search

nf-core / viralrecon

Assembly and intrahost/low-frequency variant calling for viral samples
https://nf-co.re/viralrecon
MIT License
113 stars 107 forks source link

viralrecon gets stuck on FASTQC jobs #151

Closed fbnrst closed 3 years ago

fbnrst commented 3 years ago

I try to run viralrecon for 86 samples. It seems the pipeline gets stuck and I cannot figure out why. I did run the pipeline on my local machine (14 cores, 128 GB memory) with standard configuration like this:

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

it starts to run, but then it gets stuck without an error and just seems to hang. There is no CPU usage according to htop. When I run the pipeline on our cluster, distributing jobs with SGE, I get a similar issue. First, I thought it is SGE, but now that the pipeline also gets stuck on my local machine. Getting stuck means, there is no new entry in the log for 1.5 hours now. From the log, I can see that the last jobs were FASTQC jobs. What can I do, do you need more infos? I attach the log.

`.nextflow.log`

``` 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] ```

fbnrst commented 3 years ago

Running with -profile test,singularity, I get: 

-Warning, pipeline completed, but with errored process(es) -
-Number of ignored errored process(es) : 22 -
-Number of successfully ran process(es) : 120 -
-[nf-core/viralrecon] Pipeline completed successfully-
WARN: To render the execution DAG in the required format it is required to install Graphviz -- See http://www.graphviz.org for more info.
Completed at: 29-Jan-2021 18:28:41
Duration    : 4m 51s
CPU hours   : 0.9 (12.2% failed)
Succeeded   : 120
Ignored     : 22
Failed      : 22

full log:

Jan-29 18:23:48.112 [main] DEBUG nextflow.cli.Launcher - $> nextflow run nf-core/viralrecon -profile test,singularity -r e49cee2
Jan-29 18:23:48.179 [main] INFO  nextflow.cli.CmdRun - N E X T F L O W  ~  version 20.10.0
Jan-29 18:23:48.843 [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 18:23:48.855 [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 18:23:49.043 [main] INFO  nextflow.cli.CmdRun - Launching `nf-core/viralrecon` [crazy_ampere] - revision: e49cee2f15dce2e9993736d16f08b1f9d808e292
Jan-29 18:23:49.641 [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 18:23:49.667 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/crtd_bioinf/fabirost/.nextflow/assets/nf-core/viralrecon/nextflow.config
Jan-29 18:23:49.668 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/crtd_bioinf/fabirost/.nextflow/assets/nf-core/viralrecon/nextflow.config
Jan-29 18:23:49.673 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `test,singularity`
...skipping...
"UNICYCLER_ABACAS (SAMPLE1_PE)","q3Label":"UNICYCLER_ABACAS (SAMPLE1_PE)"},"timeUsage":null,"vmem":{"mean":17145856,"min":17145856,"q1":17145856,"q2":17145856,"q3":17145856,"max":17145856,"minLabel":"UNICYCLER_ABACAS (SAMPLE2_PE)","maxLabel":"UNICYCLER_ABACAS (SAMPLE1_PE)","q1Label":"UNICYCLER_ABACAS (SAMPLE2_PE)","q2Label":"UNICYCLER_ABACAS (SAMPLE3_SE)","q3Label":"UNICYCLER_ABACAS (SAMPLE3_SE)"},"reads":{"mean":350422.33,"min":348167,"q1":349852.5,"q2":351538,"q3":351550,"max":351562,"minLabel":"UNICYCLER_ABACAS (SAMPLE2_PE)","maxLabel":"UNICYCLER_ABACAS (SAMPLE3_SE)","q1Label":"UNICYCLER_ABACAS (SAMPLE2_PE)","q2Label":"UNICYCLER_ABACAS (SAMPLE1_PE)","q3Label":"UNICYCLER_ABACAS (SAMPLE1_PE)"},"cpu":{"mean":40.97,"min":38.1,"q1":39.95,"q2":41.8,"q3":42.4,"max":43,"minLabel":"UNICYCLER_ABACAS (SAMPLE1_PE)","maxLabel":"UNICYCLER_ABACAS (SAMPLE2_PE)","q1Label":"UNICYCLER_ABACAS (SAMPLE1_PE)","q2Label":"UNICYCLER_ABACAS (SAMPLE3_SE)","q3Label":"UNICYCLER_ABACAS (SAMPLE3_SE)"},"time":{"mean":204,"min":201,"q1":201.5,"q2":202,"q3":205.5,"max":209,"minLabel":"UNICYCLER_ABACAS (SAMPLE1_PE)","maxLabel":"UNICYCLER_ABACAS (SAMPLE3_SE)","q1Label":"UNICYCLER_ABACAS (SAMPLE1_PE)","q2Label":"UNICYCLER_ABACAS (SAMPLE2_PE)","q3Label":"UNICYCLER_ABACAS (SAMPLE2_PE)"},"writes":{"mean":61585.33,"min":56387,"q1":59753.5,"q2":63120,"q3":64184.5,"max":65249,"minLabel":"UNICYCLER_ABACAS (SAMPLE3_SE)","maxLabel":"UNICYCLER_ABACAS (SAMPLE1_PE)","q1Label":"UNICYCLER_ABACAS (SAMPLE3_SE)","q2Label":"UNICYCLER_ABACAS (SAMPLE2_PE)","q3Label":"UNICYCLER_ABACAS (SAMPLE2_PE)"}},{"cpuUsage":null,"process":"UNICYCLER_VG","mem":null,"memUsage":null,"timeUsage":null,"vmem":null,"reads":null,"cpu":null,"time":{"mean":719.67,"min":704,"q1":714.5,"q2":725,"q3":727.5,"max":730,"minLabel":"UNICYCLER_VG (SAMPLE2_PE)","maxLabel":"UNICYCLER_VG (SAMPLE1_PE)","q1Label":"UNICYCLER_VG (SAMPLE2_PE)","q2Label":"UNICYCLER_VG (SAMPLE3_SE)","q3Label":"UNICYCLER_VG (SAMPLE3_SE)"},"writes":null},{"cpuUsage":{"mean":37.58,"min":35.65,"q1":36.47,"q2":37.3,"q3":38.55,"max":39.8,"minLabel":"UNICYCLER_BLAST (SAMPLE1_PE)","maxLabel":"UNICYCLER_BLAST (SAMPLE2_PE)","q1Label":"UNICYCLER_BLAST (SAMPLE1_PE)","q2Label":"UNICYCLER_BLAST (SAMPLE3_SE)","q3Label":"UNICYCLER_BLAST (SAMPLE3_SE)"},"process":"UNICYCLER_BLAST","mem":{"mean":6400682.67,"min":6029312,"q1":6135808,"q2":6242304,"q3":6586368,"max":6930432,"minLabel":"UNICYCLER_BLAST (SAMPLE3_SE)","maxLabel":"UNICYCLER_BLAST (SAMPLE2_PE)","q1Label":"UNICYCLER_BLAST (SAMPLE3_SE)","q2Label":"UNICYCLER_BLAST (SAMPLE1_PE)","q3Label":"UNICYCLER_BLAST (SAMPLE1_PE)"},"memUsage":{"mean":0.1,"min":0.09,"q1":0.1,"q2":0.1,"q3":0.1,"max":0.11,"minLabel":"UNICYCLER_BLAST (SAMPLE3_SE)","maxLabel":"UNICYCLER_BLAST (SAMPLE2_PE)","q1Label":"UNICYCLER_BLAST (SAMPLE3_SE)","q2Label":"UNICYCLER_BLAST (SAMPLE1_PE)","q3Label":"UNICYCLER_BLAST (SAMPLE1_PE)"},"timeUsage":null,"vmem":{"mean":42781354.67,"min":41611264,"q1":41940992,"q2":42270720,"q3":43366400,"max":44462080,"minLabel":"UNICYCLER_BLAST (SAMPLE3_SE)","maxLabel":"UNICYCLER_BLAST (SAMPLE2_PE)","q1Label":"UNICYCLER_BLAST (SAMPLE3_SE)","q2Label":"UNICYCLER_BLAST (SAMPLE1_PE)","q3Label":"UNICYCLER_BLAST (SAMPLE1_PE)"},"reads":{"mean":162387.67,"min":161030,"q1":162004,"q2":162978,"q3":163066.5,"max":163155,"minLabel":"UNICYCLER_BLAST (SAMPLE2_PE)","maxLabel":"UNICYCLER_BLAST (SAMPLE3_SE)","q1Label":"UNICYCLER_BLAST (SAMPLE2_PE)","q2Label":"UNICYCLER_BLAST (SAMPLE1_PE)","q3Label":"UNICYCLER_BLAST (SAMPLE1_PE)"},"cpu":{"mean":75.17,"min":71.3,"q1":72.95,"q2":74.6,"q3":77.1,"max":79.6,"minLabel":"UNICYCLER_BLAST (SAMPLE1_PE)","maxLabel":"UNICYCLER_BLAST (SAMPLE2_PE)","q1Label":"UNICYCLER_BLAST (SAMPLE1_PE)","q2Label":"UNICYCLER_BLAST (SAMPLE3_SE)","q3Label":"UNICYCLER_BLAST (SAMPLE3_SE)"},"time":{"mean":433.33,"min":412,"q1":423.5,"q2":435,"q3":444,"max":453,"minLabel":"UNICYCLER_BLAST (SAMPLE3_SE)","maxLabel":"UNICYCLER_BLAST (SAMPLE1_PE)","q1Label":"UNICYCLER_BLAST (SAMPLE3_SE)","q2Label":"UNICYCLER_BLAST (SAMPLE2_PE)","q3Label":"UNICYCLER_BLAST (SAMPLE2_PE)"},"writes":{"mean":3749,"min":2955,"q1":2959,"q2":2963,"q3":4146,"max":5329,"minLabel":"UNICYCLER_BLAST (SAMPLE1_PE)","maxLabel":"UNICYCLER_BLAST (SAMPLE2_PE)","q1Label":"UNICYCLER_BLAST (SAMPLE1_PE)","q2Label":"UNICYCLER_BLAST (SAMPLE3_SE)","q3Label":"UNICYCLER_BLAST (SAMPLE3_SE)"}},{"cpuUsage":null,"process":"UNICYCLER_PLASMIDID","mem":null,"memUsage":null,"timeUsage":{"mean":0.03,"min":0.03,"q1":0.03,"q2":0.03,"q3":0.04,"max":0.04,"minLabel":"UNICYCLER_PLASMIDID (SAMPLE2_PE)","maxLabel":"UNICYCLER_PLASMIDID (SAMPLE3_SE)","q1Label":"UNICYCLER_PLASMIDID (SAMPLE2_PE)","q2Label":"UNICYCLER_PLASMIDID (SAMPLE1_PE)","q3Label":"UNICYCLER_PLASMIDID (SAMPLE1_PE)"},"vmem":null,"reads":null,"cpu":null,"time":{"mean":14812.33,"min":14061,"q1":14557,"q2":15053,"q3":15188,"max":15323,"minLabel":"UNICYCLER_PLASMIDID (SAMPLE2_PE)","maxLabel":"UNICYCLER_PLASMIDID (SAMPLE3_SE)","q1Label":"UNICYCLER_PLASMIDID (SAMPLE2_PE)","q2Label":"UNICYCLER_PLASMIDID (SAMPLE1_PE)","q3Label":"UNICYCLER_PLASMIDID (SAMPLE1_PE)"},"writes":null},{"cpuUsage":{"mean":79.4,"min":79.4,"q1":79.4,"q2":79.4,"q3":79.4,"max":79.4,"minLabel":"UNICYCLER_QUAST","maxLabel":"UNICYCLER_QUAST","q1Label":"UNICYCLER_QUAST","q2Label":"UNICYCLER_QUAST","q3Label":"UNICYCLER_QUAST"},"process":"UNICYCLER_QUAST","mem":{"mean":142688256,"min":142688256,"q1":142688256,"q2":142688256,"q3":142688256,"max":142688256,"minLabel":"UNICYCLER_QUAST","maxLabel":"UNICYCLER_QUAST","q1Label":"UNICYCLER_QUAST","q2Label":"UNICYCLER_QUAST","q3Label":"UNICYCLER_QUAST"},"memUsage":{"mean":2.21,"min":2.21,"q1":2.21,"q2":2.21,"q3":2.21,"max":2.21,"minLabel":"UNICYCLER_QUAST","maxLabel":"UNICYCLER_QUAST","q1Label":"UNICYCLER_QUAST","q2Label":"UNICYCLER_QUAST","q3Label":"UNICYCLER_QUAST"},"timeUsage":{"mean":0.01,"min":0.01,"q1":0.01,"q2":0.01,"q3":0.01,"max":0.01,"minLabel":"UNICYCLER_QUAST","maxLabel":"UNICYCLER_QUAST","q1Label":"UNICYCLER_QUAST","q2Label":"UNICYCLER_QUAST","q3Label":"UNICYCLER_QUAST"},"vmem":{"mean":8255979520,"min":8255979520,"q1":8255979520,"q2":8255979520,"q3":8255979520,"max":8255979520,"minLabel":"UNICYCLER_QUAST","maxLabel":"UNICYCLER_QUAST","q1Label":"UNICYCLER_QUAST","q2Label":"UNICYCLER_QUAST","q3Label":"UNICYCLER_QUAST"},"reads":{"mean":141151917,"min":141151917,"q1":141151917,"q2":141151917,"q3":141151917,"max":141151917,"minLabel":"UNICYCLER_QUAST","maxLabel":"UNICYCLER_QUAST","q1Label":"UNICYCLER_QUAST","q2Label":"UNICYCLER_QUAST","q3Label":"UNICYCLER_QUAST"},"cpu":{"mean":158.8,"min":158.8,"q1":158.8,"q2":158.8,"q3":158.8,"max":158.8,"minLabel":"UNICYCLER_QUAST","maxLabel":"UNICYCLER_QUAST","q1Label":"UNICYCLER_QUAST","q2Label":"UNICYCLER_QUAST","q3Label":"UNICYCLER_QUAST"},"time":{"mean":5739,"min":5739,"q1":5739,"q2":5739,"q3":5739,"max":5739,"minLabel":"UNICYCLER_QUAST","maxLabel":"UNICYCLER_QUAST","q1Label":"UNICYCLER_QUAST","q2Label":"UNICYCLER_QUAST","q3Label":"UNICYCLER_QUAST"},"writes":{"mean":8474187,"min":8474187,"q1":8474187,"q2":8474187,"q3":8474187,"max":8474187,"minLabel":"UNICYCLER_QUAST","maxLabel":"UNICYCLER_QUAST","q1Label":"UNICYCLER_QUAST","q2Label":"UNICYCLER_QUAST","q3Label":"UNICYCLER_QUAST"}},{"cpuUsage":{"mean":64.9,"min":64.9,"q1":64.9,"q2":64.9,"q3":64.9,"max":64.9,"minLabel":"MULTIQC (1)","maxLabel":"MULTIQC (1)","q1Label":"MULTIQC (1)","q2Label":"MULTIQC (1)","q3Label":"MULTIQC (1)"},"process":"MULTIQC","mem":{"mean":547586048,"min":547586048,"q1":547586048,"q2":547586048,"q3":547586048,"max":547586048,"minLabel":"MULTIQC (1)","maxLabel":"MULTIQC (1)","q1Label":"MULTIQC (1)","q2Label":"MULTIQC (1)","q3Label":"MULTIQC (1)"},"memUsage":{"mean":8.5,"min":8.5,"q1":8.5,"q2":8.5,"q3":8.5,"max":8.5,"minLabel":"MULTIQC (1)","maxLabel":"MULTIQC (1)","q1Label":"MULTIQC (1)","q2Label":"MULTIQC (1)","q3Label":"MULTIQC (1)"},"timeUsage":{"mean":0.06,"min":0.06,"q1":0.06,"q2":0.06,"q3":0.06,"max":0.06,"minLabel":"MULTIQC (1)","maxLabel":"MULTIQC (1)","q1Label":"MULTIQC (1)","q2Label":"MULTIQC (1)","q3Label":"MULTIQC (1)"},"vmem":{"mean":4582301696,"min":4582301696,"q1":4582301696,"q2":4582301696,"q3":4582301696,"max":4582301696,"minLabel":"MULTIQC (1)","maxLabel":"MULTIQC (1)","q1Label":"MULTIQC (1)","q2Label":"MULTIQC (1)","q3Label":"MULTIQC (1)"},"reads":{"mean":247678356,"min":247678356,"q1":247678356,"q2":247678356,"q3":247678356,"max":247678356,"minLabel":"MULTIQC (1)","maxLabel":"MULTIQC (1)","q1Label":"MULTIQC (1)","q2Label":"MULTIQC (1)","q3Label":"MULTIQC (1)"},"cpu":{"mean":129.8,"min":129.8,"q1":129.8,"q2":129.8,"q3":129.8,"max":129.8,"minLabel":"MULTIQC (1)","maxLabel":"MULTIQC (1)","q1Label":"MULTIQC (1)","q2Label":"MULTIQC (1)","q3Label":"MULTIQC (1)"},"time":{"mean":25479,"min":25479,"q1":25479,"q2":25479,"q3":25479,"max":25479,"minLabel":"MULTIQC (1)","maxLabel":"MULTIQC (1)","q1Label":"MULTIQC (1)","q2Label":"MULTIQC (1)","q3Label":"MULTIQC (1)"},"writes":{"mean":32375238,"min":32375238,"q1":32375238,"q2":32375238,"q3":32375238,"max":32375238,"minLabel":"MULTIQC (1)","maxLabel":"MULTIQC (1)","q1Label":"MULTIQC (1)","q2Label":"MULTIQC (1)","q3Label":"MULTIQC (1)"}}]
Jan-29 18:28:41.892 [main] DEBUG nextflow.trace.TimelineObserver - Flow completing -- rendering html timeline
Jan-29 18:28:41.931 [main] WARN  nextflow.dag.GraphvizRenderer - To render the execution DAG in the required format it is required to install Graphviz -- See http://www.graphviz.org for more info.
Jan-29 18:28:42.119 [main] DEBUG nextflow.CacheDB - Closing CacheDB done
Jan-29 18:28:42.126 [main] DEBUG nextflow.util.SpuriousDeps - AWS S3 uploader shutdown
Jan-29 18:28:42.144 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye
Jan-29 18:23:48.112 [main] DEBUG nextflow.cli.Launcher - $> nextflow run nf-core/viralrecon -profile test,singularity -r e49cee2
Jan-29 18:23:48.179 [main] INFO  nextflow.cli.CmdRun - N E X T F L O W  ~  version 20.10.0
Jan-29 18:23:48.843 [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 18:23:48.855 [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 18:23:49.043 [main] INFO  nextflow.cli.CmdRun - Launching `nf-core/viralrecon` [crazy_ampere] - revision: e49cee2f15dce2e9993736d16f08b1f9d808e292
Jan-29 18:23:49.641 [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=b6e
20251447dff08ea213605f4bfe554b17a0ab4], Ref[refs/pull/40/head=658104370a3aab1bde5e176750a1ae15687a0b89], Ref[refs/pull/24/head=b77d015ce4720e7447ee6c50fcca8758d16a173e], Ref[refs/pull/135/head=778693daee7
a476c8cc9ed1b703bd0e801d42016], Ref[refs/pull/55/head=3bfc2ba5239baa54260a95f031523f4e212451f6], Ref[refs/heads/dsl2=c8f708819bede4b1c8f3840c6355c22b03e6d0e9], Ref[refs/pull/23/head=a87af4acb8a3afe26175da
6feeb4c5ca28b3b436], Ref[refs/pull/148/head=9ba237e45aef44056dfd137caf33782252b8c9b2], Ref[refs/pull/120/head=4461c408701db0ba78264092632e45c93f83ba4c], Ref[refs/pull/103/head=372de46851a76d35c038fdf4a80d
1207f71de073], Ref[refs/pull/68/head=487df0392fa1579abb9842d33111ebcc6e223d66], Ref[refs/pull/70/head=fb6596249daf33376ca148c6b06a9f2ebb50af8d], Ref[refs/pull/118/head=fb552abe4143334b8b6131028e029a6d9271
202a], 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/h
ead=d3c56f47a3a51a50a526590901e3f1bfe3db6049], Ref[refs/pull/116/head=e1134ed88cec082d6f7373ba96bfc4e0ecc412bc], Ref[refs/pull/119/head=43c9d78884774bfe5e419014c38cf1e8b31c6710], Ref[refs/pull/41/head=485
3f86c0869171b16a53b767401a5a341167e53], Ref[refs/pull/36/head=3eaeb42a7b15701ec7107498e5cdd5866325143c], Ref[refs/pull/52/head=9e511349d7e899310a41fa9b46269571e39034f5], Ref[refs/pull/22/head=a580cfaa8869
07f4cda826088a15cc8241a99c31], Ref[refs/pull/102/head=1b93695f72a814764cc7dbf74d6a47855042b87a], Ref[refs/pull/25/head=6ebfb8a9d9c42dc06827211f6ef576bdee232efa], Ref[refs/pull/105/head=9a46ba7d317c00e23bd
fb889dd1298c33171c99c], Ref[refs/pull/146/head=90079b0fa5d37ffd551c4a9a18cba4f9860a017b], Ref[refs/pull/49/head=fee3c68ef7053fc9bd79a11937320abd056f0948], Ref[refs/pull/88/head=00816d0ec217c4adc2fa38ea07e
f882d4dd1c822], Ref[refs/tags/1.1.0=75a2f9763e9b4c1aa20ad342ae3ce148c33cc65a], Ref[refs/pull/140/head=2898d227ba61e2920fc4cc36ed6e5cd14064b7f7], Ref[refs/pull/60/head=eaab9880c914ea28d55f9077005808b9034a6
0ab], 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/pu
ll/43/head=2e5a2b4772239651bd292cbdd1d21fc69c4d1caa], Ref[refs/pull/129/head=7b38fe2439f97927093452232263123e71368d44], Ref[refs/pull/59/head=046d91a78b5c112a93ed7ef7d185c18a19bea8b9], Ref[refs/pull/139/h
ead=60cd93051c5de0af9f79886e48d7c96c6b4ae199], Ref[refs/pull/53/head=ac36d1fcf11674ab8ccf8b77a7bfb414614b9cad], Ref[refs/pull/111/head=69326f97b1c1d1b8733a0df573cb1f3eff907e6d], Ref[refs/pull/136/head=700
2a5eb6f481075cf577e7898212bf01144e2f9], Ref[refs/pull/130/head=b0229bbbc6eda0614aa40269a3f06b4edf78c360], Ref[refs/pull/117/head=acfc523f35cb9174c383b01cede82a14c8818688], Ref[refs/pull/133/head=52a1e50ff
57cf2295e2de9b425f73f276f20bade], Ref[refs/pull/37/head=55c2a56f7101f4d9bc74fa91cbc6bf9fd81527e2], Ref[refs/pull/114/head=d0e3e179d14b95eb8a1b08c3edcea5012e741206], Ref[refs/pull/34/head=dad04235f8b75dabd
385a2e2476a895629549d98], Ref[refs/pull/50/head=fc6eb38364aa85181defa21fb32ba9c56b87bd80], Ref[refs/pull/72/head=3c810f848c21ca58d69aa31b0cecb68889cecebd], Ref[refs/pull/97/head=c6682e57fd58b9ed743e388999
c393f2cdaccd78], Ref[refs/pull/78/head=7c38d49a99fd897ac473995c29876c5579e1722d], Ref[refs/pull/91/head=b0f9b52f9d17ba097a518b4dd01e25da52c6159a], Ref[refs/pull/75/head=f9b4b596671b2325011c42734b14239027d
62c1d], Ref[refs/pull/94/head=f7004dd083f523674b0b5b7b3d98176b8887b43e], Ref[refs/pull/32/head=cb10b45cadedd90d5da6460704d5cd5f15764c01], Ref[refs/pull/77/head=ed2511444ce83e7924e9fd91584c268251bb2e31], R
ef[refs/pull/63/head=4f56a2b91f580fc4f1ff4ff9510bd675b1d512b0], Ref[refs/pull/29/head=634bf562df7712e80ffa57839263273a53b3ae6b], Ref[refs/pull/16/head=79005a50623da53a812584537ee081744631dbe2], Ref[refs/p
ull/93/head=a495c1c40bd21085c21247ad812e51bcbb90088f], Ref[refs/pull/76/head=8b7285dbb0baa5ee300a43500dbeff782b284134], Ref[refs/pull/15/head=f899da38519e283a12df70fa6f20efd0a851f053], Ref[refs/pull/126/h
ead=13331866195d9b0cc0aee95fc0df881965be7ef3], Ref[refs/pull/62/head=edb5bd0b6f40ac15432d5d234293d39334fd347f], Ref[refs/pull/92/head=ecc1fdcf1dade61baa2f65c2904f88457aa54054], Ref[refs/pull/28/head=c83b9
a771430ed9c793e78f4507b6ba50858950b], Ref[refs/pull/81/head=9b4444fc1bb6ea038245dcb57db55ff96161d977], Ref[refs/pull/79/head=d9ad5b9c6f6ee7e1c2e62c36d8df2ef13eecffc1], Ref[refs/pull/44/head=a6524572ebfc9a
9b73b1c207d7b56f3c0c37a411], Ref[refs/pull/110/head=9ea4c1a52a0b55beb8fda28d9d5d318c7909a99c], Ref[refs/pull/7/head=053508707e945f883dd611cb6eab89be73f77f56], Ref[refs/pull/127/head=0a7325e0a42b5f06afcb62
2c74962a3899157eca], Ref[refs/pull/108/head=2622959ec0ca9753ccf35fb57fa38d12a688a4f2], Ref[refs/pull/30/head=8940416aacf0648eeef5fd083cc7cc333d266be4], Ref[refs/pull/17/head=747296441fb64b4bd1137fd8d93f08
f91572f90b], 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=6c
c01895b3db2901ac33dad5ae2317664467ae35], Ref[refs/pull/19/head=29d89516b218140ce2a5ed4f04c7898d436fc390], Ref[refs/pull/100/head=85f13dd3df92feec87fbe5b367715bb53743067c], Ref[refs/pull/73/head=d07af1ccde
076f7010330c1fdd7d60a7b4c6f5be], Ref[refs/pull/96/head=2d5cdb3d8234e7f11c079fe57d8b131010423aae], Ref[refs/pull/57/head=d72c512df8fd38215b8c9bc259a2b97373536ad0], Ref[refs/pull/125/head=c9d40fb3c3f0bf413d
593d43c6483f0eca234249], Ref[refs/pull/128/head=eca1bdcdaed5aefaf74402c858a45dc1ba4d123a], Ref[refs/pull/64/head=f27a55065c359cc6f19c4ea8bd7b6d93375a8141], Ref[refs/pull/48/head=e0474ce0f9f7c198f5e4907053
6b76c70e4b2e0b], Ref[refs/pull/45/head=0687ec1ef98f3ae80c147329c193338d79f537d6], Ref[refs/pull/106/head=160438169ebb0e488fd75f4706dc6fb66888cd7f], Ref[refs/pull/109/head=a5c12fcbbe4ead170ccd13d54b2038406
757f271], 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[re
fs/heads/master=75a2f9763e9b4c1aa20ad342ae3ce148c33cc65a], Ref[refs/pull/80/head=80a8eb55a94c26d7c488cf0290ff3dc904c3c42d], Ref[refs/pull/89/head=397f25529d0ca506666c88d74a5382fcbbbb481e], Ref[refs/pull/1
44/head=b006a4187540d86a80981d28c364779ffb2c4aeb], Ref[refs/pull/147/head=80b17e725ec72e03ee63be69187b0f2feb7e8ada]]
Jan-29 18:23:49.667 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/crtd_bioinf/fabirost/.nextflow/assets/nf-core/viralrecon/nextflow.config
Jan-29 18:23:49.668 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/crtd_bioinf/fabirost/.nextflow/assets/nf-core/viralrecon/nextflow.config
Jan-29 18:23:49.673 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `test,singularity`
...skipping...
"UNICYCLER_ABACAS (SAMPLE1_PE)","q3Label":"UNICYCLER_ABACAS (SAMPLE1_PE)"},"timeUsage":null,"vmem":{"mean":17145856,"min":17145856,"q1":17145856,"q2":17145856,"q3":17145856,"max":17145856,"minLabel":"UNICYCLER_ABACAS (SAMPLE2_PE)","maxLabel":"UNICYCLER_ABACAS (SAMPLE1_PE)","q1Label":"UNICYCLER_ABACAS (SAMPLE2_PE)","q2Label":"UNICYCLER_ABACAS (SAMPLE3_SE)","q3Label":"UNICYCLER_ABACAS (SAMPLE3_SE)"},"reads":{"mean":350422.33,"min":348167,"q1":349852.5,"q2":351538,"q3":351550,"max":351562,"minLabel":"UNICYCLER_ABACAS (SAMPLE2_PE)","maxLabel":"UNICYCLER_ABACAS (SAMPLE3_SE)","q1Label":"UNICYCLER_ABACAS (SAMPLE2_PE)","q2Label":"UNICYCLER_ABACAS (SAMPLE1_PE)","q3Label":"UNICYCLER_ABACAS (SAMPLE1_PE)"},"cpu":{"mean":40.97,"min":38.1,"q1":39.95,"q2":41.8,"q3":42.4,"max":43,"minLabel":"UNICYCLER_ABACAS (SAMPLE1_PE)","maxLabel":"UNICYCLER_ABACAS (SAMPLE2_PE)","q1Label":"UNICYCLER_ABACAS (SAMPLE1_PE)","q2Label":"UNICYCLER_ABACAS (SAMPLE3_SE)","q3Label":"UNICYCLER_ABACAS (SAMPLE3_SE)"},"time":{"mean":204,"min":201,"q1":201.5,"q2":202,"q3":205.5,"max":209,"minLabel":"UNICYCLER_ABACAS (SAMPLE1_PE)","maxLabel":"UNICYCLER_ABACAS (SAMPLE3_SE)","q1Label":"UNICYCLER_ABACAS (SAMPLE1_PE)","q2Label":"UNICYCLER_ABACAS (SAMPLE2_PE)","q3Label":"UNICYCLER_ABACAS (SAMPLE2_PE)"},"writes":{"mean":61585.33,"min":56387,"q1":59753.5,"q2":63120,"q3":64184.5,"max":65249,"minLabel":"UNICYCLER_ABACAS (SAMPLE3_SE)","maxLabel":"UNICYCLER_ABACAS (SAMPLE1_PE)","q1Label":"UNICYCLER_ABACAS (SAMPLE3_SE)","q2Label":"UNICYCLER_ABACAS (SAMPLE2_PE)","q3Label":"UNICYCLER_ABACAS (SAMPLE2_PE)"}},{"cpuUsage":null,"process":"UNICYCLER_VG","mem":null,"memUsage":null,"timeUsage":null,"vmem":null,"reads":null,"cpu":null,"time":{"mean":719.67,"min":704,"q1":714.5,"q2":725,"q3":727.5,"max":730,"minLabel":"UNICYCLER_VG (SAMPLE2_PE)","maxLabel":"UNICYCLER_VG (SAMPLE1_PE)","q1Label":"UNICYCLER_VG (SAMPLE2_PE)","q2Label":"UNICYCLER_VG (SAMPLE3_SE)","q3Label":"UNICYCLER_VG (SAMPLE3_SE)"},"writes":null},{"cpuUsage":{"mean":37.58,"min":35.65,"q1":36.47,"q2":37.3,"q3":38.55,"max":39.8,"minLabel":"UNICYCLER_BLAST (SAMPLE1_PE)","maxLabel":"UNICYCLER_BLAST (SAMPLE2_PE)","q1Label":"UNICYCLER_BLAST (SAMPLE1_PE)","q2Label":"UNICYCLER_BLAST (SAMPLE3_SE)","q3Label":"UNICYCLER_BLAST (SAMPLE3_SE)"},"process":"UNICYCLER_BLAST","mem":{"mean":6400682.67,"min":6029312,"q1":6135808,"q2":6242304,"q3":6586368,"max":6930432,"minLabel":"UNICYCLER_BLAST (SAMPLE3_SE)","maxLabel":"UNICYCLER_BLAST (SAMPLE2_PE)","q1Label":"UNICYCLER_BLAST (SAMPLE3_SE)","q2Label":"UNICYCLER_BLAST (SAMPLE1_PE)","q3Label":"UNICYCLER_BLAST (SAMPLE1_PE)"},"memUsage":{"mean":0.1,"min":0.09,"q1":0.1,"q2":0.1,"q3":0.1,"max":0.11,"minLabel":"UNICYCLER_BLAST (SAMPLE3_SE)","maxLabel":"UNICYCLER_BLAST (SAMPLE2_PE)","q1Label":"UNICYCLER_BLAST (SAMPLE3_SE)","q2Label":"UNICYCLER_BLAST (SAMPLE1_PE)","q3Label":"UNICYCLER_BLAST (SAMPLE1_PE)"},"timeUsage":null,"vmem":{"mean":42781354.67,"min":41611264,"q1":41940992,"q2":42270720,"q3":43366400,"max":44462080,"minLabel":"UNICYCLER_BLAST (SAMPLE3_SE)","maxLabel":"UNICYCLER_BLAST (SAMPLE2_PE)","q1Label":"UNICYCLER_BLAST (SAMPLE3_SE)","q2Label":"UNICYCLER_BLAST (SAMPLE1_PE)","q3Label":"UNICYCLER_BLAST (SAMPLE1_PE)"},"reads":{"mean":162387.67,"min":161030,"q1":162004,"q2":162978,"q3":163066.5,"max":163155,"minLabel":"UNICYCLER_BLAST (SAMPLE2_PE)","maxLabel":"UNICYCLER_BLAST (SAMPLE3_SE)","q1Label":"UNICYCLER_BLAST (SAMPLE2_PE)","q2Label":"UNICYCLER_BLAST (SAMPLE1_PE)","q3Label":"UNICYCLER_BLAST (SAMPLE1_PE)"},"cpu":{"mean":75.17,"min":71.3,"q1":72.95,"q2":74.6,"q3":77.1,"max":79.6,"minLabel":"UNICYCLER_BLAST (SAMPLE1_PE)","maxLabel":"UNICYCLER_BLAST (SAMPLE2_PE)","q1Label":"UNICYCLER_BLAST (SAMPLE1_PE)","q2Label":"UNICYCLER_BLAST (SAMPLE3_SE)","q3Label":"UNICYCLER_BLAST (SAMPLE3_SE)"},"time":{"mean":433.33,"min":412,"q1":423.5,"q2":435,"q3":444,"max":453,"minLabel":"UNICYCLER_BLAST (SAMPLE3_SE)","maxLabel":"UNICYCLER_BLAST (SAMPLE1_PE)","q1Label":"UNICYCLER_BLAST (SAMPLE3_SE)","q2Label":"UNICYCLER_BLAST (SAMPLE2_PE)","q3Label":"UNICYCLER_BLAST (SAMPLE2_PE)"},"writes":{"mean":3749,"min":2955,"q1":2959,"q2":2963,"q3":4146,"max":5329,"minLabel":"UNICYCLER_BLAST (SAMPLE1_PE)","maxLabel":"UNICYCLER_BLAST (SAMPLE2_PE)","q1Label":"UNICYCLER_BLAST (SAMPLE1_PE)","q2Label":"UNICYCLER_BLAST (SAMPLE3_SE)","q3Label":"UNICYCLER_BLAST (SAMPLE3_SE)"}},{"cpuUsage":null,"process":"UNICYCLER_PLASMIDID","mem":null,"memUsage":null,"timeUsage":{"mean":0.03,"min":0.03,"q1":0.03,"q2":0.03,"q3":0.04,"max":0.04,"minLabel":"UNICYCLER_PLASMIDID (SAMPLE2_PE)","maxLabel":"UNICYCLER_PLASMIDID (SAMPLE3_SE)","q1Label":"UNICYCLER_PLASMIDID (SAMPLE2_PE)","q2Label":"UNICYCLER_PLASMIDID (SAMPLE1_PE)","q3Label":"UNICYCLER_PLASMIDID (SAMPLE1_PE)"},"vmem":null,"reads":null,"cpu":null,"time":{"mean":14812.33,"min":14061,"q1":14557,"q2":15053,"q3":15188,"max":15323,"minLabel":"UNICYCLER_PLASMIDID (SAMPLE2_PE)","maxLabel":"UNICYCLER_PLASMIDID (SAMPLE3_SE)","q1Label":"UNICYCLER_PLASMIDID (SAMPLE2_PE)","q2Label":"UNICYCLER_PLASMIDID (SAMPLE1_PE)","q3Label":"UNICYCLER_PLASMIDID (SAMPLE1_PE)"},"writes":null},{"cpuUsage":{"mean":79.4,"min":79.4,"q1":79.4,"q2":79.4,"q3":79.4,"max":79.4,"minLabel":"UNICYCLER_QUAST","maxLabel":"UNICYCLER_QUAST","q1Label":"UNICYCLER_QUAST","q2Label":"UNICYCLER_QUAST","q3Label":"UNICYCLER_QUAST"},"process":"UNICYCLER_QUAST","mem":{"mean":142688256,"min":142688256,"q1":142688256,"q2":142688256,"q3":142688256,"max":142688256,"minLabel":"UNICYCLER_QUAST","maxLabel":"UNICYCLER_QUAST","q1Label":"UNICYCLER_QUAST","q2Label":"UNICYCLER_QUAST","q3Label":"UNICYCLER_QUAST"},"memUsage":{"mean":2.21,"min":2.21,"q1":2.21,"q2":2.21,"q3":2.21,"max":2.21,"minLabel":"UNICYCLER_QUAST","maxLabel":"UNICYCLER_QUAST","q1Label":"UNICYCLER_QUAST","q2Label":"UNICYCLER_QUAST","q3Label":"UNICYCLER_QUAST"},"timeUsage":{"mean":0.01,"min":0.01,"q1":0.01,"q2":0.01,"q3":0.01,"max":0.01,"minLabel":"UNICYCLER_QUAST","maxLabel":"UNICYCLER_QUAST","q1Label":"UNICYCLER_QUAST","q2Label":"UNICYCLER_QUAST","q3Label":"UNICYCLER_QUAST"},"vmem":{"mean":8255979520,"min":8255979520,"q1":8255979520,"q2":8255979520,"q3":8255979520,"max":8255979520,"minLabel":"UNICYCLER_QUAST","maxLabel":"UNICYCLER_QUAST","q1Label":"UNICYCLER_QUAST","q2Label":"UNICYCLER_QUAST","q3Label":"UNICYCLER_QUAST"},"reads":{"mean":141151917,"min":141151917,"q1":141151917,"q2":141151917,"q3":141151917,"max":141151917,"minLabel":"UNICYCLER_QUAST","maxLabel":"UNICYCLER_QUAST","q1Label":"UNICYCLER_QUAST","q2Label":"UNICYCLER_QUAST","q3Label":"UNICYCLER_QUAST"},"cpu":{"mean":158.8,"min":158.8,"q1":158.8,"q2":158.8,"q3":158.8,"max":158.8,"minLabel":"UNICYCLER_QUAST","maxLabel":"UNICYCLER_QUAST","q1Label":"UNICYCLER_QUAST","q2Label":"UNICYCLER_QUAST","q3Label":"UNICYCLER_QUAST"},"time":{"mean":5739,"min":5739,"q1":5739,"q2":5739,"q3":5739,"max":5739,"minLabel":"UNICYCLER_QUAST","maxLabel":"UNICYCLER_QUAST","q1Label":"UNICYCLER_QUAST","q2Label":"UNICYCLER_QUAST","q3Label":"UNICYCLER_QUAST"},"writes":{"mean":8474187,"min":8474187,"q1":8474187,"q2":8474187,"q3":8474187,"max":8474187,"minLabel":"UNICYCLER_QUAST","maxLabel":"UNICYCLER_QUAST","q1Label":"UNICYCLER_QUAST","q2Label":"UNICYCLER_QUAST","q3Label":"UNICYCLER_QUAST"}},{"cpuUsage":{"mean":64.9,"min":64.9,"q1":64.9,"q2":64.9,"q3":64.9,"max":64.9,"minLabel":"MULTIQC (1)","maxLabel":"MULTIQC (1)","q1Label":"MULTIQC (1)","q2Label":"MULTIQC (1)","q3Label":"MULTIQC (1)"},"process":"MULTIQC","mem":{"mean":547586048,"min":547586048,"q1":547586048,"q2":547586048,"q3":547586048,"max":547586048,"minLabel":"MULTIQC (1)","maxLabel":"MULTIQC (1)","q1Label":"MULTIQC (1)","q2Label":"MULTIQC (1)","q3Label":"MULTIQC (1)"},"memUsage":{"mean":8.5,"min":8.5,"q1":8.5,"q2":8.5,"q3":8.5,"max":8.5,"minLabel":"MULTIQC (1)","maxLabel":"MULTIQC (1)","q1Label":"MULTIQC (1)","q2Label":"MULTIQC (1)","q3Label":"MULTIQC (1)"},"timeUsage":{"mean":0.06,"min":0.06,"q1":0.06,"q2":0.06,"q3":0.06,"max":0.06,"minLabel":"MULTIQC (1)","maxLabel":"MULTIQC (1)","q1Label":"MULTIQC (1)","q2Label":"MULTIQC (1)","q3Label":"MULTIQC (1)"},"vmem":{"mean":4582301696,"min":4582301696,"q1":4582301696,"q2":4582301696,"q3":4582301696,"max":4582301696,"minLabel":"MULTIQC (1)","maxLabel":"MULTIQC (1)","q1Label":"MULTIQC (1)","q2Label":"MULTIQC (1)","q3Label":"MULTIQC (1)"},"reads":{"mean":247678356,"min":247678356,"q1":247678356,"q2":247678356,"q3":247678356,"max":247678356,"minLabel":"MULTIQC (1)","maxLabel":"MULTIQC (1)","q1Label":"MULTIQC (1)","q2Label":"MULTIQC (1)","q3Label":"MULTIQC (1)"},"cpu":{"mean":129.8,"min":129.8,"q1":129.8,"q2":129.8,"q3":129.8,"max":129.8,"minLabel":"MULTIQC (1)","maxLabel":"MULTIQC (1)","q1Label":"MULTIQC (1)","q2Label":"MULTIQC (1)","q3Label":"MULTIQC (1)"},"time":{"mean":25479,"min":25479,"q1":25479,"q2":25479,"q3":25479,"max":25479,"minLabel":"MULTIQC (1)","maxLabel":"MULTIQC (1)","q1Label":"MULTIQC (1)","q2Label":"MULTIQC (1)","q3Label":"MULTIQC (1)"},"writes":{"mean":32375238,"min":32375238,"q1":32375238,"q2":32375238,"q3":32375238,"max":32375238,"minLabel":"MULTIQC (1)","maxLabel":"MULTIQC (1)","q1Label":"MULTIQC (1)","q2Label":"MULTIQC (1)","q3Label":"MULTIQC (1)"}}]
Jan-29 18:28:41.892 [main] DEBUG nextflow.trace.TimelineObserver - Flow completing -- rendering html timeline
Jan-29 18:28:41.931 [main] WARN  nextflow.dag.GraphvizRenderer - To render the execution DAG in the required format it is required to install Graphviz -- See http://www.graphviz.org for more info.
Jan-29 18:28:42.119 [main] DEBUG nextflow.CacheDB - Closing CacheDB done
Jan-29 18:28:42.126 [main] DEBUG nextflow.util.SpuriousDeps - AWS S3 uploader shutdown
Jan-29 18:28:42.144 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye
fbnrst commented 3 years ago

While running the test, the pipeline actually continued after a pause of about 2 hours. here is the continued log:

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]
Jan-29 18:02:21.391 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 18:02:21.392 [Task submitter] INFO  nextflow.Session - [f4/57df93] Submitted process > FASTP (L66091_EdenPool_Covid-DD-VIR-00229)
Jan-29 18:02:21.396 [Task submitter] DEBUG n.processor.TaskPollingMonitor - %% executor local > tasks in the submission queue: 160 -- tasks to be submitted are shown below
~> TaskHandler[id: 112; name: FASTQC (L66082_EdenPool_Covid-DD-VIR-00211); status: NEW; exit: -; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/ce/34a6407007e8893748208548afc7eb]
~> TaskHandler[id: 113; name: FASTP (L66082_EdenPool_Covid-DD-VIR-00211); status: NEW; exit: -; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/6a/39bb8c84bf9298309494de600969c0]
~> TaskHandler[id: 114; name: FASTQC (L66095_EdenPool_Covid-DD-VIR-00237); status: NEW; exit: -; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/94/a29f26ec5ec0d1a706a6bd11d40394]
~> TaskHandler[id: 115; name: FASTP (L66095_EdenPool_Covid-DD-VIR-00237); status: NEW; exit: -; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/c6/2089f8873af8b580284bf280e34393]
~> TaskHandler[id: 117; name: FASTP (L66100_EdenPool_Covid-DD-VIR-00244); status: NEW; exit: -; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/af/af101c9d7933cb0545cd421a0bde0e]
~> TaskHandler[id: 116; name: FASTQC (L66100_EdenPool_Covid-DD-VIR-00244); status: NEW; exit: -; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/05/0fea0e980b22db02fb405889c695b2]
~> TaskHandler[id: 119; name: FASTQC (L66078_EdenPool_Covid-DD-VIR-00207); status: NEW; exit: -; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/aa/487e22427c545e7f15a664101de23c]
~> TaskHandler[id: 118; name: FASTP (L66078_EdenPool_Covid-DD-VIR-00207); status: NEW; exit: -; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/ee/f4d2359d077433bc5695e2376aa7ac]
~> TaskHandler[id: 121; name: FASTP (L66090_EdenPool_Covid-DD-VIR-00226); status: NEW; exit: -; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/94/91b0f9cae0f00e7ca6935ccb368e5e]
~> TaskHandler[id: 120; name: FASTQC (L66090_EdenPool_Covid-DD-VIR-00226); status: NEW; exit: -; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/58/1d086aac4b63d9bdc5f473423090ea]
.. remaining tasks omitted.
Jan-29 18:02:21.403 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 110; name: FASTQC (L66091_EdenPool_Covid-DD-VIR-00229); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/43/666074fb5b6e4158655efd6b01e449]
Jan-29 18:02:21.406 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 18:02:21.406 [Task submitter] INFO  nextflow.Session - [ce/34a640] Submitted process > FASTQC (L66082_EdenPool_Covid-DD-VIR-00211)
Jan-29 18:02:21.417 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 2 -- submitted tasks are shown below
~> TaskHandler[id: 111; name: FASTP (L66091_EdenPool_Covid-DD-VIR-00229); status: SUBMITTED; exit: -; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/f4/57df93dad895496a3bf9c3198ce123]
~> TaskHandler[id: 112; name: FASTQC (L66082_EdenPool_Covid-DD-VIR-00211); status: SUBMITTED; exit: -; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/ce/34a6407007e8893748208548afc7eb]
Jan-29 18:02:25.613 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 112; name: FASTQC (L66082_EdenPool_Covid-DD-VIR-00211); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/ce/34a6407007e8893748208548afc7eb]
Jan-29 18:02:25.617 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 18:02:25.617 [Task submitter] INFO  nextflow.Session - [6a/39bb8c] Submitted process > FASTP (L66082_EdenPool_Covid-DD-VIR-00211)
Jan-29 18:02:29.813 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 111; name: FASTP (L66091_EdenPool_Covid-DD-VIR-00229); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/f4/57df93dad895496a3bf9c3198ce123]
Jan-29 18:02:29.815 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 18:02:29.815 [Task submitter] INFO  nextflow.Session - [94/a29f26] Submitted process > FASTQC (L66095_EdenPool_Covid-DD-VIR-00237)
Jan-29 18:02:33.644 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 113; name: FASTP (L66082_EdenPool_Covid-DD-VIR-00211); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/6a/39bb8c84bf9298309494de600969c0]
Jan-29 18:02:33.649 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 18:02:33.649 [Task submitter] INFO  nextflow.Session - [c6/2089f8] Submitted process > FASTP (L66095_EdenPool_Covid-DD-VIR-00237)
Jan-29 18:02:34.797 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 114; name: FASTQC (L66095_EdenPool_Covid-DD-VIR-00237); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/94/a29f26ec5ec0d1a706a6bd11d40394]
Jan-29 18:02:34.801 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 18:02:34.801 [Task submitter] INFO  nextflow.Session - [af/af101c] Submitted process > FASTP (L66100_EdenPool_Covid-DD-VIR-00244)
Jan-29 18:02:40.961 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 115; name: FASTP (L66095_EdenPool_Covid-DD-VIR-00237); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/c6/2089f8873af8b580284bf280e34393]
Jan-29 18:02:40.965 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 18:02:40.965 [Task submitter] INFO  nextflow.Session - [05/0fea0e] Submitted process > FASTQC (L66100_EdenPool_Covid-DD-VIR-00244)
Jan-29 18:02:45.402 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 117; name: FASTP (L66100_EdenPool_Covid-DD-VIR-00244); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/af/af101c9d7933cb0545cd421a0bde0e]
Jan-29 18:48:18.219 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 18:48:18.236 [Task submitter] INFO  nextflow.Session - [aa/487e22] Submitted process > FASTQC (L66078_EdenPool_Covid-DD-VIR-00207)
Jan-29 18:48:18.312 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 116; name: FASTQC (L66100_EdenPool_Covid-DD-VIR-00244); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/05/0fea0e980b22db02fb405889c695b2]
Jan-29 18:48:18.330 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 18:48:18.331 [Task submitter] INFO  nextflow.Session - [a6/632ffc] Submitted process > FASTQC (L66151_EdenPool_cDNA_S48_20210103-792272_01_H06)
Jan-29 18:48:18.332 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below
~> TaskHandler[id: 119; name: FASTQC (L66078_EdenPool_Covid-DD-VIR-00207); status: SUBMITTED; exit: -; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/aa/487e22427c545e7f15a664101de23c]
~> TaskHandler[id: 247; name: FASTQC (L66151_EdenPool_cDNA_S48_20210103-792272_01_H06); status: SUBMITTED; exit: -; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/a6/632ffc5f61a61b1a057f21f88ee326]
Jan-29 18:48:18.357 [Task submitter] DEBUG n.processor.TaskPollingMonitor - %% executor local > tasks in the submission queue: 156 -- tasks to be submitted are shown below
~> TaskHandler[id: 118; name: FASTP (L66078_EdenPool_Covid-DD-VIR-00207); status: NEW; exit: -; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/ee/f4d2359d077433bc5695e2376aa7ac]
~> TaskHandler[id: 121; name: FASTP (L66090_EdenPool_Covid-DD-VIR-00226); status: NEW; exit: -; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/94/91b0f9cae0f00e7ca6935ccb368e5e]
~> TaskHandler[id: 120; name: FASTQC (L66090_EdenPool_Covid-DD-VIR-00226); status: NEW; exit: -; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/58/1d086aac4b63d9bdc5f473423090ea]
~> TaskHandler[id: 122; name: FASTQC (L66094_EdenPool_Covid-DD-VIR-00236); status: NEW; exit: -; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/38/cb77a26aef209b50c03d58c6ff4001]
~> TaskHandler[id: 123; name: FASTP (L66094_EdenPool_Covid-DD-VIR-00236); status: NEW; exit: -; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/1e/eb04efed30a64ef87d55916bf6ca3b]
~> TaskHandler[id: 124; name: FASTQC (L66088_EdenPool_Covid-DD-VIR-00221); status: NEW; exit: -; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/22/4da394bcaa3d7d7ba315563dfc3a09]
~> TaskHandler[id: 125; name: FASTP (L66088_EdenPool_Covid-DD-VIR-00221); status: NEW; exit: -; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/35/df5f331ef230c5a7ca016b4bf7fc1b]
~> TaskHandler[id: 126; name: FASTQC (L66097_EdenPool_Covid-DD-VIR-00240); status: NEW; exit: -; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/61/f5c2456b978c75528e9f4b9150b705]
~> TaskHandler[id: 127; name: FASTP (L66097_EdenPool_Covid-DD-VIR-00240); status: NEW; exit: -; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/9e/551070be19d995757899526766b533]
~> TaskHandler[id: 129; name: FASTQC (L66077_EdenPool_Covid-DD-VIR-00206); status: NEW; exit: -; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/42/b3f724e79936f117ec00cdd272fef5]
.. remaining tasks omitted.
Jan-29 18:48:22.289 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 119; name: FASTQC (L66078_EdenPool_Covid-DD-VIR-00207); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/aa/487e22427c545e7f15a664101de23c]
Jan-29 18:48:22.297 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 18:48:22.297 [Task submitter] INFO  nextflow.Session - [ee/f4d235] Submitted process > FASTP (L66078_EdenPool_Covid-DD-VIR-00207)
Jan-29 18:48:23.290 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 247; name: FASTQC (L66151_EdenPool_cDNA_S48_20210103-792272_01_H06); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/a6/632ffc5f61a61b1a057f21f88ee326]
Jan-29 18:48:23.300 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 18:48:23.300 [Task submitter] INFO  nextflow.Session - [94/91b0f9] Submitted process > FASTP (L66090_EdenPool_Covid-DD-VIR-00226)
Jan-29 18:48:30.033 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 118; name: FASTP (L66078_EdenPool_Covid-DD-VIR-00207); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/ee/f4d2359d077433bc5695e2376aa7ac]
Jan-29 18:48:30.044 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 18:48:30.045 [Task submitter] INFO  nextflow.Session - [58/1d086a] Submitted process > FASTQC (L66090_EdenPool_Covid-DD-VIR-00226)
Jan-29 18:48:34.902 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 120; name: FASTQC (L66090_EdenPool_Covid-DD-VIR-00226); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/58/1d086aac4b63d9bdc5f473423090ea]
Jan-29 18:48:34.912 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 18:48:34.912 [Task submitter] INFO  nextflow.Session - [38/cb77a2] Submitted process > FASTQC (L66094_EdenPool_Covid-DD-VIR-00236)
Jan-29 18:48:36.396 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 121; name: FASTP (L66090_EdenPool_Covid-DD-VIR-00226); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/94/91b0f9cae0f00e7ca6935ccb368e5e]
Jan-29 18:48:36.404 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 18:48:36.404 [Task submitter] INFO  nextflow.Session - [1e/eb04ef] Submitted process > FASTP (L66094_EdenPool_Covid-DD-VIR-00236)
Jan-29 18:48:39.876 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 122; name: FASTQC (L66094_EdenPool_Covid-DD-VIR-00236); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/38/cb77a26aef209b50c03d58c6ff4001]
Jan-29 18:48:39.885 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 18:48:39.885 [Task submitter] INFO  nextflow.Session - [22/4da394] Submitted process > FASTQC (L66088_EdenPool_Covid-DD-VIR-00221)
Jan-29 18:48:43.921 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 124; name: FASTQC (L66088_EdenPool_Covid-DD-VIR-00221); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/22/4da394bcaa3d7d7ba315563dfc3a09]
Jan-29 18:48:43.929 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 18:48:43.929 [Task submitter] INFO  nextflow.Session - [35/df5f33] Submitted process > FASTP (L66088_EdenPool_Covid-DD-VIR-00221)
Jan-29 18:48:46.984 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 123; name: FASTP (L66094_EdenPool_Covid-DD-VIR-00236); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/1e/eb04efed30a64ef87d55916bf6ca3b]
Jan-29 18:48:46.991 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 18:48:46.992 [Task submitter] INFO  nextflow.Session - [61/f5c245] Submitted process > FASTQC (L66097_EdenPool_Covid-DD-VIR-00240)
Jan-29 18:48:50.961 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 125; name: FASTP (L66088_EdenPool_Covid-DD-VIR-00221); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/35/df5f331ef230c5a7ca016b4bf7fc1b]
Jan-29 18:48:50.971 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 18:48:50.972 [Task submitter] INFO  nextflow.Session - [9e/551070] Submitted process > FASTP (L66097_EdenPool_Covid-DD-VIR-00240)
Jan-29 18:48:51.953 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 126; name: FASTQC (L66097_EdenPool_Covid-DD-VIR-00240); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/61/f5c2456b978c75528e9f4b9150b705]
Jan-29 18:48:51.964 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 18:48:51.964 [Task submitter] INFO  nextflow.Session - [42/b3f724] Submitted process > FASTQC (L66077_EdenPool_Covid-DD-VIR-00206)
Jan-29 18:48:58.029 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 129; name: FASTQC (L66077_EdenPool_Covid-DD-VIR-00206); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/42/b3f724e79936f117ec00cdd272fef5]
Jan-29 18:48:58.036 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 18:48:58.036 [Task submitter] INFO  nextflow.Session - [c7/1841b9] Submitted process > FASTP (L66077_EdenPool_Covid-DD-VIR-00206)
Jan-29 18:48:59.057 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 127; name: FASTP (L66097_EdenPool_Covid-DD-VIR-00240); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/9e/551070be19d995757899526766b533]
Jan-29 18:48:59.064 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 18:48:59.064 [Task submitter] INFO  nextflow.Session - [a9/fee605] Submitted process > FASTQC (L66076_EdenPool_Covid-DD-VIR-00205)
Jan-29 18:49:03.985 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 130; name: FASTQC (L66076_EdenPool_Covid-DD-VIR-00205); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/a9/fee60590d60b0a2f8b06a4a49ed470]
Jan-29 18:49:03.993 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 18:49:03.994 [Task submitter] INFO  nextflow.Session - [ef/ab059f] Submitted process > FASTP (L66076_EdenPool_Covid-DD-VIR-00205)
Jan-29 18:49:06.245 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 128; name: FASTP (L66077_EdenPool_Covid-DD-VIR-00206); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/c7/1841b9b1ba66d33a47e09fe92074b0]
Jan-29 18:49:06.252 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 18:49:06.253 [Task submitter] INFO  nextflow.Session - [c9/f297ad] Submitted process > FASTQC (L66079_EdenPool_Covid-DD-VIR-00208)
Jan-29 18:49:10.205 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 132; name: FASTQC (L66079_EdenPool_Covid-DD-VIR-00208); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/c9/f297ad3e4ebc7ddaae27012065e6a6]
Jan-29 18:49:10.216 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 18:49:10.216 [Task submitter] INFO  nextflow.Session - [9d/da029f] Submitted process > FASTP (L66079_EdenPool_Covid-DD-VIR-00208)
Jan-29 18:49:16.301 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 131; name: FASTP (L66076_EdenPool_Covid-DD-VIR-00205); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/ef/ab059f7f1e799f1681aa2684df799b]
Jan-29 18:49:16.310 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 18:49:16.311 [Task submitter] INFO  nextflow.Session - [67/f0953d] Submitted process > FASTP (L66098_EdenPool_Covid-DD-VIR-00241)
Jan-29 18:49:19.653 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 133; name: FASTP (L66079_EdenPool_Covid-DD-VIR-00208); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/9d/da029fd35d1c81424b9133fe06045a]
Jan-29 18:49:19.660 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 18:49:19.660 [Task submitter] INFO  nextflow.Session - [65/a7c561] Submitted process > FASTQC (L66098_EdenPool_Covid-DD-VIR-00241)
Jan-29 18:49:23.473 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 135; name: FASTP (L66098_EdenPool_Covid-DD-VIR-00241); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/67/f0953d25d234cfeb2b63b9b51a9300]
Jan-29 18:49:23.485 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 18:49:23.486 [Task submitter] INFO  nextflow.Session - [e0/ebe33f] Submitted process > FASTP (L66081_EdenPool_Covid-DD-VIR-00210)
Jan-29 18:49:23.653 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 134; name: FASTQC (L66098_EdenPool_Covid-DD-VIR-00241); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/65/a7c5615ca2299ec9e830eb8dee9e55]
Jan-29 18:49:23.661 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 18:49:23.661 [Task submitter] INFO  nextflow.Session - [be/e01436] Submitted process > FASTQC (L66081_EdenPool_Covid-DD-VIR-00210)
Jan-29 18:49:28.597 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 136; name: FASTQC (L66081_EdenPool_Covid-DD-VIR-00210); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/be/e01436dad77857cd8fbfa02ae9c857]
Jan-29 18:49:28.605 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 18:49:28.606 [Task submitter] INFO  nextflow.Session - [1b/7f7d2e] Submitted process > FASTQC (L66092_EdenPool_Covid-DD-VIR-00231)
Jan-29 18:49:31.757 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 137; name: FASTP (L66081_EdenPool_Covid-DD-VIR-00210); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/e0/ebe33f391317372a96a64721c00934]
Jan-29 18:49:31.766 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 18:49:31.766 [Task submitter] INFO  nextflow.Session - [c5/dba527] Submitted process > FASTP (L66092_EdenPool_Covid-DD-VIR-00231)
Jan-29 18:49:32.573 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 138; name: FASTQC (L66092_EdenPool_Covid-DD-VIR-00231); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/1b/7f7d2e1bdf90b13a785c0ecd747413]
Jan-29 18:49:32.583 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 18:49:32.583 [Task submitter] INFO  nextflow.Session - [46/e074d8] Submitted process > FASTQC (L66074_EdenPool_Covid-DD-VIR-00201)
Jan-29 18:49:36.652 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 141; name: FASTQC (L66074_EdenPool_Covid-DD-VIR-00201); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/46/e074d8c9d73169017b16ce31a599b9]
Jan-29 18:49:36.662 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 18:49:36.663 [Task submitter] INFO  nextflow.Session - [98/3222c0] Submitted process > FASTP (L66074_EdenPool_Covid-DD-VIR-00201)
Jan-29 18:49:39.941 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 139; name: FASTP (L66092_EdenPool_Covid-DD-VIR-00231); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/c5/dba527232785960ed5d29524b9ee96]
Jan-29 18:49:39.949 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 18:49:39.950 [Task submitter] INFO  nextflow.Session - [91/2a4adc] Submitted process > FASTP (L66101_EdenPool_Covid-DD-VIR-00245)
Jan-29 18:49:40.989 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 140; name: FASTP (L66074_EdenPool_Covid-DD-VIR-00201); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/98/3222c0f96d43e2527dc77fb7ce2ded]
Jan-29 18:49:40.997 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 18:49:40.997 [Task submitter] INFO  nextflow.Session - [e6/c51e57] Submitted process > FASTQC (L66101_EdenPool_Covid-DD-VIR-00245)
Jan-29 18:49:45.961 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 142; name: FASTQC (L66101_EdenPool_Covid-DD-VIR-00245); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/e6/c51e57fffa5fde4cf5e1a5a3d30596]
Jan-29 18:49:45.969 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 18:49:45.969 [Task submitter] INFO  nextflow.Session - [8a/a504dd] Submitted process > FASTP (L66087_EdenPool_Covid-DD-VIR-00219)
Jan-29 18:49:48.137 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 143; name: FASTP (L66101_EdenPool_Covid-DD-VIR-00245); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/91/2a4adc8a311b3615b6ae9865947390]
Jan-29 18:49:48.148 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 18:49:48.148 [Task submitter] INFO  nextflow.Session - [65/825f65] Submitted process > FASTQC (L66087_EdenPool_Covid-DD-VIR-00219)
Jan-29 18:49:51.989 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 145; name: FASTQC (L66087_EdenPool_Covid-DD-VIR-00219); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/65/825f651df29701bdd4109066c698fc]
Jan-29 18:49:51.995 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 18:49:51.995 [Task submitter] INFO  nextflow.Session - [4a/654bdb] Submitted process > FASTQC (L66145_EdenPool_cDNA_S42_20201227-787343_01_B06)
Jan-29 18:49:54.077 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 144; name: FASTP (L66087_EdenPool_Covid-DD-VIR-00219); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/8a/a504ddef8fae31e940a893f5f8affb]
Jan-29 18:49:54.088 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 18:49:54.088 [Task submitter] INFO  nextflow.Session - [f3/f0ef0f] Submitted process > FASTP (L66145_EdenPool_cDNA_S42_20201227-787343_01_B06)
Jan-29 18:49:56.997 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 146; name: FASTQC (L66145_EdenPool_cDNA_S42_20201227-787343_01_B06); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/4a/654bdb2ee568e2f1e413cddaffbef7]
Jan-29 18:49:57.006 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 18:49:57.007 [Task submitter] INFO  nextflow.Session - [26/93cbb3] Submitted process > FASTQC (L66085_EdenPool_Covid-DD-VIR-00215)
Jan-29 18:50:01.874 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 148; name: FASTQC (L66085_EdenPool_Covid-DD-VIR-00215); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/26/93cbb3da850c01335092a590ece7c9]
Jan-29 18:50:01.881 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 18:50:01.881 [Task submitter] INFO  nextflow.Session - [be/8186fd] Submitted process > FASTP (L66085_EdenPool_Covid-DD-VIR-00215)
Jan-29 18:50:02.309 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 147; name: FASTP (L66145_EdenPool_cDNA_S42_20201227-787343_01_B06); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/f3/f0ef0fa4a095bbdcfdade055daa154]
Jan-29 18:50:02.321 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 18:50:02.321 [Task submitter] INFO  nextflow.Session - [04/56fb6c] Submitted process > FASTQC (L66144_EdenPool_cDNA_S41_20201227-787782_01_A06)
Jan-29 18:50:07.349 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 150; name: FASTQC (L66144_EdenPool_cDNA_S41_20201227-787782_01_A06); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/04/56fb6ce2d8f4c705106021c5169e5c]
Jan-29 18:50:07.363 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 18:50:07.363 [Task submitter] INFO  nextflow.Session - [50/27e2b6] Submitted process > FASTP (L66144_EdenPool_cDNA_S41_20201227-787782_01_A06)
Jan-29 18:50:14.224 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 149; name: FASTP (L66085_EdenPool_Covid-DD-VIR-00215); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/be/8186fd3adfa85a60ba13dcf8a27b0d]
Jan-29 18:50:14.230 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 18:50:14.230 [Task submitter] INFO  nextflow.Session - [9e/fa511b] Submitted process > FASTQC (L66096_EdenPool_Covid-DD-VIR-00238)
Jan-29 18:50:15.145 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 151; name: FASTP (L66144_EdenPool_cDNA_S41_20201227-787782_01_A06); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/50/27e2b63ff17efbb96f9d35049a3b4b]
Jan-29 18:50:15.154 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 18:50:15.154 [Task submitter] INFO  nextflow.Session - [68/12b18f] Submitted process > FASTP (L66096_EdenPool_Covid-DD-VIR-00238)
Jan-29 18:50:19.217 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 152; name: FASTQC (L66096_EdenPool_Covid-DD-VIR-00238); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/9e/fa511b6c0924970a2d0066956d6965]
Jan-29 18:50:19.225 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 18:50:19.225 [Task submitter] INFO  nextflow.Session - [26/052e18] Submitted process > FASTQC (L66102_EdenPool_Covid-DD-VIR-00246)
Jan-29 18:50:24.205 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 154; name: FASTQC (L66102_EdenPool_Covid-DD-VIR-00246); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/26/052e183c31f97692845fcc34140265]
Jan-29 18:50:24.212 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 18:50:24.212 [Task submitter] INFO  nextflow.Session - [7a/c07c55] Submitted process > FASTP (L66102_EdenPool_Covid-DD-VIR-00246)
Jan-29 18:50:25.697 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 153; name: FASTP (L66096_EdenPool_Covid-DD-VIR-00238); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/68/12b18fd22331f3ff2df3790380930d]
Jan-29 18:50:25.705 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 18:50:25.705 [Task submitter] INFO  nextflow.Session - [8b/2a8230] Submitted process > FASTQC (L66104_EdenPool_cDNA_S1_20210108-799934_01_A01)
Jan-29 18:50:29.685 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 156; name: FASTQC (L66104_EdenPool_cDNA_S1_20210108-799934_01_A01); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/8b/2a823086b51b008cf8f49bed882681]
Jan-29 18:50:29.693 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 18:50:29.693 [Task submitter] INFO  nextflow.Session - [0c/607566] Submitted process > FASTP (L66104_EdenPool_cDNA_S1_20210108-799934_01_A01)
Jan-29 18:50:31.409 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 155; name: FASTP (L66102_EdenPool_Covid-DD-VIR-00246); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/7a/c07c552d9e3cab2696c1656abff5b0]
Jan-29 18:50:31.419 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 18:50:31.419 [Task submitter] INFO  nextflow.Session - [c1/b87b91] Submitted process > FASTQC (L66105_EdenPool_cDNA_S2_20210106-797126_01_B01)
Jan-29 18:50:36.220 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 157; name: FASTP (L66104_EdenPool_cDNA_S1_20210108-799934_01_A01); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/0c/6075663fc6be031fefe87c39c2e6aa]
Jan-29 18:50:36.228 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 18:50:36.228 [Task submitter] INFO  nextflow.Session - [c8/45ff2b] Submitted process > FASTP (L66105_EdenPool_cDNA_S2_20210106-797126_01_B01)
Jan-29 18:50:37.338 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 158; name: FASTQC (L66105_EdenPool_cDNA_S2_20210106-797126_01_B01); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/c1/b87b91b637e03958a6bc22afa8fb18]
Jan-29 18:50:37.348 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 18:50:37.348 [Task submitter] INFO  nextflow.Session - [01/681788] Submitted process > FASTQC (L66106_EdenPool_cDNA_S3_20210104-793515_01_C01)
Jan-29 18:50:41.441 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 161; name: FASTQC (L66106_EdenPool_cDNA_S3_20210104-793515_01_C01); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/01/6817880ea9d9cc4c31d7c94922552c]
Jan-29 18:50:41.450 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 18:50:41.450 [Task submitter] INFO  nextflow.Session - [12/abc2d9] Submitted process > FASTP (L66106_EdenPool_cDNA_S3_20210104-793515_01_C01)
Jan-29 18:50:44.498 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 159; name: FASTP (L66105_EdenPool_cDNA_S2_20210106-797126_01_B01); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/c8/45ff2b8463d37d122636f4c77dc260]
Jan-29 18:50:44.504 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 18:50:44.504 [Task submitter] INFO  nextflow.Session - [3a/fabb1a] Submitted process > FASTP (L66107_EdenPool_cDNA_S4_20210110-721656_01_D01)
Jan-29 18:50:49.181 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 160; name: FASTP (L66106_EdenPool_cDNA_S3_20210104-793515_01_C01); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/12/abc2d982d6a135deed941643f1a3ba]
Jan-29 18:50:49.189 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 18:50:49.189 [Task submitter] INFO  nextflow.Session - [43/971485] Submitted process > FASTQC (L66107_EdenPool_cDNA_S4_20210110-721656_01_D01)
Jan-29 18:50:51.665 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 163; name: FASTP (L66107_EdenPool_cDNA_S4_20210110-721656_01_D01); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/3a/fabb1af083ef010cc6852c8cdb3544]
Jan-29 18:50:51.672 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 18:50:51.672 [Task submitter] INFO  nextflow.Session - [b9/99a82a] Submitted process > FASTQC (L66109_EdenPool_cDNA_S6_20210108-720624_01_F01)
Jan-29 18:50:54.145 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 162; name: FASTQC (L66107_EdenPool_cDNA_S4_20210110-721656_01_D01); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/43/9714856522488ddae7d2abb9664f2d]
Jan-29 18:50:54.154 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 18:50:54.154 [Task submitter] INFO  nextflow.Session - [21/e9d210] Submitted process > FASTP (L66109_EdenPool_cDNA_S6_20210108-720624_01_F01)
Jan-29 18:50:56.597 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 164; name: FASTQC (L66109_EdenPool_cDNA_S6_20210108-720624_01_F01); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/b9/99a82a6a3c8eabfe34ddd548d63a61]
Jan-29 18:50:56.604 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 18:50:56.604 [Task submitter] INFO  nextflow.Session - [00/0551ff] Submitted process > FASTQC (L66108_EdenPool_cDNA_S5_20210109-721159_01_E01)
Jan-29 18:51:01.478 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 166; name: FASTQC (L66108_EdenPool_cDNA_S5_20210109-721159_01_E01); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/00/0551ff7e209147012f8cd8b1e32a07]
Jan-29 18:51:01.488 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 18:51:01.488 [Task submitter] INFO  nextflow.Session - [9b/3fb68c] Submitted process > FASTP (L66108_EdenPool_cDNA_S5_20210109-721159_01_E01)
Jan-29 18:51:02.205 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 165; name: FASTP (L66109_EdenPool_cDNA_S6_20210108-720624_01_F01); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/21/e9d210ac6746187d2c9195ecc1a1d2]
Jan-29 18:51:02.211 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 18:51:02.211 [Task submitter] INFO  nextflow.Session - [39/e23b09] Submitted process > FASTQC (L66110_EdenPool_cDNA_S7_20210108-720770_01_G01)
Jan-29 18:51:06.114 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 168; name: FASTQC (L66110_EdenPool_cDNA_S7_20210108-720770_01_G01); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/39/e23b09e64ff4296e28bd83e817a423]
Jan-29 18:51:06.121 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 18:51:06.121 [Task submitter] INFO  nextflow.Session - [9b/b39f2c] Submitted process > FASTP (L66110_EdenPool_cDNA_S7_20210108-720770_01_G01)
Jan-29 18:51:09.794 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 167; name: FASTP (L66108_EdenPool_cDNA_S5_20210109-721159_01_E01); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/9b/3fb68c9c4a9271c2bbf55ac80c7eb4]
Jan-29 18:51:09.801 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 18:51:09.801 [Task submitter] INFO  nextflow.Session - [e0/a3618b] Submitted process > FASTP (L66112_EdenPool_cDNA_S9_20210108-720344_01_A02)
Jan-29 18:51:13.913 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 169; name: FASTP (L66110_EdenPool_cDNA_S7_20210108-720770_01_G01); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/9b/b39f2cc857ab84631c5546199b0633]
Jan-29 18:51:13.921 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 18:51:13.921 [Task submitter] INFO  nextflow.Session - [fa/7f6688] Submitted process > FASTQC (L66112_EdenPool_cDNA_S9_20210108-720344_01_A02)
Jan-29 18:51:18.166 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 171; name: FASTP (L66112_EdenPool_cDNA_S9_20210108-720344_01_A02); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/e0/a3618b6f6d7a64955fb7d11b584b98]
Jan-29 18:51:18.172 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 18:51:18.172 [Task submitter] INFO  nextflow.Session - [3f/219716] Submitted process > FASTP (L66111_EdenPool_cDNA_S8_20210108-720048_01_H01)
Jan-29 18:51:18.865 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 170; name: FASTQC (L66112_EdenPool_cDNA_S9_20210108-720344_01_A02); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/fa/7f66888a9f246a4d316e2c0394fcbd]
Jan-29 18:51:18.875 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 18:51:18.875 [Task submitter] INFO  nextflow.Session - [65/e5b409] Submitted process > FASTQC (L66111_EdenPool_cDNA_S8_20210108-720048_01_H01)
Jan-29 18:51:23.886 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 173; name: FASTQC (L66111_EdenPool_cDNA_S8_20210108-720048_01_H01); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/65/e5b4099f513c22bc8b2b8722b54676]
Jan-29 18:51:23.894 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 18:51:23.894 [Task submitter] INFO  nextflow.Session - [1b/cde451] Submitted process > FASTQC (L66113_EdenPool_cDNA_S10_20210107-798696_01_B02)
Jan-29 18:51:28.801 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 174; name: FASTQC (L66113_EdenPool_cDNA_S10_20210107-798696_01_B02); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/1b/cde451b733de2e119f193fc6a818cd]
Jan-29 18:51:28.809 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 18:51:28.809 [Task submitter] INFO  nextflow.Session - [be/8c8fc6] Submitted process > FASTP (L66113_EdenPool_cDNA_S10_20210107-798696_01_B02)
Jan-29 18:51:30.054 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 172; name: FASTP (L66111_EdenPool_cDNA_S8_20210108-720048_01_H01); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/3f/219716d405e98c9063d28ff1c269ca]
Jan-29 18:51:30.061 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 18:51:30.061 [Task submitter] INFO  nextflow.Session - [48/2180db] Submitted process > FASTQC (L66114_EdenPool_cDNA_S11_20210106-797945_01_C02)
Jan-29 18:51:34.073 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 177; name: FASTQC (L66114_EdenPool_cDNA_S11_20210106-797945_01_C02); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/48/2180dbe54da03c8034931db438a1ae]
Jan-29 18:51:34.080 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 18:51:34.080 [Task submitter] INFO  nextflow.Session - [5d/e8d86d] Submitted process > FASTP (L66114_EdenPool_cDNA_S11_20210106-797945_01_C02)
Jan-29 18:51:36.873 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 175; name: FASTP (L66113_EdenPool_cDNA_S10_20210107-798696_01_B02); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/be/8c8fc6bb912907c708f4be26d1a7e2]
Jan-29 18:51:36.880 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 18:51:36.880 [Task submitter] INFO  nextflow.Session - [90/1d5561] Submitted process > FASTQC (L66115_EdenPool_cDNA_S12_20210106-797963_01_D02)
Jan-29 18:51:40.597 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 176; name: FASTP (L66114_EdenPool_cDNA_S11_20210106-797945_01_C02); status: COMPLETED; exit: 0; error: -; workDir: /home/crtd_bioinf/fabirost/projects/illudev/bfx1527/nfcore/work/5d/e8d86d37ba74d0afc4882770ced5e7]
Jan-29 18:51:40.603 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 18:51:40.603 [Task submitter] INFO  nextflow.Session - [f7/189a95] Submitted process > FASTP (L66115_EdenPool_cDNA_S12_20210106-797963_01_D02)
fbnrst commented 3 years ago

Here is the result of running tests on viralrecon release 1.1.0 using nextflow 20.10.0. There are some errors

-Warning, pipeline completed, but with errored process(es) -
-Number of ignored errored process(es) : 11 -
-Number of successfully ran process(es) : 131 -
-[nf-core/viralrecon] Pipeline completed successfully-
WARN: To render the execution DAG in the required format it is required to install Graphviz -- See http://www.graphviz.org for more info.
Completed at: 01-Feb-2021 12:22:24
Duration    : 7m 11s
CPU hours   : 0.9 (0.5% failed)
Succeeded   : 131
Ignored     : 11
Failed      : 11

nextflow.log

fbnrst commented 3 years ago

One of the ignored errors from the log file I posted above:

Feb-01 13:01:26.852 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 135; name: UNICYCLER_VG (SAMPLE3_SE); status: COMPLETED; exit: 1; error: -; workDir: /home/crtd_bioinf/fabirost/temp/work/6a/9ebe2aa3590467b8fe9ad48a7b361b]

I inspected the workDir /home/crtd_bioinf/fabirost/temp/work/6a/9ebe2aa3590467b8fe9ad48a7b361b .command.out is empty. .command.log and .command.err` have the following identical content:

[M::mm_idx_gen::0.004*2.68] collected minimizers
[M::mm_idx_gen::0.005*2.41] sorted minimizers
[M::main::0.005*2.41] loaded/built the index for 1 target sequence(s)
[M::mm_mapopt_update::0.005*2.34] mid_occ = 100
[M::mm_idx_stat] kmer size: 19; skip: 10; is_hpc: 0; #seq: 1
[M::mm_idx_stat::0.005*2.29] distinct minimizers: 5470 (99.98% are singletons); average occurrences: 1.003; average spacing: 5.453
[M::worker_pipeline::0.021*1.46] mapped 2 sequences
[M::main] Version: 2.17-r941
[M::main] CMD: minimap2 -c -t 2 -x asm20 GCF_009858895.2_ASM985889v3_genomic.200409.fna SAMPLE3_SE.scaffolds.fa
[M::main] Real time: 0.022 sec; CPU: 0.032 sec; Peak RSS: 0.004 GB
[xg]: couldn't create temp directory: /xg-Pkl7wB
fbnrst commented 3 years ago

OK, so the above errors were solved by setting export TMPDIR=/tmp.

Now, I am running tests on the dev branch and I run into new errors:

-Warning, pipeline completed, but with errored process(es) -
-Number of ignored errored process(es) : 11 -
-Number of successfully ran process(es) : 142 -
-[nf-core/viralrecon] Pipeline completed successfully-
WARN: To render the execution DAG in the required format it is required to install Graphviz -- See http://www.graphviz.org for more info.
Completed at: 04-Feb-2021 17:30:06
Duration    : 4m 53s
CPU hours   : 0.9 (11.4% failed)
Succeeded   : 142
Ignored     : 11
Failed      : 11

I attach the log file.

nextflow.log

The first error I can spot in the log file is:

Feb-04 17:26:05.965 [Task monitor] INFO  nextflow.processor.TaskProcessor - [3a/9ac1e1] NOTE: Process `MINIA_PLASMIDID (SAMPLE2_PE)` terminated with an error exit status (1) -- Error is ignored

So, I also attach output from 3a/9ac1e1 command.log command.out.txt command.err.txt

There is some error in .command.err:

Namespace(group=False, input_folder='./NO_GROUP/SAMPLE2_PE')
Creating summary
must be str, not NoneType
Traceback (most recent call last):
  File "/opt/conda/envs/nf-core-viralrecon-1.2.0dev/bin/summary_report_pid.py", line 465, in <module>
    main()
  File "/opt/conda/envs/nf-core-viralrecon-1.2.0dev/bin/summary_report_pid.py", line 459, in main
    summary_to_html(input_folder, final_individual_dataframe, html_template)
  File "/opt/conda/envs/nf-core-viralrecon-1.2.0dev/bin/summary_report_pid.py", line 301, in summary_to_html
    df['images'] = df.apply(lambda x: apply_img_tag(x), axis=1)
  File "/opt/conda/envs/nf-core-viralrecon-1.2.0dev/lib/python3.6/site-packages/pandas/core/frame.py", line 7552, in apply
    return op.get_result()
  File "/opt/conda/envs/nf-core-viralrecon-1.2.0dev/lib/python3.6/site-packages/pandas/core/apply.py", line 185, in get_result
    return self.apply_standard()
  File "/opt/conda/envs/nf-core-viralrecon-1.2.0dev/lib/python3.6/site-packages/pandas/core/apply.py", line 276, in apply_standard
    results, res_index = self.apply_series_generator()
  File "/opt/conda/envs/nf-core-viralrecon-1.2.0dev/lib/python3.6/site-packages/pandas/core/apply.py", line 305, in apply_series_generator
    results[i] = self.f(v)
  File "/opt/conda/envs/nf-core-viralrecon-1.2.0dev/bin/summary_report_pid.py", line 301, in <lambda>
    df['images'] = df.apply(lambda x: apply_img_tag(x), axis=1)
  File "/opt/conda/envs/nf-core-viralrecon-1.2.0dev/bin/summary_report_pid.py", line 291, in apply_img_tag
    '</a>' + '\n' + \
TypeError: must be str, not NoneType
Traceback (most recent call last):
  File "/opt/conda/envs/nf-core-viralrecon-1.2.0dev/bin/summary_report_pid.py", line 465, in <module>
    main()
  File "/opt/conda/envs/nf-core-viralrecon-1.2.0dev/bin/summary_report_pid.py", line 459, in main
    summary_to_html(input_folder, final_individual_dataframe, html_template)
  File "/opt/conda/envs/nf-core-viralrecon-1.2.0dev/bin/summary_report_pid.py", line 301, in summary_to_html
    df['images'] = df.apply(lambda x: apply_img_tag(x), axis=1)
  File "/opt/conda/envs/nf-core-viralrecon-1.2.0dev/lib/python3.6/site-packages/pandas/core/frame.py", line 7552, in apply
    return op.get_result()
  File "/opt/conda/envs/nf-core-viralrecon-1.2.0dev/lib/python3.6/site-packages/pandas/core/apply.py", line 185, in get_result
    return self.apply_standard()
  File "/opt/conda/envs/nf-core-viralrecon-1.2.0dev/lib/python3.6/site-packages/pandas/core/apply.py", line 276, in apply_standard
    results, res_index = self.apply_series_generator()
  File "/opt/conda/envs/nf-core-viralrecon-1.2.0dev/lib/python3.6/site-packages/pandas/core/apply.py", line 305, in apply_series_generator
    results[i] = self.f(v)
  File "/opt/conda/envs/nf-core-viralrecon-1.2.0dev/bin/summary_report_pid.py", line 301, in <lambda>
    df['images'] = df.apply(lambda x: apply_img_tag(x), axis=1)
  File "/opt/conda/envs/nf-core-viralrecon-1.2.0dev/bin/summary_report_pid.py", line 291, in apply_img_tag
    '</a>' + '\n' + \
TypeError: must be str, not NoneType
fbnrst commented 3 years ago

Setting export TMPDIR=/tmp seems to solve the issue.