N E X T F L O W ~ version 23.04.1 Launching `nf-flu_v3.3.4/cfia-ncfad-nf-flu-3.3.4/workflow/main.nf` [kickass_agnesi] DSL2 - revision: 91a5d05f86 Core Nextflow options runName : kickass_agnesi containerEngine : singularity launchDir : IRVC20230831IHN-1 workDir : IRVC20230831IHN-1/IRVC20230831IHN-1_NTC_nf-flu_results/work projectDir : nf-flu_v3.3.4/cfia-ncfad-nf-flu-3.3.4/workflow userName : cbuchanan profile : singularity,slurm configFiles : nf-flu_v3.3.4/cfia-ncfad-nf-flu-3.3.4/workflow/nextflow.config Input/output options input : IRVC20230831IHN-1_NTC.csv platform : nanopore outdir : IRVC20230831IHN-1_NTC_nf-flu_results Variant calling options major_allele_fraction : 0.25 IRMA assembly options keep_ref_deletions : true skip_irma_subtyping_report: true Max job request options max_memory : 32 GB [Only displaying parameters that differ from pipeline default] ------------------------------------------------------ ------------------------------------------------------ [- ] process > NF_FLU:NANOPORE:CHECK_SAMPL... - [- ] process > NF_FLU:NANOPORE:READ_COUNT_... - [- ] process > NF_FLU:NANOPORE:READ_COUNT_... - [- ] process > NF_FLU:NANOPORE:CHECK_SAMPL... - [- ] process > NF_FLU:NANOPORE:READ_COUNT_... - [- ] process > NF_FLU:NANOPORE:READ_COUNT_... - [- ] process > NF_FLU:NANOPORE:ZSTD_DECOMP... - [- ] process > NF_FLU:NANOPORE:ZSTD_DECOMP... - [- ] process > NF_FLU:NANOPORE:BLAST_MAKEB... - [- ] process > NF_FLU:NANOPORE:CAT_NANOPOR... - [- ] process > NF_FLU:NANOPORE:IRMA - [- ] process > NF_FLU:NANOPORE:BLAST_BLAST... - [- ] process > NF_FLU:NANOPORE:PULL_TOP_RE... - [- ] process > NF_FLU:NANOPORE:SEQTK_SEQ - [- ] process > NF_FLU:NANOPORE:MINIMAP2 - [- ] process > NF_FLU:NANOPORE:MOSDEPTH_GE... - [- ] process > NF_FLU:NANOPORE:CLAIR3 - [- ] process > NF_FLU:NANOPORE:BCF_FILTER_... - [- ] process > NF_FLU:NANOPORE:VCF_FILTER_... - [- ] process > NF_FLU:NANOPORE:BCFTOOLS_STATS - [- ] process > NF_FLU:NANOPORE:COVERAGE_PLOT - [- ] process > NF_FLU:NANOPORE:BCF_CONSENSUS - [- ] process > NF_FLU:NANOPORE:CAT_CONSENSUS - [- ] process > NF_FLU:NANOPORE:BLAST_BLAST... - [- ] process > NF_FLU:NANOPORE:SUBTYPING_R... - [- ] process > NF_FLU:NANOPORE:SOFTWARE_VE... - [- ] process > NF_FLU:NANOPORE:MULTIQC - [- ] process > NF_FLU:NANOPORE:CHECK_SAMPL... [ 0%] 0 of 1 [- ] process > NF_FLU:NANOPORE:READ_COUNT_... - [- ] process > NF_FLU:NANOPORE:READ_COUNT_... - [- ] process > NF_FLU:NANOPORE:ZSTD_DECOMP... - [- ] process > NF_FLU:NANOPORE:ZSTD_DECOMP... - [- ] process > NF_FLU:NANOPORE:BLAST_MAKEB... - [- ] process > NF_FLU:NANOPORE:CAT_NANOPOR... - [- ] process > NF_FLU:NANOPORE:IRMA - [- ] process > NF_FLU:NANOPORE:BLAST_BLAST... - [- ] process > NF_FLU:NANOPORE:PULL_TOP_RE... - [- ] process > NF_FLU:NANOPORE:SEQTK_SEQ - [- ] process > NF_FLU:NANOPORE:MINIMAP2 - [- ] process > NF_FLU:NANOPORE:MOSDEPTH_GE... - [- ] process > NF_FLU:NANOPORE:CLAIR3 - [- ] process > NF_FLU:NANOPORE:BCF_FILTER_... - [- ] process > NF_FLU:NANOPORE:VCF_FILTER_... - [- ] process > NF_FLU:NANOPORE:BCFTOOLS_STATS - [- ] process > NF_FLU:NANOPORE:COVERAGE_PLOT - [- ] process > NF_FLU:NANOPORE:BCF_CONSENSUS - [- ] process > NF_FLU:NANOPORE:CAT_CONSENSUS - [- ] process > NF_FLU:NANOPORE:BLAST_BLAST... - [- ] process > NF_FLU:NANOPORE:SUBTYPING_R... - [- ] process > NF_FLU:NANOPORE:SOFTWARE_VE... - [- ] process > NF_FLU:NANOPORE:MULTIQC - executor > slurm (1) [02/4c74cc] process > NF_FLU:NANOPORE:CHECK_SAMPL... [ 0%] 0 of 1 [- ] process > NF_FLU:NANOPORE:READ_COUNT_... - [- ] process > NF_FLU:NANOPORE:READ_COUNT_... - [- ] process > NF_FLU:NANOPORE:ZSTD_DECOMP... - [- ] process > NF_FLU:NANOPORE:ZSTD_DECOMP... - [- ] process > NF_FLU:NANOPORE:BLAST_MAKEB... - [- ] process > NF_FLU:NANOPORE:CAT_NANOPOR... - [- ] process > NF_FLU:NANOPORE:IRMA - [- ] process > NF_FLU:NANOPORE:BLAST_BLAST... - [- ] process > NF_FLU:NANOPORE:PULL_TOP_RE... - [- ] process > NF_FLU:NANOPORE:SEQTK_SEQ - [- ] process > NF_FLU:NANOPORE:MINIMAP2 - [- ] process > NF_FLU:NANOPORE:MOSDEPTH_GE... - [- ] process > NF_FLU:NANOPORE:CLAIR3 - [- ] process > NF_FLU:NANOPORE:BCF_FILTER_... - [- ] process > NF_FLU:NANOPORE:VCF_FILTER_... - [- ] process > NF_FLU:NANOPORE:BCFTOOLS_STATS - [- ] process > NF_FLU:NANOPORE:COVERAGE_PLOT - [- ] process > NF_FLU:NANOPORE:BCF_CONSENSUS - [- ] process > NF_FLU:NANOPORE:CAT_CONSENSUS - [- ] process > NF_FLU:NANOPORE:BLAST_BLAST... - [- ] process > NF_FLU:NANOPORE:SUBTYPING_R... - [- ] process > NF_FLU:NANOPORE:SOFTWARE_VE... - [- ] process > NF_FLU:NANOPORE:MULTIQC - executor > slurm (1), local (1) [02/4c74cc] process > NF_FLU:NANOPORE:CHECK_SAMPL... [100%] 1 of 1 ✔ [ee/6c9b92] process > NF_FLU:NANOPORE:READ_COUNT_... [100%] 1 of 1, cached: 1 ✔ [72/3036a5] process > NF_FLU:NANOPORE:READ_COUNT_... [100%] 1 of 1 ✔ [- ] process > NF_FLU:NANOPORE:ZSTD_DECOMP... - [- ] process > NF_FLU:NANOPORE:ZSTD_DECOMP... - [- ] process > NF_FLU:NANOPORE:BLAST_MAKEB... - [a8/0167b9] process > NF_FLU:NANOPORE:CAT_NANOPOR... [100%] 3 of 3, cached: 3 ✔ [bf/7b3942] process > NF_FLU:NANOPORE:IRMA (GEN23... [ 33%] 1 of 3, cached: 1 [- ] process > NF_FLU:NANOPORE:BLAST_BLAST... - [- ] process > NF_FLU:NANOPORE:PULL_TOP_RE... - [- ] process > NF_FLU:NANOPORE:SEQTK_SEQ - [- ] process > NF_FLU:NANOPORE:MINIMAP2 - [- ] process > NF_FLU:NANOPORE:MOSDEPTH_GE... - [- ] process > NF_FLU:NANOPORE:CLAIR3 - [- ] process > NF_FLU:NANOPORE:BCF_FILTER_... - [- ] process > NF_FLU:NANOPORE:VCF_FILTER_... - [- ] process > NF_FLU:NANOPORE:BCFTOOLS_STATS - [- ] process > NF_FLU:NANOPORE:COVERAGE_PLOT - [- ] process > NF_FLU:NANOPORE:BCF_CONSENSUS - [- ] process > NF_FLU:NANOPORE:CAT_CONSENSUS - [- ] process > NF_FLU:NANOPORE:BLAST_BLAST... - [- ] process > NF_FLU:NANOPORE:SUBTYPING_R... - [- ] process > NF_FLU:NANOPORE:SOFTWARE_VE... - [- ] process > NF_FLU:NANOPORE:MULTIQC - executor > slurm (3), local (1) [02/4c74cc] process > NF_FLU:NANOPORE:CHECK_SAMPL... [100%] 1 of 1 ✔ [ee/6c9b92] process > NF_FLU:NANOPORE:READ_COUNT_... [100%] 1 of 1, cached: 1 ✔ [72/3036a5] process > NF_FLU:NANOPORE:READ_COUNT_... [100%] 1 of 1 ✔ [- ] process > NF_FLU:NANOPORE:ZSTD_DECOMP... - [- ] process > NF_FLU:NANOPORE:ZSTD_DECOMP... - [- ] process > NF_FLU:NANOPORE:BLAST_MAKEB... - [a8/0167b9] process > NF_FLU:NANOPORE:CAT_NANOPOR... [100%] 3 of 3, cached: 3 ✔ [bb/8b180f] process > NF_FLU:NANOPORE:IRMA (GEN23... [ 33%] 1 of 3, cached: 1 [- ] process > NF_FLU:NANOPORE:BLAST_BLAST... - [- ] process > NF_FLU:NANOPORE:PULL_TOP_RE... - [- ] process > NF_FLU:NANOPORE:SEQTK_SEQ - [- ] process > NF_FLU:NANOPORE:MINIMAP2 - [- ] process > NF_FLU:NANOPORE:MOSDEPTH_GE... - [- ] process > NF_FLU:NANOPORE:CLAIR3 - [- ] process > NF_FLU:NANOPORE:BCF_FILTER_... - [- ] process > NF_FLU:NANOPORE:VCF_FILTER_... - [- ] process > NF_FLU:NANOPORE:BCFTOOLS_STATS - [- ] process > NF_FLU:NANOPORE:COVERAGE_PLOT - [- ] process > NF_FLU:NANOPORE:BCF_CONSENSUS - [- ] process > NF_FLU:NANOPORE:CAT_CONSENSUS - [- ] process > NF_FLU:NANOPORE:BLAST_BLAST... - [- ] process > NF_FLU:NANOPORE:SUBTYPING_R... - [- ] process > NF_FLU:NANOPORE:SOFTWARE_VE... - [- ] process > NF_FLU:NANOPORE:MULTIQC - executor > slurm (5), local (1) [02/4c74cc] process > NF_FLU:NANOPORE:CHECK_SAMPL... [100%] 1 of 1 ✔ [ee/6c9b92] process > NF_FLU:NANOPORE:READ_COUNT_... [100%] 1 of 1, cached: 1 ✔ [72/3036a5] process > NF_FLU:NANOPORE:READ_COUNT_... [100%] 1 of 1 ✔ [- ] process > NF_FLU:NANOPORE:ZSTD_DECOMP... - [- ] process > NF_FLU:NANOPORE:ZSTD_DECOMP... - [- ] process > NF_FLU:NANOPORE:BLAST_MAKEB... - [a8/0167b9] process > NF_FLU:NANOPORE:CAT_NANOPOR... [100%] 3 of 3, cached: 3 ✔ [77/9ff718] process > NF_FLU:NANOPORE:IRMA (GEN23... [ 60%] 3 of 5, cached: 1... [- ] process > NF_FLU:NANOPORE:BLAST_BLAST... - [- ] process > NF_FLU:NANOPORE:PULL_TOP_RE... - [- ] process > NF_FLU:NANOPORE:SEQTK_SEQ - [- ] process > NF_FLU:NANOPORE:MINIMAP2 - [- ] process > NF_FLU:NANOPORE:MOSDEPTH_GE... - [- ] process > NF_FLU:NANOPORE:CLAIR3 - [- ] process > NF_FLU:NANOPORE:BCF_FILTER_... - [- ] process > NF_FLU:NANOPORE:VCF_FILTER_... - [- ] process > NF_FLU:NANOPORE:BCFTOOLS_STATS - [- ] process > NF_FLU:NANOPORE:COVERAGE_PLOT - [- ] process > NF_FLU:NANOPORE:BCF_CONSENSUS - [- ] process > NF_FLU:NANOPORE:CAT_CONSENSUS - [- ] process > NF_FLU:NANOPORE:BLAST_BLAST... - [- ] process > NF_FLU:NANOPORE:SUBTYPING_R... - [- ] process > NF_FLU:NANOPORE:SOFTWARE_VE... - [- ] process > NF_FLU:NANOPORE:MULTIQC - [83/3ae326] NOTE: Process `NF_FLU:NANOPORE:IRMA (GEN23-RTPCR-0829-NTC-3-1b)` terminated with an error exit status (1) -- Execution is retried (1) [bb/8b180f] NOTE: Process `NF_FLU:NANOPORE:IRMA (GEN23-RTPCR-0829-NTC-3-1c)` terminated with an error exit status (1) -- Execution is retried (1) executor > slurm (5), local (1) [02/4c74cc] process > NF_FLU:NANOPORE:CHECK_SAMPL... [100%] 1 of 1 ✔ [ee/6c9b92] process > NF_FLU:NANOPORE:READ_COUNT_... [100%] 1 of 1, cached: 1 ✔ [72/3036a5] process > NF_FLU:NANOPORE:READ_COUNT_... [100%] 1 of 1 ✔ [- ] process > NF_FLU:NANOPORE:ZSTD_DECOMP... - [- ] process > NF_FLU:NANOPORE:ZSTD_DECOMP... - [- ] process > NF_FLU:NANOPORE:BLAST_MAKEB... - [a8/0167b9] process > NF_FLU:NANOPORE:CAT_NANOPOR... [100%] 3 of 3, cached: 3 ✔ [77/9ff718] process > NF_FLU:NANOPORE:IRMA (GEN23... [ 60%] 3 of 5, cached: 1... [- ] process > NF_FLU:NANOPORE:BLAST_BLAST... - [- ] process > NF_FLU:NANOPORE:PULL_TOP_RE... - [- ] process > NF_FLU:NANOPORE:SEQTK_SEQ - [- ] process > NF_FLU:NANOPORE:MINIMAP2 - [- ] process > NF_FLU:NANOPORE:MOSDEPTH_GE... - [- ] process > NF_FLU:NANOPORE:CLAIR3 - [- ] process > NF_FLU:NANOPORE:BCF_FILTER_... - [- ] process > NF_FLU:NANOPORE:VCF_FILTER_... - [- ] process > NF_FLU:NANOPORE:BCFTOOLS_STATS - [- ] process > NF_FLU:NANOPORE:COVERAGE_PLOT - [- ] process > NF_FLU:NANOPORE:BCF_CONSENSUS - [- ] process > NF_FLU:NANOPORE:CAT_CONSENSUS - [- ] process > NF_FLU:NANOPORE:BLAST_BLAST... - [- ] process > NF_FLU:NANOPORE:SUBTYPING_R... - [- ] process > NF_FLU:NANOPORE:SOFTWARE_VE... - [- ] process > NF_FLU:NANOPORE:MULTIQC - Staging foreign file: https://api.figshare.com/v2/file/download/41415330 Staging foreign file: https://api.figshare.com/v2/file/download/41415333 [83/3ae326] NOTE: Process `NF_FLU:NANOPORE:IRMA (GEN23-RTPCR-0829-NTC-3-1b)` terminated with an error exit status (1) -- Execution is retried (1) [bb/8b180f] NOTE: Process `NF_FLU:NANOPORE:IRMA (GEN23-RTPCR-0829-NTC-3-1c)` terminated with an error exit status (1) -- Execution is retried (1) executor > slurm (5), local (1) [02/4c74cc] process > NF_FLU:NANOPORE:CHECK_SAMPL... [100%] 1 of 1 ✔ [ee/6c9b92] process > NF_FLU:NANOPORE:READ_COUNT_... [100%] 1 of 1, cached: 1 ✔ [72/3036a5] process > NF_FLU:NANOPORE:READ_COUNT_... [100%] 1 of 1 ✔ [- ] process > NF_FLU:NANOPORE:ZSTD_DECOMP... - [- ] process > NF_FLU:NANOPORE:ZSTD_DECOMP... - [- ] process > NF_FLU:NANOPORE:BLAST_MAKEB... - [a8/0167b9] process > NF_FLU:NANOPORE:CAT_NANOPOR... [100%] 3 of 3, cached: 3 ✔ [77/9ff718] process > NF_FLU:NANOPORE:IRMA (GEN23... [ 60%] 3 of 5, cached: 1... [- ] process > NF_FLU:NANOPORE:BLAST_BLAST... - [- ] process > NF_FLU:NANOPORE:PULL_TOP_RE... - [- ] process > NF_FLU:NANOPORE:SEQTK_SEQ - [- ] process > NF_FLU:NANOPORE:MINIMAP2 - [- ] process > NF_FLU:NANOPORE:MOSDEPTH_GE... - [- ] process > NF_FLU:NANOPORE:CLAIR3 - [- ] process > NF_FLU:NANOPORE:BCF_FILTER_... - [- ] process > NF_FLU:NANOPORE:VCF_FILTER_... - [- ] process > NF_FLU:NANOPORE:BCFTOOLS_STATS - [- ] process > NF_FLU:NANOPORE:COVERAGE_PLOT - [- ] process > NF_FLU:NANOPORE:BCF_CONSENSUS - [- ] process > NF_FLU:NANOPORE:CAT_CONSENSUS - [- ] process > NF_FLU:NANOPORE:BLAST_BLAST... - [- ] process > NF_FLU:NANOPORE:SUBTYPING_R... - [- ] process > NF_FLU:NANOPORE:SOFTWARE_VE... - [- ] process > NF_FLU:NANOPORE:MULTIQC - Staging foreign file: https://api.figshare.com/v2/file/download/41415330 Staging foreign file: https://api.figshare.com/v2/file/download/41415333 [83/3ae326] NOTE: Process `NF_FLU:NANOPORE:IRMA (GEN23-RTPCR-0829-NTC-3-1b)` terminated with an error exit status (1) -- Execution is retried (1) [bb/8b180f] NOTE: Process `NF_FLU:NANOPORE:IRMA (GEN23-RTPCR-0829-NTC-3-1c)` terminated with an error exit status (1) -- Execution is retried (1) executor > slurm (5), local (1) [02/4c74cc] process > NF_FLU:NANOPORE:CHECK_SAMPL... [100%] 1 of 1 ✔ [ee/6c9b92] process > NF_FLU:NANOPORE:READ_COUNT_... [100%] 1 of 1, cached: 1 ✔ [72/3036a5] process > NF_FLU:NANOPORE:READ_COUNT_... [100%] 1 of 1 ✔ [- ] process > NF_FLU:NANOPORE:ZSTD_DECOMP... - [- ] process > NF_FLU:NANOPORE:ZSTD_DECOMP... - [- ] process > NF_FLU:NANOPORE:BLAST_MAKEB... - [a8/0167b9] process > NF_FLU:NANOPORE:CAT_NANOPOR... [100%] 3 of 3, cached: 3 ✔ [77/9ff718] process > NF_FLU:NANOPORE:IRMA (GEN23... [ 60%] 3 of 5, cached: 1... [- ] process > NF_FLU:NANOPORE:BLAST_BLAST... - [- ] process > NF_FLU:NANOPORE:PULL_TOP_RE... - [- ] process > NF_FLU:NANOPORE:SEQTK_SEQ - [- ] process > NF_FLU:NANOPORE:MINIMAP2 - [- ] process > NF_FLU:NANOPORE:MOSDEPTH_GE... - [- ] process > NF_FLU:NANOPORE:CLAIR3 - [- ] process > NF_FLU:NANOPORE:BCF_FILTER_... - [- ] process > NF_FLU:NANOPORE:VCF_FILTER_... - [- ] process > NF_FLU:NANOPORE:BCFTOOLS_STATS - [- ] process > NF_FLU:NANOPORE:COVERAGE_PLOT - [- ] process > NF_FLU:NANOPORE:BCF_CONSENSUS - [- ] process > NF_FLU:NANOPORE:CAT_CONSENSUS - [- ] process > NF_FLU:NANOPORE:BLAST_BLAST... - [- ] process > NF_FLU:NANOPORE:SUBTYPING_R... - [- ] process > NF_FLU:NANOPORE:SOFTWARE_VE... - [- ] process > NF_FLU:NANOPORE:MULTIQC - Staging foreign file: https://api.figshare.com/v2/file/download/41415330 Staging foreign file: https://api.figshare.com/v2/file/download/41415333 [83/3ae326] NOTE: Process `NF_FLU:NANOPORE:IRMA (GEN23-RTPCR-0829-NTC-3-1b)` terminated with an error exit status (1) -- Execution is retried (1) [bb/8b180f] NOTE: Process `NF_FLU:NANOPORE:IRMA (GEN23-RTPCR-0829-NTC-3-1c)` terminated with an error exit status (1) -- Execution is retried (1) ERROR ~ Error executing process > 'NF_FLU:NANOPORE:IRMA (GEN23-RTPCR-0829-NTC-3-1b)' Caused by: Process `NF_FLU:NANOPORE:IRMA (GEN23-RTPCR-0829-NTC-3-1b)` terminated with an error exit status (1) Command executed: touch irma_config.sh echo 'SINGLE_LOCAL_PROC=16' >> irma_config.sh echo 'DOUBLE_LOCAL_PROC=8' >> irma_config.sh # default tmp in current working directory instead of defaulting to /tmp # which may be restricted in size on HPC clusters echo 'ALLOW_TMP=1' >> irma_config.sh echo 'TMP=$PWD' >> irma_config.sh if [ true ]; then echo 'DEL_TYPE="NNN"' >> irma_config.sh echo 'ALIGN_PROG="BLAT"' >> irma_config.sh fi IRMA FLU-minion GEN23-RTPCR-0829-NTC-3-1b.merged.fastq.gz GEN23-RTPCR-0829-NTC-3-1b if [ -d "GEN23-RTPCR-0829-NTC-3-1b/amended_consensus/" ]; then cat GEN23-RTPCR-0829-NTC-3-1b/amended_consensus/*.fa > GEN23-RTPCR-0829-NTC-3-1b.irma.consensus.fasta fi ln -s .command.log GEN23-RTPCR-0829-NTC-3-1b.irma.log cat <<-END_VERSIONS > versions.yml "NF_FLU:NANOPORE:IRMA": IRMA: $(IRMA | head -n1 | sed -E 's/^Iter.*IRMA\), v(\S+) .*/\1/') END_VERSIONS Command exit status: 1 Command output: Loading config file 'irma_config.sh' [2023-09-11 16:06:21] IRMA/FLU-minion started run 'GEN23-RTPCR-0829-NTC-3-1b' [2023-09-11 16:06:21] IRMA/FLU-minion found 1305.9T free space, only needed ~6.0M [2023-09-11 16:06:21] IRMA/FLU-minion pre-processed [2023-09-11 16:06:21] IRMA/FLU-minion R1 started (253) [2023-09-11 16:06:22] IRMA/FLU-minion R1 all-match with BLAT finished [2023-09-11 16:06:23] IRMA/FLU-minion R1 consolidated & cleaned [2023-09-11 16:06:23] IRMA/FLU-minion R1 aborted, no matches found [2023-09-11 16:06:23] IRMA/FLU-minion converted back to fastq [2023-09-11 16:06:23] IRMA/FLU-minion saved unmatched read patterns [2023-09-11 16:06:23] IRMA/FLU-minion skipping final assembly, no reference files found [2023-09-11 16:06:24] IRMA/FLU-minion moving project [2023-09-11 16:06:24] IRMA/FLU-minion finished! Command error: cat: can't open 'GEN23-RTPCR-0829-NTC-3-1b/amended_consensus/*.fa': No such file or directory Work dir: IRVC20230831IHN-1/IRVC20230831IHN-1_NTC_nf-flu_results/work/9a/75e6be9b2f3640fdcc85bf3b2958ae Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh` -- Check '.nextflow.log' file for details Pipeline execution summary --------------------------- Completed at : 2023-09-11T16:06:24.575616577-05:00 Duration : 19.1s Success : false Results Dir : IRVC20230831IHN-1/IRVC20230831IHN-1_NTC_nf-flu_results Work Dir : IRVC20230831IHN-1/IRVC20230831IHN-1_NTC_nf-flu_results/work Exit status : 1 Error report : Error executing process > 'NF_FLU:NANOPORE:IRMA (GEN23-RTPCR-0829-NTC-3-1b)' Caused by: Process `NF_FLU:NANOPORE:IRMA (GEN23-RTPCR-0829-NTC-3-1b)` terminated with an error exit status (1) Command executed: touch irma_config.sh echo 'SINGLE_LOCAL_PROC=16' >> irma_config.sh echo 'DOUBLE_LOCAL_PROC=8' >> irma_config.sh # default tmp in current working directory instead of defaulting to /tmp # which may be restricted in size on HPC clusters echo 'ALLOW_TMP=1' >> irma_config.sh echo 'TMP=$PWD' >> irma_config.sh if [ true ]; then echo 'DEL_TYPE="NNN"' >> irma_config.sh echo 'ALIGN_PROG="BLAT"' >> irma_config.sh fi IRMA FLU-minion GEN23-RTPCR-0829-NTC-3-1b.merged.fastq.gz GEN23-RTPCR-0829-NTC-3-1b if [ -d "GEN23-RTPCR-0829-NTC-3-1b/amended_consensus/" ]; then cat GEN23-RTPCR-0829-NTC-3-1b/amended_consensus/*.fa > GEN23-RTPCR-0829-NTC-3-1b.irma.consensus.fasta fi ln -s .command.log GEN23-RTPCR-0829-NTC-3-1b.irma.log cat <<-END_VERSIONS > versions.yml "NF_FLU:NANOPORE:IRMA": IRMA: $(IRMA | head -n1 | sed -E 's/^Iter.*IRMA\), v(\S+) .*/\1/') END_VERSIONS Command exit status: 1 Command output: Loading config file 'irma_config.sh' [2023-09-11 16:06:21] IRMA/FLU-minion started run 'GEN23-RTPCR-0829-NTC-3-1b' [2023-09-11 16:06:21] IRMA/FLU-minion found 1305.9T free space, only needed ~6.0M [2023-09-11 16:06:21] IRMA/FLU-minion pre-processed [2023-09-11 16:06:21] IRMA/FLU-minion R1 started (253) [2023-09-11 16:06:22] IRMA/FLU-minion R1 all-match with BLAT finished [2023-09-11 16:06:23] IRMA/FLU-minion R1 consolidated & cleaned [2023-09-11 16:06:23] IRMA/FLU-minion R1 aborted, no matches found [2023-09-11 16:06:23] IRMA/FLU-minion converted back to fastq [2023-09-11 16:06:23] IRMA/FLU-minion saved unmatched read patterns [2023-09-11 16:06:23] IRMA/FLU-minion skipping final assembly, no reference files found [2023-09-11 16:06:24] IRMA/FLU-minion moving project [2023-09-11 16:06:24] IRMA/FLU-minion finished! Command error: cat: can't open 'GEN23-RTPCR-0829-NTC-3-1b/amended_consensus/*.fa': No such file or directory Work dir: IRVC20230831IHN-1/IRVC20230831IHN-1_NTC_nf-flu_results/work/9a/75e6be9b2f3640fdcc85bf3b2958ae Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh` executor > slurm (5), local (1) [02/4c74cc] process > NF_FLU:NANOPORE:CHECK_SAMPL... [100%] 1 of 1 ✔ [ee/6c9b92] process > NF_FLU:NANOPORE:READ_COUNT_... [100%] 1 of 1, cached: 1 ✔ [72/3036a5] process > NF_FLU:NANOPORE:READ_COUNT_... [100%] 1 of 1 ✔ [- ] process > NF_FLU:NANOPORE:ZSTD_DECOMP... - [- ] process > NF_FLU:NANOPORE:ZSTD_DECOMP... - [- ] process > NF_FLU:NANOPORE:BLAST_MAKEB... - [a8/0167b9] process > NF_FLU:NANOPORE:CAT_NANOPOR... [100%] 3 of 3, cached: 3 ✔ [77/9ff718] process > NF_FLU:NANOPORE:IRMA (GEN23... [100%] 5 of 5, cached: 1... [- ] process > NF_FLU:NANOPORE:BLAST_BLAST... - [- ] process > NF_FLU:NANOPORE:PULL_TOP_RE... - [- ] process > NF_FLU:NANOPORE:SEQTK_SEQ - [- ] process > NF_FLU:NANOPORE:MINIMAP2 - [- ] process > NF_FLU:NANOPORE:MOSDEPTH_GE... - [- ] process > NF_FLU:NANOPORE:CLAIR3 - [- ] process > NF_FLU:NANOPORE:BCF_FILTER_... - [- ] process > NF_FLU:NANOPORE:VCF_FILTER_... - [- ] process > NF_FLU:NANOPORE:BCFTOOLS_STATS - [- ] process > NF_FLU:NANOPORE:COVERAGE_PLOT - [- ] process > NF_FLU:NANOPORE:BCF_CONSENSUS - [- ] process > NF_FLU:NANOPORE:CAT_CONSENSUS - [- ] process > NF_FLU:NANOPORE:BLAST_BLAST... - [- ] process > NF_FLU:NANOPORE:SUBTYPING_R... - [- ] process > NF_FLU:NANOPORE:SOFTWARE_VE... - [- ] process > NF_FLU:NANOPORE:MULTIQC - Staging foreign file: https://api.figshare.com/v2/file/download/41415330 Staging foreign file: https://api.figshare.com/v2/file/download/41415333 Oops... Pipeline execution stopped with the following message: cat: can't open 'GEN23-RTPCR-0829-NTC-3-1b/amended_consensus/*.fa': No such file or directory [83/3ae326] NOTE: Process `NF_FLU:NANOPORE:IRMA (GEN23-RTPCR-0829-NTC-3-1b)` terminated with an error exit status (1) -- Execution is retried (1) [bb/8b180f] NOTE: Process `NF_FLU:NANOPORE:IRMA (GEN23-RTPCR-0829-NTC-3-1c)` terminated with an error exit status (1) -- Execution is retried (1) ERROR ~ Error executing process > 'NF_FLU:NANOPORE:IRMA (GEN23-RTPCR-0829-NTC-3-1b)' Caused by: Process `NF_FLU:NANOPORE:IRMA (GEN23-RTPCR-0829-NTC-3-1b)` terminated with an error exit status (1) Command executed: touch irma_config.sh echo 'SINGLE_LOCAL_PROC=16' >> irma_config.sh echo 'DOUBLE_LOCAL_PROC=8' >> irma_config.sh # default tmp in current working directory instead of defaulting to /tmp # which may be restricted in size on HPC clusters echo 'ALLOW_TMP=1' >> irma_config.sh echo 'TMP=$PWD' >> irma_config.sh if [ true ]; then echo 'DEL_TYPE="NNN"' >> irma_config.sh echo 'ALIGN_PROG="BLAT"' >> irma_config.sh fi IRMA FLU-minion GEN23-RTPCR-0829-NTC-3-1b.merged.fastq.gz GEN23-RTPCR-0829-NTC-3-1b if [ -d "GEN23-RTPCR-0829-NTC-3-1b/amended_consensus/" ]; then cat GEN23-RTPCR-0829-NTC-3-1b/amended_consensus/*.fa > GEN23-RTPCR-0829-NTC-3-1b.irma.consensus.fasta fi ln -s .command.log GEN23-RTPCR-0829-NTC-3-1b.irma.log cat <<-END_VERSIONS > versions.yml "NF_FLU:NANOPORE:IRMA": IRMA: $(IRMA | head -n1 | sed -E 's/^Iter.*IRMA\), v(\S+) .*/\1/') END_VERSIONS Command exit status: 1 Command output: Loading config file 'irma_config.sh' [2023-09-11 16:06:21] IRMA/FLU-minion started run 'GEN23-RTPCR-0829-NTC-3-1b' [2023-09-11 16:06:21] IRMA/FLU-minion found 1305.9T free space, only needed ~6.0M [2023-09-11 16:06:21] IRMA/FLU-minion pre-processed [2023-09-11 16:06:21] IRMA/FLU-minion R1 started (253) [2023-09-11 16:06:22] IRMA/FLU-minion R1 all-match with BLAT finished [2023-09-11 16:06:23] IRMA/FLU-minion R1 consolidated & cleaned [2023-09-11 16:06:23] IRMA/FLU-minion R1 aborted, no matches found [2023-09-11 16:06:23] IRMA/FLU-minion converted back to fastq [2023-09-11 16:06:23] IRMA/FLU-minion saved unmatched read patterns [2023-09-11 16:06:23] IRMA/FLU-minion skipping final assembly, no reference files found [2023-09-11 16:06:24] IRMA/FLU-minion moving project [2023-09-11 16:06:24] IRMA/FLU-minion finished! Command error: cat: can't open 'GEN23-RTPCR-0829-NTC-3-1b/amended_consensus/*.fa': No such file or directory Work dir: IRVC20230831IHN-1/IRVC20230831IHN-1_NTC_nf-flu_results/work/9a/75e6be9b2f3640fdcc85bf3b2958ae Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh` -- Check '.nextflow.log' file for details