Issues with odgibuild
dbrami opened this issue · 4 comments
dbrami commented
This can't be a memory issue as I have 64GB on my machine and only adding 2 x 200 viral genomes
Description of the bug
odgibuild chokes but running the following completes succesfully:
nextflow run nf-core/pangenome -r dev -profile test,dockerSteps to reproduce
Steps to reproduce the behaviour:
export NXF_OPTS="-Xms8G -Xmx60G"
nextflow run nf-core/pangenome -r dev -profile docker --input 'ncbi200_??.fasta.gz' -c nfcore_ec2.config
N E X T F L O W ~ version 20.10.0
Launching `nf-core/pangenome` [pensive_galileo] - revision: 2652c2871a [dev]
----------------------------------------------------
,--./,-.
___ __ __ __ ___ /,-._.--~'
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/pangenome v1.0dev
----------------------------------------------------
executor > local (15)
[72/e5d415] process > edyeet (2) [100%] 2 of 2 ✔
[d6/66334d] process > seqwish (2) [100%] 2 of 2 ✔
[11/d228c2] process > smoothxg (2) [100%] 2 of 2 ✔
[e6/be2b2c] process > odgiBuild (7) [ 0%] 0 of 11
[- ] process > odgiStats -
[- ] process > odgiViz -
[- ] process > odgiChop -
[- ] process > odgiLayout -
[- ] process > odgiDraw -
Error executing process > 'odgiBuild (1)'
Caused by:
Process `odgiBuild (1)` terminated with an error exit status (1)
Command executed:
odgi build -g ncbi200_01.pggb-s1000-p90-n10-a90-K16-X-k8-w10000-j5000-W0-e5000-I0.seqwish.gfa ncbi200_00.pggb-s1000-p90-n10-a90-K16-X-k8-w10000-j5000-W0-e5000-I0.seqwish.gfa -o ncbi200_01.pggb-s1000-p90-n10-a90-K16-X-k8-w10000-j5000-W0-e5000-I0.seqwish.gfa ncbi200_00.pggb-s1000-p90-n10-a90-K16-X-k8-w10000-j5000-W0-e5000-I0.seqwish.gfa.og
Command exit status:
1
Command output:
(empty)
Command error:
WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
Passed in argument, but no positional arguments were ready to receive it: ncbi200_00.pggb-s1000-p90-n10-a90-K16-X-k8-w10000-j5000-W0-e5000-I0.seqwish.gfa
executor > local (15)
[72/e5d415] process > edyeet (2) [100%] 2 of 2 ✔
[d6/66334d] process > seqwish (2) [100%] 2 of 2 ✔
[11/d228c2] process > smoothxg (2) [100%] 2 of 2 ✔
[6f/1a2ca0] process > odgiBuild (2) [ 18%] 2 of 11, failed: 1
[- ] process > odgiStats -
[- ] process > odgiViz -
[- ] process > odgiChop -
[- ] process > odgiLayout -
[- ] process > odgiDraw -
Execution cancelled -- Finishing pending tasks before exit
Error executing process > 'odgiBuild (1)'
Caused by:
Process `odgiBuild (1)` terminated with an error exit status (1)
Command executed:
odgi build -g ncbi200_01.pggb-s1000-p90-n10-a90-K16-X-k8-w10000-j5000-W0-e5000-I0.seqwish.gfa ncbi200_00.pggb-s1000-p90-n10-a90-K16-X-k8-w10000-j5000-W0-e5000-I0.seqwish.gfa -o ncbi200_01.pggb-s1000-p90-n10-a90-K16-X-k8-w10000-j5000-W0-e5000-I0.seqwish.gfa ncbi200_00.pggb-s1000-p90-n10-a90-K16-X-k8-w10000-j5000-W0-e5000-I0.seqwish.gfa.og
Command exit status:
1
Command output:
(empty)
Command error:
WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
Passed in argument, but no positional arguments were ready to receive it: ncbi200_00.pggb-s1000-p90-n10-a90-K16-X-k8-w10000-j5000-W0-e5000-I0.seqwish.gfa
executor > local (15)
[72/e5d415] process > edyeet (2) [100%] 2 of 2 ✔
[d6/66334d] process > seqwish (2) [100%] 2 of 2 ✔
[11/d228c2] process > smoothxg (2) [100%] 2 of 2 ✔
[42/1ed10c] process > odgiBuild (6) [ 36%] 4 of 11, failed: 1
[- ] process > odgiStats -
[- ] process > odgiViz -
[- ] process > odgiChop -
[- ] process > odgiLayout -
[- ] process > odgiDraw -
Execution cancelled -- Finishing pending tasks before exit
Error executing process > 'odgiBuild (1)'
Caused by:
Process `odgiBuild (1)` terminated with an error exit status (1)
Command executed:
odgi build -g ncbi200_01.pggb-s1000-p90-n10-a90-K16-X-k8-w10000-j5000-W0-e5000-I0.seqwish.gfa ncbi200_00.pggb-s1000-p90-n10-a90-K16-X-k8-w10000-j5000-W0-e5000-I0.seqwish.gfa -o ncbi200_01.pggb-s1000-p90-n10-a90-K16-X-k8-w10000-j5000-W0-e5000-I0.seqwish.gfa ncbi200_00.pggb-s1000-p90-n10-a90-K16-X-k8-w10000-j5000-W0-e5000-I0.seqwish.gfa.og
Command exit status:
1
Command output:
(empty)
Command error:
WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
Passed in argument, but no positional arguments were ready to receive it: ncbi200_00.pggb-s1000-p90-n10-a90-K16-X-k8-w10000-j5000-W0-e5000-I0.seqwish.gfa
executor > local (15)
[72/e5d415] process > edyeet (2) [100%] 2 of 2 ✔
[d6/66334d] process > seqwish (2) [100%] 2 of 2 ✔
[11/d228c2] process > smoothxg (2) [100%] 2 of 2 ✔
[f5/ff32be] process > odgiBuild (5) [ 64%] 7 of 11, failed: 1
[- ] process > odgiStats -
[- ] process > odgiViz -
[- ] process > odgiChop -
[- ] process > odgiLayout -
[- ] process > odgiDraw -
Execution cancelled -- Finishing pending tasks before exit
Error executing process > 'odgiBuild (1)'
Caused by:
Process `odgiBuild (1)` terminated with an error exit status (1)
Command executed:
odgi build -g ncbi200_01.pggb-s1000-p90-n10-a90-K16-X-k8-w10000-j5000-W0-e5000-I0.seqwish.gfa ncbi200_00.pggb-s1000-p90-n10-a90-K16-X-k8-w10000-j5000-W0-e5000-I0.seqwish.gfa -o ncbi200_01.pggb-s1000-p90-n10-a90-K16-X-k8-w10000-j5000-W0-e5000-I0.seqwish.gfa ncbi200_00.pggb-s1000-p90-n10-a90-K16-X-k8-w10000-j5000-W0-e5000-I0.seqwish.gfa.og
Command exit status:
1
Command output:
(empty)
Command error:
WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
Passed in argument, but no positional arguments were ready to receive it: ncbi200_00.pggb-s1000-p90-n10-a90-K16-X-k8-w10000-j5000-W0-e5000-I0.seqwish.gfa
executor > local (15)
[72/e5d415] process > edyeet (2) [100%] 2 of 2 ✔
[d6/66334d] process > seqwish (2) [100%] 2 of 2 ✔
[11/d228c2] process > smoothxg (2) [100%] 2 of 2 ✔
[0f/6f0f89] process > odgiBuild (9) [ 73%] 8 of 11, failed: 1
[- ] process > odgiStats -
[- ] process > odgiViz -
[- ] process > odgiChop -
[- ] process > odgiLayout -
[- ] process > odgiDraw -
Execution cancelled -- Finishing pending tasks before exit
Error executing process > 'odgiBuild (1)'
Caused by:
Process `odgiBuild (1)` terminated with an error exit status (1)
Command executed:
odgi build -g ncbi200_01.pggb-s1000-p90-n10-a90-K16-X-k8-w10000-j5000-W0-e5000-I0.seqwish.gfa ncbi200_00.pggb-s1000-p90-n10-a90-K16-X-k8-w10000-j5000-W0-e5000-I0.seqwish.gfa -o ncbi200_01.pggb-s1000-p90-n10-a90-K16-X-k8-w10000-j5000-W0-e5000-I0.seqwish.gfa ncbi200_00.pggb-s1000-p90-n10-a90-K16-X-k8-w10000-j5000-W0-e5000-I0.seqwish.gfa.og
Command exit status:
1
Command output:
(empty)
Command error:
WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
Passed in argument, but no positional arguments were ready to receive it: ncbi200_00.pggb-s1000-p90-n10-a90-K16-X-k8-w10000-j5000-W0-e5000-I0.seqwish.gfa
executor > local (15)
[72/e5d415] process > edyeet (2) [100%] 2 of 2 ✔
[d6/66334d] process > seqwish (2) [100%] 2 of 2 ✔
[11/d228c2] process > smoothxg (2) [100%] 2 of 2 ✔
[e6/be2b2c] process > odgiBuild (7) [ 82%] 9 of 11, failed: 1
[- ] process > odgiStats -
[- ] process > odgiViz -
[- ] process > odgiChop -
[- ] process > odgiLayout -
[- ] process > odgiDraw -
Execution cancelled -- Finishing pending tasks before exit
Error executing process > 'odgiBuild (1)'
Caused by:
Process `odgiBuild (1)` terminated with an error exit status (1)
Command executed:
odgi build -g ncbi200_01.pggb-s1000-p90-n10-a90-K16-X-k8-w10000-j5000-W0-e5000-I0.seqwish.gfa ncbi200_00.pggb-s1000-p90-n10-a90-K16-X-k8-w10000-j5000-W0-e5000-I0.seqwish.gfa -o ncbi200_01.pggb-s1000-p90-n10-a90-K16-X-k8-w10000-j5000-W0-e5000-I0.seqwish.gfa ncbi200_00.pggb-s1000-p90-n10-a90-K16-X-k8-w10000-j5000-W0-e5000-I0.seqwish.gfa.og
Command exit status:
1
Command output:
(empty)
Command error:
WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
Passed in argument, but no positional arguments were ready to receive it: ncbi200_00.pggb-s1000-p90-n10-a90-K16-X-k8-w10000-j5000-W0-e5000-I0.seqwish.gfa
odgi build {OPTIONS}
executor > local (15)
[72/e5d415] process > edyeet (2) [100%] 2 of 2 ✔
[d6/66334d] process > seqwish (2) [100%] 2 of 2 ✔
[11/d228c2] process > smoothxg (2) [100%] 2 of 2 ✔
[e6/be2b2c] process > odgiBuild (7) [ 82%] 9 of 11, failed: 1
[- ] process > odgiStats -
[- ] process > odgiViz -
[- ] process > odgiChop -
[- ] process > odgiLayout -
[- ] process > odgiDraw -
Execution cancelled -- Finishing pending tasks before exit
Error executing process > 'odgiBuild (1)'
Caused by:
Process `odgiBuild (1)` terminated with an error exit status (1)
Command executed:
odgi build -g ncbi200_01.pggb-s1000-p90-n10-a90-K16-X-k8-w10000-j5000-W0-e5000-I0.seqwish.gfa ncbi200_00.pggb-s1000-p90-n10-a90-K16-X-k8-w10000-j5000-W0-e5000-I0.seqwish.gfa -o ncbi200_01.pggb-s1000-p90-n10-a90-K16-X-k8-w10000-j5000-W0-e5000-I0.seqwish.gfa ncbi200_00.pggb-s1000-p90-n10-a90-K16-X-k8-w10000-j5000-W0-e5000-I0.seqwish.gfa.og
Command exit status:
1
Command output:
(empty)
Command error:
WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
Passed in argument, but no positional arguments were ready to receive it: ncbi200_00.pggb-s1000-p90-n10-a90-K16-X-k8-w10000-j5000-W0-e5000-I0.seqwish.gfa
odgi build {OPTIONS}
construct a dynamic succinct variation graph
OPTIONS:
-h, --help display this help summary
-g[FILE], --gfa=[FILE] construct the graph from this GFA input
file
-o[FILE], --out=[FILE] store the graph self index in this file
-G, --to-gfa write the graph to stdout in GFA format
-s, --sort apply generalized topological sort to
the graph and set node ids to order
-t[N], --threads=[N] number of threads to use for parallel
operations
-d, --debug enable debugging
-p, --progress show progress updates
Work dir:
/home/ubuntu/covid19/1k/work/64/97145e147f3682ed595a0fbb7125bb
Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line
One more CTRL+C to force exitExpected behaviour
completion of odgibuild step
Log files
Have you provided the following extra information/files:
- see top of error log above for command
.nextflow.log
(pangenomics) ubuntu@ip-172-31-29-49:~/covid19/1k$ cat .nextflow.log
Feb-21 17:19:56.467 [main] DEBUG nextflow.cli.Launcher - $> nextflow run nf-core/pangenome -r dev -profile docker --input 'ncbi200_??.fasta.gz' -c nfcore_ec2.config
Feb-21 17:19:56.563 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 20.10.0
Feb-21 17:19:57.551 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/ubuntu/.nextflow/assets/nf-core/pangenome/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/pangenome.git
Feb-21 17:19:57.561 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/ubuntu/.nextflow/assets/nf-core/pangenome/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/pangenome.git
Feb-21 17:19:57.743 [main] INFO nextflow.cli.CmdRun - Launching `nf-core/pangenome` [pensive_galileo] - revision: 2652c2871a [dev]
Feb-21 17:19:58.003 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/ubuntu/.nextflow/assets/nf-core/pangenome/nextflow.config
Feb-21 17:19:58.005 [main] DEBUG nextflow.config.ConfigBuilder - User config file: /home/ubuntu/covid19/1k/nfcore_ec2.config
Feb-21 17:19:58.005 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/ubuntu/.nextflow/assets/nf-core/pangenome/nextflow.config
Feb-21 17:19:58.006 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/ubuntu/covid19/1k/nfcore_ec2.config
Feb-21 17:19:58.011 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `docker`
Feb-21 17:19:58.605 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `docker`
Feb-21 17:19:58.635 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [cfc_dev, denbi_qbic, bi, genotoul, bigpurple, uppmax, abims, imperial_mb, oist, docker, gis, utd_ganymede, mpcdf, conda, singularity, icr_davros, munin, prince, podman, czbiohub_aws, hebbe, cfc, uzh, ccga_med, debug, test, genouest, cbe, ebc, ccga_dx, crick, google, kraken, phoenix, seg_globe, shh, awsbatch, pasteur, uct_hpc, imperial, test_full, binac]
Feb-21 17:19:58.682 [main] DEBUG nextflow.Session - Session uuid: ca1b3660-790a-4c80-85f1-bb2424b9e2ab
Feb-21 17:19:58.682 [main] DEBUG nextflow.Session - Run name: pensive_galileo
Feb-21 17:19:58.682 [main] DEBUG nextflow.Session - Executor pool size: 32
Feb-21 17:19:58.703 [main] DEBUG nextflow.cli.CmdRun -
Version: 20.10.0 build 5430
Created: 01-11-2020 15:14 UTC
System: Linux 5.4.0-1037-aws
Runtime: Groovy 3.0.5 on OpenJDK 64-Bit Server VM 1.8.0_152-release-1056-b12
Encoding: UTF-8 (UTF-8)
Process: 108877@ip-172-31-29-49 [172.31.29.49]
CPUs: 32 - Mem: 62.1 GB (60 GB) - Swap: 0 (0)
Feb-21 17:19:58.715 [main] DEBUG nextflow.Session - Work-dir: /home/ubuntu/covid19/1k/work [ext2/ext3]
Feb-21 17:19:58.769 [main] DEBUG nextflow.Session - Observer factory: TowerFactory
Feb-21 17:19:58.771 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Feb-21 17:19:58.998 [main] DEBUG nextflow.Session - Session start invoked
Feb-21 17:19:59.001 [main] DEBUG nextflow.trace.TraceFileObserver - Flow starting -- trace file: /home/ubuntu/covid19/1k/results/pipeline_info/execution_trace.txt
Feb-21 17:19:59.574 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Feb-21 17:19:59.656 [main] INFO nextflow.Nextflow - ----------------------------------------------------
,--./,-.
___ __ __ __ ___ /,-._.--~'
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/pangenome v1.0dev
----------------------------------------------------
Feb-21 17:19:59.658 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: seqwish, odgiStats, odgiChop, odgiViz, odgiDraw, smoothxg, edyeet, odgiLayout, odgiBuild
Feb-21 17:19:59.706 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:edyeet` matches process edyeet
Feb-21 17:19:59.711 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-21 17:19:59.711 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-21 17:19:59.715 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
Feb-21 17:19:59.719 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=32; memory=62.1 GB; capacity=32; pollInterval=100ms; dumpInterval=5m
Feb-21 17:19:59.778 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:seqwish` matches process seqwish
Feb-21 17:19:59.779 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-21 17:19:59.779 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-21 17:19:59.784 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:smoothxg` matches process smoothxg
Feb-21 17:19:59.785 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-21 17:19:59.785 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-21 17:19:59.802 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-21 17:19:59.802 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-21 17:19:59.810 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-21 17:19:59.810 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-21 17:19:59.824 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-21 17:19:59.824 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-21 17:19:59.832 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-21 17:19:59.832 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-21 17:19:59.837 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:odgiLayout` matches process odgiLayout
Feb-21 17:19:59.838 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-21 17:19:59.838 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-21 17:19:59.843 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Feb-21 17:19:59.843 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Feb-21 17:19:59.846 [main] DEBUG nextflow.Session - Ignite dataflow network (11)
Feb-21 17:19:59.852 [PathVisitor-1] DEBUG nextflow.file.PathVisitor - files for syntax: glob; folder: ./; pattern: ncbi200_??.fasta.gz; options: [:]
Feb-21 17:19:59.852 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > edyeet
Feb-21 17:19:59.853 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > seqwish
Feb-21 17:19:59.853 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > smoothxg
Feb-21 17:19:59.854 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > odgiBuild
Feb-21 17:19:59.854 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > odgiStats
Feb-21 17:19:59.855 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > odgiViz
Feb-21 17:19:59.856 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > odgiChop
Feb-21 17:19:59.859 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > odgiLayout
Feb-21 17:19:59.860 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > odgiDraw
Feb-21 17:19:59.861 [main] DEBUG nextflow.script.ScriptRunner - > Await termination
Feb-21 17:19:59.861 [main] DEBUG nextflow.Session - Session await
Feb-21 17:20:00.058 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-21 17:20:00.063 [Task submitter] INFO nextflow.Session - [4e/c0b0b0] Submitted process > edyeet (1)
Feb-21 17:20:02.128 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: edyeet (1); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/covid19/1k/work/4e/c0b0b06122abc248f0df55ac374e07]
Feb-21 17:20:02.135 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-21 17:20:02.136 [Task submitter] INFO nextflow.Session - [72/e5d415] Submitted process > edyeet (2)
Feb-21 17:20:04.248 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 2; name: edyeet (2); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/covid19/1k/work/72/e5d415e32467b49cf0f2ff7a4257f2]
Feb-21 17:20:04.254 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-21 17:20:04.255 [Task submitter] INFO nextflow.Session - [91/1b9515] Submitted process > seqwish (1)
Feb-21 17:20:07.566 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 3; name: seqwish (1); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/covid19/1k/work/91/1b9515299b6cac1ccdaf53aefabc98]
Feb-21 17:20:07.573 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-21 17:20:07.573 [Task submitter] INFO nextflow.Session - [d6/66334d] Submitted process > seqwish (2)
Feb-21 17:20:11.045 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 4; name: seqwish (2); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/covid19/1k/work/d6/66334dfe99c0e515877d0d9104e3a0]
Feb-21 17:20:11.049 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-21 17:20:11.051 [Task submitter] INFO nextflow.Session - [5a/22ef1f] Submitted process > smoothxg (1)
Feb-21 17:20:24.281 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 5; name: smoothxg (1); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/covid19/1k/work/5a/22ef1fe3d9a99c09b3f1313062a791]
Feb-21 17:20:24.284 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-21 17:20:24.285 [Task submitter] INFO nextflow.Session - [11/d228c2] Submitted process > smoothxg (2)
Feb-21 17:20:37.238 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6; name: smoothxg (2); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/covid19/1k/work/11/d228c2551fa6f50fe3cbfde6f2be2a]
Feb-21 17:20:37.244 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-21 17:20:37.244 [Task submitter] INFO nextflow.Session - [64/97145e] Submitted process > odgiBuild (1)
Feb-21 17:20:37.251 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-21 17:20:37.251 [Task submitter] INFO nextflow.Session - [6f/1a2ca0] Submitted process > odgiBuild (2)
Feb-21 17:20:37.257 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-21 17:20:37.258 [Task submitter] INFO nextflow.Session - [35/c9ffaa] Submitted process > odgiBuild (3)
Feb-21 17:20:37.264 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-21 17:20:37.265 [Task submitter] INFO nextflow.Session - [00/2e50e7] Submitted process > odgiBuild (4)
Feb-21 17:20:37.270 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-21 17:20:37.270 [Task submitter] INFO nextflow.Session - [f5/ff32be] Submitted process > odgiBuild (5)
Feb-21 17:20:37.278 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-21 17:20:37.278 [Task submitter] INFO nextflow.Session - [42/1ed10c] Submitted process > odgiBuild (6)
Feb-21 17:20:37.285 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-21 17:20:37.286 [Task submitter] INFO nextflow.Session - [93/c1fbcb] Submitted process > odgiBuild (8)
Feb-21 17:20:37.291 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-21 17:20:37.292 [Task submitter] INFO nextflow.Session - [0f/6f0f89] Submitted process > odgiBuild (9)
Feb-21 17:20:38.736 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 7; name: odgiBuild (1); status: COMPLETED; exit: 1; error: -; workDir: /home/ubuntu/covid19/1k/work/64/97145e147f3682ed595a0fbb7125bb]
Feb-21 17:20:38.740 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Feb-21 17:20:38.740 [Task submitter] INFO nextflow.Session - [e6/be2b2c] Submitted process > odgiBuild (7)
Feb-21 17:20:38.756 [Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing process > 'odgiBuild (1)'
Caused by:
Process `odgiBuild (1)` terminated with an error exit status (1)
Command executed:
odgi build -g ncbi200_01.pggb-s1000-p90-n10-a90-K16-X-k8-w10000-j5000-W0-e5000-I0.seqwish.gfa ncbi200_00.pggb-s1000-p90-n10-a90-K16-X-k8-w10000-j5000-W0-e5000-I0.seqwish.gfa -o ncbi200_01.pggb-s1000-p90-n10-a90-K16-X-k8-w10000-j5000-W0-e5000-I0.seqwish.gfa ncbi200_00.pggb-s1000-p90-n10-a90-K16-X-k8-w10000-j5000-W0-e5000-I0.seqwish.gfa.og
Command exit status:
1
Command output:
(empty)
Command error:
WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
Passed in argument, but no positional arguments were ready to receive it: ncbi200_00.pggb-s1000-p90-n10-a90-K16-X-k8-w10000-j5000-W0-e5000-I0.seqwish.gfa
odgi build {OPTIONS}
construct a dynamic succinct variation graph
OPTIONS:
-h, --help display this help summary
-g[FILE], --gfa=[FILE] construct the graph from this GFA input
file
-o[FILE], --out=[FILE] store the graph self index in this file
-G, --to-gfa write the graph to stdout in GFA format
-s, --sort apply generalized topological sort to
the graph and set node ids to order
-t[N], --threads=[N] number of threads to use for parallel
operations
-d, --debug enable debugging
-p, --progress show progress updates
Work dir:
/home/ubuntu/covid19/1k/work/64/97145e147f3682ed595a0fbb7125bb
Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line
Feb-21 17:20:38.762 [Task monitor] INFO nextflow.Session - Execution cancelled -- Finishing pending tasks before exit
Feb-21 17:20:38.767 [main] DEBUG nextflow.Session - Session await > all process finished
Feb-21 17:20:38.917 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 8; name: odgiBuild (2); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/covid19/1k/work/6f/1a2ca03c5f86cf3f7e80194141be8d]
Feb-21 17:20:39.133 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 9; name: odgiBuild (3); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/covid19/1k/work/35/c9ffaa3083edc3b337ba216e245cff]
Feb-21 17:20:39.143 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 12; name: odgiBuild (6); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/covid19/1k/work/42/1ed10c7dc13a281644c45ee02875a9]
Feb-21 17:20:39.218 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 10; name: odgiBuild (4); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/covid19/1k/work/00/2e50e72f8cea4e5d1bee56fb00f7e4]
Feb-21 17:20:39.284 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 14; name: odgiBuild (8); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/covid19/1k/work/93/c1fbcb70eb3a257c5c5bbed9c53350]
Feb-21 17:20:39.348 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 11; name: odgiBuild (5); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/covid19/1k/work/f5/ff32beec67cafb605bc4962960ab33]
Feb-21 17:20:39.415 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 15; name: odgiBuild (9); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/covid19/1k/work/0f/6f0f89881f72465dc241363cc8efa3]
Feb-21 17:20:40.183 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 13; name: odgiBuild (7); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/covid19/1k/work/e6/be2b2cfc860739a0569bc5747d427f]
Feb-21 17:20:53.935 [SIGINT handler] DEBUG nextflow.Session - Session aborted -- Cause: SIGINT
Feb-21 17:20:53.948 [main] DEBUG nextflow.Session - Session await > all barriers passed
Feb-21 17:20:53.955 [main] DEBUG nextflow.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=14; failedCount=1; ignoredCount=0; cachedCount=0; pendingCount=2; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=17m 45s; failedDuration=1.4s; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=8; peakCpus=32; peakMemory=56 GB; ]
Feb-21 17:20:53.955 [main] DEBUG nextflow.trace.TraceFileObserver - Flow completing -- flushing trace file
Feb-21 17:20:53.957 [main] DEBUG nextflow.trace.ReportObserver - Flow completing -- rendering html report
Feb-21 17:20:53.995 [main] DEBUG nextflow.trace.ReportObserver - Execution report summary data:
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(1)","q2Label":"edyeet (1)","q3Label":"edyeet (1)"},"reads":{"mean":8531422,"min":8288934,"q1":8410178,"q2":8531422,"q3":8652666,"max":8773910,"minLabel":"edyeet (1)","maxLabel":"edyeet (2)","q1Label":"edyeet (1)","q2Label":"edyeet (1)","q3Label":"edyeet (1)"},"cpu":{"mean":1763.55,"min":1733.9,"q1":1748.73,"q2":1763.55,"q3":1778.38,"max":1793.2,"minLabel":"edyeet (1)","maxLabel":"edyeet (2)","q1Label":"edyeet (1)","q2Label":"edyeet (1)","q3Label":"edyeet (1)"},"time":{"mean":1432.5,"min":1427,"q1":1429.75,"q2":1432.5,"q3":1435.25,"max":1438,"minLabel":"edyeet (1)","maxLabel":"edyeet (2)","q1Label":"edyeet (1)","q2Label":"edyeet (1)","q3Label":"edyeet (1)"},"writes":{"mean":9861364.5,"min":9152765,"q1":9507064.75,"q2":9861364.5,"q3":10215664.25,"max":10569964,"minLabel":"edyeet (1)","maxLabel":"edyeet (2)","q1Label":"edyeet (1)","q2Label":"edyeet (1)","q3Label":"edyeet (1)"}},{"cpuUsage":{"mean":13.63,"min":13.54,"q1":13.59,"q2":13.63,"q3":13.67,"max":13.71,"minLabel":"seqwish (2)","maxLabel":"seqwish (1)","q1Label":"seqwish (2)","q2Label":"seqwish (2)","q3Label":"seqwish (2)"},"process":"seqwish","mem":{"mean":309073920,"min":308404224,"q1":308739072,"q2":309073920,"q3":309408768,"max":309743616,"minLabel":"seqwish (1)","maxLabel":"seqwish (2)","q1Label":"seqwish (1)","q2Label":"seqwish (1)","q3Label":"seqwish (1)"},"memUsage":{"mean":4.11,"min":4.1,"q1":4.11,"q2":4.11,"q3":4.12,"max":4.12,"minLabel":"seqwish (1)","maxLabel":"seqwish (2)","q1Label":"seqwish (1)","q2Label":"seqwish (1)","q3Label":"seqwish (1)"},"timeUsage":{"mean":0.02,"min":0.02,"q1":0.02,"q2":0.02,"q3":0.02,"max":0.02,"minLabel":"seqwish (1)","maxLabel":"seqwish (2)","q1Label":"seqwish (1)","q2Label":"seqwish (1)","q3Label":"seqwish (1)"},"vmem":{"mean":2790244352,"min":2789535744,"q1":2789890048,"q2":2790244352,"q3":2790598656,"max":2790952960,"minLabel":"seqwish (1)","maxLabel":"seqwish (2)","q1Label":"seqwish (1)","q2Label":"seqwish (1)","q3Label":"seqwish (1)"},"reads":{"mean":8925805.5,"min":8342255,"q1":8634030.25,"q2":8925805.5,"q3":9217580.75,"max":9509356,"minLabel":"seqwish (1)","maxLabel":"seqwish (2)","q1Label":"seqwish (1)","q2Label":"seqwish (1)","q3Label":"seqwish (1)"},"cpu":{"mean":436.1,"min":433.4,"q1":434.75,"q2":436.1,"q3":437.45,"max":438.8,"minLabel":"seqwish (2)","maxLabel":"seqwish (1)","q1Label":"seqwish (2)","q2Label":"seqwish (2)","q3Label":"seqwish (2)"},"time":{"mean":2734.5,"min":2627,"q1":2680.75,"q2":2734.5,"q3":2788.25,"max":2842,"minLabel":"seqwish (1)","maxLabel":"seqwish (2)","q1Label":"seqwish (1)","q2Label":"seqwish (1)","q3Label":"seqwish (1)"},"writes":{"mean":22461965.5,"min":21945142,"q1":22203553.75,"q2":22461965.5,"q3":22720377.25,"max":22978789,"minLabel":"seqwish (2)","maxLabel":"seqwish (1)","q1Label":"seqwish (2)","q2Label":"seqwish (2)","q3Label":"seqwish (2)"}},{"cpuUsage":{"mean":45.86,"min":45.71,"q1":45.79,"q2":45.86,"q3":45.94,"max":46.01,"minLabel":"smoothxg (2)","maxLabel":"smoothxg (1)","q1Label":"smoothxg (2)","q2Label":"smoothxg (2)","q3Label":"smoothxg (2)"},"process":"smoothxg","mem":{"mean":158607360,"min":157413376,"q1":158010368,"q2":158607360,"q3":159204352,"max":159801344,"minLabel":"smoothxg (2)","maxLabel":"smoothxg (1)","q1Label":"smoothxg (2)","q2Label":"smoothxg (2)","q3Label":"smoothxg (2)"},"memUsage":{"mean":2.11,"min":2.09,"q1":2.1,"q2":2.11,"q3":2.12,"max":2.13,"minLabel":"smoothxg (2)","maxLabel":"smoothxg (1)","q1Label":"smoothxg (2)","q2Label":"smoothxg (2)","q3Label":"smoothxg (2)"},"timeUsage":{"mean":0.09,"min":0.09,"q1":0.09,"q2":0.09,"q3":0.09,"max":0.09,"minLabel":"smoothxg (2)","maxLabel":"smoothxg (1)","q1Label":"smoothxg (2)","q2Label":"smoothxg (2)","q3Label":"smoothxg (2)"},"vmem":{"mean":4910694400,"min":4893085696,"q1":4901890048,"q2":4910694400,"q3":4919498752,"max":4928303104,"minLabel":"smoothxg (1)","maxLabel":"smoothxg (2)","q1Label":"smoothxg (1)","q2Label":"smoothxg (1)","q3Label":"smoothxg (1)"},"reads":{"mean":683634,"min":680499,"q1":682066.5,"q2":683634,"q3":685201.5,"max":686769,"minLabel":"smoothxg (1)","maxLabel":"smoothxg (2)","q1Label":"smoothxg (1)","q2Label":"smoothxg (1)","q3Label":"smoothxg (1)"},"cpu":{"mean":1467.6,"min":1462.8,"q1":1465.2,"q2":1467.6,"q3":1470,"max":1472.4,"minLabel":"smoothxg (2)","maxLabel":"smoothxg (1)","q1Label":"smoothxg (2)","q2Label":"smoothxg (2)","q3Label":"smoothxg (2)"},"time":{"mean":12464,"min":12321,"q1":12392.5,"q2":12464,"q3":12535.5,"max":12607,"minLabel":"smoothxg (2)","maxLabel":"smoothxg (1)","q1Label":"smoothxg (2)","q2Label":"smoothxg (2)","q3Label":"smoothxg (2)"},"writes":{"mean":166984954.5,"min":159681754,"q1":163333354.25,"q2":166984954.5,"q3":170636554.75,"max":174288155,"minLabel":"smoothxg (2)","maxLabel":"smoothxg (1)","q1Label":"smoothxg (2)","q2Label":"smoothxg (2)","q3Label":"smoothxg (2)"}},{"cpuUsage":{"mean":91.21,"min":78.7,"q1":86.13,"q2":91.85,"q3":94.9,"max":102.4,"minLabel":"odgiBuild (3)","maxLabel":"odgiBuild (8)","q1Label":"odgiBuild (4)","q2Label":"odgiBuild (6)","q3Label":"odgiBuild (2)"},"process":"odgiBuild","mem":{"mean":9841664,"min":7434240,"q1":9765888,"q2":9863168,"q3":10107904,"max":11767808,"minLabel":"odgiBuild (2)","maxLabel":"odgiBuild (7)","q1Label":"odgiBuild (9)","q2Label":"odgiBuild (3)","q3Label":"odgiBuild (4)"},"memUsage":{"mean":0.13,"min":0.1,"q1":0.13,"q2":0.13,"q3":0.13,"max":0.16,"minLabel":"odgiBuild (2)","maxLabel":"odgiBuild (7)","q1Label":"odgiBuild (9)","q2Label":"odgiBuild (3)","q3Label":"odgiBuild (4)"},"timeUsage":{"mean":0,"min":0,"q1":0,"q2":0,"q3":0,"max":0.01,"minLabel":"odgiBuild (6)","maxLabel":"odgiBuild (1)","q1Label":"odgiBuild (4)","q2Label":"odgiBuild (8)","q3Label":"odgiBuild (7)"},"vmem":{"mean":17021952,"min":15572992,"q1":16760832,"q2":16766976,"q3":16990208,"max":19230720,"minLabel":"odgiBuild (2)","maxLabel":"odgiBuild (7)","q1Label":"odgiBuild (6)","q2Label":"odgiBuild (9)","q3Label":"odgiBuild (3)"},"reads":{"mean":48518.38,"min":48509,"q1":48516.5,"q2":48520,"q3":48522,"max":48524,"minLabel":"odgiBuild (2)","maxLabel":"odgiBuild (6)","q1Label":"odgiBuild (7)","q2Label":"odgiBuild (8)","q3Label":"odgiBuild (4)"},"cpu":{"mean":91.21,"min":78.7,"q1":86.13,"q2":91.85,"q3":94.9,"max":102.4,"minLabel":"odgiBuild (3)","maxLabel":"odgiBuild (8)","q1Label":"odgiBuild (4)","q2Label":"odgiBuild (6)","q3Label":"odgiBuild (2)"},"time":{"mean":236.78,"min":28,"q1":29,"q2":33,"q3":234,"max":1398,"minLabel":"odgiBuild (6)","maxLabel":"odgiBuild (1)","q1Label":"odgiBuild (4)","q2Label":"odgiBuild (8)","q3Label":"odgiBuild (7)"},"writes":{"mean":1794090.63,"min":778618,"q1":784742,"q2":845022.5,"q3":1792265.75,"max":4960143,"minLabel":"odgiBuild (6)","maxLabel":"odgiBuild (2)","q1Label":"odgiBuild (5)","q2Label":"odgiBuild (4)","q3Label":"odgiBuild (3)"}}]
Feb-21 17:20:54.722 [main] DEBUG nextflow.trace.TimelineObserver - Flow completing -- rendering html timeline
Feb-21 17:20:54.760 [main] DEBUG nextflow.CacheDB - Closing CacheDB done
Feb-21 17:20:54.763 [main] DEBUG nextflow.util.SpuriousDeps - AWS S3 uploader shutdown
Feb-21 17:20:54.767 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- GoodbyeSystem
- Hardware: AWS c5a.8xlarge
- Executor: local
- OS: ubuntu
- Version 20.04
Nextflow Installation
- Version: 20.10
Container engine
- Engine: <Docker
- version: Docker version 19.03.13, build cd8016b6bc
- Image tag: nfcore/pangenome:dev
Additional context
subwaystation commented
dbrami commented
Thank you Simon.
I found the requirement to have a wildcard character within the
command line for the input file name misleading as I specifically split up
my input multi-fasta into multiple files to comply with the wildcard
requirement...
…On Mon, Feb 22, 2021 at 12:38 PM Simon Heumos ***@***.***> wrote:
Hi @dbrami <https://github.com/dbrami>
I suspect you ran into the same issues as in #41
<#41> and #39
<#39> .
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
<#42 (comment)>,
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.
subwaystation commented
Oh. Now I understand the confusion! Sorry Daniel.
I will update the README to reflect the what pangenome is capable of.
subwaystation commented
This is already tracked in #39