF, PLEKHG7, DEC1, HIST1H2BI, MUM1, KIAA1107, AKAP2, NEBL, HN1L, SLC35E2, WWTR1, NOV, DCDC1, C10orf12, ZASP, HYAL1, MICALCL, QARS, LOXL2, CC2D2B, GIF, RAB34, C16orf47, TMEM257, C17orf47, ARHGAP42, MARS, TXNRD3, RRM2, HIST1H2BE, SEPT6, SEM1, C9orf47, DUPD1 snapshotDate(): 2022-10-31 see ?depmap and browseVignettes('depmap') for documentation loading from cache snapshotDate(): 2022-10-31 see ?depmap and browseVignettes('depmap') for documentation loading from cache snapshotDate(): 2022-10-31 see ?depmap and browseVignettes('depmap') for documentation loading from cache snapshotDate(): 2022-10-31 see ?depmap and browseVignettes('depmap') for documentation loading from cache 2024-07-03 19:14:43 # Enrichment analysis of Positive and Negative selected genes ... 2024-07-03 19:14:43 # Running KEGG+REACTOME+GOBP+Complex enrichment analysis 446 genes are mapped ... 2024-07-03 19:14:52 # Running KEGG+REACTOME+GOBP+Complex enrichment analysis 330 genes are mapped ... 2024-07-03 19:15:07 # Starting plot kegg pathways for Group A Info: Downloading xml files for hsa04115, 1/1 pathways.. Info: Downloading png files for hsa04115, 1/1 pathways.. 'select()' returned 1:1 mapping between keys and columns Info: Working in directory /jsimonlab/scratch/jsimon/nextflow/work/20/2cd6d926916e086179100326a47cbe Info: Writing image file hsa04115.pathview.multi.png Info: Downloading xml files for hsa04215, 1/1 pathways.. Info: Downloading png files for hsa04215, 1/1 pathways.. 'select()' returned 1:1 mapping between keys and columns Info: Working in directory /jsimonlab/scratch/jsimon/nextflow/work/20/2cd6d926916e086179100326a47cbe Info: Writing image file hsa04215.pathview.multi.png Info: some node width is different from others, and hence adjusted! pathview failed for hsa04215 Info: Downloading xml files for hsa05222, 1/1 pathways.. Info: Downloading png files for hsa05222, 1/1 pathways.. 'select()' returned 1:1 mapping between keys and columns Info: Working in directory /jsimonlab/scratch/jsimon/nextflow/work/20/2cd6d926916e086179100326a47cbe Info: Writing image file hsa05222.pathview.multi.png Info: Downloading xml files for hsa04210, 1/1 pathways.. Info: Downloading png files for hsa04210, 1/1 pathways.. 'select()' returned 1:1 mapping between keys and columns Info: Working in directory /jsimonlab/scratch/jsimon/nextflow/work/20/2cd6d926916e086179100326a47cbe Info: Writing image file hsa04210.pathview.multi.png Info: Downloading xml files for hsa01524, 1/1 pathways.. Info: Downloading png files for hsa01524, 1/1 pathways.. 'select()' returned 1:1 mapping between keys and columns Info: Working in directory /jsimonlab/scratch/jsimon/nextflow/work/20/2cd6d926916e086179100326a47cbe Info: Writing image file hsa01524.pathview.multi.png Error in png::readPNG(figure, native = FALSE) : file is not in PNG format Calls: FluteMLE ... arrangePathview -> lapply -> FUN -> -> In addition: There were 12 warnings (use warnings() to see them) Execution halted Work dir: /jsimonlab/scratch/jsimon/nextflow/work/20/2cd6d926916e086179100326a47cbe Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out` -- Check '.nextflow.log' file for details ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting -- Check '.nextflow.log' file for details executor > slurm (26) [76/fb3df4] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 9 of 9 ✔ [57/f7c2cd] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 1 of 1 ✔ [c9/a864f4] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [0b/a038f8] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [d1/27ea4b] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [58/cab0b1] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [92/d268b6] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [54/d3c636] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [20/2cd6d9] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [ 50%] 1 of 2, failed: 1 [2e/7bad33] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - Execution cancelled -- Finishing pending tasks before exit ERROR ~ Error executing process > 'NFCORE_CRISPRSEQ:CRISPRSEQ_SCREENING:MAGECK_FLUTEMLE_CONTRASTS (treated_5hr_vs_control)' Caused by: Process `NFCORE_CRISPRSEQ:CRISPRSEQ_SCREENING:MAGECK_FLUTEMLE_CONTRASTS (treated_5hr_vs_control)` terminated with an error exit status (1) Command executed [/homes8/jsimon/.nextflow/assets/nf-core/crisprseq/templates/template_fluteMLE.R]: #!/usr/bin/env Rscript #### author: Laurence Kuhlburger #### Released under the MIT license. See git repository (https://github.com/nf-core/crisprseq) for full license text. #### #### graphs mageck MLE library(MAGeCKFlute) library(clusterProfiler) library(ggplot2) library(pathview) options(ggrepel.max.overlaps = Inf) mle <- read.table("treated_5hr_vs_control.gene_summary.txt", header = TRUE, sep = " ", stringsAsFactors = FALSE) if("treated_5hr_vs_control" == "day0") { beta_strings <- grep("\\.beta", colnames(mle), value = TRUE) before_beta <- sub("\\.beta.*", "", beta_strings) unique_strings <- unique(before_beta) for(i in unique_strings) { FluteMLE(mle, treatname= i, proj=i, pathview.top=5) } } else { beta_strings <- grep("\\.beta", colnames(mle), value = TRUE) before_beta <- sub("\\.beta.*", "", beta_strings) unique_strings <- unique(before_beta) for(i in unique_strings) { FluteMLE(mle, treatname= i, proj=i, , pathview.top=5) } } version_file_path <- "versions.yml" version_flute <- paste(unlist(packageVersion("MAGeCKFlute")), collapse = ".") version_ggplot <- paste(unlist(packageVersion("ggplot2")), collapse = ".") version_clusterprofiler <- paste(unlist(packageVersion("clusterProfiler")), collapse = ".") version_pathview <- paste(unlist(packageVersion("pathview")), collapse = ".") f <- file(version_file_path, "w") writeLines('"NFCORE_CRISPRSEQ:CRISPRSEQ_SCREENING:MAGECK_FLUTEMLE_CONTRASTS":', f) writeLines(" MAGeCKFlute: ", f, sep = "") writeLines(version_flute, f) writeLines(" ggplot2: ", f, sep = "") writeLines(version_ggplot, f) writeLines(" clusterProfiler: ", f, sep = "") writeLines(version_clusterprofiler, f) writeLines(" pathview: ", f, sep = "") writeLines(version_pathview, f) close(f) Command exit status: 1 Command output: (empty) Command error: 36 genes have duplicate Entrez IDs: HIST1H2BC, HIST1H2BG, HIST1H2BF, PLEKHG7, DEC1, HIST1H2BI, MUM1, KIAA1107, AKAP2, NEBL, HN1L, SLC35E2, WWTR1, NOV, DCDC1, C10orf12, ZASP, HYAL1, MICALCL, QARS, LOXL2, CC2D2B, GIF, RAB34, C16orf47, TMEM257, C17orf47, ARHGAP42, MARS, TXNRD3, RRM2, HIST1H2BE, SEPT6, SEM1, C9orf47, DUPD1 snapshotDate(): 2022-10-31 see ?depmap and browseVignettes('depmap') for documentation loading from cache snapshotDate(): 2022-10-31 see ?depmap and browseVignettes('depmap') for documentation loading from cache snapshotDate(): 2022-10-31 see ?depmap and browseVignettes('depmap') for documentation loading from cache snapshotDate(): 2022-10-31 see ?depmap and browseVignettes('depmap') for documentation loading from cache 2024-07-03 19:14:43 # Enrichment analysis of Positive and Negative selected genes ... 2024-07-03 19:14:43 # Running KEGG+REACTOME+GOBP+Complex enrichment analysis 446 genes are mapped ... 2024-07-03 19:14:52 # Running KEGG+REACTOME+GOBP+Complex enrichment analysis 330 genes are mapped ... 2024-07-03 19:15:07 # Starting plot kegg pathways for Group A Info: Downloading xml files for hsa04115, 1/1 pathways.. Info: Downloading png files for hsa04115, 1/1 pathways.. 'select()' returned 1:1 mapping between keys and columns Info: Working in directory /jsimonlab/scratch/jsimon/nextflow/work/20/2cd6d926916e086179100326a47cbe Info: Writing image file hsa04115.pathview.multi.png Info: Downloading xml files for hsa04215, 1/1 pathways.. Info: Downloading png files for hsa04215, 1/1 pathways.. 'select()' returned 1:1 mapping between keys and columns Info: Working in directory /jsimonlab/scratch/jsimon/nextflow/work/20/2cd6d926916e086179100326a47cbe Info: Writing image file hsa04215.pathview.multi.png Info: some node width is different from others, and hence adjusted! pathview failed for hsa04215 Info: Downloading xml files for hsa05222, 1/1 pathways.. Info: Downloading png files for hsa05222, 1/1 pathways.. 'select()' returned 1:1 mapping between keys and columns Info: Working in directory /jsimonlab/scratch/jsimon/nextflow/work/20/2cd6d926916e086179100326a47cbe Info: Writing image file hsa05222.pathview.multi.png Info: Downloading xml files for hsa04210, 1/1 pathways.. Info: Downloading png files for hsa04210, 1/1 pathways.. 'select()' returned 1:1 mapping between keys and columns Info: Working in directory /jsimonlab/scratch/jsimon/nextflow/work/20/2cd6d926916e086179100326a47cbe Info: Writing image file hsa04210.pathview.multi.png Info: Downloading xml files for hsa01524, 1/1 pathways.. Info: Downloading png files for hsa01524, 1/1 pathways.. 'select()' returned 1:1 mapping between keys and columns Info: Working in directory /jsimonlab/scratch/jsimon/nextflow/work/20/2cd6d926916e086179100326a47cbe Info: Writing image file hsa01524.pathview.multi.png Error in png::readPNG(figure, native = FALSE) : file is not in PNG format Calls: FluteMLE ... arrangePathview -> lapply -> FUN -> -> In addition: There were 12 warnings (use warnings() to see them) Execution halted Work dir: /jsimonlab/scratch/jsimon/nextflow/work/20/2cd6d926916e086179100326a47cbe Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out` -- Check '.nextflow.log' file for details ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting -- Check '.nextflow.log' file for details executor > slurm (26) [76/fb3df4] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 9 of 9 ✔ [57/f7c2cd] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 1 of 1 ✔ [c9/a864f4] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [0b/a038f8] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [d1/27ea4b] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [58/cab0b1] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [92/d268b6] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [54/d3c636] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [5b/f8c309] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2, failed: 2 ✘ [2e/7bad33] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - -[nf-core/crisprseq] Pipeline completed with errors- ERROR ~ Error executing process > 'NFCORE_CRISPRSEQ:CRISPRSEQ_SCREENING:MAGECK_FLUTEMLE_CONTRASTS (treated_5hr_vs_control)' Caused by: Process `NFCORE_CRISPRSEQ:CRISPRSEQ_SCREENING:MAGECK_FLUTEMLE_CONTRASTS (treated_5hr_vs_control)` terminated with an error exit status (1) Command executed [/homes8/jsimon/.nextflow/assets/nf-core/crisprseq/templates/template_fluteMLE.R]: #!/usr/bin/env Rscript #### author: Laurence Kuhlburger #### Released under the MIT license. See git repository (https://github.com/nf-core/crisprseq) for full license text. #### #### graphs mageck MLE library(MAGeCKFlute) library(clusterProfiler) library(ggplot2) library(pathview) options(ggrepel.max.overlaps = Inf) mle <- read.table("treated_5hr_vs_control.gene_summary.txt", header = TRUE, sep = " ", stringsAsFactors = FALSE) if("treated_5hr_vs_control" == "day0") { beta_strings <- grep("\\.beta", colnames(mle), value = TRUE) before_beta <- sub("\\.beta.*", "", beta_strings) unique_strings <- unique(before_beta) for(i in unique_strings) { FluteMLE(mle, treatname= i, proj=i, pathview.top=5) } } else { beta_strings <- grep("\\.beta", colnames(mle), value = TRUE) before_beta <- sub("\\.beta.*", "", beta_strings) unique_strings <- unique(before_beta) for(i in unique_strings) { FluteMLE(mle, treatname= i, proj=i, , pathview.top=5) } } version_file_path <- "versions.yml" version_flute <- paste(unlist(packageVersion("MAGeCKFlute")), collapse = ".") version_ggplot <- paste(unlist(packageVersion("ggplot2")), collapse = ".") version_clusterprofiler <- paste(unlist(packageVersion("clusterProfiler")), collapse = ".") version_pathview <- paste(unlist(packageVersion("pathview")), collapse = ".") f <- file(version_file_path, "w") writeLines('"NFCORE_CRISPRSEQ:CRISPRSEQ_SCREENING:MAGECK_FLUTEMLE_CONTRASTS":', f) writeLines(" MAGeCKFlute: ", f, sep = "") writeLines(version_flute, f) writeLines(" ggplot2: ", f, sep = "") writeLines(version_ggplot, f) writeLines(" clusterProfiler: ", f, sep = "") writeLines(version_clusterprofiler, f) writeLines(" pathview: ", f, sep = "") writeLines(version_pathview, f) close(f) Command exit status: 1 Command output: (empty) Command error: 36 genes have duplicate Entrez IDs: HIST1H2BC, HIST1H2BG, HIST1H2BF, PLEKHG7, DEC1, HIST1H2BI, MUM1, KIAA1107, AKAP2, NEBL, HN1L, SLC35E2, WWTR1, NOV, DCDC1, C10orf12, ZASP, HYAL1, MICALCL, QARS, LOXL2, CC2D2B, GIF, RAB34, C16orf47, TMEM257, C17orf47, ARHGAP42, MARS, TXNRD3, RRM2, HIST1H2BE, SEPT6, SEM1, C9orf47, DUPD1 snapshotDate(): 2022-10-31 see ?depmap and browseVignettes('depmap') for documentation loading from cache snapshotDate(): 2022-10-31 see ?depmap and browseVignettes('depmap') for documentation loading from cache snapshotDate(): 2022-10-31 see ?depmap and browseVignettes('depmap') for documentation loading from cache snapshotDate(): 2022-10-31 see ?depmap and browseVignettes('depmap') for documentation loading from cache 2024-07-03 19:14:43 # Enrichment analysis of Positive and Negative selected genes ... 2024-07-03 19:14:43 # Running KEGG+REACTOME+GOBP+Complex enrichment analysis 446 genes are mapped ... 2024-07-03 19:14:52 # Running KEGG+REACTOME+GOBP+Complex enrichment analysis 330 genes are mapped ... 2024-07-03 19:15:07 # Starting plot kegg pathways for Group A Info: Downloading xml files for hsa04115, 1/1 pathways.. Info: Downloading png files for hsa04115, 1/1 pathways.. 'select()' returned 1:1 mapping between keys and columns Info: Working in directory /jsimonlab/scratch/jsimon/nextflow/work/20/2cd6d926916e086179100326a47cbe Info: Writing image file hsa04115.pathview.multi.png Info: Downloading xml files for hsa04215, 1/1 pathways.. Info: Downloading png files for hsa04215, 1/1 pathways.. 'select()' returned 1:1 mapping between keys and columns Info: Working in directory /jsimonlab/scratch/jsimon/nextflow/work/20/2cd6d926916e086179100326a47cbe Info: Writing image file hsa04215.pathview.multi.png Info: some node width is different from others, and hence adjusted! pathview failed for hsa04215 Info: Downloading xml files for hsa05222, 1/1 pathways.. Info: Downloading png files for hsa05222, 1/1 pathways.. 'select()' returned 1:1 mapping between keys and columns Info: Working in directory /jsimonlab/scratch/jsimon/nextflow/work/20/2cd6d926916e086179100326a47cbe Info: Writing image file hsa05222.pathview.multi.png Info: Downloading xml files for hsa04210, 1/1 pathways.. Info: Downloading png files for hsa04210, 1/1 pathways.. 'select()' returned 1:1 mapping between keys and columns Info: Working in directory /jsimonlab/scratch/jsimon/nextflow/work/20/2cd6d926916e086179100326a47cbe Info: Writing image file hsa04210.pathview.multi.png Info: Downloading xml files for hsa01524, 1/1 pathways.. Info: Downloading png files for hsa01524, 1/1 pathways.. 'select()' returned 1:1 mapping between keys and columns Info: Working in directory /jsimonlab/scratch/jsimon/nextflow/work/20/2cd6d926916e086179100326a47cbe Info: Writing image file hsa01524.pathview.multi.png Error in png::readPNG(figure, native = FALSE) : file is not in PNG format Calls: FluteMLE ... arrangePathview -> lapply -> FUN -> -> In addition: There were 12 warnings (use warnings() to see them) Execution halted Work dir: /jsimonlab/scratch/jsimon/nextflow/work/20/2cd6d926916e086179100326a47cbe Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out` -- Check '.nextflow.log' file for details ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting -- Check '.nextflow.log' file for details executor > slurm (26) [76/fb3df4] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 9 of 9 ✔ [57/f7c2cd] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 1 of 1 ✔ [c9/a864f4] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [0b/a038f8] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [d1/27ea4b] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [58/cab0b1] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [92/d268b6] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [54/d3c636] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [5b/f8c309] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2, failed: 2 ✘ [2e/7bad33] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... [100%] 2 of 2 ✔ [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_... - -[nf-core/crisprseq] Pipeline completed with errors- ERROR ~ Error executing process > 'NFCORE_CRISPRSEQ:CRISPRSEQ_SCREENING:MAGECK_FLUTEMLE_CONTRASTS (treated_5hr_vs_control)' Caused by: Process `NFCORE_CRISPRSEQ:CRISPRSEQ_SCREENING:MAGECK_FLUTEMLE_CONTRASTS (treated_5hr_vs_control)` terminated with an error exit status (1) Command executed [/homes8/jsimon/.nextflow/assets/nf-core/crisprseq/templates/template_fluteMLE.R]: #!/usr/bin/env Rscript #### author: Laurence Kuhlburger #### Released under the MIT license. See git repository (https://github.com/nf-core/crisprseq) for full license text. #### #### graphs mageck MLE library(MAGeCKFlute) library(clusterProfiler) library(ggplot2) library(pathview) options(ggrepel.max.overlaps = Inf) mle <- read.table("treated_5hr_vs_control.gene_summary.txt", header = TRUE, sep = " ", stringsAsFactors = FALSE) if("treated_5hr_vs_control" == "day0") { beta_strings <- grep("\\.beta", colnames(mle), value = TRUE) before_beta <- sub("\\.beta.*", "", beta_strings) unique_strings <- unique(before_beta) for(i in unique_strings) { FluteMLE(mle, treatname= i, proj=i, pathview.top=5) } } else { beta_strings <- grep("\\.beta", colnames(mle), value = TRUE) before_beta <- sub("\\.beta.*", "", beta_strings) unique_strings <- unique(before_beta) for(i in unique_strings) { FluteMLE(mle, treatname= i, proj=i, , pathview.top=5) } } version_file_path <- "versions.yml" version_flute <- paste(unlist(packageVersion("MAGeCKFlute")), collapse = ".") version_ggplot <- paste(unlist(packageVersion("ggplot2")), collapse = ".") version_clusterprofiler <- paste(unlist(packageVersion("clusterProfiler")), collapse = ".") version_pathview <- paste(unlist(packageVersion("pathview")), collapse = ".") f <- file(version_file_path, "w") writeLines('"NFCORE_CRISPRSEQ:CRISPRSEQ_SCREENING:MAGECK_FLUTEMLE_CONTRASTS":', f) writeLines(" MAGeCKFlute: ", f, sep = "") writeLines(version_flute, f) writeLines(" ggplot2: ", f, sep = "") writeLines(version_ggplot, f) writeLines(" clusterProfiler: ", f, sep = "") writeLines(version_clusterprofiler, f) writeLines(" pathview: ", f, sep = "") writeLines(version_pathview, f) close(f) Command exit status: 1 Command output: (empty) Command error: 36 genes have duplicate Entrez IDs: HIST1H2BC, HIST1H2BG, HIST1H2BF, PLEKHG7, DEC1, HIST1H2BI, MUM1, KIAA1107, AKAP2, NEBL, HN1L, SLC35E2, WWTR1, NOV, DCDC1, C10orf12, ZASP, HYAL1, MICALCL, QARS, LOXL2, CC2D2B, GIF, RAB34, C16orf47, TMEM257, C17orf47, ARHGAP42, MARS, TXNRD3, RRM2, HIST1H2BE, SEPT6, SEM1, C9orf47, DUPD1 snapshotDate(): 2022-10-31 see ?depmap and browseVignettes('depmap') for documentation loading from cache snapshotDate(): 2022-10-31 see ?depmap and browseVignettes('depmap') for documentation loading from cache snapshotDate(): 2022-10-31 see ?depmap and browseVignettes('depmap') for documentation loading from cache snapshotDate(): 2022-10-31 see ?depmap and browseVignettes('depmap') for documentation loading from cache 2024-07-03 19:14:43 # Enrichment analysis of Positive and Negative selected genes ... 2024-07-03 19:14:43 # Running KEGG+REACTOME+GOBP+Complex enrichment analysis 446 genes are mapped ... 2024-07-03 19:14:52 # Running KEGG+REACTOME+GOBP+Complex enrichment analysis 330 genes are mapped ... 2024-07-03 19:15:07 # Starting plot kegg pathways for Group A Info: Downloading xml files for hsa04115, 1/1 pathways.. Info: Downloading png files for hsa04115, 1/1 pathways.. 'select()' returned 1:1 mapping between keys and columns Info: Working in directory /jsimonlab/scratch/jsimon/nextflow/work/20/2cd6d926916e086179100326a47cbe Info: Writing image file hsa04115.pathview.multi.png Info: Downloading xml files for hsa04215, 1/1 pathways.. Info: Downloading png files for hsa04215, 1/1 pathways.. 'select()' returned 1:1 mapping between keys and columns Info: Working in directory /jsimonlab/scratch/jsimon/nextflow/work/20/2cd6d926916e086179100326a47cbe Info: Writing image file hsa04215.pathview.multi.png Info: some node width is different from others, and hence adjusted! pathview failed for hsa04215 Info: Downloading xml files for hsa05222, 1/1 pathways.. Info: Downloading png files for hsa05222, 1/1 pathways.. 'select()' returned 1:1 mapping between keys and columns Info: Working in directory /jsimonlab/scratch/jsimon/nextflow/work/20/2cd6d926916e086179100326a47cbe Info: Writing image file hsa05222.pathview.multi.png Info: Downloading xml files for hsa04210, 1/1 pathways.. Info: Downloading png files for hsa04210, 1/1 pathways.. 'select()' returned 1:1 mapping between keys and columns Info: Working in directory /jsimonlab/scratch/jsimon/nextflow/work/20/2cd6d926916e086179100326a47cbe Info: Writing image file hsa04210.pathview.multi.png Info: Downloading xml files for hsa01524, 1/1 pathways.. Info: Downloading png files for hsa01524, 1/1 pathways.. 'select()' returned 1:1 mapping between keys and columns Info: Working in directory /jsimonlab/scratch/jsimon/nextflow/work/20/2cd6d926916e086179100326a47cbe Info: Writing image file hsa01524.pathview.multi.png Error in png::readPNG(figure, native = FALSE) : file is not in PNG format Calls: FluteMLE ... arrangePathview -> lapply -> FUN -> -> In addition: There were 12 warnings (use warnings() to see them) Execution halted Work dir: /jsimonlab/scratch/jsimon/nextflow/work/20/2cd6d926916e086179100326a47cbe Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out` -- Check '.nextflow.log' file for details ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting -- Check '.nextflow.log' file for details