Jan-29 16:04:40.079 [main] DEBUG nextflow.cli.Launcher - $> nextflow run nf-core/viralrecon --input /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore//samples.csv --protocol amplicon --amplicon_bed /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore//../primer/Eden_processed/Eden_primers.bed --amplicon_fasta /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore//../primer/Eden_processed/Eden_primers.fa --genome MN908947.3 --skip_assembly --outdir /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore//results -profile singularity -with-singularity /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore//singularity.dev.961b10463ae1.sif -r e49cee2
Jan-29 16:04:40.130 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 20.10.0
Jan-29 16:04:40.824 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/crtd_bioinf/fabirost/.nextflow/assets/nf-core/viralrecon/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/viralrecon.git
Jan-29 16:04:40.835 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/crtd_bioinf/fabirost/.nextflow/assets/nf-core/viralrecon/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/viralrecon.git
Jan-29 16:04:41.024 [main] INFO nextflow.cli.CmdRun - Launching `nf-core/viralrecon` [condescending_volhard] - revision: e49cee2f15dce2e9993736d16f08b1f9d808e292
Jan-29 16:04:41.596 [main] DEBUG nextflow.scm.AssetManager - WARN: Cannot find any Git revision matching: null; ls-remote: [Ref[refs/pull/104/head=e21a9d69c8a80c902e8ed67ead97269ae040daa8], Ref[refs/pull/71/head=de556ff67b80ef002b437391fe3e8ae86ddfcca7], Ref[refs/pull/85/head=cea8613b4a939db7dc36fb639b0b05de07a9aaed], Ref[refs/tags/1.0.0=7422b0d353b1a295fb7cda47f2f7750c3bd890d1], Ref[refs/pull/69/head=b6e20251447dff08ea213605f4bfe554b17a0ab4], Ref[refs/pull/40/head=658104370a3aab1bde5e176750a1ae15687a0b89], Ref[refs/pull/24/head=b77d015ce4720e7447ee6c50fcca8758d16a173e], Ref[refs/pull/135/head=778693daee7a476c8cc9ed1b703bd0e801d42016], Ref[refs/pull/55/head=3bfc2ba5239baa54260a95f031523f4e212451f6], Ref[refs/heads/dsl2=c8f708819bede4b1c8f3840c6355c22b03e6d0e9], Ref[refs/pull/23/head=a87af4acb8a3afe26175da6feeb4c5ca28b3b436], Ref[refs/pull/148/head=9ba237e45aef44056dfd137caf33782252b8c9b2], Ref[refs/pull/120/head=4461c408701db0ba78264092632e45c93f83ba4c], Ref[refs/pull/103/head=372de46851a76d35c038fdf4a80d1207f71de073], Ref[refs/pull/68/head=487df0392fa1579abb9842d33111ebcc6e223d66], Ref[refs/pull/70/head=fb6596249daf33376ca148c6b06a9f2ebb50af8d], Ref[refs/pull/118/head=fb552abe4143334b8b6131028e029a6d9271202a], Ref[refs/pull/150/head=74e32eeb8efa98fea152899ae9e5f43f0aefe087], Ref[refs/pull/38/head=6030094912cb345c1b16584a713c0b94595003e0], Ref[refs/pull/134/head=abcd646b49cd7bccc8e8c4ddf164782731e1eb56], Ref[refs/pull/54/head=4c4103b9fda02bf60c8f77e424ab11d0b783e43e], Ref[refs/pull/99/head=6756a4e3a518e2cac416550168a6b89c57975785], Ref[refs/pull/98/head=afc1fd67c633482675226db3906f9e0ed93ab56f], Ref[refs/pull/84/head=52db59ea24b462f0760896bdeb2f743c85a8b781], Ref[refs/pull/11/head=886c2f681f33e75858deb6e9d1c914fdb299c035], Ref[refs/pull/39/head=0b12a3e4f87ca8f0f83fbde0737466268e15785c], Ref[refs/pull/87/head=d3c56f47a3a51a50a526590901e3f1bfe3db6049], Ref[refs/pull/116/head=e1134ed88cec082d6f7373ba96bfc4e0ecc412bc], Ref[refs/pull/119/head=43c9d78884774bfe5e419014c38cf1e8b31c6710], Ref[refs/pull/41/head=4853f86c0869171b16a53b767401a5a341167e53], Ref[refs/pull/36/head=3eaeb42a7b15701ec7107498e5cdd5866325143c], Ref[refs/pull/52/head=9e511349d7e899310a41fa9b46269571e39034f5], Ref[refs/pull/22/head=a580cfaa886907f4cda826088a15cc8241a99c31], Ref[refs/pull/102/head=1b93695f72a814764cc7dbf74d6a47855042b87a], Ref[refs/pull/25/head=6ebfb8a9d9c42dc06827211f6ef576bdee232efa], Ref[refs/pull/105/head=9a46ba7d317c00e23bdfb889dd1298c33171c99c], Ref[refs/pull/146/head=90079b0fa5d37ffd551c4a9a18cba4f9860a017b], Ref[refs/pull/49/head=fee3c68ef7053fc9bd79a11937320abd056f0948], Ref[refs/pull/88/head=00816d0ec217c4adc2fa38ea07ef882d4dd1c822], Ref[refs/tags/1.1.0=75a2f9763e9b4c1aa20ad342ae3ce148c33cc65a], Ref[refs/pull/140/head=2898d227ba61e2920fc4cc36ed6e5cd14064b7f7], Ref[refs/pull/60/head=eaab9880c914ea28d55f9077005808b9034a60ab], Ref[refs/pull/18/head=23ef7e0cacaa1726777c2a00dd7d138948f99fe8], Ref[refs/pull/82/head=7f8c7988f95c339debce2b3570df0f399fc230e0], Ref[refs/pull/21/head=4a485b793c961d148fae1bbf7f202b49a28307a3], Ref[refs/pull/65/head=3d6512ac4e109958c5fbf719ccbbd14ed9004017], Ref[refs/pull/27/head=775379f647f9e2e41a0dee869dd31d9fef06a9df], Ref[refs/pull/145/head=1ca31f1e8fec66a159e9442c45ccd926d265844e], Ref[refs/pull/43/head=2e5a2b4772239651bd292cbdd1d21fc69c4d1caa], Ref[refs/pull/129/head=7b38fe2439f97927093452232263123e71368d44], Ref[refs/pull/59/head=046d91a78b5c112a93ed7ef7d185c18a19bea8b9], Ref[refs/pull/139/head=60cd93051c5de0af9f79886e48d7c96c6b4ae199], Ref[refs/pull/53/head=ac36d1fcf11674ab8ccf8b77a7bfb414614b9cad], Ref[refs/pull/111/head=69326f97b1c1d1b8733a0df573cb1f3eff907e6d], Ref[refs/pull/136/head=7002a5eb6f481075cf577e7898212bf01144e2f9], Ref[refs/pull/130/head=b0229bbbc6eda0614aa40269a3f06b4edf78c360], Ref[refs/pull/117/head=acfc523f35cb9174c383b01cede82a14c8818688], Ref[refs/pull/133/head=52a1e50ff57cf2295e2de9b425f73f276f20bade], Ref[refs/pull/37/head=55c2a56f7101f4d9bc74fa91cbc6bf9fd81527e2], Ref[refs/pull/114/head=d0e3e179d14b95eb8a1b08c3edcea5012e741206], Ref[refs/pull/34/head=dad04235f8b75dabd385a2e2476a895629549d98], Ref[refs/pull/50/head=fc6eb38364aa85181defa21fb32ba9c56b87bd80], Ref[refs/pull/72/head=3c810f848c21ca58d69aa31b0cecb68889cecebd], Ref[refs/pull/97/head=c6682e57fd58b9ed743e388999c393f2cdaccd78], Ref[refs/pull/78/head=7c38d49a99fd897ac473995c29876c5579e1722d], Ref[refs/pull/91/head=b0f9b52f9d17ba097a518b4dd01e25da52c6159a], Ref[refs/pull/75/head=f9b4b596671b2325011c42734b14239027d62c1d], Ref[refs/pull/94/head=f7004dd083f523674b0b5b7b3d98176b8887b43e], Ref[refs/pull/32/head=cb10b45cadedd90d5da6460704d5cd5f15764c01], Ref[refs/pull/77/head=ed2511444ce83e7924e9fd91584c268251bb2e31], Ref[refs/pull/63/head=4f56a2b91f580fc4f1ff4ff9510bd675b1d512b0], Ref[refs/pull/29/head=634bf562df7712e80ffa57839263273a53b3ae6b], Ref[refs/pull/16/head=79005a50623da53a812584537ee081744631dbe2], Ref[refs/pull/93/head=a495c1c40bd21085c21247ad812e51bcbb90088f], Ref[refs/pull/76/head=8b7285dbb0baa5ee300a43500dbeff782b284134], Ref[refs/pull/15/head=f899da38519e283a12df70fa6f20efd0a851f053], Ref[refs/pull/126/head=13331866195d9b0cc0aee95fc0df881965be7ef3], Ref[refs/pull/62/head=edb5bd0b6f40ac15432d5d234293d39334fd347f], Ref[refs/pull/92/head=ecc1fdcf1dade61baa2f65c2904f88457aa54054], Ref[refs/pull/28/head=c83b9a771430ed9c793e78f4507b6ba50858950b], Ref[refs/pull/81/head=9b4444fc1bb6ea038245dcb57db55ff96161d977], Ref[refs/pull/79/head=d9ad5b9c6f6ee7e1c2e62c36d8df2ef13eecffc1], Ref[refs/pull/44/head=a6524572ebfc9a9b73b1c207d7b56f3c0c37a411], Ref[refs/pull/110/head=9ea4c1a52a0b55beb8fda28d9d5d318c7909a99c], Ref[refs/pull/7/head=053508707e945f883dd611cb6eab89be73f77f56], Ref[refs/pull/127/head=0a7325e0a42b5f06afcb622c74962a3899157eca], Ref[refs/pull/108/head=2622959ec0ca9753ccf35fb57fa38d12a688a4f2], Ref[refs/pull/30/head=8940416aacf0648eeef5fd083cc7cc333d266be4], Ref[refs/pull/17/head=747296441fb64b4bd1137fd8d93f08f91572f90b], Ref[refs/pull/74/head=72d240b1e367193672c4e8914ffd7d51c93fa39b], Ref[HEAD=75a2f9763e9b4c1aa20ad342ae3ce148c33cc65a], Ref[refs/pull/35/head=3781ff8ee824eb0c63644145a48e45221e22de9a], Ref[refs/pull/132/head=5b355cd205b4fa66a6658500d3080481d02bc736], Ref[refs/pull/90/head=b2eef6ca9038df66be27c985372ca1125fc3d8a7], Ref[refs/pull/58/head=5d42f5891d40e249a27a5cc1dcff8e9c13ce78af], Ref[refs/pull/131/head=30db7f95649e6e4f309067f3acb15b86c4499c6d], Ref[refs/pull/20/head=5c7bd7013a253a9785b346f65cf9bfc898da48f6], Ref[refs/pull/137/head=ee5b7b7a47ddabc6b44ef203ce13599ed3e42079], Ref[refs/pull/51/head=6cc01895b3db2901ac33dad5ae2317664467ae35], Ref[refs/pull/19/head=29d89516b218140ce2a5ed4f04c7898d436fc390], Ref[refs/pull/100/head=85f13dd3df92feec87fbe5b367715bb53743067c], Ref[refs/pull/73/head=d07af1ccde076f7010330c1fdd7d60a7b4c6f5be], Ref[refs/pull/96/head=2d5cdb3d8234e7f11c079fe57d8b131010423aae], Ref[refs/pull/57/head=d72c512df8fd38215b8c9bc259a2b97373536ad0], Ref[refs/pull/125/head=c9d40fb3c3f0bf413d593d43c6483f0eca234249], Ref[refs/pull/128/head=eca1bdcdaed5aefaf74402c858a45dc1ba4d123a], Ref[refs/pull/64/head=f27a55065c359cc6f19c4ea8bd7b6d93375a8141], Ref[refs/pull/48/head=e0474ce0f9f7c198f5e49070536b76c70e4b2e0b], Ref[refs/pull/45/head=0687ec1ef98f3ae80c147329c193338d79f537d6], Ref[refs/pull/106/head=160438169ebb0e488fd75f4706dc6fb66888cd7f], Ref[refs/pull/109/head=a5c12fcbbe4ead170ccd13d54b2038406757f271], Ref[refs/heads/TEMPLATE=1ca31f1e8fec66a159e9442c45ccd926d265844e], Ref[refs/heads/dev=e49cee2f15dce2e9993736d16f08b1f9d808e292], Ref[refs/pull/83/head=d9589698b6189d60f996fc722d566f84c28215c2], Ref[refs/pull/86/head=5ac0f286bc4acf243ba7ea53a665fe24ab02f85b], Ref[refs/pull/141/head=052e9a8cdaa1260a6007571b97acc855b7513086], Ref[refs/pull/131/merge=103c74d77174b79e1060b5757209a016c1e26aa6], Ref[refs/heads/master=75a2f9763e9b4c1aa20ad342ae3ce148c33cc65a], Ref[refs/pull/80/head=80a8eb55a94c26d7c488cf0290ff3dc904c3c42d], Ref[refs/pull/89/head=397f25529d0ca506666c88d74a5382fcbbbb481e], Ref[refs/pull/144/head=b006a4187540d86a80981d28c364779ffb2c4aeb], Ref[refs/pull/147/head=80b17e725ec72e03ee63be69187b0f2feb7e8ada]]
Jan-29 16:04:41.629 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/crtd_bioinf/fabirost/.nextflow/assets/nf-core/viralrecon/nextflow.config
Jan-29 16:04:41.630 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/crtd_bioinf/fabirost/.nextflow/assets/nf-core/viralrecon/nextflow.config
Jan-29 16:04:41.640 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `singularity`
Jan-29 16:04:42.104 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [cfc_dev, test_sispa, denbi_qbic, bi, genotoul, bigpurple, uppmax, abims, imperial_mb, docker, gis, utd_ganymede, mpcdf, conda, test_full_sispa, singularity, icr_davros, munin, prince, podman, test_sra, czbiohub_aws, hebbe, cfc, uzh, ccga_med, debug, test, genouest, cbe, ebc, ccga_dx, crick, google, kraken, phoenix, seg_globe, shh, awsbatch, pasteur, uct_hpc, imperial, test_full, binac]
Jan-29 16:04:42.116 [main] DEBUG nextflow.config.ConfigBuilder - Enabling execution in Singularity container as requested by cli option `-with-singularity null`
Jan-29 16:04:42.154 [main] DEBUG nextflow.Session - Session uuid: d50953bf-81a8-400d-bca1-9b94a03c8b75
Jan-29 16:04:42.154 [main] DEBUG nextflow.Session - Run name: condescending_volhard
Jan-29 16:04:42.155 [main] DEBUG nextflow.Session - Executor pool size: 28
Jan-29 16:04:42.172 [main] DEBUG nextflow.cli.CmdRun -
Version: 20.10.0 build 5430
Created: 01-11-2020 15:14 UTC (16:14 CEST)
System: Linux 5.4.0-58-generic
Runtime: Groovy 3.0.5 on OpenJDK 64-Bit Server VM 11.0.8-internal+0-adhoc..src
Encoding: UTF-8 (UTF-8)
Process: 3558564@cbioinfws1 [127.0.1.1]
CPUs: 28 - Mem: 125.5 GB (47.1 GB) - Swap: 14 GB (13.9 GB)
Jan-29 16:04:42.187 [main] DEBUG nextflow.Session - Work-dir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work [zfs]
Jan-29 16:04:42.230 [main] DEBUG nextflow.Session - Observer factory: TowerFactory
Jan-29 16:04:42.234 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Jan-29 16:04:42.408 [main] DEBUG nextflow.Session - Session start invoked
Jan-29 16:04:42.411 [main] DEBUG nextflow.trace.TraceFileObserver - Flow starting -- trace file: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/results/pipeline_info/execution_trace.txt
Jan-29 16:04:45.536 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Jan-29 16:04:45.543 [main] DEBUG nextflow.Session - Workflow process names [dsl1]: MOSDEPTH_GENOME, UNICYCLER_PLASMIDID, UNICYCLER_SNPEFF, MINIA_BLAST, output_documentation, UNICYCLER_VG, IVAR_CONSENSUS, SORT_BAM, FASTP, SRA_FASTQ_FTP, UNICYCLER_ABACAS, PICARD_MARKDUPLICATES, MINIA, VARSCAN2, BCFTOOLS_CONSENSUS, CAT_FASTQ, METASPADES_SNPEFF, GUNZIP_GFF, SPADES_VG, UNICYCLER_QUAST, PICARD_METRICS, KRAKEN2, SPADES_PLASMIDID, METASPADES_QUAST, BCFTOOLS_VARIANTS, BCFTOOLS_SNPEFF, MAKE_BLAST_DB, MOSDEPTH_AMPLICON, METASPADES, IVAR_VARIANTS, FASTQC, BOWTIE2_INDEX, SPADES, METASPADES_VG, SPADES_ABACAS, METASPADES_PLASMIDID, SPADES_SNPEFF, UNICYCLER, MULTIQC, CUTADAPT, KRAKEN2_BUILD, IVAR_TRIM, IVAR_QUAST, UNICYCLER_BLAST, VARSCAN2_QUAST, METASPADES_ABACAS, MINIA_VG, MINIA_ABACAS, get_software_versions, SPADES_BLAST, MINIA_SNPEFF, SPADES_QUAST, MAKE_SNPEFF_DB, BCFTOOLS_QUAST, SAMTOOLS_MPILEUP, GUNZIP_FASTA, METASPADES_BLAST, BCFTOOLS_ISEC, VARSCAN2_SNPEFF, MINIA_QUAST, UNTAR_KRAKEN2_DB, MOSDEPTH_AMPLICON_PLOT, SRA_FASTQ_DUMP, MINIA_PLASMIDID, BOWTIE2, IVAR_SNPEFF, CHECK_SAMPLESHEET, VARSCAN2_CONSENSUS
Jan-29 16:04:45.772 [main] INFO nextflow.Nextflow - ----------------------------------------------------
,--./,-.
___ __ __ __ ___ /,-._.--~'
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/viralrecon v1.2.0dev
----------------------------------------------------
Jan-29 16:04:45.775 [main] INFO nextflow.Nextflow - Run Name : condescending_volhard
Samplesheet : /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore//samples.csv
Protocol : amplicon
Amplicon Fasta File : /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore//../primer/Eden_processed/Eden_primers.fa
Amplicon BED File : /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore//../primer/Eden_processed/Eden_primers.bed
Amplicon Left Suffix : _LEFT
Amplicon Right Suffix : _RIGHT
Viral Genome : MN908947.3
Viral Fasta File : https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/genome/MN908947.3/GCA_009858895.3_ASM985889v3_genomic.200409.fna.gz
Viral GFF : https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/genome/MN908947.3/GCA_009858895.3_ASM985889v3_genomic.200409.gff.gz
Fastp Mean Qual : 30
Fastp Qual Phred : 30
Fastp Unqual % Limit : 10
Fastp Min Trim Length : 50
Variant Calling Tools : varscan2,ivar,bcftools
Min Mapped Reads : 1000
iVar Trim Min Len : 20
iVar Trim Min Qual : 20
iVar Trim Window : 4
Mpileup Depth : 0
Min Base Quality : 20
Min Read Depth : 10
Min Allele Freq : 0.25
Max Allele Freq : 0.75
Varscan2 Strand Filter: Yes
Skip Kraken2 : Yes
Skip Assembly : Yes
Max Resources : 128.GB memory, 16 cpus, 240.h time per job
Container : singularity - /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore//singularity.dev.961b10463ae1.sif
Output dir : /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore//results
Publish dir mode : copy
Launch dir : /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore
Working dir : /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work
Script dir : /home/crtd_bioinf/fabirost/.nextflow/assets/nf-core/viralrecon
User : fabirost
Config Profile : singularity
Jan-29 16:04:45.775 [main] INFO nextflow.Nextflow - ----------------------------------------------------
Jan-29 16:04:45.814 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_retry` matches label `error_retry` for process with name GUNZIP_FASTA
Jan-29 16:04:45.816 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:45.816 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:45.820 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
Jan-29 16:04:45.824 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=28; memory=125.5 GB; capacity=28; pollInterval=100ms; dumpInterval=5m
Jan-29 16:04:46.130 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_retry` matches label `error_retry` for process with name GUNZIP_GFF
Jan-29 16:04:46.132 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.132 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.137 [Actor Thread 3] DEBUG n.util.BlockingThreadExecutorFactory - Thread pool name=FileTransfer; maxThreads=84; maxQueueSize=252; keepAlive=1m
Jan-29 16:04:46.148 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.148 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.148 [FileTransfer-thread-1] DEBUG nextflow.file.FilePorter - Copying foreign file https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/genome/MN908947.3/GCA_009858895.3_ASM985889v3_genomic.200409.fna.gz to work dir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/stage/d4/6f01f2da9b3e9df329929a24dab4e4/GCA_009858895.3_ASM985889v3_genomic.200409.fna.gz
Jan-29 16:04:46.216 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name SRA_FASTQ_FTP
Jan-29 16:04:46.217 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_retry` matches label `error_retry` for process with name SRA_FASTQ_FTP
Jan-29 16:04:46.217 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.217 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.227 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name SRA_FASTQ_DUMP
Jan-29 16:04:46.227 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_retry` matches label `error_retry` for process with name SRA_FASTQ_DUMP
Jan-29 16:04:46.228 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.228 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.244 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.244 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.249 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name FASTQC
Jan-29 16:04:46.250 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.250 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.255 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name FASTP
Jan-29 16:04:46.255 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.255 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.261 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name BOWTIE2_INDEX
Jan-29 16:04:46.261 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.261 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.265 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches label `process_low` for process with name MAKE_SNPEFF_DB
Jan-29 16:04:46.266 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.266 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.276 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name BOWTIE2
Jan-29 16:04:46.277 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.277 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.283 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name SORT_BAM
Jan-29 16:04:46.284 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.284 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.292 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name IVAR_TRIM
Jan-29 16:04:46.292 [FileTransfer-thread-2] DEBUG nextflow.file.FilePorter - Copying foreign file https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/genome/MN908947.3/GCA_009858895.3_ASM985889v3_genomic.200409.gff.gz to work dir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/stage/65/d4783068a1abebd25f22a3dc83edcd/GCA_009858895.3_ASM985889v3_genomic.200409.gff.gz
Jan-29 16:04:46.292 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.292 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.297 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name PICARD_MARKDUPLICATES
Jan-29 16:04:46.298 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.298 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.303 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name PICARD_METRICS
Jan-29 16:04:46.303 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.303 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.307 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:46.307 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name MOSDEPTH_GENOME
Jan-29 16:04:46.308 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.308 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.310 [Task submitter] INFO nextflow.Session - [02/05e8a9] Submitted process > CHECK_SAMPLESHEET (samples.csv)
Jan-29 16:04:46.314 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name MOSDEPTH_AMPLICON
Jan-29 16:04:46.314 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.314 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.321 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name MOSDEPTH_AMPLICON_PLOT
Jan-29 16:04:46.321 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.321 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.324 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name SAMTOOLS_MPILEUP
Jan-29 16:04:46.325 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.325 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.329 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name VARSCAN2
Jan-29 16:04:46.330 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.330 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.336 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:46.336 [Task submitter] INFO nextflow.Session - [0e/cd6472] Submitted process > GUNZIP_FASTA
Jan-29 16:04:46.339 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name VARSCAN2_CONSENSUS
Jan-29 16:04:46.340 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.340 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.346 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name VARSCAN2_SNPEFF
Jan-29 16:04:46.346 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.346 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.351 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name VARSCAN2_QUAST
Jan-29 16:04:46.351 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.352 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.358 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name IVAR_VARIANTS
Jan-29 16:04:46.358 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.358 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.364 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name IVAR_CONSENSUS
Jan-29 16:04:46.364 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.364 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.368 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name IVAR_SNPEFF
Jan-29 16:04:46.368 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.368 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.372 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name IVAR_QUAST
Jan-29 16:04:46.373 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.373 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.376 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name BCFTOOLS_VARIANTS
Jan-29 16:04:46.376 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.376 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.381 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name BCFTOOLS_CONSENSUS
Jan-29 16:04:46.381 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.381 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.384 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name BCFTOOLS_SNPEFF
Jan-29 16:04:46.385 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.385 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.388 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name BCFTOOLS_QUAST
Jan-29 16:04:46.388 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.388 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.393 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name BCFTOOLS_ISEC
Jan-29 16:04:46.393 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_ignore` matches label `error_ignore` for process with name BCFTOOLS_ISEC
Jan-29 16:04:46.393 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.393 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.396 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name MAKE_BLAST_DB
Jan-29 16:04:46.396 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.396 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.398 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:46.400 [Task submitter] INFO nextflow.Session - [e1/00bc46] Submitted process > GUNZIP_GFF
Jan-29 16:04:46.401 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches label `process_high` for process with name SPADES
Jan-29 16:04:46.401 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_ignore` matches label `error_ignore` for process with name SPADES
Jan-29 16:04:46.402 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.402 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.405 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name SPADES_BLAST
Jan-29 16:04:46.405 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_ignore` matches label `error_ignore` for process with name SPADES_BLAST
Jan-29 16:04:46.406 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.406 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.409 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name SPADES_ABACAS
Jan-29 16:04:46.409 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_ignore` matches label `error_ignore` for process with name SPADES_ABACAS
Jan-29 16:04:46.409 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.409 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.413 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name SPADES_PLASMIDID
Jan-29 16:04:46.413 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_ignore` matches label `error_ignore` for process with name SPADES_PLASMIDID
Jan-29 16:04:46.413 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.413 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.418 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name SPADES_QUAST
Jan-29 16:04:46.418 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_ignore` matches label `error_ignore` for process with name SPADES_QUAST
Jan-29 16:04:46.418 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.418 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.423 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name SPADES_VG
Jan-29 16:04:46.423 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_ignore` matches label `error_ignore` for process with name SPADES_VG
Jan-29 16:04:46.423 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.423 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.426 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name SPADES_SNPEFF
Jan-29 16:04:46.427 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_ignore` matches label `error_ignore` for process with name SPADES_SNPEFF
Jan-29 16:04:46.427 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.427 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.430 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches label `process_high` for process with name METASPADES
Jan-29 16:04:46.431 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_ignore` matches label `error_ignore` for process with name METASPADES
Jan-29 16:04:46.431 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.431 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.434 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name METASPADES_BLAST
Jan-29 16:04:46.434 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_ignore` matches label `error_ignore` for process with name METASPADES_BLAST
Jan-29 16:04:46.434 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.434 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.438 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name METASPADES_ABACAS
Jan-29 16:04:46.438 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_ignore` matches label `error_ignore` for process with name METASPADES_ABACAS
Jan-29 16:04:46.438 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.438 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.442 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name METASPADES_PLASMIDID
Jan-29 16:04:46.442 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_ignore` matches label `error_ignore` for process with name METASPADES_PLASMIDID
Jan-29 16:04:46.443 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.443 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.446 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name METASPADES_QUAST
Jan-29 16:04:46.446 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_ignore` matches label `error_ignore` for process with name METASPADES_QUAST
Jan-29 16:04:46.447 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.447 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.451 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name METASPADES_VG
Jan-29 16:04:46.451 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_ignore` matches label `error_ignore` for process with name METASPADES_VG
Jan-29 16:04:46.451 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.451 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.454 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name METASPADES_SNPEFF
Jan-29 16:04:46.455 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_ignore` matches label `error_ignore` for process with name METASPADES_SNPEFF
Jan-29 16:04:46.455 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.455 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.458 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches label `process_high` for process with name UNICYCLER
Jan-29 16:04:46.458 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_ignore` matches label `error_ignore` for process with name UNICYCLER
Jan-29 16:04:46.458 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.458 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.462 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name UNICYCLER_BLAST
Jan-29 16:04:46.462 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_ignore` matches label `error_ignore` for process with name UNICYCLER_BLAST
Jan-29 16:04:46.463 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.463 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.467 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name UNICYCLER_ABACAS
Jan-29 16:04:46.468 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_ignore` matches label `error_ignore` for process with name UNICYCLER_ABACAS
Jan-29 16:04:46.468 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.468 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.472 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name UNICYCLER_PLASMIDID
Jan-29 16:04:46.473 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_ignore` matches label `error_ignore` for process with name UNICYCLER_PLASMIDID
Jan-29 16:04:46.473 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.473 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.476 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name UNICYCLER_QUAST
Jan-29 16:04:46.477 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_ignore` matches label `error_ignore` for process with name UNICYCLER_QUAST
Jan-29 16:04:46.477 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.477 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.481 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name UNICYCLER_VG
Jan-29 16:04:46.481 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_ignore` matches label `error_ignore` for process with name UNICYCLER_VG
Jan-29 16:04:46.481 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.481 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.485 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name UNICYCLER_SNPEFF
Jan-29 16:04:46.485 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_ignore` matches label `error_ignore` for process with name UNICYCLER_SNPEFF
Jan-29 16:04:46.485 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.485 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.489 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches label `process_high` for process with name MINIA
Jan-29 16:04:46.489 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_ignore` matches label `error_ignore` for process with name MINIA
Jan-29 16:04:46.489 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.489 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.493 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name MINIA_BLAST
Jan-29 16:04:46.493 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_ignore` matches label `error_ignore` for process with name MINIA_BLAST
Jan-29 16:04:46.493 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.493 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.496 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name MINIA_ABACAS
Jan-29 16:04:46.496 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_ignore` matches label `error_ignore` for process with name MINIA_ABACAS
Jan-29 16:04:46.496 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.496 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.500 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name MINIA_PLASMIDID
Jan-29 16:04:46.500 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_ignore` matches label `error_ignore` for process with name MINIA_PLASMIDID
Jan-29 16:04:46.500 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.500 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.503 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name MINIA_QUAST
Jan-29 16:04:46.504 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_ignore` matches label `error_ignore` for process with name MINIA_QUAST
Jan-29 16:04:46.504 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.504 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.507 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name MINIA_VG
Jan-29 16:04:46.507 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_ignore` matches label `error_ignore` for process with name MINIA_VG
Jan-29 16:04:46.508 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.508 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.511 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name MINIA_SNPEFF
Jan-29 16:04:46.511 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_ignore` matches label `error_ignore` for process with name MINIA_SNPEFF
Jan-29 16:04:46.511 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.511 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.524 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:get_software_versions` matches process get_software_versions
Jan-29 16:04:46.524 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.524 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.555 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:46.555 [Task submitter] INFO nextflow.Session - [99/ab7350] Submitted process > get_software_versions
Jan-29 16:04:46.586 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name MULTIQC
Jan-29 16:04:46.587 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.587 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.597 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 16:04:46.598 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 16:04:46.602 [main] DEBUG nextflow.script.ScriptRunner - > Await termination
Jan-29 16:04:46.602 [main] DEBUG nextflow.Session - Session await
Jan-29 16:04:46.611 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:46.613 [Task submitter] INFO nextflow.Session - [3f/dfd1ac] Submitted process > output_documentation
Jan-29 16:04:46.702 [Actor Thread 4] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 1; slices: 1; internal sort time: 0.001 s; external sort time: 0.011 s; total time: 0.012 s
Jan-29 16:04:46.713 [Actor Thread 4] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /tmp/8318f1e9fe9f83c0c4c05c6503d98304.collect-file
Jan-29 16:04:46.719 [Actor Thread 4] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-14007747180325198031
Jan-29 16:04:46.776 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: GUNZIP_FASTA; status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/0e/cd64726e576234d6afd243e60470a4]
Jan-29 16:04:46.813 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:46.813 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 2; name: GUNZIP_GFF; status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/e1/00bc46cbdd23a0a62eeddc73ee8b94]
Jan-29 16:04:46.813 [Task submitter] INFO nextflow.Session - [2b/435f49] Submitted process > BOWTIE2_INDEX (GCA_009858895.3_ASM985889v3_genomic.200409.fna)
Jan-29 16:04:46.829 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:46.829 [Task submitter] INFO nextflow.Session - [22/49fc18] Submitted process > MAKE_SNPEFF_DB (GCA_009858895.3_ASM985889v3_genomic.200409.fa)
Jan-29 16:04:46.854 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 3; name: CHECK_SAMPLESHEET (samples.csv); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/02/05e8a99959b4753cc597633450f804]
Jan-29 16:04:46.856 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process `CHECK_SAMPLESHEET (samples.csv)` is unable to find [UnixPath]: `/home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/02/05e8a99959b4753cc597633450f804/sra_run_info.tsv` (pattern: `sra_run_info.tsv`)
Jan-29 16:04:46.942 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process CHECK_SAMPLESHEET > Skipping output binding because one or more optional files are missing: fileoutparam<1>
Jan-29 16:04:47.261 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:47.261 [Task submitter] INFO nextflow.Session - [9d/c9edcd] Submitted process > CAT_FASTQ (L66086_EdenPool_Covid-DD-VIR-00218)
Jan-29 16:04:47.368 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:47.368 [Task submitter] INFO nextflow.Session - [c9/38ae42] Submitted process > CAT_FASTQ (L66089_EdenPool_Covid-DD-VIR-00225)
Jan-29 16:04:47.372 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:47.372 [Task submitter] INFO nextflow.Session - [23/47d98a] Submitted process > CAT_FASTQ (L66099_EdenPool_Covid-DD-VIR-00243)
Jan-29 16:04:47.377 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:47.378 [Task submitter] INFO nextflow.Session - [b6/c5cc2e] Submitted process > CAT_FASTQ (L66075_EdenPool_Covid-DD-VIR-00203)
Jan-29 16:04:47.382 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:47.383 [Task submitter] INFO nextflow.Session - [10/4619d2] Submitted process > CAT_FASTQ (L66084_EdenPool_Covid-DD-VIR-00213)
Jan-29 16:04:47.388 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:47.389 [Task submitter] INFO nextflow.Session - [7b/ee6817] Submitted process > CAT_FASTQ (L66080_EdenPool_Covid-DD-VIR-00209)
Jan-29 16:04:47.394 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:47.394 [Task submitter] INFO nextflow.Session - [53/5de058] Submitted process > CAT_FASTQ (L66083_EdenPool_Covid-DD-VIR-00212)
Jan-29 16:04:47.481 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 7; name: BOWTIE2_INDEX (GCA_009858895.3_ASM985889v3_genomic.200409.fna); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/2b/435f49b16c5b5dcc5d9a8ca1dfd157]
Jan-29 16:04:47.488 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:47.489 [Task submitter] INFO nextflow.Session - [dd/794e12] Submitted process > CAT_FASTQ (L66093_EdenPool_Covid-DD-VIR-00235)
Jan-29 16:04:47.495 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:47.495 [Task submitter] INFO nextflow.Session - [d2/0ab361] Submitted process > CAT_FASTQ (L66091_EdenPool_Covid-DD-VIR-00229)
Jan-29 16:04:47.498 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:47.499 [Task submitter] INFO nextflow.Session - [5b/808949] Submitted process > CAT_FASTQ (L66082_EdenPool_Covid-DD-VIR-00211)
Jan-29 16:04:47.503 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:47.505 [Task submitter] INFO nextflow.Session - [0f/a9d31b] Submitted process > CAT_FASTQ (L66100_EdenPool_Covid-DD-VIR-00244)
Jan-29 16:04:47.509 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:47.509 [Task submitter] INFO nextflow.Session - [91/da743d] Submitted process > CAT_FASTQ (L66095_EdenPool_Covid-DD-VIR-00237)
Jan-29 16:04:47.513 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:47.513 [Task submitter] INFO nextflow.Session - [81/4f7d3a] Submitted process > CAT_FASTQ (L66078_EdenPool_Covid-DD-VIR-00207)
Jan-29 16:04:47.578 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 5; name: output_documentation; status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/3f/dfd1ac62f7ef2fb814e8b064d80f69]
Jan-29 16:04:47.582 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:47.583 [Task submitter] INFO nextflow.Session - [fc/9de7d1] Submitted process > CAT_FASTQ (L66088_EdenPool_Covid-DD-VIR-00221)
Jan-29 16:04:47.628 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 21; name: CAT_FASTQ (L66086_EdenPool_Covid-DD-VIR-00218); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/9d/c9edcdd2549682ed2c4b8e90962be0]
Jan-29 16:04:47.633 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:47.633 [Task submitter] INFO nextflow.Session - [35/b68bc5] Submitted process > CAT_FASTQ (L66090_EdenPool_Covid-DD-VIR-00226)
Jan-29 16:04:48.048 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 34; name: CAT_FASTQ (L66099_EdenPool_Covid-DD-VIR-00243); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/23/47d98a6a017a12cec1f39351ec4f4e]
Jan-29 16:04:48.052 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:48.052 [Task submitter] INFO nextflow.Session - [21/f7ef2c] Submitted process > CAT_FASTQ (L66094_EdenPool_Covid-DD-VIR-00236)
Jan-29 16:04:48.089 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 15; name: CAT_FASTQ (L66080_EdenPool_Covid-DD-VIR-00209); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/7b/ee681796965d59b6601a420e6b9705]
Jan-29 16:04:48.093 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:48.101 [Task submitter] INFO nextflow.Session - [8c/eb1e12] Submitted process > CAT_FASTQ (L66097_EdenPool_Covid-DD-VIR-00240)
Jan-29 16:04:48.169 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 24; name: CAT_FASTQ (L66089_EdenPool_Covid-DD-VIR-00225); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/c9/38ae42802f24319657933d43c11a88]
Jan-29 16:04:48.172 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:48.173 [Task submitter] INFO nextflow.Session - [15/592959] Submitted process > CAT_FASTQ (L66077_EdenPool_Covid-DD-VIR-00206)
Jan-29 16:04:48.175 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 10; name: CAT_FASTQ (L66075_EdenPool_Covid-DD-VIR-00203); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/b6/c5cc2eaa84bde00df51f2b9defdaaf]
Jan-29 16:04:48.180 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:48.180 [Task submitter] INFO nextflow.Session - [96/91d0cf] Submitted process > CAT_FASTQ (L66076_EdenPool_Covid-DD-VIR-00205)
Jan-29 16:04:48.209 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 20; name: CAT_FASTQ (L66084_EdenPool_Covid-DD-VIR-00213); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/10/4619d25993a419d6bf78914274350b]
Jan-29 16:04:48.216 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 18; name: CAT_FASTQ (L66083_EdenPool_Covid-DD-VIR-00212); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/53/5de058b8baff74a31723f581bac17f]
Jan-29 16:04:48.217 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:48.218 [Task submitter] INFO nextflow.Session - [9a/86c686] Submitted process > CAT_FASTQ (L66098_EdenPool_Covid-DD-VIR-00241)
Jan-29 16:04:48.227 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:48.227 [Task submitter] INFO nextflow.Session - [9c/76507b] Submitted process > CAT_FASTQ (L66079_EdenPool_Covid-DD-VIR-00208)
Jan-29 16:04:48.329 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 28; name: CAT_FASTQ (L66093_EdenPool_Covid-DD-VIR-00235); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/dd/794e1280831b70961b7616298e8de4]
Jan-29 16:04:48.332 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:48.332 [Task submitter] INFO nextflow.Session - [38/1fbe20] Submitted process > CAT_FASTQ (L66081_EdenPool_Covid-DD-VIR-00210)
Jan-29 16:04:48.417 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 26; name: CAT_FASTQ (L66091_EdenPool_Covid-DD-VIR-00229); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/d2/0ab3613df6a009215572ea4b8bf876]
Jan-29 16:04:48.423 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:48.424 [Task submitter] INFO nextflow.Session - [e5/7db6cd] Submitted process > CAT_FASTQ (L66092_EdenPool_Covid-DD-VIR-00231)
Jan-29 16:04:48.516 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 17; name: CAT_FASTQ (L66082_EdenPool_Covid-DD-VIR-00211); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/5b/80894983db70c8227739ee8f242635]
Jan-29 16:04:48.519 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:48.519 [Task submitter] INFO nextflow.Session - [81/23ed74] Submitted process > CAT_FASTQ (L66074_EdenPool_Covid-DD-VIR-00201)
Jan-29 16:04:48.730 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 30; name: CAT_FASTQ (L66095_EdenPool_Covid-DD-VIR-00237); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/91/da743ddc120f3302595b241ec606a4]
Jan-29 16:04:48.732 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:48.732 [Task submitter] INFO nextflow.Session - [a4/5d0aa3] Submitted process > CAT_FASTQ (L66101_EdenPool_Covid-DD-VIR-00245)
Jan-29 16:04:48.806 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 35; name: CAT_FASTQ (L66100_EdenPool_Covid-DD-VIR-00244); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/0f/a9d31b11a58ba6896acfcfbf2083d8]
Jan-29 16:04:48.811 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:48.811 [Task submitter] INFO nextflow.Session - [b0/e41d54] Submitted process > CAT_FASTQ (L66087_EdenPool_Covid-DD-VIR-00219)
Jan-29 16:04:48.814 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 13; name: CAT_FASTQ (L66078_EdenPool_Covid-DD-VIR-00207); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/81/4f7d3ab01d35df8434dede990722c9]
Jan-29 16:04:48.820 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:48.820 [Task submitter] INFO nextflow.Session - [24/b4bee7] Submitted process > CAT_FASTQ (L66085_EdenPool_Covid-DD-VIR-00215)
Jan-29 16:04:48.824 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 25; name: CAT_FASTQ (L66090_EdenPool_Covid-DD-VIR-00226); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/35/b68bc5ca082cac0a2dfeb834217ea3]
Jan-29 16:04:48.828 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:48.828 [Task submitter] INFO nextflow.Session - [19/8f7b2e] Submitted process > CAT_FASTQ (L66144_EdenPool_cDNA_S41_20201227-787782_01_A06)
Jan-29 16:04:48.832 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 29; name: CAT_FASTQ (L66094_EdenPool_Covid-DD-VIR-00236); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/21/f7ef2cc87ae61f24496d13329203b5]
Jan-29 16:04:48.839 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:48.839 [Task submitter] INFO nextflow.Session - [97/1600e2] Submitted process > CAT_FASTQ (L66145_EdenPool_cDNA_S42_20201227-787343_01_B06)
Jan-29 16:04:48.906 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 8; name: MAKE_SNPEFF_DB (GCA_009858895.3_ASM985889v3_genomic.200409.fa); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/22/49fc18a973328f28a8ba8c964c0f62]
Jan-29 16:04:48.912 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 22; name: CAT_FASTQ (L66088_EdenPool_Covid-DD-VIR-00221); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/fc/9de7d19fa9899b1018ed7f9c130d08]
Jan-29 16:04:48.913 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:48.914 [Task submitter] INFO nextflow.Session - [ac/a64d0e] Submitted process > CAT_FASTQ (L66096_EdenPool_Covid-DD-VIR-00238)
Jan-29 16:04:48.921 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:48.921 [Task submitter] INFO nextflow.Session - [e2/db0d35] Submitted process > CAT_FASTQ (L66102_EdenPool_Covid-DD-VIR-00246)
Jan-29 16:04:48.927 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:48.927 [Task submitter] INFO nextflow.Session - [98/f973c4] Submitted process > CAT_FASTQ (L66104_EdenPool_cDNA_S1_20210108-799934_01_A01)
Jan-29 16:04:48.969 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 32; name: CAT_FASTQ (L66097_EdenPool_Covid-DD-VIR-00240); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/8c/eb1e125072237010566b835ef69cf8]
Jan-29 16:04:48.975 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:48.975 [Task submitter] INFO nextflow.Session - [3a/4085ea] Submitted process > CAT_FASTQ (L66105_EdenPool_cDNA_S2_20210106-797126_01_B01)
Jan-29 16:04:49.170 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 12; name: CAT_FASTQ (L66077_EdenPool_Covid-DD-VIR-00206); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/15/592959d487540f1fcfc692d9df55e9]
Jan-29 16:04:49.174 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:49.174 [Task submitter] INFO nextflow.Session - [38/92454e] Submitted process > CAT_FASTQ (L66106_EdenPool_cDNA_S3_20210104-793515_01_C01)
Jan-29 16:04:49.181 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 11; name: CAT_FASTQ (L66076_EdenPool_Covid-DD-VIR-00205); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/96/91d0cf4dde4d86b574f632b32d9d16]
Jan-29 16:04:49.185 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:49.185 [Task submitter] INFO nextflow.Session - [13/473b1a] Submitted process > CAT_FASTQ (L66107_EdenPool_cDNA_S4_20210110-721656_01_D01)
Jan-29 16:04:49.308 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 14; name: CAT_FASTQ (L66079_EdenPool_Covid-DD-VIR-00208); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/9c/76507b682b4350379f34c3fed7195d]
Jan-29 16:04:49.311 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:49.311 [Task submitter] INFO nextflow.Session - [c9/699aeb] Submitted process > CAT_FASTQ (L66108_EdenPool_cDNA_S5_20210109-721159_01_E01)
Jan-29 16:04:49.341 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 33; name: CAT_FASTQ (L66098_EdenPool_Covid-DD-VIR-00241); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/9a/86c6865743e7dc7b5f3ea393164f62]
Jan-29 16:04:49.343 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:49.343 [Task submitter] INFO nextflow.Session - [6c/486b0a] Submitted process > CAT_FASTQ (L66109_EdenPool_cDNA_S6_20210108-720624_01_F01)
Jan-29 16:04:49.349 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 16; name: CAT_FASTQ (L66081_EdenPool_Covid-DD-VIR-00210); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/38/1fbe2088e24fcf2d8d71bcb4216027]
Jan-29 16:04:49.356 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:49.356 [Task submitter] INFO nextflow.Session - [ee/e1ae84] Submitted process > CAT_FASTQ (L66110_EdenPool_cDNA_S7_20210108-720770_01_G01)
Jan-29 16:04:49.523 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 27; name: CAT_FASTQ (L66092_EdenPool_Covid-DD-VIR-00231); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/e5/7db6cd3ae948f35c8426a4892d9b19]
Jan-29 16:04:49.526 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:49.526 [Task submitter] INFO nextflow.Session - [6c/67207e] Submitted process > CAT_FASTQ (L66111_EdenPool_cDNA_S8_20210108-720048_01_H01)
Jan-29 16:04:49.530 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 9; name: CAT_FASTQ (L66074_EdenPool_Covid-DD-VIR-00201); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/81/23ed7411e836ceb3f47e131a72f506]
Jan-29 16:04:49.538 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 36; name: CAT_FASTQ (L66101_EdenPool_Covid-DD-VIR-00245); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/a4/5d0aa31e8e2a2a1c41d55d325eb433]
Jan-29 16:04:49.541 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:49.541 [Task submitter] INFO nextflow.Session - [4f/5893ff] Submitted process > CAT_FASTQ (L66112_EdenPool_cDNA_S9_20210108-720344_01_A02)
Jan-29 16:04:49.545 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:49.545 [Task submitter] INFO nextflow.Session - [09/68b04a] Submitted process > CAT_FASTQ (L66113_EdenPool_cDNA_S10_20210107-798696_01_B02)
Jan-29 16:04:49.597 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 23; name: CAT_FASTQ (L66087_EdenPool_Covid-DD-VIR-00219); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/b0/e41d544e0ae93b3b1a13948a0fa86c]
Jan-29 16:04:49.600 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:49.600 [Task submitter] INFO nextflow.Session - [03/d660b8] Submitted process > CAT_FASTQ (L66114_EdenPool_cDNA_S11_20210106-797945_01_C02)
Jan-29 16:04:49.684 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 79; name: CAT_FASTQ (L66145_EdenPool_cDNA_S42_20201227-787343_01_B06); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/97/1600e2676fd9a3bd5bd5c78bf8e2ca]
Jan-29 16:04:49.690 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:49.691 [Task submitter] INFO nextflow.Session - [41/56446c] Submitted process > CAT_FASTQ (L66115_EdenPool_cDNA_S12_20210106-797963_01_D02)
Jan-29 16:04:49.764 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 19; name: CAT_FASTQ (L66085_EdenPool_Covid-DD-VIR-00215); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/24/b4bee76330bb6c1266aec7a46cb40d]
Jan-29 16:04:49.768 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:49.769 [Task submitter] INFO nextflow.Session - [fe/7bfe33] Submitted process > CAT_FASTQ (L66116_EdenPool_cDNA_S13_20210108-720393_01_E02)
Jan-29 16:04:49.816 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 78; name: CAT_FASTQ (L66144_EdenPool_cDNA_S41_20201227-787782_01_A06); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/19/8f7b2e585d49d0d23342cc1da5ad71]
Jan-29 16:04:49.820 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:49.820 [Task submitter] INFO nextflow.Session - [80/b9b465] Submitted process > CAT_FASTQ (L66117_EdenPool_cDNA_S14_20210104-795197_01_F02)
Jan-29 16:04:49.821 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 31; name: CAT_FASTQ (L66096_EdenPool_Covid-DD-VIR-00238); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/ac/a64d0e124058f4106ca369069c6f3d]
Jan-29 16:04:49.828 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:49.828 [Task submitter] INFO nextflow.Session - [2e/e8da82] Submitted process > CAT_FASTQ (L66118_EdenPool_cDNA_S15_20210104-794211_01_G02)
Jan-29 16:04:49.861 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 37; name: CAT_FASTQ (L66102_EdenPool_Covid-DD-VIR-00246); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/e2/db0d35b8d6a044b4960e78d7ee7d77]
Jan-29 16:04:49.865 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:49.865 [Task submitter] INFO nextflow.Session - [fa/684ec6] Submitted process > CAT_FASTQ (L66119_EdenPool_cDNA_S16_20210104-794508_01_H02)
Jan-29 16:04:49.976 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 38; name: CAT_FASTQ (L66104_EdenPool_cDNA_S1_20210108-799934_01_A01); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/98/f973c416041bf56ec445e28726a069]
Jan-29 16:04:49.979 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:49.979 [Task submitter] INFO nextflow.Session - [07/869e09] Submitted process > CAT_FASTQ (L66120_EdenPool_cDNA_S17_20210105-796034_01_A03)
Jan-29 16:04:50.076 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 39; name: CAT_FASTQ (L66105_EdenPool_cDNA_S2_20210106-797126_01_B01); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/3a/4085ea0836ae79dfe1c111c2e8d755]
Jan-29 16:04:50.080 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:50.080 [Task submitter] INFO nextflow.Session - [3f/d866ed] Submitted process > CAT_FASTQ (L66121_EdenPool_cDNA_S18_20210105-796550_01_B03)
Jan-29 16:04:50.120 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 40; name: CAT_FASTQ (L66106_EdenPool_cDNA_S3_20210104-793515_01_C01); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/38/92454ea4b5231b19b684b3921d9c9b]
Jan-29 16:04:50.123 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:50.123 [Task submitter] INFO nextflow.Session - [6c/d366b6] Submitted process > CAT_FASTQ (L66122_EdenPool_cDNA_S19_20210106-797851_01_C03)
Jan-29 16:04:50.126 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 41; name: CAT_FASTQ (L66107_EdenPool_cDNA_S4_20210110-721656_01_D01); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/13/473b1aed59cb54dc087c438fcb6dfb]
Jan-29 16:04:50.128 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:50.128 [Task submitter] INFO nextflow.Session - [14/24e7bd] Submitted process > CAT_FASTQ (L66123_EdenPool_cDNA_S20_20210103-793929_01_D03)
Jan-29 16:04:50.164 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 43; name: CAT_FASTQ (L66109_EdenPool_cDNA_S6_20210108-720624_01_F01); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/6c/486b0aff6c030480268baaf8fe9f5f]
Jan-29 16:04:50.166 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:50.167 [Task submitter] INFO nextflow.Session - [c0/43a774] Submitted process > CAT_FASTQ (L66124_EdenPool_cDNA_S21_20210103-793393_01_E03)
Jan-29 16:04:50.197 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 42; name: CAT_FASTQ (L66108_EdenPool_cDNA_S5_20210109-721159_01_E01); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/c9/699aeb8603c2812b655bd57ff95c49]
Jan-29 16:04:50.200 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:50.200 [Task submitter] INFO nextflow.Session - [9d/5e0847] Submitted process > CAT_FASTQ (L66125_EdenPool_cDNA_S22_20210103-793390_01_F03)
Jan-29 16:04:50.337 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 44; name: CAT_FASTQ (L66110_EdenPool_cDNA_S7_20210108-720770_01_G01); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/ee/e1ae8489bd48a0e79b3e2843e15c91]
Jan-29 16:04:50.341 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:50.341 [Task submitter] INFO nextflow.Session - [b1/be8b52] Submitted process > CAT_FASTQ (L66126_EdenPool_cDNA_S23_20210103-793439_01_G03)
Jan-29 16:04:50.452 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 46; name: CAT_FASTQ (L66112_EdenPool_cDNA_S9_20210108-720344_01_A02); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/4f/5893ff34ca2604897a89b20918db9c]
Jan-29 16:04:50.454 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:50.454 [Task submitter] INFO nextflow.Session - [17/071bea] Submitted process > CAT_FASTQ (L66127_EdenPool_cDNA_S24_20210102-792782_01_H03)
Jan-29 16:04:50.484 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 45; name: CAT_FASTQ (L66111_EdenPool_cDNA_S8_20210108-720048_01_H01); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/6c/67207e44eac9f050eb8e70be1f6054]
Jan-29 16:04:50.487 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:50.487 [Task submitter] INFO nextflow.Session - [b2/91340c] Submitted process > CAT_FASTQ (L66128_EdenPool_cDNA_S25_20210101-792223_01_A04)
Jan-29 16:04:50.580 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 47; name: CAT_FASTQ (L66113_EdenPool_cDNA_S10_20210107-798696_01_B02); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/09/68b04ae1b388bc18c01a823327eaed]
Jan-29 16:04:50.584 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:50.585 [Task submitter] INFO nextflow.Session - [76/c8f1e9] Submitted process > CAT_FASTQ (L66129_EdenPool_cDNA_S26_20201230-791215_01_B04)
Jan-29 16:04:50.586 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 48; name: CAT_FASTQ (L66114_EdenPool_cDNA_S11_20210106-797945_01_C02); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/03/d660b80221c6dcbe01ed75b36bf501]
Jan-29 16:04:50.590 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:50.590 [Task submitter] INFO nextflow.Session - [bb/a4b504] Submitted process > CAT_FASTQ (L66130_EdenPool_cDNA_S27_20201230-790456_01_C04)
Jan-29 16:04:50.608 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 49; name: CAT_FASTQ (L66115_EdenPool_cDNA_S12_20210106-797963_01_D02); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/41/56446c28275b4e533aa15d00c3b587]
Jan-29 16:04:50.611 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:50.611 [Task submitter] INFO nextflow.Session - [06/777eeb] Submitted process > CAT_FASTQ (L66131_EdenPool_cDNA_S28_20201230-790289_01_D04)
Jan-29 16:04:50.770 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 52; name: CAT_FASTQ (L66118_EdenPool_cDNA_S15_20210104-794211_01_G02); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/2e/e8da822dda73c481c282b570bd1472]
Jan-29 16:04:50.773 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:50.773 [Task submitter] INFO nextflow.Session - [09/d9e151] Submitted process > CAT_FASTQ (L66132_EdenPool_cDNA_S29_20201230-790328_01_E04)
Jan-29 16:04:50.804 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 50; name: CAT_FASTQ (L66116_EdenPool_cDNA_S13_20210108-720393_01_E02); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/fe/7bfe333ce9dc422811ebb230642f8d]
Jan-29 16:04:50.808 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:50.808 [Task submitter] INFO nextflow.Session - [34/fb6bae] Submitted process > CAT_FASTQ (L66133_EdenPool_cDNA_S30_20201230-790469_01_F04)
Jan-29 16:04:50.810 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 53; name: CAT_FASTQ (L66119_EdenPool_cDNA_S16_20210104-794508_01_H02); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/fa/684ec6e9967ecdc9c8842ad4d7d37a]
Jan-29 16:04:50.816 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:50.816 [Task submitter] INFO nextflow.Session - [72/0b7b4a] Submitted process > CAT_FASTQ (L66134_EdenPool_cDNA_S31_20201230-790388_01_G04)
Jan-29 16:04:50.968 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 51; name: CAT_FASTQ (L66117_EdenPool_cDNA_S14_20210104-795197_01_F02); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/80/b9b46584d249056903b64f468881ce]
Jan-29 16:04:50.972 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:50.972 [Task submitter] INFO nextflow.Session - [f4/662279] Submitted process > CAT_FASTQ (L66135_EdenPool_cDNA_S32_20201230-790275_01_H04)
Jan-29 16:04:50.996 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 54; name: CAT_FASTQ (L66120_EdenPool_cDNA_S17_20210105-796034_01_A03); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/07/869e091f43a5b4c0bbba297fe0eb0f]
Jan-29 16:04:51.001 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:51.001 [Task submitter] INFO nextflow.Session - [a0/7746cd] Submitted process > CAT_FASTQ (L66136_EdenPool_cDNA_S33_20201230-791165_01_A05)
Jan-29 16:04:51.121 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 55; name: CAT_FASTQ (L66121_EdenPool_cDNA_S18_20210105-796550_01_B03); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/3f/d866ed926d80550ae0e50ea5eec4fe]
Jan-29 16:04:51.125 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:51.125 [Task submitter] INFO nextflow.Session - [d1/43fc04] Submitted process > CAT_FASTQ (L66137_EdenPool_cDNA_S34_20201229-789657_01_B05)
Jan-29 16:04:51.288 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 56; name: CAT_FASTQ (L66122_EdenPool_cDNA_S19_20210106-797851_01_C03); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/6c/d366b6ff4aca91634251e9d5b294cb]
Jan-29 16:04:51.291 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:51.291 [Task submitter] INFO nextflow.Session - [3c/d49ad1] Submitted process > CAT_FASTQ (L66138_EdenPool_cDNA_S35_20201228-788665_01_C05)
Jan-29 16:04:51.344 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 58; name: CAT_FASTQ (L66124_EdenPool_cDNA_S21_20210103-793393_01_E03); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/c0/43a774ac84a96f18f39f465c19749e]
Jan-29 16:04:51.346 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:51.346 [Task submitter] INFO nextflow.Session - [e1/b63762] Submitted process > CAT_FASTQ (L66139_EdenPool_cDNA_S36_20201228-788797_01_D05)
Jan-29 16:04:51.388 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 57; name: CAT_FASTQ (L66123_EdenPool_cDNA_S20_20210103-793929_01_D03); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/14/24e7bdb4a1991f4a6bff51aa8edc0c]
Jan-29 16:04:51.390 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:51.390 [Task submitter] INFO nextflow.Session - [12/424e0e] Submitted process > CAT_FASTQ (L66140_EdenPool_cDNA_S37_20201228-788712_01_E05)
Jan-29 16:04:51.421 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 59; name: CAT_FASTQ (L66125_EdenPool_cDNA_S22_20210103-793390_01_F03); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/9d/5e08477bbf93045cdfa858ee58bed9]
Jan-29 16:04:51.423 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:51.423 [Task submitter] INFO nextflow.Session - [4a/5590a4] Submitted process > CAT_FASTQ (L66141_EdenPool_cDNA_S38_20201228-788358_01_F05)
Jan-29 16:04:51.500 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 60; name: CAT_FASTQ (L66126_EdenPool_cDNA_S23_20210103-793439_01_G03); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/b1/be8b52e7592f8c89c2f47f97c0b1c6]
Jan-29 16:04:51.505 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:51.505 [Task submitter] INFO nextflow.Session - [ac/90e40a] Submitted process > CAT_FASTQ (L66142_EdenPool_cDNA_S39_20201228-788063_01_G05)
Jan-29 16:04:51.529 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 63; name: CAT_FASTQ (L66129_EdenPool_cDNA_S26_20201230-791215_01_B04); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/76/c8f1e96eacc74e74a336836b7b5e72]
Jan-29 16:04:51.533 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:51.533 [Task submitter] INFO nextflow.Session - [4d/c43fd3] Submitted process > CAT_FASTQ (L66143_EdenPool_cDNA_S40_20201228-787781_01_H05)
Jan-29 16:04:51.612 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 61; name: CAT_FASTQ (L66127_EdenPool_cDNA_S24_20210102-792782_01_H03); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/17/071beac07e8ed046765cdfac48ec11]
Jan-29 16:04:51.614 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:51.614 [Task submitter] INFO nextflow.Session - [79/3c3b41] Submitted process > CAT_FASTQ (L66146_EdenPool_cDNA_S43_20201227-787460_01_C06)
Jan-29 16:04:51.618 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 62; name: CAT_FASTQ (L66128_EdenPool_cDNA_S25_20210101-792223_01_A04); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/b2/91340cba5bc697ecf038adcf64c94f]
Jan-29 16:04:51.625 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:51.625 [Task submitter] INFO nextflow.Session - [ea/13c5cd] Submitted process > CAT_FASTQ (L66147_EdenPool_cDNA_S44_20201226-787053_01_D06)
Jan-29 16:04:51.712 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 64; name: CAT_FASTQ (L66130_EdenPool_cDNA_S27_20201230-790456_01_C04); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/bb/a4b50431fd7e3b4495b3dc4484ff2d]
Jan-29 16:04:51.715 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:51.715 [Task submitter] INFO nextflow.Session - [e6/d017db] Submitted process > CAT_FASTQ (L66148_EdenPool_cDNA_S45_20210103-793417_01_E06)
Jan-29 16:04:51.897 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 65; name: CAT_FASTQ (L66131_EdenPool_cDNA_S28_20201230-790289_01_D04); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/06/777eebea303557608d93be7ce982fa]
Jan-29 16:04:51.900 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:51.900 [Task submitter] INFO nextflow.Session - [9c/1344e9] Submitted process > CAT_FASTQ (L66149_EdenPool_cDNA_S46_20210103-793617_01_F06)
Jan-29 16:04:51.948 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 67; name: CAT_FASTQ (L66133_EdenPool_cDNA_S30_20201230-790469_01_F04); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/34/fb6baec0289e0b3725045a248600a9]
Jan-29 16:04:51.950 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:51.950 [Task submitter] INFO nextflow.Session - [f8/bba5f8] Submitted process > CAT_FASTQ (L66150_EdenPool_cDNA_S47_20210103-793411_01_G06)
Jan-29 16:04:52.061 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 68; name: CAT_FASTQ (L66134_EdenPool_cDNA_S31_20201230-790388_01_G04); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/72/0b7b4a90309edcb1c0194e38a8fcc3]
Jan-29 16:04:52.065 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:52.065 [Task submitter] INFO nextflow.Session - [d4/cd8a88] Submitted process > CAT_FASTQ (L66151_EdenPool_cDNA_S48_20210103-792272_01_H06)
Jan-29 16:04:52.068 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 69; name: CAT_FASTQ (L66135_EdenPool_cDNA_S32_20201230-790275_01_H04); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/f4/662279be13bc1ef173978f609794e5]
Jan-29 16:04:52.073 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:52.073 [Task submitter] INFO nextflow.Session - [cf/1f2fc8] Submitted process > CAT_FASTQ (L66152_EdenPool_Covid-DD-VIR-00103)
Jan-29 16:04:52.089 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 4; name: get_software_versions; status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/99/ab7350c18e31255310114459b124bb]
Jan-29 16:04:52.093 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 66; name: CAT_FASTQ (L66132_EdenPool_cDNA_S29_20201230-790328_01_E04); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/09/d9e15114e1459fa14a46ef7fc7eaed]
Jan-29 16:04:52.093 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:52.093 [Task submitter] INFO nextflow.Session - [33/aa3b31] Submitted process > CAT_FASTQ (L66153_EdenPool_FH_0152)
Jan-29 16:04:52.098 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 70; name: CAT_FASTQ (L66136_EdenPool_cDNA_S33_20201230-791165_01_A05); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/a0/7746cda21070cfeb6fed4e05353473]
Jan-29 16:04:52.098 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:52.098 [Task submitter] INFO nextflow.Session - [9f/d91a4c] Submitted process > CAT_FASTQ (L66154_EdenPool_FH_0170)
Jan-29 16:04:52.105 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:52.105 [Task submitter] INFO nextflow.Session - [d7/2d078d] Submitted process > CAT_FASTQ (L66155_EdenPool_FH_0455)
Jan-29 16:04:52.253 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 72; name: CAT_FASTQ (L66138_EdenPool_cDNA_S35_20201228-788665_01_C05); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/3c/d49ad142687482d29992645cb56a0e]
Jan-29 16:04:52.257 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:52.257 [Task submitter] INFO nextflow.Session - [8e/5a9863] Submitted process > CAT_FASTQ (L66156_EdenPool_FH_0769)
Jan-29 16:04:52.337 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 71; name: CAT_FASTQ (L66137_EdenPool_cDNA_S34_20201229-789657_01_B05); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/d1/43fc04b80fe00fcfe25cc33dd805b8]
Jan-29 16:04:52.340 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:52.341 [Task submitter] INFO nextflow.Session - [75/ac8598] Submitted process > CAT_FASTQ (L66157_EdenPool_FH_0770)
Jan-29 16:04:52.488 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 73; name: CAT_FASTQ (L66139_EdenPool_cDNA_S36_20201228-788797_01_D05); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/e1/b63762e4f4dc53e2f9f43ef97424a4]
Jan-29 16:04:52.493 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:52.494 [Task submitter] INFO nextflow.Session - [50/474db9] Submitted process > CAT_FASTQ (L66158_EdenPool_FH_0790)
Jan-29 16:04:52.620 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 75; name: CAT_FASTQ (L66141_EdenPool_cDNA_S38_20201228-788358_01_F05); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/4a/5590a4395b3018a9c04538ca18c2f9]
Jan-29 16:04:52.625 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:52.626 [Task submitter] INFO nextflow.Session - [79/851e6d] Submitted process > CAT_FASTQ (L66159_EdenPool_Covid-DD-VIR-00247)
Jan-29 16:04:52.626 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 76; name: CAT_FASTQ (L66142_EdenPool_cDNA_S39_20201228-788063_01_G05); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/ac/90e40a1f35178f1e802356616f0917]
Jan-29 16:04:52.721 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 74; name: CAT_FASTQ (L66140_EdenPool_cDNA_S37_20201228-788712_01_E05); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/12/424e0effc8a49be5aac16864a66e3d]
Jan-29 16:04:52.769 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 77; name: CAT_FASTQ (L66143_EdenPool_cDNA_S40_20201228-787781_01_H05); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/4d/c43fd32e0f2f749fd4b01ce15aa6f2]
Jan-29 16:04:52.773 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 80; name: CAT_FASTQ (L66146_EdenPool_cDNA_S43_20201227-787460_01_C06); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/79/3c3b4148c68c5dde4a2b9b2d33502f]
Jan-29 16:04:52.845 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 81; name: CAT_FASTQ (L66147_EdenPool_cDNA_S44_20201226-787053_01_D06); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/ea/13c5cdd02ca360651d5b6de72820e4]
Jan-29 16:04:52.933 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 82; name: CAT_FASTQ (L66148_EdenPool_cDNA_S45_20210103-793417_01_E06); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/e6/d017db51f9a720c6dfc800cbc75314]
Jan-29 16:04:52.936 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:52.936 [Task submitter] INFO nextflow.Session - [9b/70cee0] Submitted process > FASTQC (L66086_EdenPool_Covid-DD-VIR-00218)
Jan-29 16:04:52.969 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 83; name: CAT_FASTQ (L66149_EdenPool_cDNA_S46_20210103-793617_01_F06); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/9c/1344e9d6f0cacc0131caa9fcf9e04b]
Jan-29 16:04:53.037 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 84; name: CAT_FASTQ (L66150_EdenPool_cDNA_S47_20210103-793411_01_G06); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/f8/bba5f80219b0f124fd0122b89660e9]
Jan-29 16:04:53.060 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 85; name: CAT_FASTQ (L66151_EdenPool_cDNA_S48_20210103-792272_01_H06); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/d4/cd8a88a697a1c1d567219162f70be1]
Jan-29 16:04:53.260 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 86; name: CAT_FASTQ (L66152_EdenPool_Covid-DD-VIR-00103); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/cf/1f2fc85c66414ce28c5eb878f6a2a8]
Jan-29 16:04:53.266 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 87; name: CAT_FASTQ (L66153_EdenPool_FH_0152); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/33/aa3b319dc3166a54fe83826aee3754]
Jan-29 16:04:53.364 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 88; name: CAT_FASTQ (L66154_EdenPool_FH_0170); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/9f/d91a4c3783006c6da9fd2b64ba8c03]
Jan-29 16:04:53.366 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:53.366 [Task submitter] INFO nextflow.Session - [b9/9c83de] Submitted process > FASTP (L66086_EdenPool_Covid-DD-VIR-00218)
Jan-29 16:04:53.448 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 89; name: CAT_FASTQ (L66155_EdenPool_FH_0455); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/d7/2d078d47553332a8028a32e528991e]
Jan-29 16:04:53.455 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 90; name: CAT_FASTQ (L66156_EdenPool_FH_0769); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/8e/5a9863bccaac2d59b67050f59999bb]
Jan-29 16:04:53.493 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 91; name: CAT_FASTQ (L66157_EdenPool_FH_0770); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/75/ac8598497ef7801737fb468b48ff7a]
Jan-29 16:04:53.609 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 92; name: CAT_FASTQ (L66158_EdenPool_FH_0790); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/50/474db92fd3d9b409f02d0aea6b4597]
Jan-29 16:04:53.676 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 93; name: CAT_FASTQ (L66159_EdenPool_Covid-DD-VIR-00247); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/79/851e6dbd68d3e21b855c0de399c578]
Jan-29 16:04:58.277 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 95; name: FASTQC (L66086_EdenPool_Covid-DD-VIR-00218); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/9b/70cee026491c6b3868f42bf7b63f48]
Jan-29 16:04:58.285 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:04:58.285 [Task submitter] INFO nextflow.Session - [72/7c6b51] Submitted process > FASTQC (L66099_EdenPool_Covid-DD-VIR-00243)
Jan-29 16:05:03.201 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 96; name: FASTQC (L66099_EdenPool_Covid-DD-VIR-00243); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/72/7c6b518ac1f5250300a57eadb16d34]
Jan-29 16:05:03.205 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:05:03.206 [Task submitter] INFO nextflow.Session - [41/32b6eb] Submitted process > FASTP (L66099_EdenPool_Covid-DD-VIR-00243)
Jan-29 16:05:05.552 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 94; name: FASTP (L66086_EdenPool_Covid-DD-VIR-00218); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/b9/9c83defbd8e71dbf0802bfcb1f8246]
Jan-29 16:05:05.557 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:05:05.557 [Task submitter] INFO nextflow.Session - [c9/b3b26f] Submitted process > FASTQC (L66080_EdenPool_Covid-DD-VIR-00209)
Jan-29 16:05:10.393 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 98; name: FASTQC (L66080_EdenPool_Covid-DD-VIR-00209); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/c9/b3b26faee1218913255be20f92783a]
Jan-29 16:05:10.397 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:05:10.397 [Task submitter] INFO nextflow.Session - [b0/3bd9ff] Submitted process > FASTP (L66080_EdenPool_Covid-DD-VIR-00209)
Jan-29 16:05:11.357 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 97; name: FASTP (L66099_EdenPool_Covid-DD-VIR-00243); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/41/32b6ebc91a6e9c44e1d2a6227b5294]
Jan-29 16:05:11.361 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:05:11.361 [Task submitter] INFO nextflow.Session - [77/15a96a] Submitted process > FASTQC (L66089_EdenPool_Covid-DD-VIR-00225)
Jan-29 16:05:16.309 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 100; name: FASTQC (L66089_EdenPool_Covid-DD-VIR-00225); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/77/15a96a627858e29aa57ed4d737a670]
Jan-29 16:05:16.314 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:05:16.314 [Task submitter] INFO nextflow.Session - [b9/73eb29] Submitted process > FASTP (L66089_EdenPool_Covid-DD-VIR-00225)
Jan-29 16:05:18.521 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 99; name: FASTP (L66080_EdenPool_Covid-DD-VIR-00209); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/b0/3bd9ffa974be35acb098e64e735915]
Jan-29 16:05:18.526 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:05:18.526 [Task submitter] INFO nextflow.Session - [14/139f49] Submitted process > FASTP (L66075_EdenPool_Covid-DD-VIR-00203)
Jan-29 16:05:25.597 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 103; name: FASTP (L66075_EdenPool_Covid-DD-VIR-00203); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/14/139f49a415a39389f105874bdd6ccd]
Jan-29 16:05:25.601 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:05:25.602 [Task submitter] INFO nextflow.Session - [15/c9f701] Submitted process > FASTQC (L66075_EdenPool_Covid-DD-VIR-00203)
Jan-29 16:05:26.601 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 101; name: FASTP (L66089_EdenPool_Covid-DD-VIR-00225); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/b9/73eb295f19bd2702d3cba1138d4053]
Jan-29 16:05:26.605 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:05:26.605 [Task submitter] INFO nextflow.Session - [c1/94a425] Submitted process > FASTQC (L66084_EdenPool_Covid-DD-VIR-00213)
Jan-29 16:05:31.545 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 102; name: FASTQC (L66075_EdenPool_Covid-DD-VIR-00203); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/15/c9f701f860de8cb4bccaa5f620202e]
Jan-29 16:05:31.549 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:05:31.549 [Task submitter] INFO nextflow.Session - [3f/9b4d47] Submitted process > FASTP (L66084_EdenPool_Covid-DD-VIR-00213)
Jan-29 16:05:31.589 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 104; name: FASTQC (L66084_EdenPool_Covid-DD-VIR-00213); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/c1/94a4258145cd345cc8545de512e5d5]
Jan-29 16:05:31.593 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:05:31.593 [Task submitter] INFO nextflow.Session - [e4/f1464d] Submitted process > FASTQC (L66083_EdenPool_Covid-DD-VIR-00212)
Jan-29 16:05:35.513 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 106; name: FASTQC (L66083_EdenPool_Covid-DD-VIR-00212); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/e4/f1464d64eeba0abeb39754b6dcb871]
Jan-29 16:05:35.518 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:05:35.518 [Task submitter] INFO nextflow.Session - [db/dfa667] Submitted process > FASTP (L66083_EdenPool_Covid-DD-VIR-00212)
Jan-29 16:05:39.618 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 105; name: FASTP (L66084_EdenPool_Covid-DD-VIR-00213); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/3f/9b4d477164f19c68dfde1fdba02f4f]
Jan-29 16:05:39.622 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:05:39.622 [Task submitter] INFO nextflow.Session - [7d/08c5e8] Submitted process > FASTP (L66093_EdenPool_Covid-DD-VIR-00235)
Jan-29 16:05:45.580 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 107; name: FASTP (L66083_EdenPool_Covid-DD-VIR-00212); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/db/dfa667a5de08f25b485aed706c4341]
Jan-29 16:05:45.585 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:05:45.585 [Task submitter] INFO nextflow.Session - [69/7a513e] Submitted process > FASTQC (L66093_EdenPool_Covid-DD-VIR-00235)
Jan-29 16:05:47.617 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 109; name: FASTP (L66093_EdenPool_Covid-DD-VIR-00235); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/7d/08c5e824285d6f441e629421060421]
Jan-29 16:05:47.621 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 16:05:47.622 [Task submitter] INFO nextflow.Session - [43/666074] Submitted process > FASTQC (L66091_EdenPool_Covid-DD-VIR-00229)
Jan-29 16:05:50.605 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 108; name: FASTQC (L66093_EdenPool_Covid-DD-VIR-00235); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/69/7a513e68614cd5c9f90dc7ef873bfa]