EnTAP-nfのインストールができません！！！
解決したいこと
EnTAP(Eukaryotic Non-Model Transcriptome Annotation Pipeline:EnTAP)という遺伝子のアノテーションツールがあります。詳しくは、農研機構の内藤先生の記事を参考にしてください。
これをNextflowで動かすバージョンがEnTAP-nfという名前で公開されているのですが、それのインストール方法がよくわかりません。結論から言うと、
dockerとかnextflowとかの権限がよくわからない～！
ということで、EnTAP-nfをインストールしようとした経緯を載せました。
私自身、今後はワークフロー開発に挑戦したいと思っていて、nextflowにももちろん挑戦したいです。
素人で、不勉強で、申し訳ございませんが、先輩方のご助言をいただけますと幸いです。
私の実行環境は以下の通りです。
- WSL2 + Ubuntu(22.04)
ちなみに、Ubuntuのバージョン確認の方法は以下を参考にしました。
①Nextflowのインストール
まずは、Ubuntu環境にNextflowをインストールしました。これは以下を参考にさせていただくことでうまくいきました。
nextflowのインストール
sudo apt install openjdk-19-jre-headless -y
curl -s https://get.nextflow.io | bash
インストール後にnextflowをmvコマンドで/usr/local/binに移動
sudo mv nextflow /usr/local/bin/
②dockerのインストール
以下の記事を参考にさせていただき、進めました。
(1) 事前準備
Dockerのインストールってこんなに複雑な過程を経るんだなと思いました...。
必要なパッケージのインストール
sudo apt update
sudo apt install ca-certificates curl gnupg
リポジトリの追加
sudo install -m 0755 -d /etc/apt/keyrings
sudo curl -fsSL https://download.docker.com/linux/ubuntu/gpg -o /etc/apt/keyrings/docker.asc
sudo chmod a+r /etc/apt/keyrings/docker.asc
# Add the repository to Apt sources:[訳: aptに追加(?)]
echo \
"deb [arch=$(dpkg --print-architecture) signed-by=/etc/apt/keyrings/docker.asc] https://download.docker.com/linux/ubuntu \
$(. /etc/os-release && echo "$VERSION_CODENAME") stable" | \
sudo tee /etc/apt/sources.list.d/docker.list > /dev/null
sudo apt update
docker グループ作成・ユーザー所属(ユーザー名: username)
sudo groupadd docker
sudo usermod -aG docker usename
(2) Docker Engineのインストール
参考にしたサイトには、Docker Engine のインストールを推奨しているという記載があり、それに倣ってDocker Engineをインストールすることにしました。
Docker関連パッケージのインストール
sudo apt install docker-ce docker-ce-cli containerd.io \
docker-buildx-plugin docker-compose-plugin
Docker のインストール確認
docker --version
最新バージョンの Docker には docker-compose もデフォルトで付属しているはずなので、以下のようにして確認
docker compose version #ハイフンは不要
③EnTAP-nfのインストール
EnTAP-nfのサイト
これを参考にし、テストデータとともに、EnTAP-nfを試験的にインストールしてみました。
試験的なインストール
#nextflow run systemsgenetics/entapnf -profile test,<docker/singularity/podman/shifter/charliecloud/conda/institute>
nextflow run systemsgenetics/entapnf -profile test,docker
その結果...以下のようなエラーが生じました。
長いので、まとめています。
エラー結果
エラー結果
N E X T F L O W ~ version 24.04.4
Pulling systemsgenetics/entapnf ...
downloaded from https://github.com/SystemsGenetics/EnTAPnf.git
Launching `https://github.com/systemsgenetics/entapnf` [exotic_perlman] DSL2 - revision: 5c715c990c [master]
------------------------------------------------------
systemsgenetics/entapnf v0.1.0
------------------------------------------------------
Core Nextflow options
revision : master
runName : exotic_perlman
containerEngine : docker
container : [DIAMOND_BLASTP:systemsgenetics/entap:flask, DIAMOND_BLASTX:systemsgenetics/entap:flask]
launchDir : /home/username
workDir : /home/username/work
projectDir : /home/username/.nextflow/assets/systemsgenetics/entapnf
userName : username
profile : test,docker
configFiles : /home/username/.nextflow/assets/systemsgenetics/entapnf/nextflow.config
Databases
data_sprot : /home/username/.nextflow/assets/systemsgenetics/entapnf/assets/demo/uniprot_sprot
data_refseq : /home/username/.nextflow/assets/systemsgenetics/entapnf/assets/demo/refseq
Input/output options
input : /home/username/.nextflow/assets/systemsgenetics/entapnf/assets/demo/Osativa.demo.faa
outdir : ./results
taxonomy_ID : 2711
skip_entap : true
Institutional config options
config_profile_name : Test profile
config_profile_description: Minimal test dataset to check pipeline function
Max job request options
max_cpus : 2
max_memory : 6.GB
max_time : 6.h
Reference genome options
igenomes_ignore : true
Generic options
publish_dir_mode : link
!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
If you use systemsgenetics/entapnf for your analysis please cite:
* The nf-core framework
https://doi.org/10.1038/s41587-020-0439-x
* Software dependencies
https://github.com/systemsgenetics/entapnf/blob/master/CITATIONS.md
------------------------------------------------------
executor > local (4)
[83/6160e2] process > SYSTEMSGENETICS_ENTAPNF:ENTAPNF:blastp_sprot (Osativa.demo.1.faa_vs_sprot) [ 0%] 0 of 1
[c7/19e599] process > SYSTEMSGENETICS_ENTAPNF:ENTAPNF:parse_blastp_sprot (Osativa.demo.1.faa_vs_sprot) [ 0%] 0 of 1
[- ] process > SYSTEMSGENETICS_ENTAPNF:ENTAPNF:combine_blastp_sprot -
[e9/35e30f] process > SYSTEMSGENETICS_ENTAPNF:ENTAPNF:blastp_refseq (Osativa.demo.1.faa_vs_refseq) [ 0%] 0 of 1
[6d/669391] process > SYSTEMSGENETICS_ENTAPNF:ENTAPNF:parse_blastp_refseq (Osativa.demo.1.faa_vs_refseq) [ 0%] 0 of 1
[- ] process > SYSTEMSGENETICS_ENTAPNF:ENTAPNF:combine_blastp_refseq -
WARN: Undocumented setting `docker.userEmulation` is not supported any more - please remove it from your config
ERROR ~ Failed to publish file: /home/username/work/e9/35e30f1a9a8f62f8dd9dba78f7c8cb/Osativa.demo.1.faa_vs_refseq.xml; to: /home/username/results/DIAMOND/Osativa.demo.1.faa_vs_refseq.xml [link] -- See log file for details
-- Check '.nextflow.log' file for details
ERROR ~ Failed to publish file: /home/username/work/83/6160e2ea364d5db46ddbdefed6d652/Osativa.demo.1.faa_vs_sprot.xml; to: /home/username/results/DIAMOND/Osativa.demo.1.faa_vs_sprot.xml [link] -- See log file for details
executor > local (4)
[83/6160e2] process > SYSTEMSGENETICS_ENTAPNF:ENTAPNF:blastp_sprot (Osativa.demo.1.faa_vs_sprot) [100%] 1 of 1 ✔
[c7/19e599] process > SYSTEMSGENETICS_ENTAPNF:ENTAPNF:parse_blastp_sprot (Osativa.demo.1.faa_vs_sprot) [100%] 1 of 1
[- ] process > SYSTEMSGENETICS_ENTAPNF:ENTAPNF:combine_blastp_sprot -
[e9/35e30f] process > SYSTEMSGENETICS_ENTAPNF:ENTAPNF:blastp_refseq (Osativa.demo.1.faa_vs_refseq) [100%] 1 of 1 ✔
[6d/669391] process > SYSTEMSGENETICS_ENTAPNF:ENTAPNF:parse_blastp_refseq (Osativa.demo.1.faa_vs_refseq) [100%] 1 of 1
[- ] process > SYSTEMSGENETICS_ENTAPNF:ENTAPNF:combine_blastp_refseq -
WARN: Undocumented setting `docker.userEmulation` is not supported any more - please remove it from your config
ERROR ~ Failed to publish file: /home/username/work/e9/35e30f1a9a8f62f8dd9dba78f7c8cb/Osativa.demo.1.faa_vs_refseq.xml; to: /home/username/results/DIAMOND/Osativa.demo.1.faa_vs_refseq.xml [link] -- See log file for details
-- Check '.nextflow.log' file for details
まとめると、
どうも、dockerとかnextflowとかの権限の問題で先に進めないようです。
-- Check '.nextflow.log' file for details
とのことなので、.nextflow.logを載せます。
.nextflow.log
Oct-13 13:34:09.848 [main] DEBUG nextflow.cli.Launcher - $> nextflow run systemsgenetics/entapnf -profile test,docker
Oct-13 13:34:09.952 [main] DEBUG nextflow.cli.CmdRun - N E X T F L O W ~ version 24.04.4
Oct-13 13:34:09.981 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/home/ryoma/.nextflow/plugins; core-plugins: nf-amazon@2.5.3,nf-azure@1.6.1,nf-cloudcache@0.4.1,nf-codecommit@0.2.1,nf-console@1.1.3,nf-ga4gh@1.3.0,nf-google@1.13.2-patch1,nf-tower@1.9.1,nf-wave@1.4.2-patch1
Oct-13 13:34:09.996 [main] INFO o.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Oct-13 13:34:09.997 [main] INFO o.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Oct-13 13:34:10.001 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.12.0 in 'deployment' mode
Oct-13 13:34:10.015 [main] INFO org.pf4j.AbstractPluginManager - No plugins
Oct-13 13:34:10.029 [main] DEBUG nextflow.scm.ProviderConfig - Using SCM config path: /home/ryoma/.nextflow/scm
Oct-13 13:34:10.997 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/ryoma/.nextflow/assets/systemsgenetics/entapnf/.git/config; branch: master; remote: origin; url: https://github.com/SystemsGenetics/EnTAPnf.git
Oct-13 13:34:11.037 [main] DEBUG nextflow.scm.RepositoryFactory - Found Git repository result: [RepositoryFactory]
Oct-13 13:34:11.048 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/ryoma/.nextflow/assets/systemsgenetics/entapnf/.git/config; branch: master; remote: origin; url: https://github.com/SystemsGenetics/EnTAPnf.git
Oct-13 13:34:12.281 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/ryoma/.nextflow/assets/systemsgenetics/entapnf/nextflow.config
Oct-13 13:34:12.286 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/ryoma/.nextflow/assets/systemsgenetics/entapnf/nextflow.config
Oct-13 13:34:12.312 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /home/ryoma/.nextflow/secrets/store.json
Oct-13 13:34:12.317 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@3dce6dd8] - activable => nextflow.secret.LocalSecretsProvider@3dce6dd8
Oct-13 13:34:12.325 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `test,docker`
Oct-13 13:34:13.365 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [bih, cfc_dev, uzl_omics, ifb_core, embl_hd, denbi_qbic, alice, mjolnir_globe, uppmax, incliva, ilifu, uge, rosalind_uge, lugh, mccleary, unibe_ibu, vai, czbiohub_aws, jax, roslin, ccga_med, tes, scw, unc_longleaf, tigem, tubingen_apg, google, apollo, ipop_up, vsc_calcua, pdc_kth, googlels, stjude, daisybio, eddie, medair, biowulf, bi, bigpurple, adcra, cedars, pawsey_setonix, vsc_kul_uhasselt, pawsey_nimbus, ucl_myriad, utd_ganymede, charliecloud, icr_davros, ceres, munin, rosalind, hasta, cfc, uzh, ebi_codon_slurm, ebc, ccga_dx, crick, ku_sund_danhead, marvin, biohpc_gen, shifter, mana, mamba, york_viking, unc_lccc, wehi, awsbatch, wustl_htcf, arcc, imperial, maestro, software_license, genotoul, nci_gadi, abims, janelia, nu_genomics, googlebatch, oist, sahmri, mpcdf, leicester, vsc_ugent, create, sage, cambridge, jex, podman, ebi_codon, cheaha, xanadu, nyu_hpc, test, marjorie, computerome, ucd_sonic, seg_globe, sanger, dkfz, bluebear, pasteur, einstein, ethz_euler, m3c, test_full, imb, ucl_cscluster, tuos_stanage, azurebatch, hki, crukmi, csiro_petrichor, qmul_apocrita, docker, engaging, gis, hypatia, psmn, eva, nygc, fgcz, conda, crg, singularity, mpcdf_viper, pe2, self_hosted_runner, tufts, uw_hyak_pedslabs, debug, genouest, cbe, phoenix, gitpod, seawulf, uod_hpc, fub_curta, uct_hpc, aws_tower, binac]
Oct-13 13:34:13.415 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declaration
Oct-13 13:34:13.416 [main] DEBUG nextflow.cli.CmdRun - Launching `https://github.com/systemsgenetics/entapnf` [hungry_brenner] DSL2 - revision: 5c715c990c [master]
Oct-13 13:34:13.418 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Oct-13 13:34:13.418 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[]
Oct-13 13:34:13.479 [main] DEBUG nextflow.Session - Session UUID: ad983d37-7e7c-43dd-9e4d-4713db08b3cb
Oct-13 13:34:13.480 [main] DEBUG nextflow.Session - Run name: hungry_brenner
Oct-13 13:34:13.481 [main] DEBUG nextflow.Session - Executor pool size: 8
Oct-13 13:34:13.489 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null
Oct-13 13:34:13.496 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=24; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
Oct-13 13:34:13.531 [main] DEBUG nextflow.cli.CmdRun -
Version: 24.04.4 build 5917
Created: 01-08-2024 07:05 UTC (16:05 JDT)
System: Linux 5.15.153.1-microsoft-standard-WSL2
Runtime: Groovy 4.0.21 on OpenJDK 64-Bit Server VM 19.0.2+7-Ubuntu-0ubuntu322.04
Encoding: UTF-8 (UTF-8)
Process: 121671@MYCOMPUTER [127.0.1.1]
CPUs: 8 - Mem: 15.5 GB (14 GB) - Swap: 4 GB (4 GB)
Oct-13 13:34:13.552 [main] DEBUG nextflow.Session - Work-dir: /home/ryoma/work [ext2/ext3]
Oct-13 13:34:13.600 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Oct-13 13:34:13.614 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Oct-13 13:34:13.707 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Oct-13 13:34:13.717 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 9; maxThreads: 1000
Oct-13 13:34:13.797 [main] DEBUG nextflow.Session - Session start
Oct-13 13:34:13.799 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /home/ryoma/results/pipeline_info/execution_trace_2024-10-13_13-34-13.txt
Oct-13 13:34:13.808 [main] DEBUG nextflow.Session - Using default localLib path: /home/ryoma/.nextflow/assets/systemsgenetics/entapnf/lib
Oct-13 13:34:13.814 [main] DEBUG nextflow.Session - Adding to the classpath library: /home/ryoma/.nextflow/assets/systemsgenetics/entapnf/lib
Oct-13 13:34:13.814 [main] DEBUG nextflow.Session - Adding to the classpath library: /home/ryoma/.nextflow/assets/systemsgenetics/entapnf/lib/nfcore_external_java_deps.jar
Oct-13 13:34:14.609 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Oct-13 13:34:14.779 [main] INFO nextflow.Nextflow -
-[2m----------------------------------------------------[0m-
[0;35m systemsgenetics/entapnf v0.1.0[0m
-[2m----------------------------------------------------[0m-
[1mCore Nextflow options[0m
[0;34mrevision : [0;32mmaster[0m
[0;34mrunName : [0;32mhungry_brenner[0m
[0;34mcontainerEngine : [0;32mdocker[0m
[0;34mcontainer : [0;32m[DIAMOND_BLASTP:systemsgenetics/entap:flask, DIAMOND_BLASTX:systemsgenetics/entap:flask][0m
[0;34mlaunchDir : [0;32m/home/ryoma[0m
[0;34mworkDir : [0;32m/home/ryoma/work[0m
[0;34mprojectDir : [0;32m/home/ryoma/.nextflow/assets/systemsgenetics/entapnf[0m
[0;34muserName : [0;32mryoma[0m
[0;34mprofile : [0;32mtest,docker[0m
[0;34mconfigFiles : [0;32m/home/ryoma/.nextflow/assets/systemsgenetics/entapnf/nextflow.config[0m
[1mDatabases[0m
[0;34mdata_sprot : [0;32m/home/ryoma/.nextflow/assets/systemsgenetics/entapnf/assets/demo/uniprot_sprot[0m
[0;34mdata_refseq : [0;32m/home/ryoma/.nextflow/assets/systemsgenetics/entapnf/assets/demo/refseq[0m
[1mInput/output options[0m
[0;34minput : [0;32m/home/ryoma/.nextflow/assets/systemsgenetics/entapnf/assets/demo/Osativa.demo.faa[0m
[0;34moutdir : [0;32m./results[0m
[0;34mtaxonomy_ID : [0;32m2711[0m
[0;34mskip_entap : [0;32mtrue[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
[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
[1mReference genome options[0m
[0;34migenomes_ignore : [0;32mtrue[0m
[1mGeneric options[0m
[0;34mpublish_dir_mode : [0;32mlink[0m
!! Only displaying parameters that differ from the pipeline defaults !!
-[2m----------------------------------------------------[0m-
If you use systemsgenetics/entapnf for your analysis please cite:
* The nf-core framework
https://doi.org/10.1038/s41587-020-0439-x
* Software dependencies
https://github.com/systemsgenetics/entapnf/blob/master/CITATIONS.md
-[2m----------------------------------------------------[0m-
Oct-13 13:34:16.179 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name SYSTEMSGENETICS_ENTAPNF:ENTAPNF:blastp_sprot
Oct-13 13:34:16.181 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:DIAMOND_BLASTP` matches process SYSTEMSGENETICS_ENTAPNF:ENTAPNF:blastp_sprot
Oct-13 13:34:16.198 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-13 13:34:16.198 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-13 13:34:16.207 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
Oct-13 13:34:16.214 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=8; memory=15.5 GB; capacity=8; pollInterval=100ms; dumpInterval=5m
Oct-13 13:34:16.218 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: local)
Oct-13 13:34:16.289 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name SYSTEMSGENETICS_ENTAPNF:ENTAPNF:parse_blastp_sprot
Oct-13 13:34:16.290 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:PARSE_BLASTXML` matches process SYSTEMSGENETICS_ENTAPNF:ENTAPNF:parse_blastp_sprot
Oct-13 13:34:16.292 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-13 13:34:16.292 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-13 13:34:16.316 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name SYSTEMSGENETICS_ENTAPNF:ENTAPNF:combine_blastp_sprot
Oct-13 13:34:16.318 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BLAST_COMBINE` matches process SYSTEMSGENETICS_ENTAPNF:ENTAPNF:combine_blastp_sprot
Oct-13 13:34:16.320 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-13 13:34:16.321 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-13 13:34:16.335 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name SYSTEMSGENETICS_ENTAPNF:ENTAPNF:blastp_refseq
Oct-13 13:34:16.336 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:DIAMOND_BLASTP` matches process SYSTEMSGENETICS_ENTAPNF:ENTAPNF:blastp_refseq
Oct-13 13:34:16.340 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-13 13:34:16.341 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-13 13:34:16.348 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name SYSTEMSGENETICS_ENTAPNF:ENTAPNF:parse_blastp_refseq
Oct-13 13:34:16.349 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:PARSE_BLASTXML` matches process SYSTEMSGENETICS_ENTAPNF:ENTAPNF:parse_blastp_refseq
Oct-13 13:34:16.354 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-13 13:34:16.354 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-13 13:34:16.364 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name SYSTEMSGENETICS_ENTAPNF:ENTAPNF:combine_blastp_refseq
Oct-13 13:34:16.365 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BLAST_COMBINE` matches process SYSTEMSGENETICS_ENTAPNF:ENTAPNF:combine_blastp_refseq
Oct-13 13:34:16.369 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-13 13:34:16.369 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-13 13:34:16.375 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: parse_blastx_trembl, entap_config, blastp_trembl, blastx_refseq, parse_blastp_sprot, PARSE_BLASTXML, combine_blastx_trembl, parse_blastx_sprot, combine_blastp_trembl, SYSTEMSGENETICS_ENTAPNF:ENTAPNF:blastp_refseq, parse_blastx_refseq, blastp_orthodb, combine_blastp_sprot, SYSTEMSGENETICS_ENTAPNF:ENTAPNF:blastp_sprot, blastx_string, combine_blastx_sprot, blastp_sprot, blastx_nr, blastx_trembl, interproscan_combine, blastp_nr, INTERPROSCAN, blastp_string, parse_blastp_nr, FIND_ORTHO_GROUPS, DIAMOND_BLASTX, parse_blastx_nr, DIAMOND_BLASTP, SYSTEMSGENETICS_ENTAPNF:ENTAPNF:combine_blastp_refseq, interproscan_nuc, FIND_EC_NUMBERS, INTERPROSCAN_COMBINE, ENTAP_CONFIG, find_ortho_groups, SYSTEMSGENETICS_ENTAPNF:ENTAPNF:parse_blastp_sprot, entap_run, find_ec_numbers, SYSTEMSGENETICS_ENTAPNF:ENTAPNF:combine_blastp_sprot, parse_blastp_refseq, interproscan_pep, blastx_orthodb, SYSTEMSGENETICS_ENTAPNF:ENTAPNF:parse_blastp_refseq, BLAST_COMBINE, blastp_refseq, ENTAP_RUN, parse_blastp_trembl, blastx_sprot, combine_blastx_nr, combine_blastp_nr, CUSTOM_DUMPSOFTWAREVERSIONS, combine_blastx_refseq, combine_blastp_refseq
Oct-13 13:34:16.382 [main] DEBUG nextflow.Session - Igniting dataflow network (8)
Oct-13 13:34:16.391 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > SYSTEMSGENETICS_ENTAPNF:ENTAPNF:blastp_sprot
Oct-13 13:34:16.392 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > SYSTEMSGENETICS_ENTAPNF:ENTAPNF:parse_blastp_sprot
Oct-13 13:34:16.392 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > SYSTEMSGENETICS_ENTAPNF:ENTAPNF:combine_blastp_sprot
Oct-13 13:34:16.392 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > SYSTEMSGENETICS_ENTAPNF:ENTAPNF:blastp_refseq
Oct-13 13:34:16.392 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > SYSTEMSGENETICS_ENTAPNF:ENTAPNF:parse_blastp_refseq
Oct-13 13:34:16.392 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > SYSTEMSGENETICS_ENTAPNF:ENTAPNF:combine_blastp_refseq
Oct-13 13:34:16.393 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files:
Script_93c8d4a30582a3e1: /home/ryoma/.nextflow/assets/systemsgenetics/entapnf/./workflows/../modules/local/find_EC_numbers.nf
Script_7f2769f39fed9f7a: /home/ryoma/.nextflow/assets/systemsgenetics/entapnf/./workflows/../modules/nf-core/diamond/blastx/main.nf
Script_ca8edc702d48ff3c: /home/ryoma/.nextflow/assets/systemsgenetics/entapnf/./workflows/../modules/local/parse_blastxml.nf
Script_58ad3329b35131c3: /home/ryoma/.nextflow/assets/systemsgenetics/entapnf/./workflows/../modules/local/interproscan_combine.nf
Script_2147ecd6482e0906: /home/ryoma/.nextflow/assets/systemsgenetics/entapnf/./workflows/entapnf.nf
Script_9a8e88d44d8a512d: /home/ryoma/.nextflow/assets/systemsgenetics/entapnf/./workflows/../modules/local/entap/entap_run/main.nf
Script_2f4a8253cb9c2e87: /home/ryoma/.nextflow/assets/systemsgenetics/entapnf/./workflows/../modules/local/blast_combine.nf
Script_c5343b75722c2953: /home/ryoma/.nextflow/assets/systemsgenetics/entapnf/main.nf
Script_ce4c93de1e51fb0d: /home/ryoma/.nextflow/assets/systemsgenetics/entapnf/./workflows/../modules/local/interproscan/main.nf
Script_1549d41dabf8bd2e: /home/ryoma/.nextflow/assets/systemsgenetics/entapnf/./workflows/../modules/nf-core/custom/dumpsoftwareversions/main.nf
Script_a92f467a9c957eff: /home/ryoma/.nextflow/assets/systemsgenetics/entapnf/./workflows/../modules/local/entap/entap_config/main.nf
Script_9eb82e693a8469e0: /home/ryoma/.nextflow/assets/systemsgenetics/entapnf/./workflows/../modules/local/find_ortho_groups.nf
Script_aa89f411951ebac3: /home/ryoma/.nextflow/assets/systemsgenetics/entapnf/./workflows/../modules/nf-core/diamond/blastp/main.nf
Oct-13 13:34:16.393 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination
Oct-13 13:34:16.393 [main] DEBUG nextflow.Session - Session await
Oct-13 13:34:16.402 [Actor Thread 9] DEBUG nextflow.util.HashBuilder - Hash asset file sha-256: /home/ryoma/.nextflow/assets/systemsgenetics/entapnf/assets/demo/Osativa.demo.faa
Oct-13 13:34:16.411 [Actor Thread 9] DEBUG n.splitter.AbstractTextSplitter - Splitter `Fasta` collector path: nextflow.splitter.TextFileCollector$CachePath(/home/ryoma/work/c8/a5cc69dd1dd4d2b3a0bbf7bf0be9f2/Osativa.demo.faa, null)
Oct-13 13:34:16.575 [Actor Thread 3] DEBUG nextflow.util.HashBuilder - Unable to get file attributes file: Osativa.demo.1.faa_vs_sprot -- Cause: java.nio.file.NoSuchFileException: Osativa.demo.1.faa_vs_sprot
Oct-13 13:34:16.575 [Actor Thread 7] DEBUG nextflow.util.HashBuilder - Unable to get file attributes file: Osativa.demo.1.faa_vs_refseq -- Cause: java.nio.file.NoSuchFileException: Osativa.demo.1.faa_vs_refseq
Oct-13 13:34:16.576 [Actor Thread 3] DEBUG nextflow.util.HashBuilder - Hash asset file sha-256: /home/ryoma/.nextflow/assets/systemsgenetics/entapnf/assets/demo/uniprot_sprot/uniprot_sprot.dmnd
Oct-13 13:34:16.576 [Actor Thread 7] DEBUG nextflow.util.HashBuilder - Hash asset file sha-256: /home/ryoma/.nextflow/assets/systemsgenetics/entapnf/assets/demo/refseq/refseq_plant.protein.dmnd
Oct-13 13:34:16.682 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Oct-13 13:34:16.684 [Task submitter] INFO nextflow.Session - [04/8ab8bf] Submitted process > SYSTEMSGENETICS_ENTAPNF:ENTAPNF:blastp_sprot (Osativa.demo.1.faa_vs_sprot)
Oct-13 13:34:16.700 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Oct-13 13:34:16.702 [Task submitter] INFO nextflow.Session - [de/d63363] Submitted process > SYSTEMSGENETICS_ENTAPNF:ENTAPNF:blastp_refseq (Osativa.demo.1.faa_vs_refseq)
Oct-13 13:34:18.158 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 2; name: SYSTEMSGENETICS_ENTAPNF:ENTAPNF:blastp_sprot (Osativa.demo.1.faa_vs_sprot); status: COMPLETED; exit: 0; error: -; workDir: /home/ryoma/work/04/8ab8bfe8cc2494e659cc20e7bcd5ef]
Oct-13 13:34:18.159 [Task monitor] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'TaskFinalizer' minSize=10; maxSize=24; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
Oct-13 13:34:18.284 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: SYSTEMSGENETICS_ENTAPNF:ENTAPNF:blastp_refseq (Osativa.demo.1.faa_vs_refseq); status: COMPLETED; exit: 0; error: -; workDir: /home/ryoma/work/de/d633637ee32eee0efea48659016981]
Oct-13 13:34:18.336 [TaskFinalizer-2] DEBUG nextflow.processor.TaskProcessor - Process SYSTEMSGENETICS_ENTAPNF:ENTAPNF:blastp_refseq > Skipping output binding because one or more optional files are missing: fileoutparam<0:1>
Oct-13 13:34:18.336 [TaskFinalizer-1] DEBUG nextflow.processor.TaskProcessor - Process SYSTEMSGENETICS_ENTAPNF:ENTAPNF:blastp_sprot > Skipping output binding because one or more optional files are missing: fileoutparam<0:1>
Oct-13 13:34:18.338 [TaskFinalizer-2] DEBUG nextflow.processor.TaskProcessor - Process SYSTEMSGENETICS_ENTAPNF:ENTAPNF:blastp_refseq > Skipping output binding because one or more optional files are missing: fileoutparam<2:1>
Oct-13 13:34:18.338 [TaskFinalizer-1] DEBUG nextflow.processor.TaskProcessor - Process SYSTEMSGENETICS_ENTAPNF:ENTAPNF:blastp_sprot > Skipping output binding because one or more optional files are missing: fileoutparam<2:1>
Oct-13 13:34:18.338 [TaskFinalizer-2] DEBUG nextflow.processor.TaskProcessor - Process SYSTEMSGENETICS_ENTAPNF:ENTAPNF:blastp_refseq > Skipping output binding because one or more optional files are missing: fileoutparam<3:1>
Oct-13 13:34:18.338 [TaskFinalizer-1] DEBUG nextflow.processor.TaskProcessor - Process SYSTEMSGENETICS_ENTAPNF:ENTAPNF:blastp_sprot > Skipping output binding because one or more optional files are missing: fileoutparam<3:1>
Oct-13 13:34:18.338 [TaskFinalizer-2] DEBUG nextflow.processor.TaskProcessor - Process SYSTEMSGENETICS_ENTAPNF:ENTAPNF:blastp_refseq > Skipping output binding because one or more optional files are missing: fileoutparam<4:1>
Oct-13 13:34:18.338 [TaskFinalizer-2] DEBUG nextflow.processor.TaskProcessor - Process SYSTEMSGENETICS_ENTAPNF:ENTAPNF:blastp_refseq > Skipping output binding because one or more optional files are missing: fileoutparam<5:1>
Oct-13 13:34:18.338 [TaskFinalizer-1] DEBUG nextflow.processor.TaskProcessor - Process SYSTEMSGENETICS_ENTAPNF:ENTAPNF:blastp_sprot > Skipping output binding because one or more optional files are missing: fileoutparam<4:1>
Oct-13 13:34:18.338 [TaskFinalizer-2] DEBUG nextflow.processor.TaskProcessor - Process SYSTEMSGENETICS_ENTAPNF:ENTAPNF:blastp_refseq > Skipping output binding because one or more optional files are missing: fileoutparam<6:1>
Oct-13 13:34:18.338 [TaskFinalizer-1] DEBUG nextflow.processor.TaskProcessor - Process SYSTEMSGENETICS_ENTAPNF:ENTAPNF:blastp_sprot > Skipping output binding because one or more optional files are missing: fileoutparam<5:1>
Oct-13 13:34:18.339 [TaskFinalizer-1] DEBUG nextflow.processor.TaskProcessor - Process SYSTEMSGENETICS_ENTAPNF:ENTAPNF:blastp_sprot > Skipping output binding because one or more optional files are missing: fileoutparam<6:1>
Oct-13 13:34:18.371 [Actor Thread 3] DEBUG nextflow.util.HashBuilder - Unable to get file attributes file: Osativa.demo.1.faa_vs_sprot -- Cause: java.nio.file.NoSuchFileException: Osativa.demo.1.faa_vs_sprot
Oct-13 13:34:18.371 [Actor Thread 9] DEBUG nextflow.util.HashBuilder - Unable to get file attributes file: Osativa.demo.1.faa_vs_refseq -- Cause: java.nio.file.NoSuchFileException: Osativa.demo.1.faa_vs_refseq
Oct-13 13:34:18.371 [Actor Thread 3] DEBUG nextflow.util.HashBuilder - Hash asset file sha-256: /home/ryoma/.nextflow/assets/systemsgenetics/entapnf/bin/parse_blastxml.py
Oct-13 13:34:18.397 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Oct-13 13:34:18.397 [Task submitter] INFO nextflow.Session - [a3/1f3e82] Submitted process > SYSTEMSGENETICS_ENTAPNF:ENTAPNF:parse_blastp_refseq (Osativa.demo.1.faa_vs_refseq)
Oct-13 13:34:18.407 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Oct-13 13:34:18.408 [Task submitter] INFO nextflow.Session - [37/98c666] Submitted process > SYSTEMSGENETICS_ENTAPNF:ENTAPNF:parse_blastp_sprot (Osativa.demo.1.faa_vs_sprot)
Oct-13 13:34:18.743 [TaskFinalizer-1] DEBUG nextflow.processor.PublishDir - Failed to publish file: /home/ryoma/work/04/8ab8bfe8cc2494e659cc20e7bcd5ef/Osativa.demo.1.faa_vs_sprot.xml; to: /home/ryoma/results/DIAMOND/Osativa.demo.1.faa_vs_sprot.xml [link] -- attempt: 1; reason: /home/ryoma/results/DIAMOND/Osativa.demo.1.faa_vs_sprot.xml -> /home/ryoma/work/04/8ab8bfe8cc2494e659cc20e7bcd5ef/Osativa.demo.1.faa_vs_sprot.xml: Operation not permitted
Oct-13 13:34:18.780 [TaskFinalizer-2] DEBUG nextflow.processor.PublishDir - Failed to publish file: /home/ryoma/work/de/d633637ee32eee0efea48659016981/Osativa.demo.1.faa_vs_refseq.xml; to: /home/ryoma/results/DIAMOND/Osativa.demo.1.faa_vs_refseq.xml [link] -- attempt: 1; reason: /home/ryoma/results/DIAMOND/Osativa.demo.1.faa_vs_refseq.xml -> /home/ryoma/work/de/d633637ee32eee0efea48659016981/Osativa.demo.1.faa_vs_refseq.xml: Operation not permitted
Oct-13 13:34:19.477 [TaskFinalizer-2] DEBUG nextflow.processor.PublishDir - Failed to publish file: /home/ryoma/work/de/d633637ee32eee0efea48659016981/Osativa.demo.1.faa_vs_refseq.xml; to: /home/ryoma/results/DIAMOND/Osativa.demo.1.faa_vs_refseq.xml [link] -- attempt: 2; reason: /home/ryoma/results/DIAMOND/Osativa.demo.1.faa_vs_refseq.xml -> /home/ryoma/work/de/d633637ee32eee0efea48659016981/Osativa.demo.1.faa_vs_refseq.xml: Operation not permitted
Oct-13 13:34:19.605 [TaskFinalizer-1] DEBUG nextflow.processor.PublishDir - Failed to publish file: /home/ryoma/work/04/8ab8bfe8cc2494e659cc20e7bcd5ef/Osativa.demo.1.faa_vs_sprot.xml; to: /home/ryoma/results/DIAMOND/Osativa.demo.1.faa_vs_sprot.xml [link] -- attempt: 2; reason: /home/ryoma/results/DIAMOND/Osativa.demo.1.faa_vs_sprot.xml -> /home/ryoma/work/04/8ab8bfe8cc2494e659cc20e7bcd5ef/Osativa.demo.1.faa_vs_sprot.xml: Operation not permitted
Oct-13 13:34:20.225 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 3; name: SYSTEMSGENETICS_ENTAPNF:ENTAPNF:parse_blastp_refseq (Osativa.demo.1.faa_vs_refseq); status: COMPLETED; exit: 0; error: -; workDir: /home/ryoma/work/a3/1f3e8271e31666b377239af6bbb568]
Oct-13 13:34:20.313 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 4; name: SYSTEMSGENETICS_ENTAPNF:ENTAPNF:parse_blastp_sprot (Osativa.demo.1.faa_vs_sprot); status: COMPLETED; exit: 0; error: -; workDir: /home/ryoma/work/37/98c66688430fcaa64a124aad24e490]
Oct-13 13:34:20.556 [TaskFinalizer-3] DEBUG nextflow.processor.PublishDir - Failed to publish file: /home/ryoma/work/a3/1f3e8271e31666b377239af6bbb568/Osativa.demo.1.faa_vs_refseq.txt; to: /home/ryoma/results/DIAMOND/Osativa.demo.1.faa_vs_refseq.txt [link] -- attempt: 1; reason: /home/ryoma/results/DIAMOND/Osativa.demo.1.faa_vs_refseq.txt -> /home/ryoma/work/a3/1f3e8271e31666b377239af6bbb568/Osativa.demo.1.faa_vs_refseq.txt: Operation not permitted
Oct-13 13:34:20.691 [TaskFinalizer-2] DEBUG nextflow.processor.PublishDir - Failed to publish file: /home/ryoma/work/de/d633637ee32eee0efea48659016981/Osativa.demo.1.faa_vs_refseq.xml; to: /home/ryoma/results/DIAMOND/Osativa.demo.1.faa_vs_refseq.xml [link] -- attempt: 3; reason: /home/ryoma/results/DIAMOND/Osativa.demo.1.faa_vs_refseq.xml -> /home/ryoma/work/de/d633637ee32eee0efea48659016981/Osativa.demo.1.faa_vs_refseq.xml: Operation not permitted
Oct-13 13:34:20.737 [TaskFinalizer-4] DEBUG nextflow.processor.PublishDir - Failed to publish file: /home/ryoma/work/37/98c66688430fcaa64a124aad24e490/Osativa.demo.1.faa_vs_sprot.txt; to: /home/ryoma/results/DIAMOND/Osativa.demo.1.faa_vs_sprot.txt [link] -- attempt: 1; reason: /home/ryoma/results/DIAMOND/Osativa.demo.1.faa_vs_sprot.txt -> /home/ryoma/work/37/98c66688430fcaa64a124aad24e490/Osativa.demo.1.faa_vs_sprot.txt: Operation not permitted
Oct-13 13:34:20.737 [TaskFinalizer-1] DEBUG nextflow.processor.PublishDir - Failed to publish file: /home/ryoma/work/04/8ab8bfe8cc2494e659cc20e7bcd5ef/Osativa.demo.1.faa_vs_sprot.xml; to: /home/ryoma/results/DIAMOND/Osativa.demo.1.faa_vs_sprot.xml [link] -- attempt: 3; reason: /home/ryoma/results/DIAMOND/Osativa.demo.1.faa_vs_sprot.xml -> /home/ryoma/work/04/8ab8bfe8cc2494e659cc20e7bcd5ef/Osativa.demo.1.faa_vs_sprot.xml: Operation not permitted
Oct-13 13:34:21.375 [TaskFinalizer-3] DEBUG nextflow.processor.PublishDir - Failed to publish file: /home/ryoma/work/a3/1f3e8271e31666b377239af6bbb568/Osativa.demo.1.faa_vs_refseq.txt; to: /home/ryoma/results/DIAMOND/Osativa.demo.1.faa_vs_refseq.txt [link] -- attempt: 2; reason: /home/ryoma/results/DIAMOND/Osativa.demo.1.faa_vs_refseq.txt -> /home/ryoma/work/a3/1f3e8271e31666b377239af6bbb568/Osativa.demo.1.faa_vs_refseq.txt: Operation not permitted
Oct-13 13:34:21.598 [TaskFinalizer-4] DEBUG nextflow.processor.PublishDir - Failed to publish file: /home/ryoma/work/37/98c66688430fcaa64a124aad24e490/Osativa.demo.1.faa_vs_sprot.txt; to: /home/ryoma/results/DIAMOND/Osativa.demo.1.faa_vs_sprot.txt [link] -- attempt: 2; reason: /home/ryoma/results/DIAMOND/Osativa.demo.1.faa_vs_sprot.txt -> /home/ryoma/work/37/98c66688430fcaa64a124aad24e490/Osativa.demo.1.faa_vs_sprot.txt: Operation not permitted
Oct-13 13:34:22.677 [TaskFinalizer-3] DEBUG nextflow.processor.PublishDir - Failed to publish file: /home/ryoma/work/a3/1f3e8271e31666b377239af6bbb568/Osativa.demo.1.faa_vs_refseq.txt; to: /home/ryoma/results/DIAMOND/Osativa.demo.1.faa_vs_refseq.txt [link] -- attempt: 3; reason: /home/ryoma/results/DIAMOND/Osativa.demo.1.faa_vs_refseq.txt -> /home/ryoma/work/a3/1f3e8271e31666b377239af6bbb568/Osativa.demo.1.faa_vs_refseq.txt: Operation not permitted
Oct-13 13:34:22.805 [TaskFinalizer-4] DEBUG nextflow.processor.PublishDir - Failed to publish file: /home/ryoma/work/37/98c66688430fcaa64a124aad24e490/Osativa.demo.1.faa_vs_sprot.txt; to: /home/ryoma/results/DIAMOND/Osativa.demo.1.faa_vs_sprot.txt [link] -- attempt: 3; reason: /home/ryoma/results/DIAMOND/Osativa.demo.1.faa_vs_sprot.txt -> /home/ryoma/work/37/98c66688430fcaa64a124aad24e490/Osativa.demo.1.faa_vs_sprot.txt: Operation not permitted
Oct-13 13:34:23.668 [TaskFinalizer-2] DEBUG nextflow.processor.PublishDir - Failed to publish file: /home/ryoma/work/de/d633637ee32eee0efea48659016981/Osativa.demo.1.faa_vs_refseq.xml; to: /home/ryoma/results/DIAMOND/Osativa.demo.1.faa_vs_refseq.xml [link] -- attempt: 4; reason: /home/ryoma/results/DIAMOND/Osativa.demo.1.faa_vs_refseq.xml -> /home/ryoma/work/de/d633637ee32eee0efea48659016981/Osativa.demo.1.faa_vs_refseq.xml: Operation not permitted
Oct-13 13:34:23.670 [TaskFinalizer-2] ERROR nextflow.processor.PublishDir - Failed to publish file: /home/ryoma/work/de/d633637ee32eee0efea48659016981/Osativa.demo.1.faa_vs_refseq.xml; to: /home/ryoma/results/DIAMOND/Osativa.demo.1.faa_vs_refseq.xml [link] -- See log file for details
dev.failsafe.FailsafeException: java.nio.file.FileSystemException: /home/ryoma/results/DIAMOND/Osativa.demo.1.faa_vs_refseq.xml -> /home/ryoma/work/de/d633637ee32eee0efea48659016981/Osativa.demo.1.faa_vs_refseq.xml: Operation not permitted
at dev.failsafe.FailsafeExecutor.call(FailsafeExecutor.java:444)
at dev.failsafe.FailsafeExecutor.get(FailsafeExecutor.java:129)
at nextflow.processor.PublishDir.retryableProcessFile(PublishDir.groovy:396)
at nextflow.processor.PublishDir.safeProcessFile(PublishDir.groovy:367)
at nextflow.processor.PublishDir.apply1(PublishDir.groovy:339)
at nextflow.processor.PublishDir.apply0(PublishDir.groovy:246)
at nextflow.processor.PublishDir.apply(PublishDir.groovy:304)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.processor.TaskProcessor.publishOutputs0(TaskProcessor.groovy:1410)
at nextflow.processor.TaskProcessor.publishOutputs(TaskProcessor.groovy:1385)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.processor.TaskProcessor.finalizeTask0(TaskProcessor.groovy:2424)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.selectMethod(IndyInterface.java:355)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.processor.TaskProcessor.finalizeTask(TaskProcessor.groovy:2395)
at nextflow.processor.TaskPollingMonitor.finalizeTask(TaskPollingMonitor.groovy:686)
at nextflow.processor.TaskPollingMonitor.safeFinalizeTask(TaskPollingMonitor.groovy:676)
at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:104)
at java.base/java.lang.reflect.Method.invoke(Method.java:578)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328)
at groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1333)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1088)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007)
at org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:645)
at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:628)
at org.codehaus.groovy.runtime.InvokerHelper.invokeMethodSafe(InvokerHelper.java:82)
at nextflow.processor.TaskPollingMonitor$_checkTaskStatus_lambda8.doCall(TaskPollingMonitor.groovy:666)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:577)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642)
at java.base/java.lang.Thread.run(Thread.java:1589)
Caused by: java.nio.file.FileSystemException: /home/ryoma/results/DIAMOND/Osativa.demo.1.faa_vs_refseq.xml -> /home/ryoma/work/de/d633637ee32eee0efea48659016981/Osativa.demo.1.faa_vs_refseq.xml: Operation not permitted
at java.base/sun.nio.fs.UnixException.translateToIOException(UnixException.java:100)
at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:106)
at java.base/sun.nio.fs.UnixFileSystemProvider.createLink(UnixFileSystemProvider.java:492)
at java.base/java.nio.file.Files.createLink(Files.java:1112)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.extension.FilesEx.createLinkImpl(FilesEx.groovy:1504)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.extension.FilesEx.mklink(FilesEx.groovy:1490)
at nextflow.processor.PublishDir.processFileImpl(PublishDir.groovy:501)
at nextflow.processor.PublishDir.processFile(PublishDir.groovy:406)
at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:104)
at java.base/java.lang.reflect.Method.invoke(Method.java:578)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328)
at groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1333)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1088)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007)
at org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:645)
at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:628)
at org.codehaus.groovy.runtime.InvokerHelper.invokeMethodSafe(InvokerHelper.java:82)
at nextflow.processor.PublishDir$_retryableProcessFile_closure2.doCall(PublishDir.groovy:397)
at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:104)
at java.base/java.lang.reflect.Method.invoke(Method.java:578)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328)
at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:279)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007)
at groovy.lang.Closure.call(Closure.java:433)
at org.codehaus.groovy.runtime.ConvertedClosure.invokeCustom(ConvertedClosure.java:52)
at org.codehaus.groovy.runtime.ConversionHandler.invoke(ConversionHandler.java:113)
at jdk.proxy2/jdk.proxy2.$Proxy35.get(Unknown Source)
at dev.failsafe.Functions.lambda$get$0(Functions.java:46)
at dev.failsafe.internal.RetryPolicyExecutor.lambda$apply$0(RetryPolicyExecutor.java:75)
at dev.failsafe.SyncExecutionImpl.executeSync(SyncExecutionImpl.java:176)
at dev.failsafe.FailsafeExecutor.call(FailsafeExecutor.java:437)
... 32 common frames omitted
Oct-13 13:34:23.689 [TaskFinalizer-2] DEBUG nextflow.Session - Session aborted -- Cause: java.nio.file.FileSystemException: /home/ryoma/results/DIAMOND/Osativa.demo.1.faa_vs_refseq.xml -> /home/ryoma/work/de/d633637ee32eee0efea48659016981/Osativa.demo.1.faa_vs_refseq.xml: Operation not permitted
Oct-13 13:34:23.721 [TaskFinalizer-2] DEBUG nextflow.Session - The following nodes are still active:
[process] SYSTEMSGENETICS_ENTAPNF:ENTAPNF:parse_blastp_sprot
status=ACTIVE
port 0: (queue) OPEN ; channel: -
port 1: (cntrl) - ; channel: $
[process] SYSTEMSGENETICS_ENTAPNF:ENTAPNF:combine_blastp_sprot
status=ACTIVE
port 0: (value) OPEN ; channel: outfiles
port 1: (value) bound ; channel: blast_type
port 2: (value) bound ; channel: sequence_filename
port 3: (value) bound ; channel: db_name
port 4: (cntrl) - ; channel: $
[process] SYSTEMSGENETICS_ENTAPNF:ENTAPNF:parse_blastp_refseq
status=ACTIVE
port 0: (queue) OPEN ; channel: -
port 1: (cntrl) - ; channel: $
[process] SYSTEMSGENETICS_ENTAPNF:ENTAPNF:combine_blastp_refseq
status=ACTIVE
port 0: (value) OPEN ; channel: outfiles
port 1: (value) bound ; channel: blast_type
port 2: (value) bound ; channel: sequence_filename
port 3: (value) bound ; channel: db_name
port 4: (cntrl) - ; channel: $
Oct-13 13:34:23.723 [main] DEBUG nextflow.Session - Session await > all processes finished
Oct-13 13:34:23.724 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: local) - terminating tasks monitor poll loop
Oct-13 13:34:23.725 [main] DEBUG nextflow.Session - Session await > all barriers passed
Oct-13 13:34:23.728 [TaskFinalizer-3] ERROR nextflow.processor.PublishDir - Failed to publish file: /home/ryoma/work/a3/1f3e8271e31666b377239af6bbb568/Osativa.demo.1.faa_vs_refseq.txt; to: /home/ryoma/results/DIAMOND/Osativa.demo.1.faa_vs_refseq.txt [link] -- See log file for details
dev.failsafe.FailsafeException: java.lang.InterruptedException: sleep interrupted
at dev.failsafe.FailsafeExecutor.call(FailsafeExecutor.java:444)
at dev.failsafe.FailsafeExecutor.get(FailsafeExecutor.java:129)
at nextflow.processor.PublishDir.retryableProcessFile(PublishDir.groovy:396)
at nextflow.processor.PublishDir.safeProcessFile(PublishDir.groovy:367)
at nextflow.processor.PublishDir.apply1(PublishDir.groovy:339)
at nextflow.processor.PublishDir.apply0(PublishDir.groovy:246)
at nextflow.processor.PublishDir.apply(PublishDir.groovy:304)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.processor.TaskProcessor.publishOutputs0(TaskProcessor.groovy:1410)
at nextflow.processor.TaskProcessor.publishOutputs(TaskProcessor.groovy:1385)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.processor.TaskProcessor.finalizeTask0(TaskProcessor.groovy:2424)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.processor.TaskProcessor.finalizeTask(TaskProcessor.groovy:2395)
at nextflow.processor.TaskPollingMonitor.finalizeTask(TaskPollingMonitor.groovy:686)
at nextflow.processor.TaskPollingMonitor.safeFinalizeTask(TaskPollingMonitor.groovy:676)
at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:104)
at java.base/java.lang.reflect.Method.invoke(Method.java:578)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328)
at groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1333)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1088)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007)
at org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:645)
at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:628)
at org.codehaus.groovy.runtime.InvokerHelper.invokeMethodSafe(InvokerHelper.java:82)
at nextflow.processor.TaskPollingMonitor$_checkTaskStatus_lambda8.doCall(TaskPollingMonitor.groovy:666)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:577)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642)
at java.base/java.lang.Thread.run(Thread.java:1589)
Caused by: java.lang.InterruptedException: sleep interrupted
at java.base/java.lang.Thread.sleep0(Native Method)
at java.base/java.lang.Thread.sleep(Thread.java:465)
at dev.failsafe.internal.RetryPolicyExecutor.lambda$apply$0(RetryPolicyExecutor.java:90)
at dev.failsafe.SyncExecutionImpl.executeSync(SyncExecutionImpl.java:176)
at dev.failsafe.FailsafeExecutor.call(FailsafeExecutor.java:437)
... 31 common frames omitted
Oct-13 13:34:23.728 [TaskFinalizer-4] ERROR nextflow.processor.PublishDir - Failed to publish file: /home/ryoma/work/37/98c66688430fcaa64a124aad24e490/Osativa.demo.1.faa_vs_sprot.txt; to: /home/ryoma/results/DIAMOND/Osativa.demo.1.faa_vs_sprot.txt [link] -- See log file for details
dev.failsafe.FailsafeException: java.lang.InterruptedException: sleep interrupted
at dev.failsafe.FailsafeExecutor.call(FailsafeExecutor.java:444)
at dev.failsafe.FailsafeExecutor.get(FailsafeExecutor.java:129)
at nextflow.processor.PublishDir.retryableProcessFile(PublishDir.groovy:396)
at nextflow.processor.PublishDir.safeProcessFile(PublishDir.groovy:367)
at nextflow.processor.PublishDir.apply1(PublishDir.groovy:339)
at nextflow.processor.PublishDir.apply0(PublishDir.groovy:246)
at nextflow.processor.PublishDir.apply(PublishDir.groovy:304)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.processor.TaskProcessor.publishOutputs0(TaskProcessor.groovy:1410)
at nextflow.processor.TaskProcessor.publishOutputs(TaskProcessor.groovy:1385)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.processor.TaskProcessor.finalizeTask0(TaskProcessor.groovy:2424)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.processor.TaskProcessor.finalizeTask(TaskProcessor.groovy:2395)
at nextflow.processor.TaskPollingMonitor.finalizeTask(TaskPollingMonitor.groovy:686)
at nextflow.processor.TaskPollingMonitor.safeFinalizeTask(TaskPollingMonitor.groovy:676)
at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:104)
at java.base/java.lang.reflect.Method.invoke(Method.java:578)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328)
at groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1333)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1088)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007)
at org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:645)
at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:628)
at org.codehaus.groovy.runtime.InvokerHelper.invokeMethodSafe(InvokerHelper.java:82)
at nextflow.processor.TaskPollingMonitor$_checkTaskStatus_lambda8.doCall(TaskPollingMonitor.groovy:666)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:577)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642)
at java.base/java.lang.Thread.run(Thread.java:1589)
Caused by: java.lang.InterruptedException: sleep interrupted
at java.base/java.lang.Thread.sleep0(Native Method)
at java.base/java.lang.Thread.sleep(Thread.java:465)
at dev.failsafe.internal.RetryPolicyExecutor.lambda$apply$0(RetryPolicyExecutor.java:90)
at dev.failsafe.SyncExecutionImpl.executeSync(SyncExecutionImpl.java:176)
at dev.failsafe.FailsafeExecutor.call(FailsafeExecutor.java:437)
... 31 common frames omitted
Oct-13 13:34:23.728 [TaskFinalizer-1] ERROR nextflow.processor.PublishDir - Failed to publish file: /home/ryoma/work/04/8ab8bfe8cc2494e659cc20e7bcd5ef/Osativa.demo.1.faa_vs_sprot.xml; to: /home/ryoma/results/DIAMOND/Osativa.demo.1.faa_vs_sprot.xml [link] -- See log file for details
dev.failsafe.FailsafeException: java.lang.InterruptedException: sleep interrupted
at dev.failsafe.FailsafeExecutor.call(FailsafeExecutor.java:444)
at dev.failsafe.FailsafeExecutor.get(FailsafeExecutor.java:129)
at nextflow.processor.PublishDir.retryableProcessFile(PublishDir.groovy:396)
at nextflow.processor.PublishDir.safeProcessFile(PublishDir.groovy:367)
at nextflow.processor.PublishDir.apply1(PublishDir.groovy:339)
at nextflow.processor.PublishDir.apply0(PublishDir.groovy:246)
at nextflow.processor.PublishDir.apply(PublishDir.groovy:304)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.processor.TaskProcessor.publishOutputs0(TaskProcessor.groovy:1410)
at nextflow.processor.TaskProcessor.publishOutputs(TaskProcessor.groovy:1385)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.processor.TaskProcessor.finalizeTask0(TaskProcessor.groovy:2424)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.processor.TaskProcessor.finalizeTask(TaskProcessor.groovy:2395)
at nextflow.processor.TaskPollingMonitor.finalizeTask(TaskPollingMonitor.groovy:686)
at nextflow.processor.TaskPollingMonitor.safeFinalizeTask(TaskPollingMonitor.groovy:676)
at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:104)
at java.base/java.lang.reflect.Method.invoke(Method.java:578)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328)
at groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1333)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1088)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007)
at org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:645)
at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:628)
at org.codehaus.groovy.runtime.InvokerHelper.invokeMethodSafe(InvokerHelper.java:82)
at nextflow.processor.TaskPollingMonitor$_checkTaskStatus_lambda8.doCall(TaskPollingMonitor.groovy:666)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:577)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642)
at java.base/java.lang.Thread.run(Thread.java:1589)
Caused by: java.lang.InterruptedException: sleep interrupted
at java.base/java.lang.Thread.sleep0(Native Method)
at java.base/java.lang.Thread.sleep(Thread.java:465)
at dev.failsafe.internal.RetryPolicyExecutor.lambda$apply$0(RetryPolicyExecutor.java:90)
at dev.failsafe.SyncExecutionImpl.executeSync(SyncExecutionImpl.java:176)
at dev.failsafe.FailsafeExecutor.call(FailsafeExecutor.java:437)
... 31 common frames omitted
Oct-13 13:34:23.733 [main] INFO nextflow.Nextflow - -[0;35m[systemsgenetics/entapnf][0;31m Pipeline completed with errors[0m-
Oct-13 13:34:23.741 [main] DEBUG n.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=1; failedCount=0; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=3; retriesCount=0; abortedCount=0; succeedDuration=529ms; failedDuration=0ms; cachedDuration=0ms;loadCpus=5; loadMemory=18 GB; peakRunning=4; peakCpus=6; peakMemory=24 GB; ]
Oct-13 13:34:23.741 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow completed -- saving trace file
Oct-13 13:34:23.754 [main] DEBUG nextflow.trace.ReportObserver - Workflow completed -- rendering execution report
Oct-13 13:34:23.772 [main] WARN nextflow.trace.ReportObserver - Failed to render execution report -- see the log file for details
java.util.ConcurrentModificationException: null
at java.base/java.util.LinkedHashMap$LinkedHashIterator.nextNode(LinkedHashMap.java:764)
at java.base/java.util.LinkedHashMap$LinkedKeyIterator.next(LinkedHashMap.java:786)
at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2393)
at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2379)
at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2432)
at nextflow.trace.ResourcesAggregator.computeSummaryMap(ResourcesAggregator.groovy:64)
at nextflow.trace.ResourcesAggregator.computeSummaryList(ResourcesAggregator.groovy:90)
at nextflow.trace.ResourcesAggregator.renderSummaryJson(ResourcesAggregator.groovy:105)
at nextflow.trace.ReportObserver.renderSummaryJson(ReportObserver.groovy:244)
at nextflow.trace.ReportObserver.renderPayloadJson(ReportObserver.groovy:248)
at nextflow.trace.ReportObserver.renderHtml(ReportObserver.groovy:259)
at nextflow.trace.ReportObserver.onFlowComplete(ReportObserver.groovy:143)
at nextflow.Session.notifyFlowComplete(Session.groovy:1115)
at nextflow.Session.shutdown0(Session.groovy:738)
at nextflow.Session.destroy(Session.groovy:683)
at nextflow.script.ScriptRunner.shutdown(ScriptRunner.groovy:260)
at nextflow.script.ScriptRunner.execute(ScriptRunner.groovy:146)
at nextflow.cli.CmdRun.run(CmdRun.groovy:372)
at nextflow.cli.Launcher.run(Launcher.groovy:503)
at nextflow.cli.Launcher.main(Launcher.groovy:657)
Oct-13 13:34:23.773 [main] DEBUG nextflow.trace.TimelineObserver - Workflow completed -- rendering execution timeline
Oct-13 13:34:23.914 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done
Oct-13 13:34:23.928 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye
おわりに
すみません。すごく投げ出した形になってしまいました。
ChatGPTで解決を試みましたが、うまくいきません。。。
もしよろしければ、お力を頂きたいと思っています。
また、通常のEnTAPの記事は別にあります。
そちらの方はうまく動きます。
改善し次第、この質問を本記事にアップロードしようと思います。
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