Closed olgabot closed 2 years ago
pditommaso
commented
2 years ago Hi Olga! it looks like there's something messed up with the container configuration, in particular it's suspect the last line
However, think is should be reported to https://github.com/nf-core/rnaseq/, because it looks related to the pipeline. tagging @drpatelh for details.
drpatelh
commented
2 years ago Hi @olgabot ! Long time no hear! Hope you are doing well :)
Unfortunately, I don't have any concrete suggestions for you. I have kinda been spoilt by always interacting with AWS Batch via Nextflow Tower. Feel free to push an issue to the nf-core/rnaseq repo because it could be useful for others encountering the same issue.
A couple of suggestions that may be worth playing with:
bbio-nf-awsbatch.config since some of these settings will already by set when you import the relevant -profile. e.g.params {
awsqueue = "our-queue-name"
awsregion = 'us-west-1'
awscli = '/usr/bin/aws'
}
workDir = "s3://nextflow-bucket/work"Check that the value of AWS CLI should instead be: awscli = '/home/ec2-user/miniconda/bin/aws'
Try a simpler pipeline to get yourself up and running first e.g. nextflow-io/rnaseq-nf
Hope that helps!
olgabot
commented
2 years ago Hi @drpatelh and @pditommaso! Thank you so much for your help and long time no see :)
The nextflow run hello pipeline worked on AWS for me, but I think something is weird with either our permissions for the container registry, or the AMI doesn't have docker installed
3. Check that the value of AWS CLI should instead be:
awscli = '/home/ec2-user/miniconda/bin/aws'
This was actually not working for me earlier, because which -a aws within the container produced /usr/bin/aws, so I changed the value of awscli.
4. Try a simpler pipeline to get yourself up and running first e.g. nextflow-io/rnaseq-nf
Yay, new error! :)
The good thing is that salmon index at least runs, which tells me that the container is getting attached.
Forking nextflow-io/rnaseq-nf and adding these commands to double-check the container setup showed:
which -a python
which -a aws
which -a salmon
python --version
# Show whether you're in a docker container
# From: http://youdidwhatwithtsql.com/how-to-tell-if-youre-in-a-docker-container/2466/
grep :/docker /proc/self/cgroup | wc -lHere's the output from just these new commands
Command output:
/opt/conda/bin/python
/usr/bin/python
/usr/bin/aws
/opt/conda/bin/salmon
Python 3.9.5
0
... redacted "salmon index" output ...The output of grep :/docker /proc/self/cgroup | wc -l being 0 is concerning to me.. doesn't that mean this command wasn't performed inside a docker container?
olgabot
commented
2 years ago BTW, FASTQC fails independently for a locale reason:
(nf-core)
✘ Tue 24 May - 17:27 ~/nf-workflow-runs/exonchecker origin ☊ master 3☀ 1●
nextflow run olgabot/rnaseq-nf -c bbio-nf-awsbatch.config -latest -profile batch
N E X T F L O W ~ version 22.04.0
Pulling olgabot/rnaseq-nf ...
Fast-forward
Launching `https://github.com/olgabot/rnaseq-nf` [berserk_carson] DSL2 - revision: 6b6f25e4f2 [master]
R N A S E Q - N F P I P E L I N E
===================================
transcriptome: s3://rnaseq-nf/data/ggal/transcript.fa
reads : s3://rnaseq-nf/data/ggal/lung_{1,2}.fq
outdir : results
Uploading local `bin` scripts folder to s3://nextflow-bucket/work/tmp/f1/b06b6522e336dfa55dec99a200fb19/bin
executor > awsbatch (2)
[81/da838f] process > RNASEQ:INDEX (transcript) [ 0%] 0 of 1
[1b/62f1bb] process > RNASEQ:FASTQC (FASTQC on lung) [ 0%] 0 of 1
executor > awsbatch (2)
[- ] process > RNASEQ:INDEX (transcript) -
[1b/62f1bb] process > RNASEQ:FASTQC (FASTQC on lung) [100%] 1 of 1, failed: 1 ✘
[- ] process > RNASEQ:QUANT -
[- ] process > MULTIQC -
Error executing process > 'RNASEQ:FASTQC (FASTQC on lung)'
Caused by:
Missing output file(s) `fastqc_lung_logs` expected by process `RNASEQ:FASTQC (FASTQC on lung)`
Command executed:
fastqc.sh "lung" "lung_1.fq lung_2.fq"
Command exit status:
0
Command output:
(empty)
Command error:
/bin/bash: warning: setlocale: LC_ALL: cannot change locale (C.UTF-8)
bash: warning: setlocale: LC_ALL: cannot change locale (C.UTF-8)
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
arLANGUAGE = (unset),
perl: LC_ALL = "C.UTF-8",
LANG = "C.UTF-8"
are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
Work dir:
s3://nextflow-bucket/work/1b/62f1bb2f1483b6ad74a437e77d6edb
Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`
Since these are battle-tested pipelines, I wouldn't expect these errors which look like some configuration issue. Do you have any ideas?
olgabot
commented
2 years ago Adding -with-docker created new errors about the shared object files and probably the LD_LIBRARY_PATH
Using a modified rnaseq-nf pipeline with a few more verbose messages:
Command executed:
which -a python
which -a aws
which -a salmon
python --version
# Show whether you're in a docker container
# From: http://youdidwhatwithtsql.com/how-to-tell-if-youre-in-a-docker-container/2466/
grep :/docker /proc/self/cgroup | wc -l
ls -lha
salmon index --threads 1 -t transcript.fa -i index
ls -lha
Command exit status:
127
Command output:
/opt/conda/bin/python
/usr/bin/python
/usr/bin/aws
/opt/conda/bin/salmon
Python 3.9.5
0
Command error:
bash: warning: setlocale: LC_ALL: cannot change locale (C.UTF-8)
bash: warning: setlocale: LC_ALL: cannot change locale (C.UTF-8)
nxf-scratch-dir ip-10-0-5-206.us-west-1.compute.internal:/tmp/nxf.nHlsYEV6f1
grep: error while loading shared libraries: libpcre.so.1: cannot open shared object file: No such file or directory
grep: error while loading shared libraries: libpcre.so.1: cannot open shared object file: No such file or directory
[Errno 32] Broken pipe
Exception ignored in: <_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>
BrokenPipeError: [Errno 32] Broken pipe
[Errno 32] Broken pipe
Exception ignored in: <_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>
BrokenPipeError: [Errno 32] Broken pipe
/bin/bash: warning: setlocale: LC_ALL: cannot change locale (C.UTF-8)
/opt/conda/bin/python
/usr/bin/python
/usr/bin/aws
/opt/conda/bin/salmon
Python 3.9.5
grep: error while loading shared libraries: libpcre.so.1: cannot open shared object file: No such file or directory
0
ls: error while loading shared libraries: libcap.so.2: cannot open shared object file: No such file or directory
What I'm really confused about is this log, which uses the container quay.io/biocontainers/python:3.8.3, but which -a python returns /usr/bin/python when it should be /usr/local/bin/python and python --version is 2.7. Do you know what may be happening?
(base)
Tue 24 May - 20:19 ~/nf-workflow-runs/exonchecker origin ☊ master 3☀ 1●
docker run -it quay.io/biocontainers/python:3.8.3 bash
bash-4.2# which -a python
/usr/local/bin/python
bash-4.2# python --version
Python 3.8.3FYI, here is the fix: https://github.com/aws-samples/aws-genomics-workflows/issues/202#issuecomment-1147996363
New versions of AWS CLI v2 on the host instances have a different path to aws. I have no idea how, but this change fixed everything:
aws.batch.cliPath = "/opt/aws-cli/bin/aws"
GallVp
commented
5 months ago Hi @olgabot
Thanks for the hint. In my case, I was experiencing the same issue because of installing aws-cli in /usr/local/bin and setting aws.batch.cliPath='/usr/local/bin'. This created a conflict due to container mount paths. This is documented here:
https://www.nextflow.io/docs/latest/aws.html#aws-cli-installation
I moved the cli installation to an uncommon path and the pipeline started working.
Bug report
Expected behavior and actual behavior
Hello, hope you are doing well!
I expected to be able to run
nf-core/rnasequsing AWS Batch. We created a the first two CloudFormation stacks as listed on the AWS Genomics Workflows, and they look to have the right permissions. However, the containers don't seem to get started at all and I can't run evennf-core/rnaseq.Steps to reproduce the problem
Here is the nextflow command:
Here is our configuration:
Contents of `bbio-nf-awsbatch.config`
``` params { awsqueue = "our-queue-name" awsregion = 'us-west-1' } process.queue = "our-queue-name" aws.region = 'us-west-1' aws.batch.cliPath = "/usr/bin/aws" workDir = "s3://nextflow-bucket/work" docker.enabled = true docker.userEmulation = true singularity.enabled = false podman.enabled = false shifter.enabled = false charliecloud.enabled = false process.container = 'quay.io/biocontainers/python:3.8.3' ```Looking in the
.command.runfile, there is no even mention ofdockerProgram output
`.nextflow.log` file
``` May-23 18:39:12.191 [main] DEBUG nextflow.cli.Launcher - $> nextflow run nf-core/rnaseq -profile test,docker,awsbatch -c nf-workflow-runs/exonchecker/bbio-nf-awsbatch.config --outdir 's3://nextflow-bucket/output/nf-core--rnaseq/test/' May-23 18:39:12.261 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 22.04.0 May-23 18:39:13.557 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/olgabot/.nextflow/assets/nf-core/rnaseq/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/rnaseq.git May-23 18:39:13.570 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/olgabot/.nextflow/assets/nf-core/rnaseq/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/rnaseq.git May-23 18:39:14.127 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/olgabot/.nextflow/assets/nf-core/rnaseq/nextflow.config May-23 18:39:14.129 [main] DEBUG nextflow.config.ConfigBuilder - User config file: /home/olgabot/nf-workflow-runs/exonchecker/bbio-nf-awsbatch.config May-23 18:39:14.130 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/olgabot/.nextflow/assets/nf-core/rnaseq/nextflow.config May-23 18:39:14.130 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/olgabot/nf-workflow-runs/exonchecker/bbio-nf-awsbatch.config May-23 18:39:14.138 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `test,docker,awsbatch` May-23 18:39:14.362 [main] DEBUG nextflow.plugin.PluginsFacade - Using Default plugins manager May-23 18:39:14.371 [main] INFO org.pf4j.DefaultPluginStatusProvider - Enabled plugins: [] May-23 18:39:14.372 [main] INFO org.pf4j.DefaultPluginStatusProvider - Disabled plugins: [] May-23 18:39:14.375 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode May-23 18:39:14.379 [main] DEBUG nextflow.plugin.PluginsFacade - Using Default plugins manager May-23 18:39:14.665 [main] DEBUG nextflow.plugin.PluginsFacade - Using Default plugins manager May-23 18:39:14.665 [main] DEBUG nextflow.plugin.PluginsFacade - Using Default plugins manager May-23 18:39:14.875 [main] DEBUG nextflow.plugin.PluginsFacade - Using Default plugins manager May-23 18:39:14.876 [main] DEBUG nextflow.plugin.PluginsFacade - Using Default plugins manager May-23 18:39:15.815 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `test,docker,awsbatch` May-23 18:39:15.842 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [cfc_dev, ifb_core, denbi_qbic, genotoul, alice, uppmax, abims, nihbiowulf, nu_genomics, oist, sahmri, mpcdf, leicester, lugh, vsc_ugent, cambridge, unibe_ibu, vai, podman, czbiohub_aws, jax, cheaha, ccga_med, test, google, computerome, seg_globe, sanger, pasteur, test_full, eddie, azurebatch, bi, bigpurple, cedars, docker, gis, eva, utd_ganymede, charliecloud, fgcz, conda, singularity, icr_davros, munin, rosalind, prince, hasta, hebbe, cfc, utd_sysbio, uzh, debug, genouest, cbe, ebc, ccga_dx, crick, marvin, phoenix, biohpc_gen, shifter, awsbatch, uct_hpc, imperial, maestro, aws_tower, binac] May-23 18:39:15.895 [main] INFO nextflow.cli.CmdRun - Launching `https://github.com/nf-core/rnaseq` [trusting_snyder] DSL2 - revision: e0dfce9af5 [master] May-23 18:39:15.896 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; plugins-dir=/home/olgabot/.nextflow/plugins; core-plugins: nf-amazon@1.7.1,nf-azure@0.13.1,nf-console@1.0.3,nf-ga4gh@1.0.3,nf-google@1.1.4,nf-sqldb@0.4.0,nf-tower@1.4.0 May-23 18:39:15.897 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[nf-amazon@1.7.1] May-23 18:39:15.901 [main] INFO org.pf4j.DefaultPluginStatusProvider - Enabled plugins: [] May-23 18:39:15.901 [main] INFO org.pf4j.DefaultPluginStatusProvider - Disabled plugins: [] May-23 18:39:15.903 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode May-23 18:39:15.909 [main] INFO org.pf4j.AbstractPluginManager - No plugins May-23 18:39:15.909 [main] DEBUG nextflow.plugin.PluginUpdater - Installing plugin nf-amazon version: 1.7.1 May-23 18:39:15.915 [main] INFO org.pf4j.AbstractPluginManager - Plugin 'nf-amazon@1.7.1' resolved May-23 18:39:15.915 [main] INFO org.pf4j.AbstractPluginManager - Start plugin 'nf-amazon@1.7.1' May-23 18:39:15.927 [main] DEBUG nextflow.plugin.BasePlugin - Plugin started nf-amazon@1.7.1 May-23 18:39:15.941 [main] DEBUG nextflow.file.FileHelper - > Added 'S3FileSystemProvider' to list of installed providers [s3] May-23 18:39:15.941 [main] DEBUG nextflow.plugin.PluginUpdater - Installing plugin nf-tower version: 1.4.0 May-23 18:39:15.942 [main] INFO org.pf4j.AbstractPluginManager - Plugin 'nf-tower@1.4.0' resolved May-23 18:39:15.942 [main] INFO org.pf4j.AbstractPluginManager - Start plugin 'nf-tower@1.4.0' May-23 18:39:15.945 [main] DEBUG nextflow.plugin.BasePlugin - Plugin started nf-tower@1.4.0 May-23 18:39:15.991 [main] DEBUG nextflow.Session - Session uuid: ffc30461-54a5-4716-8a80-6d3e1b2b92c3 May-23 18:39:15.991 [main] DEBUG nextflow.Session - Run name: trusting_snyder May-23 18:39:15.991 [main] DEBUG nextflow.Session - Executor pool size: 8 May-23 18:39:16.000 [main] DEBUG nextflow.file.FileHelper - Creating a file system instance for provider: S3FileSystemProvider May-23 18:39:16.005 [main] DEBUG nextflow.Global - Using AWS credential defined in `default` section in file: /home/olgabot/.aws/credentials May-23 18:39:16.005 [main] DEBUG nextflow.file.FileHelper - AWS S3 config details: {secret_key=m9t67j.., region=us-west-1, max_error_retry=5, access_key=AKIA36..} May-23 18:39:16.365 [main] DEBUG c.u.s3fs.S3FileSystemProvider - Using S3 multi-part downloader May-23 18:39:16.367 [main] DEBUG c.u.s3fs.ng.S3ParallelDownload - Creating S3 download thread pool: workers=10; chunkSize=10 MB; queueSize=10000; max-mem=1 GB; maxAttempts=5; maxDelay=1m 30s; pool-capacity=103 May-23 18:39:16.411 [main] DEBUG nextflow.cli.CmdRun - Version: 22.04.0 build 5697 Created: 23-04-2022 18:00 UTC System: Linux 4.14.262-200.489.amzn2.x86_64 Runtime: Groovy 3.0.10 on OpenJDK 64-Bit Server VM 11.0.9.1-internal+0-adhoc..src Encoding: UTF-8 (UTF-8) Process: 15739@ip-172-31-9-54.us-west-1.compute.internal [172.31.9.54] CPUs: 8 - Mem: 30.6 GB (3 GB) - Swap: 0 (0) May-23 18:39:16.695 [main] WARN com.amazonaws.util.Base64 - JAXB is unavailable. Will fallback to SDK implementation which may be less performant.If you are using Java 9+, you will need to include javax.xml.bind:jaxb-api as a dependency. May-23 18:39:16.703 [main] DEBUG nextflow.file.FileHelper - Can't check if specified path is NFS (1): /nextflow-bucket/work May-23 18:39:16.703 [main] DEBUG nextflow.Session - Work-dir: s3://nextflow-bucket/work [null] May-23 18:39:16.779 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[AwsBatchExecutor] May-23 18:39:16.799 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory May-23 18:39:16.823 [main] DEBUG nextflow.Session - Observer factory: TowerFactory May-23 18:39:16.940 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory May-23 18:39:16.949 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 9; maxThreads: 1000 May-23 18:39:17.013 [main] DEBUG nextflow.Session - Session start invoked May-23 18:39:17.016 [main] DEBUG nextflow.trace.TraceFileObserver - Flow starting -- trace file: /nextflow-bucket/output/nf-core--rnaseq/test/pipeline_info/execution_trace_2022-05-23_18-39-15.txt May-23 18:39:17.112 [main] DEBUG nextflow.Session - Using default localLib path: /home/olgabot/.nextflow/assets/nf-core/rnaseq/lib May-23 18:39:17.116 [main] DEBUG nextflow.Session - Adding to the classpath library: /home/olgabot/.nextflow/assets/nf-core/rnaseq/lib May-23 18:39:17.116 [main] DEBUG nextflow.Session - Adding to the classpath library: /home/olgabot/.nextflow/assets/nf-core/rnaseq/lib/nfcore_external_java_deps.jar May-23 18:39:18.104 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution May-23 18:39:18.312 [main] WARN nextflow.Nextflow - Found unexpected parameters: * --awscli: /home/ec2-user/miniconda/bin/aws * --awsregion: us-west-1 * --awsqueue: our-queue-name May-23 18:39:18.313 [main] INFO nextflow.Nextflow - - [2mIgnore this warning: params.schema_ignore_params = "awscli,awsregion,awsqueue" [0m May-23 18:39:18.326 [main] INFO nextflow.Nextflow - -[2m----------------------------------------------------[0m- [0;32m,--.[0;30m/[0;32m,-.[0m [0;34m ___ __ __ __ ___ [0;32m/,-._.--~'[0m [0;34m |\ | |__ __ / ` / \ |__) |__ [0;33m} {[0m [0;34m | \| | \__, \__/ | \ |___ [0;32m\`-._,-`-,[0m [0;32m`._,._,'[0m [0;35m nf-core/rnaseq v3.7[0m -[2m----------------------------------------------------[0m- [1mCore Nextflow options[0m [0;34mrevision : [0;32mmaster[0m [0;34mrunName : [0;32mtrusting_snyder[0m [0;34mcontainerEngine : [0;32mdocker[0m [0;34mcontainer : [0;32mquay.io/biocontainers/python:3.8.3[0m [0;34mlaunchDir : [0;32m/home/olgabot[0m [0;34mworkDir : [0;32m/nextflow-bucket/work[0m [0;34mprojectDir : [0;32m/home/olgabot/.nextflow/assets/nf-core/rnaseq[0m [0;34muserName : [0;32molgabot[0m [0;34mprofile : [0;32mtest,docker,awsbatch[0m [0;34mconfigFiles : [0;32m/home/olgabot/.nextflow/assets/nf-core/rnaseq/nextflow.config, /home/olgabot/nf-workflow-runs/exonchecker/bbio-nf-awsbatch.config[0m [1mInput/output options[0m [0;34minput : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/samplesheet/v3.4/samplesheet_test.csv[0m [0;34moutdir : [0;32ms3://nextflow-bucket/output/nf-core--rnaseq/test/[0m [1mUMI options[0m [0;34mumitools_bc_pattern : [0;32mNNNN[0m [1mRead filtering options[0m [0;34mbbsplit_fasta_list : [0;32mhttps://github.com/nf-core/test-datasets/raw/rnaseq/reference/bbsplit_fasta_list.txt[0m [0;34mskip_bbsplit : [0;32mfalse[0m [1mReference genome options[0m [0;34mfasta : [0;32mhttps://github.com/nf-core/test-datasets/raw/rnaseq/reference/genome.fasta[0m [0;34mgtf : [0;32mhttps://github.com/nf-core/test-datasets/raw/rnaseq/reference/genes.gtf.gz[0m [0;34mgff : [0;32mhttps://github.com/nf-core/test-datasets/raw/rnaseq/reference/genes.gff.gz[0m [0;34mtranscript_fasta : [0;32mhttps://github.com/nf-core/test-datasets/raw/rnaseq/reference/transcriptome.fasta[0m [0;34madditional_fasta : [0;32mhttps://github.com/nf-core/test-datasets/raw/rnaseq/reference/gfp.fa.gz[0m [0;34mhisat2_index : [0;32mhttps://github.com/nf-core/test-datasets/raw/rnaseq/reference/hisat2.tar.gz[0m [0;34mrsem_index : [0;32mhttps://github.com/nf-core/test-datasets/raw/rnaseq/reference/rsem.tar.gz[0m [0;34msalmon_index : [0;32mhttps://github.com/nf-core/test-datasets/raw/rnaseq/reference/salmon.tar.gz[0m [1mAlignment options[0m [0;34mpseudo_aligner : [0;32msalmon[0m [1mInstitutional config options[0m [0;34mconfig_profile_name : [0;32mTest profile[0m [0;34mconfig_profile_description: [0;32mMinimal test dataset to check pipeline function[0m [0;34mconfig_profile_contact : [0;32mAlexander Peltzer (@apeltzer)[0m [0;34mconfig_profile_url : [0;32mhttps://aws.amazon.com/batch/[0m [1mMax job request options[0m [0;34mmax_cpus : [0;32m2[0m [0;34mmax_memory : [0;32m6.GB[0m [0;34mmax_time : [0;32m6.h[0m !! Only displaying parameters that differ from the pipeline defaults !! -[2m----------------------------------------------------[0m- If you use nf-core/rnaseq for your analysis please cite: * The pipeline https://doi.org/10.5281/zenodo.1400710 * The nf-core framework https://doi.org/10.1038/s41587-020-0439-x * Software dependencies https://github.com/nf-core/rnaseq/blob/master/CITATIONS.md -[2m----------------------------------------------------[0m- May-23 18:39:19.169 [main] WARN nextflow.Nextflow - ============================================================================= Both '--gtf' and '--gff' parameters have been provided. Using GTF file as priority. =================================================================================== May-23 18:39:19.170 [main] WARN nextflow.Nextflow - ============================================================================= '--transcript_fasta' parameter has been provided. Make sure transcript names in this file match those in the GFF/GTF file. Please see: https://github.com/nf-core/rnaseq/issues/753 =================================================================================== May-23 18:39:31.254 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_GTF May-23 18:39:31.256 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GUNZIP_.*|MAKE_TRANSCRIPTS_FASTA` matches process NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_GTF May-23 18:39:31.267 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: awsbatch May-23 18:39:31.267 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'awsbatch' May-23 18:39:31.268 [main] DEBUG nextflow.executor.Executor - [warm up] executor > awsbatch May-23 18:39:31.279 [main] DEBUG nextflow.util.ThrottlingExecutor - Creating throttling executor with opts: nextflow.util.ThrottlingExecutor$Options(poolName:AWSBatch-executor, limiter:RateLimiter[stableRate=50.0qps], poolSize:40, maxPoolSize:40, queueSize:5000, maxRetries:10, keepAlive:1m, autoThrottle:true, errorBurstDelay:1s, rampUpInterval:100, rampUpFactor:1.2, rampUpMaxRate:1.7976931348623157E308, backOffFactor:2.0, backOffMinRate:0.0166666667, retryDelay:1s) May-23 18:39:31.284 [main] DEBUG nextflow.util.ThrottlingExecutor - Creating throttling executor with opts: nextflow.util.ThrottlingExecutor$Options(poolName:AWSBatch-reaper, limiter:RateLimiter[stableRate=50.0qps], poolSize:40, maxPoolSize:40, queueSize:5000, maxRetries:10, keepAlive:1m, autoThrottle:true, errorBurstDelay:1s, rampUpInterval:100, rampUpFactor:1.2, rampUpMaxRate:1.7976931348623157E308, backOffFactor:2.0, backOffMinRate:0.0166666667, retryDelay:1s) May-23 18:39:31.285 [main] DEBUG n.cloud.aws.batch.AwsBatchExecutor - Creating parallel monitor for executor 'awsbatch' > pollInterval=10s; dumpInterval=5m May-23 18:39:31.528 [main] INFO n.cloud.aws.batch.AwsBatchExecutor - Uploading local `bin` scripts folder to s3://nextflow-bucket/work/tmp/59/57c99dbb2c36549875d666144cea88/bin May-23 18:39:32.271 [main] DEBUG nextflow.Global - Using AWS credential defined in `default` section in file: /home/olgabot/.aws/credentials May-23 18:39:32.302 [main] DEBUG n.cloud.aws.batch.AwsBatchExecutor - [AWS BATCH] Executor options=AwsOptions(cliPath:/usr/bin/aws, storageClass:null, storageEncryption:null, remoteBinDir:/nextflow-bucket/work/tmp/59/57c99dbb2c36549875d666144cea88/bin, region:us-west-1, maxParallelTransfers:4, maxTransferAttempts:5, delayBetweenAttempts:10s, retryMode:standard, maxSpotAttempts:5, debug:null, fetchInstanceType:false, jobRole:null, volumes:[], awsCli:/usr/bin/aws --region us-west-1) May-23 18:39:32.377 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA May-23 18:39:32.377 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GUNZIP_.*|MAKE_TRANSCRIPTS_FASTA` matches process NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA May-23 18:39:32.380 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: awsbatch May-23 18:39:32.381 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'awsbatch' May-23 18:39:32.392 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CAT_ADDITIONAL_FASTA` matches process NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:CAT_ADDITIONAL_FASTA May-23 18:39:32.395 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: awsbatch May-23 18:39:32.395 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'awsbatch' May-23 18:39:32.402 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF2BED May-23 18:39:32.402 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GTF2BED` matches process NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF2BED May-23 18:39:32.403 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: awsbatch May-23 18:39:32.403 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'awsbatch' May-23 18:39:32.410 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES May-23 18:39:32.410 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CUSTOM_GETCHROMSIZES` matches process NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES May-23 18:39:32.412 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: awsbatch May-23 18:39:32.412 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'awsbatch' May-23 18:39:32.457 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:BBMAP_BBSPLIT May-23 18:39:32.457 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BBMAP_BBSPLIT` matches process NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:BBMAP_BBSPLIT May-23 18:39:32.459 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:PREPARE_GENOME:BBMAP_BBSPLIT` matches process NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:BBMAP_BBSPLIT May-23 18:39:32.461 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: awsbatch May-23 18:39:32.461 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'awsbatch' May-23 18:39:32.471 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE May-23 18:39:32.472 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNTAR_.*|STAR_GENOMEGENERATE|HISAT2_BUILD` matches process NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE May-23 18:39:32.474 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: awsbatch May-23 18:39:32.474 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'awsbatch' May-23 18:39:32.483 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:UNTAR_SALMON_INDEX May-23 18:39:32.484 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNTAR_.*` matches process NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:UNTAR_SALMON_INDEX May-23 18:39:32.484 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNTAR_.*|STAR_GENOMEGENERATE|HISAT2_BUILD` matches process NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:UNTAR_SALMON_INDEX May-23 18:39:32.487 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: awsbatch May-23 18:39:32.487 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'awsbatch' May-23 18:39:32.499 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMPLESHEET_CHECK` matches process NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK May-23 18:39:32.501 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: awsbatch May-23 18:39:32.501 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'awsbatch' May-23 18:39:32.518 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_RNASEQ:RNASEQ:CAT_FASTQ May-23 18:39:32.518 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CAT_FASTQ` matches process NFCORE_RNASEQ:RNASEQ:CAT_FASTQ May-23 18:39:32.520 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: awsbatch May-23 18:39:32.520 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'awsbatch' May-23 18:39:32.535 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC May-23 18:39:32.535 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:FASTQC_UMITOOLS_TRIMGALORE:FASTQC` matches process NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC May-23 18:39:32.536 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: awsbatch May-23 18:39:32.537 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'awsbatch' May-23 18:39:32.551 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE May-23 18:39:32.552 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE` matches process NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE May-23 18:39:32.554 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: awsbatch May-23 18:39:32.554 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'awsbatch' May-23 18:39:32.569 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name NFCORE_RNASEQ:RNASEQ:BBMAP_BBSPLIT May-23 18:39:32.569 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BBMAP_BBSPLIT` matches process NFCORE_RNASEQ:RNASEQ:BBMAP_BBSPLIT May-23 18:39:32.571 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: awsbatch May-23 18:39:32.571 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'awsbatch' May-23 18:39:32.587 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN May-23 18:39:32.588 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:ALIGN_STAR:STAR_ALIGN` matches process NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN May-23 18:39:32.589 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: awsbatch May-23 18:39:32.589 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'awsbatch' May-23 18:39:32.599 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT May-23 18:39:32.600 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_RNASEQ:RNASEQ:.*:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT` matches process NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT May-23 18:39:32.601 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: awsbatch May-23 18:39:32.601 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'awsbatch' May-23 18:39:32.608 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX May-23 18:39:32.609 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_RNASEQ:RNASEQ:.*:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX` matches process NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX May-23 18:39:32.610 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: awsbatch May-23 18:39:32.610 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'awsbatch' May-23 18:39:32.630 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS May-23 18:39:32.630 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_RNASEQ:RNASEQ:.*:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:.*` matches process NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS May-23 18:39:32.631 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: awsbatch May-23 18:39:32.631 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'awsbatch' May-23 18:39:32.636 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT May-23 18:39:32.637 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_RNASEQ:RNASEQ:.*:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:.*` matches process NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT May-23 18:39:32.637 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: awsbatch May-23 18:39:32.637 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'awsbatch' May-23 18:39:32.643 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS May-23 18:39:32.643 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_RNASEQ:RNASEQ:.*:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:.*` matches process NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS May-23 18:39:32.644 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: awsbatch May-23 18:39:32.644 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'awsbatch' May-23 18:39:32.653 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT May-23 18:39:32.653 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:QUANTIFY_STAR_SALMON:SALMON_QUANT` matches process NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT May-23 18:39:32.654 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: awsbatch May-23 18:39:32.654 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'awsbatch' May-23 18:39:32.661 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE May-23 18:39:32.661 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:QUANTIFY_STAR_SALMON:SALMON_TX2GENE` matches process NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE May-23 18:39:32.662 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: awsbatch May-23 18:39:32.662 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'awsbatch' May-23 18:39:32.668 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT May-23 18:39:32.668 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT` matches process NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT May-23 18:39:32.669 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: awsbatch May-23 18:39:32.669 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'awsbatch' May-23 18:39:32.674 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE May-23 18:39:32.675 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:QUANTIFY_STAR_SALMON:SALMON_SE_.*` matches process NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE May-23 18:39:32.676 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: awsbatch May-23 18:39:32.676 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'awsbatch' May-23 18:39:32.680 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED May-23 18:39:32.680 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:QUANTIFY_STAR_SALMON:SALMON_SE_.*` matches process NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED May-23 18:39:32.680 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: awsbatch May-23 18:39:32.680 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'awsbatch' May-23 18:39:32.683 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED May-23 18:39:32.684 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:QUANTIFY_STAR_SALMON:SALMON_SE_.*` matches process NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED May-23 18:39:32.684 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: awsbatch May-23 18:39:32.684 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'awsbatch' May-23 18:39:32.688 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT May-23 18:39:32.688 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:QUANTIFY_STAR_SALMON:SALMON_SE_.*` matches process NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT May-23 18:39:32.689 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: awsbatch May-23 18:39:32.689 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'awsbatch' May-23 18:39:32.694 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON May-23 18:39:32.694 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:DESEQ2_QC_STAR_SALMON` matches process NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON May-23 18:39:32.695 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: awsbatch May-23 18:39:32.696 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'awsbatch' May-23 18:39:32.713 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MULTIQC_TSV_FAIL_MAPPED` matches process NFCORE_RNASEQ:RNASEQ:MULTIQC_TSV_FAIL_MAPPED May-23 18:39:32.714 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local May-23 18:39:32.714 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-23 18:39:32.716 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local May-23 18:39:32.719 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=8; memory=30.6 GB; capacity=8; pollInterval=100ms; dumpInterval=5m May-23 18:39:32.722 [main] WARN nextflow.executor.LocalExecutor - Local executor only supports default file system -- Check work directory: s3://nextflow-bucket/work May-23 18:39:32.729 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium,error_ignore` for process with name NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP May-23 18:39:32.729 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_ignore` matches labels `process_medium,error_ignore` for process with name NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP May-23 18:39:32.730 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:PRESEQ_LCEXTRAP` matches process NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP May-23 18:39:32.731 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: awsbatch May-23 18:39:32.731 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'awsbatch' May-23 18:39:32.741 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES May-23 18:39:32.741 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES` matches process NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES May-23 18:39:32.742 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: awsbatch May-23 18:39:32.742 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'awsbatch' May-23 18:39:32.750 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX May-23 18:39:32.750 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX` matches process NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX May-23 18:39:32.751 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: awsbatch May-23 18:39:32.752 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'awsbatch' May-23 18:39:32.765 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS May-23 18:39:32.765 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:.*` matches process NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS May-23 18:39:32.766 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: awsbatch May-23 18:39:32.766 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'awsbatch' May-23 18:39:32.773 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT May-23 18:39:32.774 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:.*` matches process NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT May-23 18:39:32.774 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: awsbatch May-23 18:39:32.775 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'awsbatch' May-23 18:39:32.781 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS May-23 18:39:32.781 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:.*` matches process NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS May-23 18:39:32.781 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: awsbatch May-23 18:39:32.782 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'awsbatch' May-23 18:39:32.789 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE May-23 18:39:32.789 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:STRINGTIE_STRINGTIE` matches process NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE May-23 18:39:32.790 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: awsbatch May-23 18:39:32.790 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'awsbatch' May-23 18:39:32.809 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS May-23 18:39:32.809 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SUBREAD_FEATURECOUNTS` matches process NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS May-23 18:39:32.810 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: awsbatch May-23 18:39:32.810 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'awsbatch' May-23 18:39:32.815 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MULTIQC_CUSTOM_BIOTYPE` matches process NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE May-23 18:39:32.816 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: awsbatch May-23 18:39:32.816 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'awsbatch' May-23 18:39:32.822 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV May-23 18:39:32.822 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BEDTOOLS_GENOMECOV` matches process NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV May-23 18:39:32.823 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: awsbatch May-23 18:39:32.823 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'awsbatch' May-23 18:39:32.828 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP May-23 18:39:32.828 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP` matches process NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP May-23 18:39:32.829 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: awsbatch May-23 18:39:32.829 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'awsbatch' May-23 18:39:32.834 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG May-23 18:39:32.834 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG` matches process NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG May-23 18:39:32.835 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: awsbatch May-23 18:39:32.835 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'awsbatch' May-23 18:39:32.840 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP May-23 18:39:32.840 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP` matches process NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP May-23 18:39:32.841 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: awsbatch May-23 18:39:32.841 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'awsbatch' May-23 18:39:32.846 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG May-23 18:39:32.846 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG` matches process NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG May-23 18:39:32.847 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: awsbatch May-23 18:39:32.847 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'awsbatch' May-23 18:39:32.857 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ May-23 18:39:32.857 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:QUALIMAP_RNASEQ` matches process NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ May-23 18:39:32.858 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: awsbatch May-23 18:39:32.858 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'awsbatch' May-23 18:39:32.863 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_long` matches labels `process_long` for process with name NFCORE_RNASEQ:RNASEQ:DUPRADAR May-23 18:39:32.863 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:DUPRADAR` matches process NFCORE_RNASEQ:RNASEQ:DUPRADAR May-23 18:39:32.864 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: awsbatch May-23 18:39:32.864 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'awsbatch' May-23 18:39:32.871 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT May-23 18:39:32.871 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:RSEQC:RSEQC_BAMSTAT` matches process NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT May-23 18:39:32.872 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: awsbatch May-23 18:39:32.872 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'awsbatch' May-23 18:39:32.879 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE May-23 18:39:32.879 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:RSEQC:RSEQC_INNERDISTANCE` matches process NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE May-23 18:39:32.880 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: awsbatch May-23 18:39:32.880 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'awsbatch' May-23 18:39:32.886 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT May-23 18:39:32.887 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:RSEQC:RSEQC_INFEREXPERIMENT` matches process NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT May-23 18:39:32.887 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: awsbatch May-23 18:39:32.887 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'awsbatch' May-23 18:39:32.896 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION May-23 18:39:32.897 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:RSEQC:RSEQC_JUNCTIONANNOTATION` matches process NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION May-23 18:39:32.898 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: awsbatch May-23 18:39:32.898 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'awsbatch' May-23 18:39:32.906 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION May-23 18:39:32.906 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:RSEQC:RSEQC_JUNCTIONSATURATION` matches process NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION May-23 18:39:32.907 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: awsbatch May-23 18:39:32.907 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'awsbatch' May-23 18:39:32.913 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION May-23 18:39:32.913 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:RSEQC:RSEQC_READDISTRIBUTION` matches process NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION May-23 18:39:32.913 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: awsbatch May-23 18:39:32.913 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'awsbatch' May-23 18:39:32.920 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION May-23 18:39:32.921 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:RSEQC:RSEQC_READDUPLICATION` matches process NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION May-23 18:39:32.921 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: awsbatch May-23 18:39:32.922 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'awsbatch' May-23 18:39:32.933 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MULTIQC_TSV_STRAND_CHECK` matches process NFCORE_RNASEQ:RNASEQ:MULTIQC_TSV_STRAND_CHECK May-23 18:39:32.935 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local May-23 18:39:32.935 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-23 18:39:32.940 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_QUANT May-23 18:39:32.941 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:QUANTIFY_SALMON:SALMON_QUANT` matches process NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_QUANT May-23 18:39:32.941 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: awsbatch May-23 18:39:32.941 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'awsbatch' May-23 18:39:32.947 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_TX2GENE May-23 18:39:32.948 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:QUANTIFY_SALMON:SALMON_TX2GENE` matches process NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_TX2GENE May-23 18:39:32.948 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: awsbatch May-23 18:39:32.948 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'awsbatch' May-23 18:39:32.954 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_TXIMPORT May-23 18:39:32.955 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:QUANTIFY_SALMON:SALMON_TXIMPORT` matches process NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_TXIMPORT May-23 18:39:32.955 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: awsbatch May-23 18:39:32.955 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'awsbatch' May-23 18:39:32.960 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_SE_GENE May-23 18:39:32.961 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:QUANTIFY_SALMON:SALMON_SE_.*` matches process NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_SE_GENE May-23 18:39:32.961 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: awsbatch May-23 18:39:32.961 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'awsbatch' May-23 18:39:32.966 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_SE_GENE_LENGTH_SCALED May-23 18:39:32.966 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:QUANTIFY_SALMON:SALMON_SE_.*` matches process NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_SE_GENE_LENGTH_SCALED May-23 18:39:32.967 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: awsbatch May-23 18:39:32.967 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'awsbatch' May-23 18:39:32.971 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_SE_GENE_SCALED May-23 18:39:32.971 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:QUANTIFY_SALMON:SALMON_SE_.*` matches process NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_SE_GENE_SCALED May-23 18:39:32.972 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: awsbatch May-23 18:39:32.972 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'awsbatch' May-23 18:39:32.975 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_SE_TRANSCRIPT May-23 18:39:32.976 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:QUANTIFY_SALMON:SALMON_SE_.*` matches process NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_SE_TRANSCRIPT May-23 18:39:32.976 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: awsbatch May-23 18:39:32.976 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'awsbatch' May-23 18:39:32.981 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_SALMON May-23 18:39:32.982 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:DESEQ2_QC_SALMON` matches process NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_SALMON May-23 18:39:32.982 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: awsbatch May-23 18:39:32.982 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'awsbatch' May-23 18:39:33.057 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_RNASEQ:RNASEQ:CUSTOM_DUMPSOFTWAREVERSIONS May-23 18:39:33.057 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CUSTOM_DUMPSOFTWAREVERSIONS` matches process NFCORE_RNASEQ:RNASEQ:CUSTOM_DUMPSOFTWAREVERSIONS May-23 18:39:33.058 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: awsbatch May-23 18:39:33.058 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'awsbatch' May-23 18:39:33.153 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:MULTIQC May-23 18:39:33.154 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MULTIQC` matches process NFCORE_RNASEQ:RNASEQ:MULTIQC May-23 18:39:33.154 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: awsbatch May-23 18:39:33.154 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'awsbatch' May-23 18:39:33.169 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: DUPRADAR, NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION, RSEM_PREPAREREFERENCE, CAT_ADDITIONAL_FASTA, NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON, DESEQ2_QC_SALMON, NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE, RSEQC_READDISTRIBUTION, NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:UNTAR_SALMON_INDEX, NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN, NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX, NFCORE_RNASEQ:RNASEQ:CUSTOM_DUMPSOFTWAREVERSIONS, GFFREAD, RSEQC_JUNCTIONSATURATION, RSEQC_READDUPLICATION, NFCORE_RNASEQ:RNASEQ:MULTIQC_TSV_STRAND_CHECK, NFCORE_RNASEQ:RNASEQ:CAT_FASTQ, CAT_FASTQ, GUNZIP, NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES, SAMTOOLS_STATS, NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT, GUNZIP_GFF, NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG, HISAT2_BUILD, NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED, NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT, TRIMGALORE, BEDTOOLS_GENOMECOV, SALMON_TX2GENE, SORTMERNA, NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP, NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_GTF, NFCORE_RNASEQ:RNASEQ:DUPRADAR, NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS, SAMTOOLS_INDEX, NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV, PRESEQ_LCEXTRAP, FASTQC, NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG, UCSC_BEDCLIP, NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT, UCSC_BEDGRAPHTOBIGWIG, NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS, MULTIQC, GTF2BED, NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE, GUNZIP_GTF, SALMON_INDEX, UMITOOLS_EXTRACT, UNTAR_HISAT2_INDEX, NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK, NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_SE_GENE, UNTAR_BBSPLIT_INDEX, NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:BBMAP_BBSPLIT, SAMTOOLS_FLAGSTAT, SAMPLESHEET_CHECK, NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_SE_GENE_SCALED, DESEQ2_QC_RSEM, GUNZIP_FASTA, NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS, NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES, RSEM_PREPAREREFERENCE_GENOME, UNTAR_RSEM_INDEX, NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION, NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE, SALMON_SE_GENE_SCALED, NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT, SALMON_QUANT, MULTIQC_CUSTOM_BIOTYPE, NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:CAT_ADDITIONAL_FASTA, RSEM_CALCULATEEXPRESSION, DESEQ2_QC_STAR_SALMON, NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_SE_TRANSCRIPT, GUNZIP_TRANSCRIPT_FASTA, MAKE_TRANSCRIPTS_FASTA, NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC, MULTIQC_TSV_FAIL_MAPPED, SALMON_SE_GENE_LENGTH_SCALED, DESEQ2_QC, NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX, PICARD_MARKDUPLICATES, RSEM_MERGE_COUNTS, SALMON_SE_GENE, NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS, NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_TX2GENE, UNTAR, NFCORE_RNASEQ:RNASEQ:MULTIQC_TSV_FAIL_MAPPED, SALMON_SUMMARIZEDEXPERIMENT, RSEQC_INNERDISTANCE, NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE, GTF_GENE_FILTER, RSEQC_BAMSTAT, NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT, NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_SALMON, QUALIMAP_RNASEQ, RSEQC_INFEREXPERIMENT, NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT, NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE, STAR_ALIGN, MULTIQC_TSV_STRAND_CHECK, NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_TXIMPORT, NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS, NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA, RSEQC_JUNCTIONANNOTATION, NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_QUANT, SALMON_TXIMPORT, NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE, CUSTOM_GETCHROMSIZES, NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP, SAMTOOLS_SORT, SUBREAD_FEATURECOUNTS, NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT, GUNZIP_GENE_BED, UNTAR_STAR_INDEX, UNTAR_SALMON_INDEX, HISAT2_ALIGN, NFCORE_RNASEQ:RNASEQ:BBMAP_BBSPLIT, NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT, BBMAP_BBSPLIT, NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED, RSEQC_TIN, MULTIQC_TSV_FROM_LIST, NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ, UMITOOLS_DEDUP, STRINGTIE_STRINGTIE, HISAT2_EXTRACTSPLICESITES, SALMON_SE_TRANSCRIPT, NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE, NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF2BED, NFCORE_RNASEQ:RNASEQ:MULTIQC, SAMTOOLS_IDXSTATS, NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP, STAR_GENOMEGENERATE, CUSTOM_DUMPSOFTWAREVERSIONS, GUNZIP_ADDITIONAL_FASTA, NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION, NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_SE_GENE_LENGTH_SCALED, NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION May-23 18:39:33.177 [main] DEBUG nextflow.Session - Ignite dataflow network (142) May-23 18:39:33.178 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_GTF May-23 18:39:33.178 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA May-23 18:39:33.180 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:CAT_ADDITIONAL_FASTA May-23 18:39:33.181 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF2BED May-23 18:39:33.181 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES May-23 18:39:33.181 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:BBMAP_BBSPLIT May-23 18:39:33.181 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE May-23 18:39:33.181 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:UNTAR_SALMON_INDEX May-23 18:39:33.181 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK May-23 18:39:33.181 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ May-23 18:39:33.186 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC May-23 18:39:33.188 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE May-23 18:39:33.188 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:BBMAP_BBSPLIT May-23 18:39:33.189 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN May-23 18:39:33.189 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT May-23 18:39:33.189 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX May-23 18:39:33.190 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS May-23 18:39:33.191 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT May-23 18:39:33.191 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS May-23 18:39:33.191 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT May-23 18:39:33.191 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE May-23 18:39:33.191 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT May-23 18:39:33.191 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE May-23 18:39:33.191 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED May-23 18:39:33.191 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED May-23 18:39:33.191 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT May-23 18:39:33.191 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON May-23 18:39:33.192 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:MULTIQC_TSV_FAIL_MAPPED May-23 18:39:33.192 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP May-23 18:39:33.192 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES May-23 18:39:33.192 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX May-23 18:39:33.192 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS May-23 18:39:33.192 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT May-23 18:39:33.192 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS May-23 18:39:33.192 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE May-23 18:39:33.192 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS May-23 18:39:33.192 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE May-23 18:39:33.192 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV May-23 18:39:33.192 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP May-23 18:39:33.192 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG May-23 18:39:33.192 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP May-23 18:39:33.192 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG May-23 18:39:33.192 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ May-23 18:39:33.192 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:DUPRADAR May-23 18:39:33.192 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT May-23 18:39:33.193 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE May-23 18:39:33.193 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT May-23 18:39:33.193 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION May-23 18:39:33.193 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION May-23 18:39:33.193 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION May-23 18:39:33.193 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION May-23 18:39:33.193 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:MULTIQC_TSV_STRAND_CHECK May-23 18:39:33.196 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_QUANT May-23 18:39:33.196 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_TX2GENE May-23 18:39:33.196 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_TXIMPORT May-23 18:39:33.196 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_SE_GENE May-23 18:39:33.203 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_SE_GENE_LENGTH_SCALED May-23 18:39:33.204 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_SE_GENE_SCALED May-23 18:39:33.204 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_SE_TRANSCRIPT May-23 18:39:33.204 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_SALMON May-23 18:39:33.204 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:CUSTOM_DUMPSOFTWAREVERSIONS May-23 18:39:33.204 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:MULTIQC May-23 18:39:33.204 [main] DEBUG nextflow.script.ScriptRunner - > Await termination May-23 18:39:33.205 [main] DEBUG nextflow.Session - Session await May-23 18:39:33.342 [Actor Thread 12] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 1; slices: 1; internal sort time: 0.001 s; external sort time: 0.013 s; total time: 0.014 s May-23 18:39:33.378 [Actor Thread 14] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=4; maxSize=4; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false May-23 18:39:33.441 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/samplesheet/v3.4/samplesheet_test.csv at s3://nextflow-bucket/work/stage/b3/6a31b4d61a7a567fd0579ce5495999/samplesheet_test.csv May-23 18:39:33.496 [Actor Thread 14] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /home/olgabot/.nextflow/assets/nf-core/rnaseq/bin/check_samplesheet.py May-23 18:39:33.505 [Actor Thread 12] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /tmp/992aebd7427e6dc806feae39b82e6bcc.collect-file May-23 18:39:33.514 [Actor Thread 12] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-9719905170109097748 May-23 18:39:33.829 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://github.com/nf-core/test-datasets/raw/rnaseq/reference/genes.gtf.gz at s3://nextflow-bucket/work/stage/a3/6e635fa1c320e077a16dd25de029b9/genes.gtf.gz May-23 18:39:33.835 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://github.com/nf-core/test-datasets/raw/rnaseq/reference/gfp.fa.gz at s3://nextflow-bucket/work/stage/d1/1dc25d9994ea2c7500a9325499ec71/gfp.fa.gz May-23 18:39:33.925 [AWSBatch-executor-1] DEBUG n.c.aws.batch.AwsBatchTaskHandler - [AWS BATCH] [AWS BATCH] Found job definition name=nf-quay-io-biocontainers-python-3-9--1:1; container=quay.io/biocontainers/python:3.9--1 May-23 18:39:33.959 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://github.com/nf-core/test-datasets/raw/rnaseq/reference/salmon.tar.gz at s3://nextflow-bucket/work/stage/77/98eb1d5b249826ae57b570a92fdd42/salmon.tar.gz May-23 18:39:34.051 [AWSBatch-executor-2] DEBUG n.c.aws.batch.AwsBatchTaskHandler - [AWS BATCH] [AWS BATCH] Found job definition name=nf-ubuntu-20-04:1; container=ubuntu:20.04 May-23 18:39:34.055 [AWSBatch-executor-1] DEBUG n.c.aws.batch.AwsBatchTaskHandler - [AWS BATCH] submitted > job=e6c5c07c-a08f-4e11-8a31-3f669aaf37fa; work-dir=s3://nextflow-bucket/work/4b/3e4254443d207235b90d933c1855df May-23 18:39:34.055 [AWSBatch-executor-1] INFO nextflow.Session - [4b/3e4254] Submitted process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet_test.csv) May-23 18:39:34.140 [AWSBatch-executor-2] DEBUG n.c.aws.batch.AwsBatchTaskHandler - [AWS BATCH] submitted > job=e44ae3c1-aa6c-4ded-a63d-cba633f4c7ac; work-dir=s3://nextflow-bucket/work/8f/56a1acf67b84c3516ade4694427031 May-23 18:39:34.140 [AWSBatch-executor-2] INFO nextflow.Session - [8f/56a1ac] Submitted process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes.gtf.gz) May-23 18:39:34.170 [AWSBatch-executor-3] DEBUG n.c.aws.batch.AwsBatchTaskHandler - [AWS BATCH] submitted > job=c501e360-9987-4842-b7d5-fcb47e7e5e4b; work-dir=s3://nextflow-bucket/work/99/3130248465fde5bd971fc09add62d1 May-23 18:39:34.170 [AWSBatch-executor-3] INFO nextflow.Session - [99/313024] Submitted process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz) May-23 18:39:34.227 [AWSBatch-executor-4] DEBUG n.c.aws.batch.AwsBatchTaskHandler - [AWS BATCH] submitted > job=23c7e540-8dc2-4d8f-bfe8-2b6e48f95e4a; work-dir=s3://nextflow-bucket/work/13/4cd45a08da00ea4d613e11dde4a474 May-23 18:39:34.227 [AWSBatch-executor-4] INFO nextflow.Session - [13/4cd45a] Submitted process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:UNTAR_SALMON_INDEX (salmon.tar.gz) May-23 18:42:31.372 [Task monitor] DEBUG c.u.s3fs.S3FileSystemProvider - S3 parallel download with direct buffer: s3://nextflow-bucket/work/8f/56a1acf67b84c3516ade4694427031/.exitcode May-23 18:42:31.567 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 4; name: NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes.gtf.gz); status: COMPLETED; exit: 0; error: -; workDir: s3://nextflow-bucket/work/8f/56a1acf67b84c3516ade4694427031] May-23 18:42:31.765 [Task monitor] DEBUG c.u.s3fs.S3FileSystemProvider - S3 parallel download with direct buffer: s3://nextflow-bucket/work/8f/56a1acf67b84c3516ade4694427031/.command.trace May-23 18:42:31.819 [Task monitor] DEBUG c.u.s3fs.S3FileSystemProvider - S3 parallel download with direct buffer: s3://nextflow-bucket/work/99/3130248465fde5bd971fc09add62d1/.exitcode May-23 18:42:31.865 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz); status: COMPLETED; exit: 0; error: -; workDir: s3://nextflow-bucket/work/99/3130248465fde5bd971fc09add62d1] May-23 18:42:31.917 [Task monitor] DEBUG c.u.s3fs.S3FileSystemProvider - S3 parallel download with direct buffer: s3://nextflow-bucket/work/99/3130248465fde5bd971fc09add62d1/.command.trace May-23 18:42:31.954 [Task monitor] DEBUG c.u.s3fs.S3FileSystemProvider - S3 parallel download with direct buffer: s3://nextflow-bucket/work/13/4cd45a08da00ea4d613e11dde4a474/.exitcode May-23 18:42:31.994 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 3; name: NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:UNTAR_SALMON_INDEX (salmon.tar.gz); status: COMPLETED; exit: 0; error: -; workDir: s3://nextflow-bucket/work/13/4cd45a08da00ea4d613e11dde4a474] May-23 18:42:32.042 [Task monitor] DEBUG c.u.s3fs.S3FileSystemProvider - S3 parallel download with direct buffer: s3://nextflow-bucket/work/13/4cd45a08da00ea4d613e11dde4a474/.command.trace May-23 18:42:32.747 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://github.com/nf-core/test-datasets/raw/rnaseq/reference/genome.fasta at s3://nextflow-bucket/work/stage/93/30fed0dafdcfa665c23f6dd7cd5870/genome.fasta May-23 18:42:32.817 [Actor Thread 9] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /home/olgabot/.nextflow/assets/nf-core/rnaseq/bin/fasta2gtf.py May-23 18:42:33.036 [AWSBatch-executor-23] DEBUG n.c.aws.batch.AwsBatchTaskHandler - [AWS BATCH] submitted > job=cd9e572f-07eb-47bb-97fa-45e4570defac; work-dir=s3://nextflow-bucket/work/8d/dad22c76cbe7daff2a2bee39ed11dc May-23 18:42:33.036 [AWSBatch-executor-23] INFO nextflow.Session - [8d/dad22c] Submitted process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:CAT_ADDITIONAL_FASTA (gfp.fa) May-23 18:42:51.386 [Task monitor] DEBUG c.u.s3fs.S3FileSystemProvider - S3 parallel download with direct buffer: s3://nextflow-bucket/work/4b/3e4254443d207235b90d933c1855df/.exitcode May-23 18:42:51.435 [Task monitor] DEBUG n.c.aws.batch.AwsBatchTaskHandler - [AWS BATCH] Cannot read exitstatus for task: `NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet_test.csv)` | /nextflow-bucket/work/4b/3e4254443d207235b90d933c1855df/.exitcode May-23 18:42:51.604 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 2; name: NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet_test.csv); status: COMPLETED; exit: -; error: nextflow.exception.ProcessUnrecoverableException: Task failed to start - CannotStartContainerError: Error response from daemon: OCI runtime create failed: container_linux.go:380: starting container process caused: exec: "/usr/local/env-execute": stat /usr/local/env-execute: no such file or directory: unknown; workDir: s3://nextflow-bucket/work/4b/3e4254443d207235b90d933c1855df] May-23 18:42:51.635 [Task monitor] DEBUG nextflow.processor.TaskRun - Unable to dump output of process 'NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet_test.csv)' -- Cause: java.nio.file.NoSuchFileException: /tmp/temp-s3-12583512661127037527/.command.out May-23 18:42:51.655 [Task monitor] DEBUG nextflow.processor.TaskRun - Unable to dump error of process 'NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet_test.csv)' -- Cause: java.nio.file.NoSuchFileException: /tmp/temp-s3-5591907900688274529/.command.err May-23 18:42:51.672 [Task monitor] DEBUG nextflow.processor.TaskRun - Unable to dump error of process 'NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet_test.csv)' -- Cause: java.nio.file.NoSuchFileException: /tmp/temp-s3-5341739717464023779/.command.log May-23 18:42:51.673 [Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing process > 'NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet_test.csv)' Caused by: Task failed to start - CannotStartContainerError: Error response from daemon: OCI runtime create failed: container_linux.go:380: starting container process caused: exec: "/usr/local/env-execute": stat /usr/local/env-execute: no such file or directory: unknown Command executed: check_samplesheet.py \ samplesheet_test.csv \ samplesheet.valid.csv cat <<-END_VERSIONS > versions.yml "NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK": python: $(python --version | sed 's/Python //g') END_VERSIONS Command exit status: - Command output: (empty) Work dir: s3://nextflow-bucket/work/4b/3e4254443d207235b90d933c1855df Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out` May-23 18:42:51.676 [Task monitor] DEBUG c.u.s3fs.S3FileSystemProvider - S3 parallel download with direct buffer: s3://nextflow-bucket/work/4b/3e4254443d207235b90d933c1855df/.command.trace May-23 18:42:51.690 [Task monitor] INFO nextflow.Session - Execution cancelled -- Finishing pending tasks before exit May-23 18:42:51.691 [Task monitor] DEBUG c.u.s3fs.S3FileSystemProvider - S3 parallel download with direct buffer: s3://nextflow-bucket/work/4b/3e4254443d207235b90d933c1855df/.command.trace May-23 18:42:51.704 [Task monitor] DEBUG c.u.s3fs.S3FileSystemProvider - S3 parallel download with direct buffer: s3://nextflow-bucket/work/4b/3e4254443d207235b90d933c1855df/.command.trace May-23 18:42:51.717 [Task monitor] DEBUG c.u.s3fs.S3FileSystemProvider - S3 parallel download with direct buffer: s3://nextflow-bucket/work/4b/3e4254443d207235b90d933c1855df/.command.trace May-23 18:42:51.728 [Task monitor] DEBUG c.u.s3fs.S3FileSystemProvider - S3 parallel download with direct buffer: s3://nextflow-bucket/work/4b/3e4254443d207235b90d933c1855df/.command.trace May-23 18:42:51.740 [Task monitor] DEBUG c.u.s3fs.S3FileSystemProvider - S3 parallel download with direct buffer: s3://nextflow-bucket/work/4b/3e4254443d207235b90d933c1855df/.command.trace May-23 18:42:51.752 [Task monitor] DEBUG c.u.s3fs.S3FileSystemProvider - S3 parallel download with direct buffer: s3://nextflow-bucket/work/4b/3e4254443d207235b90d933c1855df/.command.trace May-23 18:42:51.764 [Task monitor] DEBUG c.u.s3fs.S3FileSystemProvider - S3 parallel download with direct buffer: s3://nextflow-bucket/work/4b/3e4254443d207235b90d933c1855df/.command.trace May-23 18:42:51.789 [Task monitor] DEBUG nextflow.processor.TaskRun - Unable to dump error of process 'NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet_test.csv)' -- Cause: java.nio.file.NoSuchFileException: /tmp/temp-s3-4297356990755602898/.command.err May-23 18:42:51.802 [Task monitor] DEBUG nextflow.processor.TaskRun - Unable to dump output of process 'NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet_test.csv)' -- Cause: java.nio.file.NoSuchFileException: /tmp/temp-s3-8826672131291160384/.command.out May-23 18:42:51.803 [main] DEBUG nextflow.Session - Session await > all process finished May-23 18:42:51.812 [Actor Thread 38] WARN nextflow.util.CacheHelper - Unable to get file attributes file: s3://nextflow-bucket/work/99/3130248465fde5bd971fc09add62d1/versions.yml -- Cause: com.amazonaws.AbortedException: May-23 18:42:51.812 [Actor Thread 38] WARN nextflow.util.CacheHelper - Unable to get file attributes file: s3://nextflow-bucket/work/8f/56a1acf67b84c3516ade4694427031/versions.yml -- Cause: com.amazonaws.AbortedException: May-23 18:42:51.813 [Actor Thread 38] WARN nextflow.util.CacheHelper - Unable to get file attributes file: s3://nextflow-bucket/work/13/4cd45a08da00ea4d613e11dde4a474/versions.yml -- Cause: com.amazonaws.AbortedException: May-23 18:42:51.814 [Actor Thread 38] WARN nextflow.util.CacheHelper - Unable to get file attributes file: s3://nextflow-bucket/work/99/3130248465fde5bd971fc09add62d1/versions.yml -- Cause: com.amazonaws.AbortedException: May-23 18:42:51.815 [Actor Thread 38] WARN nextflow.util.CacheHelper - Unable to get file attributes file: s3://nextflow-bucket/work/13/4cd45a08da00ea4d613e11dde4a474/versions.yml -- Cause: com.amazonaws.AbortedException: May-23 18:42:51.815 [Actor Thread 38] WARN nextflow.util.CacheHelper - Unable to get file attributes file: s3://nextflow-bucket/work/99/3130248465fde5bd971fc09add62d1/versions.yml -- Cause: com.amazonaws.AbortedException: May-23 18:42:51.816 [Actor Thread 38] WARN nextflow.util.CacheHelper - Unable to get file attributes file: s3://nextflow-bucket/work/13/4cd45a08da00ea4d613e11dde4a474/versions.yml -- Cause: com.amazonaws.AbortedException: May-23 18:42:51.816 [Actor Thread 38] WARN nextflow.util.CacheHelper - Unable to get file attributes file: s3://nextflow-bucket/work/8f/56a1acf67b84c3516ade4694427031/versions.yml -- Cause: com.amazonaws.AbortedException: May-23 18:42:51.818 [Actor Thread 38] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 3; slices: 1; internal sort time: 0.007 s; external sort time: 0.001 s; total time: 0.008 s May-23 18:42:51.821 [Actor Thread 38] ERROR nextflow.extension.OperatorEx - @unknown com.amazonaws.AbortedException: at com.amazonaws.http.AmazonHttpClient$RequestExecutor.handleInterruptedException(AmazonHttpClient.java:877) at com.amazonaws.http.AmazonHttpClient$RequestExecutor.execute(AmazonHttpClient.java:755) at com.amazonaws.http.AmazonHttpClient$RequestExecutor.access$500(AmazonHttpClient.java:713) at com.amazonaws.http.AmazonHttpClient$RequestExecutionBuilderImpl.execute(AmazonHttpClient.java:695) at com.amazonaws.http.AmazonHttpClient.execute(AmazonHttpClient.java:559) at com.amazonaws.http.AmazonHttpClient.execute(AmazonHttpClient.java:539) at com.amazonaws.services.s3.AmazonS3Client.invoke(AmazonS3Client.java:5453) at com.amazonaws.services.s3.AmazonS3Client.invoke(AmazonS3Client.java:5400) at com.amazonaws.services.s3.AmazonS3Client.invoke(AmazonS3Client.java:5394) at com.amazonaws.services.s3.AmazonS3Client.listObjects(AmazonS3Client.java:928) at com.upplication.s3fs.AmazonS3Client.listObjects(AmazonS3Client.java:129) at com.upplication.s3fs.util.S3ObjectSummaryLookup.lookup(S3ObjectSummaryLookup.java:113) at com.upplication.s3fs.S3FileSystemProvider.readAttributes(S3FileSystemProvider.java:709) at java.base/java.nio.file.Files.readAttributes(Files.java:1763) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107) at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323) at org.codehaus.groovy.runtime.callsite.StaticMetaMethodSite.invoke(StaticMetaMethodSite.java:44) at org.codehaus.groovy.runtime.callsite.StaticMetaMethodSite.call(StaticMetaMethodSite.java:89) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:148) at nextflow.extension.FilesEx.createDirIfNotExists(FilesEx.groovy:1253) at nextflow.file.FileCollector.saveTo0(FileCollector.groovy:225) at nextflow.file.FileCollector.saveTo(FileCollector.groovy:250) at nextflow.file.FileCollector$saveTo.call(Unknown Source) at nextflow.extension.CollectFileOp.emitItems(CollectFileOp.groovy:191) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107) at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1268) at groovy.lang.MetaClassImpl.invokeMethodClosure(MetaClassImpl.java:1048) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1142) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1035) at groovy.lang.Closure.call(Closure.java:412) at groovy.lang.Closure.call(Closure.java:428) at groovy.lang.Closure$call.call(Unknown Source) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47) at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.call(PogoMetaClassSite.java:53) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:139) at nextflow.extension.DataflowHelper$3.afterStop(DataflowHelper.groovy:255) at groovyx.gpars.dataflow.operator.DataflowProcessor.fireAfterStop(DataflowProcessor.java:324) at groovyx.gpars.dataflow.operator.DataflowProcessorActor.afterStop(DataflowProcessorActor.java:59) at jdk.internal.reflect.GeneratedMethodAccessor208.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107) at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1268) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1035) at org.codehaus.groovy.runtime.InvokerHelper.invokePojoMethod(InvokerHelper.java:1017) at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:1008) at groovyx.gpars.actor.Actor.callDynamic(Actor.java:369) at groovyx.gpars.actor.Actor.handleTermination(Actor.java:320) at groovyx.gpars.actor.AbstractLoopingActor$1.handleMessage(AbstractLoopingActor.java:86) at groovyx.gpars.util.AsyncMessagingCore.run(AsyncMessagingCore.java:132) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:834) Caused by: com.amazonaws.http.timers.client.SdkInterruptedException: null at com.amazonaws.http.AmazonHttpClient$RequestExecutor.checkInterrupted(AmazonHttpClient.java:932) at com.amazonaws.http.AmazonHttpClient$RequestExecutor.checkInterrupted(AmazonHttpClient.java:918) at com.amazonaws.http.AmazonHttpClient$RequestExecutor.executeHelper(AmazonHttpClient.java:1112) at com.amazonaws.http.AmazonHttpClient$RequestExecutor.doExecute(AmazonHttpClient.java:811) at com.amazonaws.http.AmazonHttpClient$RequestExecutor.executeWithTimer(AmazonHttpClient.java:779) at com.amazonaws.http.AmazonHttpClient$RequestExecutor.execute(AmazonHttpClient.java:753) ... 61 common frames omitted May-23 18:42:51.829 [Actor Thread 38] DEBUG nextflow.Session - Session aborted -- Cause: com.amazonaws.AbortedException: May-23 18:42:51.858 [Actor Thread 38] DEBUG nextflow.Session - The following nodes are still active: [operator] collectFile May-23 18:42:51.858 [Actor Thread 38] WARN nextflow.util.SimpleAgent - Got an interrupted exception while taking agent result | java.lang.InterruptedException May-23 18:42:51.875 [Actor Thread 38] DEBUG nextflow.processor.TaskRun - Unable to dump error of process 'NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet_test.csv)' -- Cause: java.nio.file.NoSuchFileException: /tmp/temp-s3-6391416332089775439/.command.err May-23 18:42:51.888 [Actor Thread 38] DEBUG nextflow.processor.TaskRun - Unable to dump output of process 'NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet_test.csv)' -- Cause: java.nio.file.NoSuchFileException: /tmp/temp-s3-3814873576661632441/.command.out May-23 18:42:51.888 [main] DEBUG nextflow.Session - Session await > all barriers passed May-23 18:42:51.910 [main] DEBUG nextflow.processor.TaskRun - Unable to dump error of process 'NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet_test.csv)' -- Cause: java.nio.file.NoSuchFileException: /tmp/temp-s3-14336677328131709019/.command.err May-23 18:42:51.919 [main] DEBUG nextflow.processor.TaskRun - Unable to dump output of process 'NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet_test.csv)' -- Cause: java.nio.file.NoSuchFileException: /tmp/temp-s3-5196691416074903981/.command.out May-23 18:42:51.920 [main] INFO nextflow.Nextflow - -[0;35m[nf-core/rnaseq][0;31m Pipeline completed with errors[0m- May-23 18:42:51.924 [main] WARN n.processor.TaskPollingMonitor - Killing running tasks (1) May-23 18:42:51.932 [main] DEBUG nextflow.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=3; failedCount=1; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=1; runningCount=-1; retriesCount=0; abortedCount=1; succeedDuration=114ms; failedDuration=221ms; cachedDuration=0ms;loadCpus=-1; loadMemory=0; peakRunning=3; peakCpus=6; peakMemory=18 GB; ] May-23 18:42:51.932 [main] DEBUG nextflow.trace.TraceFileObserver - Flow completing -- flushing trace file May-23 18:42:51.985 [main] DEBUG nextflow.trace.ReportObserver - Flow completing -- rendering html report May-23 18:42:52.011 [main] DEBUG nextflow.trace.ReportObserver - Execution report summary data: [{"cpuUsage":{"mean":22.2,"min":22.2,"q1":22.2,"q2":22.2,"q3":22.2,"max":22.2,"minLabel":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes.gtf.gz)","maxLabel":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes.gtf.gz)","q1Label":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes.gtf.gz)","q2Label":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes.gtf.gz)","q3Label":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes.gtf.gz)"},"process":"GUNZIP_GTF","mem":{"mean":2494464,"min":2494464,"q1":2494464,"q2":2494464,"q3":2494464,"max":2494464,"minLabel":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes.gtf.gz)","maxLabel":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes.gtf.gz)","q1Label":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes.gtf.gz)","q2Label":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes.gtf.gz)","q3Label":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes.gtf.gz)"},"memUsage":{"mean":0.04,"min":0.04,"q1":0.04,"q2":0.04,"q3":0.04,"max":0.04,"minLabel":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes.gtf.gz)","maxLabel":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes.gtf.gz)","q1Label":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes.gtf.gz)","q2Label":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes.gtf.gz)","q3Label":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes.gtf.gz)"},"timeUsage":null,"vmem":{"mean":11841536,"min":11841536,"q1":11841536,"q2":11841536,"q3":11841536,"max":11841536,"minLabel":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes.gtf.gz)","maxLabel":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes.gtf.gz)","q1Label":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes.gtf.gz)","q2Label":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes.gtf.gz)","q3Label":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes.gtf.gz)"},"reads":{"mean":75293,"min":75293,"q1":75293,"q2":75293,"q3":75293,"max":75293,"minLabel":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes.gtf.gz)","maxLabel":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes.gtf.gz)","q1Label":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes.gtf.gz)","q2Label":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes.gtf.gz)","q3Label":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes.gtf.gz)"},"cpu":{"mean":44.4,"min":44.4,"q1":44.4,"q2":44.4,"q3":44.4,"max":44.4,"minLabel":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes.gtf.gz)","maxLabel":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes.gtf.gz)","q1Label":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes.gtf.gz)","q2Label":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes.gtf.gz)","q3Label":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes.gtf.gz)"},"time":{"mean":13,"min":13,"q1":13,"q2":13,"q3":13,"max":13,"minLabel":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes.gtf.gz)","maxLabel":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes.gtf.gz)","q1Label":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes.gtf.gz)","q2Label":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes.gtf.gz)","q3Label":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes.gtf.gz)"},"writes":{"mean":205210,"min":205210,"q1":205210,"q2":205210,"q3":205210,"max":205210,"minLabel":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes.gtf.gz)","maxLabel":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes.gtf.gz)","q1Label":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes.gtf.gz)","q2Label":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes.gtf.gz)","q3Label":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes.gtf.gz)"}},{"cpuUsage":{"mean":40,"min":40,"q1":40,"q2":40,"q3":40,"max":40,"minLabel":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz)","maxLabel":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz)","q1Label":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz)","q2Label":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz)","q3Label":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz)"},"process":"GUNZIP_ADDITIONAL_FASTA","mem":{"mean":2498560,"min":2498560,"q1":2498560,"q2":2498560,"q3":2498560,"max":2498560,"minLabel":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz)","maxLabel":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz)","q1Label":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz)","q2Label":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz)","q3Label":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz)"},"memUsage":{"mean":0.04,"min":0.04,"q1":0.04,"q2":0.04,"q3":0.04,"max":0.04,"minLabel":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz)","maxLabel":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz)","q1Label":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz)","q2Label":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz)","q3Label":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz)"},"timeUsage":null,"vmem":{"mean":11841536,"min":11841536,"q1":11841536,"q2":11841536,"q3":11841536,"max":11841536,"minLabel":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz)","maxLabel":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz)","q1Label":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz)","q2Label":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz)","q3Label":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz)"},"reads":{"mean":65179,"min":65179,"q1":65179,"q2":65179,"q3":65179,"max":65179,"minLabel":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz)","maxLabel":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA 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(salmon.tar.gz)"},"reads":{"mean":1724417,"min":1724417,"q1":1724417,"q2":1724417,"q3":1724417,"max":1724417,"minLabel":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:UNTAR_SALMON_INDEX (salmon.tar.gz)","maxLabel":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:UNTAR_SALMON_INDEX (salmon.tar.gz)","q1Label":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:UNTAR_SALMON_INDEX (salmon.tar.gz)","q2Label":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:UNTAR_SALMON_INDEX (salmon.tar.gz)","q3Label":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:UNTAR_SALMON_INDEX (salmon.tar.gz)"},"cpu":{"mean":80,"min":80,"q1":80,"q2":80,"q3":80,"max":80,"minLabel":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:UNTAR_SALMON_INDEX (salmon.tar.gz)","maxLabel":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:UNTAR_SALMON_INDEX (salmon.tar.gz)","q1Label":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:UNTAR_SALMON_INDEX (salmon.tar.gz)","q2Label":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:UNTAR_SALMON_INDEX (salmon.tar.gz)","q3Label":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:UNTAR_SALMON_INDEX (salmon.tar.gz)"},"time":{"mean":29,"min":29,"q1":29,"q2":29,"q3":29,"max":29,"minLabel":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:UNTAR_SALMON_INDEX (salmon.tar.gz)","maxLabel":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:UNTAR_SALMON_INDEX (salmon.tar.gz)","q1Label":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:UNTAR_SALMON_INDEX (salmon.tar.gz)","q2Label":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:UNTAR_SALMON_INDEX (salmon.tar.gz)","q3Label":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:UNTAR_SALMON_INDEX (salmon.tar.gz)"},"writes":{"mean":1744198,"min":1744198,"q1":1744198,"q2":1744198,"q3":1744198,"max":1744198,"minLabel":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:UNTAR_SALMON_INDEX (salmon.tar.gz)","maxLabel":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:UNTAR_SALMON_INDEX (salmon.tar.gz)","q1Label":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:UNTAR_SALMON_INDEX (salmon.tar.gz)","q2Label":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:UNTAR_SALMON_INDEX (salmon.tar.gz)","q3Label":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:UNTAR_SALMON_INDEX (salmon.tar.gz)"}},{"cpuUsage":null,"process":"SAMPLESHEET_CHECK","mem":null,"memUsage":null,"timeUsage":null,"vmem":null,"reads":null,"cpu":null,"time":{"mean":221,"min":221,"q1":221,"q2":221,"q3":221,"max":221,"minLabel":"NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet_test.csv)","maxLabel":"NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet_test.csv)","q1Label":"NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet_test.csv)","q2Label":"NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet_test.csv)","q3Label":"NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet_test.csv)"},"writes":null},{"cpuUsage":null,"process":"CAT_ADDITIONAL_FASTA","mem":null,"memUsage":null,"timeUsage":null,"vmem":null,"reads":null,"cpu":null,"time":null,"writes":null}] May-23 18:42:52.099 [AWSBatch-reaper-1] DEBUG n.c.aws.batch.AwsBatchTaskHandler - [AWS BATCH] killing job=cd9e572f-07eb-47bb-97fa-45e4570defac; response={} May-23 18:42:52.325 [Actor Thread 38] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 3; slices: 1; internal sort time: 0.232 s; external sort time: 0.198 s; total time: 0.43 s May-23 18:42:52.348 [Actor Thread 38] DEBUG c.u.s3fs.S3FileSystemProvider - S3 parallel download with direct buffer: s3://nextflow-bucket/work/13/4cd45a08da00ea4d613e11dde4a474/versions.yml May-23 18:42:52.386 [Actor Thread 38] DEBUG c.u.s3fs.S3FileSystemProvider - S3 parallel download with direct buffer: s3://nextflow-bucket/work/13/4cd45a08da00ea4d613e11dde4a474/versions.yml May-23 18:42:52.417 [Actor Thread 38] DEBUG c.u.s3fs.S3FileSystemProvider - S3 parallel download with direct buffer: s3://nextflow-bucket/work/8f/56a1acf67b84c3516ade4694427031/versions.yml May-23 18:42:52.452 [Actor Thread 38] DEBUG c.u.s3fs.S3FileSystemProvider - S3 parallel download with direct buffer: s3://nextflow-bucket/work/8f/56a1acf67b84c3516ade4694427031/versions.yml May-23 18:42:52.486 [Actor Thread 38] DEBUG c.u.s3fs.S3FileSystemProvider - S3 parallel download with direct buffer: s3://nextflow-bucket/work/99/3130248465fde5bd971fc09add62d1/versions.yml May-23 18:42:52.522 [Actor Thread 38] DEBUG c.u.s3fs.S3FileSystemProvider - S3 parallel download with direct buffer: s3://nextflow-bucket/work/99/3130248465fde5bd971fc09add62d1/versions.yml May-23 18:42:52.586 [Actor Thread 38] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /tmp/e7a907e76dcacb3449be8b5f9b22c31a.collect-file May-23 18:42:52.590 [Actor Thread 38] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-15125001686207343865 May-23 18:42:52.591 [Actor Thread 38] ERROR nextflow.extension.DataflowHelper - @unknown java.lang.IllegalStateException: A DataflowVariable can only be assigned once. Use bind() to allow for equal values to be passed into already-bound variables. at groovyx.gpars.dataflow.expression.DataflowExpression.bindUnique(DataflowExpression.java:383) at groovyx.gpars.actor.AbstractLoopingActor$1.handleMessage(AbstractLoopingActor.java:88) at groovyx.gpars.util.AsyncMessagingCore.run(AsyncMessagingCore.java:132) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:834) May-23 18:42:53.030 [main] DEBUG nextflow.trace.TimelineObserver - Flow completing -- rendering html timeline May-23 18:42:53.488 [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. May-23 18:42:53.491 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done May-23 18:42:53.492 [main] INFO org.pf4j.AbstractPluginManager - Stop plugin 'nf-tower@1.4.0' May-23 18:42:53.492 [main] DEBUG nextflow.plugin.BasePlugin - Plugin stopped nf-tower May-23 18:42:53.492 [main] INFO org.pf4j.AbstractPluginManager - Stop plugin 'nf-amazon@1.7.1' May-23 18:42:53.492 [main] DEBUG nextflow.plugin.BasePlugin - Plugin stopped nf-amazon May-23 18:42:53.492 [main] DEBUG c.u.s3fs.ng.S3ParallelDownload - Shutdown S3 downloader May-23 18:42:53.494 [main] DEBUG c.u.s3fs.ng.S3ParallelDownload - Shutdown S3 downloader - done May-23 18:42:53.509 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye ```Looking in the
.command.runfile, there is no mention ofdockerat all, which seems weird since Docker should be enabled.`.command.run` file
``` #!/bin/bash # NEXTFLOW TASK: NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet_test.csv) set -e set -u NXF_DEBUG=${NXF_DEBUG:=0}; [[ $NXF_DEBUG > 1 ]] && set -x NXF_ENTRY=${1:-nxf_main} nxf_tree() { local pid=$1 declare -a ALL_CHILDREN while read P PP;do ALL_CHILDREN[$PP]+=" $P" done < <(ps -e -o pid= -o ppid=) pstat() { local x_pid=$1 local STATUS=$(2> /dev/null < /proc/$1/status egrep 'Vm|ctxt') if [ $? = 0 ]; then local x_vsz=$(echo "$STATUS" | grep VmSize | awk '{print $2}' || echo -n '0') local x_rss=$(echo "$STATUS" | grep VmRSS | awk '{print $2}' || echo -n '0') local x_peak=$(echo "$STATUS" | egrep 'VmPeak|VmHWM' | sed 's/^.*:\s*//' | sed 's/[\sa-zA-Z]*$//' | tr '\n' ' ' || echo -n '0 0') local x_pmem=$(awk -v rss=$x_rss -v mem_tot=$mem_tot 'BEGIN {printf "%.0f", rss/mem_tot*100*10}' || echo -n '0') local vol_ctxt=$(echo "$STATUS" | grep '\bvoluntary_ctxt_switches' | awk '{print $2}' || echo -n '0') local inv_ctxt=$(echo "$STATUS" | grep '\bnonvoluntary_ctxt_switches' | awk '{print $2}' || echo -n '0') cpu_stat[x_pid]="$x_pid $x_pmem $x_vsz $x_rss $x_peak $vol_ctxt $inv_ctxt" fi } pwalk() { pstat $1 for i in ${ALL_CHILDREN[$1]:=}; do pwalk $i; done } pwalk $1 } nxf_stat() { cpu_stat=() nxf_tree $1 declare -a sum=(0 0 0 0 0 0 0 0) local pid local i for pid in "${!cpu_stat[@]}"; do local row=(${cpu_stat[pid]}) [ $NXF_DEBUG = 1 ] && echo "++ stat mem=${row[*]}" for i in "${!row[@]}"; do if [ $i != 0 ]; then sum[i]=$((sum[i]+row[i])) fi done done [ $NXF_DEBUG = 1 ] && echo -e "++ stat SUM=${sum[*]}" for i in {1..7}; do if [ ${sum[i]} -lt ${cpu_peak[i]} ]; then sum[i]=${cpu_peak[i]} else cpu_peak[i]=${sum[i]} fi done [ $NXF_DEBUG = 1 ] && echo -e "++ stat PEAK=${sum[*]}\n" nxf_stat_ret=(${sum[*]}) } nxf_mem_watch() { set -o pipefail local pid=$1 local trace_file=.command.trace local count=0; declare -a cpu_stat=(0 0 0 0 0 0 0 0) declare -a cpu_peak=(0 0 0 0 0 0 0 0) local mem_tot=$(< /proc/meminfo grep MemTotal | awk '{print $2}') local timeout local DONE local STOP='' [ $NXF_DEBUG = 1 ] && nxf_sleep 0.2 && ps fx while true; do nxf_stat $pid if [ $count -lt 10 ]; then timeout=1; elif [ $count -lt 120 ]; then timeout=5; else timeout=30; fi read -t $timeout -r DONE || true [[ $DONE ]] && break if [ ! -e /proc/$pid ]; then [ ! $STOP ] && STOP=$(nxf_date) [ $(($(nxf_date)-STOP)) -gt 10000 ] && break fi count=$((count+1)) done echo "%mem=${nxf_stat_ret[1]}" >> $trace_file echo "vmem=${nxf_stat_ret[2]}" >> $trace_file echo "rss=${nxf_stat_ret[3]}" >> $trace_file echo "peak_vmem=${nxf_stat_ret[4]}" >> $trace_file echo "peak_rss=${nxf_stat_ret[5]}" >> $trace_file echo "vol_ctxt=${nxf_stat_ret[6]}" >> $trace_file echo "inv_ctxt=${nxf_stat_ret[7]}" >> $trace_file } nxf_write_trace() { echo "nextflow.trace/v2" > $trace_file echo "realtime=$wall_time" >> $trace_file echo "%cpu=$ucpu" >> $trace_file echo "rchar=${io_stat1[0]}" >> $trace_file echo "wchar=${io_stat1[1]}" >> $trace_file echo "syscr=${io_stat1[2]}" >> $trace_file echo "syscw=${io_stat1[3]}" >> $trace_file echo "read_bytes=${io_stat1[4]}" >> $trace_file echo "write_bytes=${io_stat1[5]}" >> $trace_file } nxf_trace_mac() { local start_millis=$(nxf_date) /bin/bash -ue .command.sh local end_millis=$(nxf_date) local wall_time=$((end_millis-start_millis)) local ucpu='' local io_stat1=('' '' '' '' '' '') nxf_write_trace } nxf_fd() { local FD=11 while [ -e /proc/$$/fd/$FD ]; do FD=$((FD+1)); done echo $FD } nxf_trace_linux() { local pid=$$ command -v ps &>/dev/null || { >&2 echo "Command 'ps' required by nextflow to collect task metrics cannot be found"; exit 1; } local num_cpus=$(< /proc/cpuinfo grep '^processor' -c) local tot_time0=$(grep '^cpu ' /proc/stat | awk '{sum=$2+$3+$4+$5+$6+$7+$8+$9; printf "%.0f",sum}') local cpu_time0=$(2> /dev/null < /proc/$pid/stat awk '{printf "%.0f", ($16+$17)*10 }' || echo -n 'X') local io_stat0=($(2> /dev/null < /proc/$pid/io sed 's/^.*:\s*//' | head -n 6 | tr '\n' ' ' || echo -n '0 0 0 0 0 0')) local start_millis=$(nxf_date) trap 'kill $mem_proc' ERR /bin/bash -ue .command.sh & local task=$! mem_fd=$(nxf_fd) eval "exec $mem_fd> >(nxf_mem_watch $task)" local mem_proc=$! wait $task local end_millis=$(nxf_date) local tot_time1=$(grep '^cpu ' /proc/stat | awk '{sum=$2+$3+$4+$5+$6+$7+$8+$9; printf "%.0f",sum}') local cpu_time1=$(2> /dev/null < /proc/$pid/stat awk '{printf "%.0f", ($16+$17)*10 }' || echo -n 'X') local ucpu=$(awk -v p1=$cpu_time1 -v p0=$cpu_time0 -v t1=$tot_time1 -v t0=$tot_time0 -v n=$num_cpus 'BEGIN { pct=(p1-p0)/(t1-t0)*100*n; printf("%.0f", pct>0 ? pct : 0) }' ) local io_stat1=($(2> /dev/null < /proc/$pid/io sed 's/^.*:\s*//' | head -n 6 | tr '\n' ' ' || echo -n '0 0 0 0 0 0')) local i for i in {0..5}; do io_stat1[i]=$((io_stat1[i]-io_stat0[i])) done local wall_time=$((end_millis-start_millis)) [ $NXF_DEBUG = 1 ] && echo "+++ STATS %CPU=$ucpu TIME=$wall_time I/O=${io_stat1[*]}" echo "nextflow.trace/v2" > $trace_file echo "realtime=$wall_time" >> $trace_file echo "%cpu=$ucpu" >> $trace_file echo "rchar=${io_stat1[0]}" >> $trace_file echo "wchar=${io_stat1[1]}" >> $trace_file echo "syscr=${io_stat1[2]}" >> $trace_file echo "syscw=${io_stat1[3]}" >> $trace_file echo "read_bytes=${io_stat1[4]}" >> $trace_file echo "write_bytes=${io_stat1[5]}" >> $trace_file [ -e /proc/$mem_proc ] && eval "echo 'DONE' >&$mem_fd" || true wait $mem_proc 2>/dev/null || true while [ -e /proc/$mem_proc ]; do nxf_sleep 0.1; done } nxf_trace() { local trace_file=.command.trace touch $trace_file if [[ $(uname) = Darwin ]]; then nxf_trace_mac else nxf_trace_linux fi } # bash helper functions nxf_cp_retry() { local max_attempts=5 local timeout=10 local attempt=0 local exitCode=0 while (( $attempt < $max_attempts )) do if "$@" then return 0 else exitCode=$? fi if [[ $exitCode == 0 ]] then break fi nxf_sleep $timeout attempt=$(( attempt + 1 )) timeout=$(( timeout * 2 )) done } nxf_parallel() { IFS=$'\n' local cmd=("$@") local cpus=$(nproc 2>/dev/null || < /proc/cpuinfo grep '^process' -c) local max=$(if (( cpus>4 )); then echo 4; else echo $cpus; fi) local i=0 local pid=() ( set +u while ((i<${#cmd[@]})); do local copy=() for x in "${pid[@]}"; do [[ -e /proc/$x ]] && copy+=($x) done pid=("${copy[@]}") if ((${#pid[@]}>=$max)); then nxf_sleep 0.2 else eval "${cmd[$i]}" & pid+=($!) ((i+=1)) fi done for p in "${pid[@]}"; do wait $p done ) unset IFS } # aws cli retry config export AWS_RETRY_MODE=standard export AWS_MAX_ATTEMPTS=5 # aws helper nxf_s3_upload() { local name=$1 local s3path=$2 if [[ "$name" == - ]]; then /usr/bin/aws --region us-west-1 s3 cp --only-show-errors --storage-class STANDARD - "$s3path" elif [[ -d "$name" ]]; then /usr/bin/aws --region us-west-1 s3 cp --only-show-errors --recursive --storage-class STANDARD "$name" "$s3path/$name" else /usr/bin/aws --region us-west-1 s3 cp --only-show-errors --storage-class STANDARD "$name" "$s3path/$name" fi } nxf_s3_download() { local source=$1 local target=$2 local file_name=$(basename $1) local is_dir=$(/usr/bin/aws --region us-west-1 s3 ls $source | grep -F "PRE ${file_name}/" -c) if [[ $is_dir == 1 ]]; then /usr/bin/aws --region us-west-1 s3 cp --only-show-errors --recursive "$source" "$target" else /usr/bin/aws --region us-west-1 s3 cp --only-show-errors "$source" "$target" fi } nxf_sleep() { sleep $1 2>/dev/null || sleep 1; } nxf_date() { local ts=$(date +%s%3N); if [[ ${#ts} == 10 ]]; then echo ${ts}000 elif [[ $ts == *%3N ]]; then echo ${ts/\%3N/000} elif [[ $ts == *3N ]]; then echo ${ts/3N/000} elif [[ ${#ts} == 13 ]]; then echo $ts else echo "Unexpected timestamp value: $ts"; exit 1 fi } nxf_env() { echo '============= task environment =============' env | sort | sed "s/\(.*\)AWS\(.*\)=\(.\{6\}\).*/\1AWS\2=\3xxxxxxxxxxxxx/" echo '============= task output ==================' } nxf_kill() { declare -a children while read P PP;do children[$PP]+=" $P" done < <(ps -e -o pid= -o ppid=) kill_all() { [[ $1 != $$ ]] && kill $1 2>/dev/null || true for i in ${children[$1]:=}; do kill_all $i; done } kill_all $1 } nxf_mktemp() { local base=${1:-/tmp} if [[ $(uname) = Darwin ]]; then mktemp -d $base/nxf.XXXXXXXXXX else TMPDIR="$base" mktemp -d -t nxf.XXXXXXXXXX fi } nxf_fs_copy() { local source=$1 local target=$2 local basedir=$(dirname $1) mkdir -p $target/$basedir cp -fRL $source $target/$basedir } nxf_fs_move() { local source=$1 local target=$2 local basedir=$(dirname $1) mkdir -p $target/$basedir mv -f $source $target/$basedir } nxf_fs_rsync() { rsync -rRl $1 $2 } on_exit() { exit_status=${nxf_main_ret:=$?} printf $exit_status | nxf_s3_upload - s3://nextflow-bucket/work/4b/3e4254443d207235b90d933c1855df/.exitcode || true set +u [[ "$tee1" ]] && kill $tee1 2>/dev/null [[ "$tee2" ]] && kill $tee2 2>/dev/null [[ "$ctmp" ]] && rm -rf $ctmp || true rm -rf $NXF_SCRATCH || true exit $exit_status } on_term() { set +e [[ "$pid" ]] && nxf_kill $pid } nxf_launch() { /bin/bash .command.run nxf_trace } nxf_stage() { true # stage input files downloads=(true) rm -f samplesheet_test.csv rm -f .command.sh rm -f .command.run downloads+=("nxf_s3_download s3://nextflow-bucket/work/stage/b3/6a31b4d61a7a567fd0579ce5495999/samplesheet_test.csv samplesheet_test.csv") downloads+=("nxf_s3_download s3://nextflow-bucket/work/4b/3e4254443d207235b90d933c1855df/.command.sh .command.sh") downloads+=("nxf_s3_download s3://nextflow-bucket/work/4b/3e4254443d207235b90d933c1855df/.command.run .command.run") nxf_parallel "${downloads[@]}" } nxf_unstage() { true nxf_s3_upload .command.out s3://nextflow-bucket/work/4b/3e4254443d207235b90d933c1855df || true nxf_s3_upload .command.err s3://nextflow-bucket/work/4b/3e4254443d207235b90d933c1855df || true nxf_s3_upload .command.trace s3://nextflow-bucket/work/4b/3e4254443d207235b90d933c1855df || true [[ ${nxf_main_ret:=0} != 0 ]] && return uploads=() IFS=$'\n' for name in $(eval "ls -1d *.csv versions.yml" | sort | uniq); do uploads+=("nxf_s3_upload '$name' s3://nextflow-bucket/work/4b/3e4254443d207235b90d933c1855df") done unset IFS nxf_parallel "${uploads[@]}" } nxf_main() { trap on_exit EXIT trap on_term TERM INT USR2 trap '' USR1 [[ "${NXF_CHDIR:-}" ]] && cd "$NXF_CHDIR" NXF_SCRATCH="$(set +u; nxf_mktemp $TMPDIR)" [[ $NXF_DEBUG > 0 ]] && nxf_env echo start | nxf_s3_upload - s3://nextflow-bucket/work/4b/3e4254443d207235b90d933c1855df/.command.begin set +u set -u /usr/bin/aws --region us-west-1 s3 cp --recursive --only-show-errors s3://nextflow-bucket/work/tmp/59/57c99dbb2c36549875d666144cea88/bin $PWD/nextflow-bin chmod +x $PWD/nextflow-bin/* export PATH=$PWD/nextflow-bin:$PATH export R_ENVIRON_USER="/.Renviron" export PYTHONNOUSERSITE="1" export R_PROFILE_USER="/.Rprofile" export JULIA_DEPOT_PATH="/usr/local/share/julia" [[ $NXF_SCRATCH ]] && echo "nxf-scratch-dir $HOSTNAME:$NXF_SCRATCH" && cd $NXF_SCRATCH nxf_stage set +e ctmp=$(set +u; nxf_mktemp /dev/shm 2>/dev/null || nxf_mktemp $TMPDIR) local cout=$ctmp/.command.out; mkfifo $cout local cerr=$ctmp/.command.err; mkfifo $cerr tee .command.out < $cout & tee1=$! tee .command.err < $cerr >&2 & tee2=$! ( nxf_launch ) >$cout 2>$cerr & pid=$! wait $pid || nxf_main_ret=$? wait $tee1 $tee2 nxf_unstage } $NXF_ENTRY ```Environment
$SHELL --version)Additional context
Originally, I was debugging a separate workflow where the container wasn't even getting attached. The Python version detected in the script was 2.7 while the container clearly stated 3.8. But the fact that I can't even get
nf-core/rnaseqto work tells me that there is some more fundamental error in our AWS Batch setup.Thank you so much for your help! Warmest, Olga