Error on VIPR4

[Ritzttk]

Dear I met this error when running VIPR4 pipeline, please help me. This is the log file

root@vi-dengue:~# cat .nextflow.log
Sep-20 10:00:08.987 [main] DEBUG nextflow.cli.Launcher - $> /usr/local/bin/nextflow run vipr/ -params-file vi.yaml -profile docker
Sep-20 10:00:09.097 [main] INFO  nextflow.cli.CmdRun - N E X T F L O W  ~  version 0.31.1
Sep-20 10:00:09.591 [main] INFO  nextflow.cli.CmdRun - Launching `vipr/main.nf` [nice_hoover] - revision: 26fe4451e5
Sep-20 10:00:09.605 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/vi/vipr/nextflow.config
Sep-20 10:00:09.606 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/vi/vipr/nextflow.config
Sep-20 10:00:09.613 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `docker`
Sep-20 10:00:09.687 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [standard, gis, conda, awsbatch, singularity, docker]
Sep-20 10:00:09.755 [main] DEBUG nextflow.Session - Session uuid: 40df97f6-a0ea-4127-a041-2b75d8ffbe9c
Sep-20 10:00:09.755 [main] DEBUG nextflow.Session - Run name: nice_hoover
Sep-20 10:00:09.756 [main] DEBUG nextflow.Session - Executor pool size: 5
Sep-20 10:00:09.939 [main] DEBUG nextflow.cli.CmdRun -
  Version: 0.31.1 build 4886
  Modified: 07-08-2018 15:53 UTC
  System: Linux 4.4.0-133-generic
  Runtime: Groovy 2.4.15 on Java HotSpot(TM) 64-Bit Server VM 1.8.0_181-b13
  Encoding: UTF-8 (UTF-8)
  Process: 1620@localhost null
  CPUs: 5 - Mem: 15.3 GB (383.4 MB) - Swap: 31.2 GB (31.2 GB)
Sep-20 10:00:09.964 [main] DEBUG nextflow.Session - Work-dir: /home/vi/work [ext2/ext3]
Sep-20 10:00:09.964 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /home/vi/vipr/bin
Sep-20 10:00:10.229 [main] DEBUG nextflow.Session - Session start invoked
Sep-20 10:00:10.233 [main] DEBUG nextflow.processor.TaskDispatcher - Dispatcher > start
Sep-20 10:00:10.233 [main] DEBUG nextflow.trace.TraceFileObserver - Flow starting -- trace file: /home/vi/results/pipeline_info/nfcore-vipr_trace.txt
Sep-20 10:00:10.238 [main] DEBUG nextflow.script.ScriptRunner - > Script parsing
Sep-20 10:00:10.283 [main] DEBUG nextflow.Session - Session aborted -- Cause: startup failed:
_nf_script_1396a082: 94: unexpected token: } @ line 94, column 1.
}
^

1 error

Sep-20 10:00:10.296 [main] ERROR nextflow.cli.Launcher - startup failed:
_nf_script_1396a082: 94: unexpected token: } @ line 94, column 1.
}
^

1 error

[ewels]

@apeltzer - looks like your AWS batch code could be broken?

https://github.com/nf-core/vipr/blob/5dd7e163c66b9c124939bc624391eaab6b424118/main.nf#L91-L94

[apeltzer]

We have a techtalk in a couple of minutes - will have a look later on this one!

[apeltzer]

Thats not mine - the one I added to some pipelines is found here in Vipr:

https://github.com/nf-core/vipr/blob/5dd7e163c66b9c124939bc624391eaab6b424118/main.nf#L54-L59

[ewels]

Git blame would beg to differ 😉 https://github.com/nf-core/vipr/commit/7ec2297a2774d92bbea23048593fc38204dfa130#diff-28b7bea57b04f15beeb4c1de0ee78382R93

[apeltzer]

Looks like there are two - I will remove the line 90+ one then :-( Sorry, apparently my fault indeed.

[ewels]

No problem 😉 We should get the CI tests up and running on this repo to spot this kind of thing.

[ewels]

Hi @Ritzttk - the bug has hopefully been fixed now. If you could try pulling the latest version of the code and trying again, that would be great!

[Ritzttk]

Hi @ewels - With the new code, I ran over that error. But I met another error. I will create a new issue for that error.

Thanks, Kien

[ewels]

Great, thanks! 👍