Error on bamCoverage

[bioinfo-dirty-jobs]

I try to install in another machine cipher-workflow. When try to run the example files I have now this other error:

Sep-14 22:22:47.869 [Task submitter] INFO  nextflow.Session - [30/e5e179] Submit
ted process > mapping_bowtie2 (2)
Sep-14 22:22:47.874 [Actor Thread 19] DEBUG nextflow.Session - <<< barrier arriv
e (process: post_fastqc)
Sep-14 22:23:09.901 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! exe
cutor local > tasks to be completed: 1 -- pending tasks are shown below
~> TaskHandler[id: 12; name: mapping_bowtie2 (2); status: RUNNING; exit: -; erro
r: -; workDir: /home/centos/cipher-workflow-platform/work/30/e5e17934b2b587b54f5
4daa676cd09]
Sep-14 22:24:08.389 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task c
ompleted > TaskHandler[id: 12; name: mapping_bowtie2 (2); status: COMPLETED; exi
t: 0; error: -; workDir: /home/centos/cipher-workflow-platform/work/30/e5e17934b
2b587b54f54daa676cd09]
Sep-14 22:24:08.390 [Task submitter] INFO  nextflow.Session - [58/80b5fd] Submit
ted process > multiqc
Sep-14 22:24:08.400 [Actor Thread 21] DEBUG nextflow.Session - <<< barrier arriv
e (process: mapping_bowtie2)
Sep-14 22:24:08.407 [Actor Thread 24] DEBUG nextflow.Session - <<< barrier arriv
e (process: merge_bams)
Sep-14 22:24:08.411 [Actor Thread 29] WARN  nextflow.processor.TaskProcessor - I
nput tuple does not match input set cardinality declared by process `bamCoverage
` -- offending value: [Input, Input_Rep1, /home/centos/cipher-workflow-platform/
work/85/0da34454d38c168eb38075e88ef71b/Input_Rep1.sorted.mapped.bam, control1, i
nput, /home/centos/cipher-workflow-platform/work/85/0da34454d38c168eb38075e88ef7
1b/Input_Rep1.sorted.mapped.bam.bai]
Sep-14 22:24:13.007 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task c
ompleted > TaskHandler[id: 13; name: multiqc; status: COMPLETED; exit: 0; error:
 -; workDir: /home/centos/cipher-workflow-platform/work/58/80b5fdf66e9d4df840071
1beeb4976]
Sep-14 22:24:13.008 [Task submitter] INFO  nextflow.Session - [25/2418bb] Submit
ted process > estimate_fragment_size (1)
Sep-14 22:24:13.012 [Actor Thread 24] DEBUG nextflow.Session - <<< barrier arriv
e (process: multiqc)
Sep-14 22:24:59.465 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task c
ompleted > TaskHandler[id: 14; name: estimate_fragment_size (1); status: COMPLET
ED; exit: 0; error: -; workDir: /home/centos/cipher-workflow-platform/work/25/24
18bbb5884f168b703c9607e39ecd]
Sep-14 22:24:59.509 [Task submitter] INFO  nextflow.Session - [fe/2d68b3] Submit
ted process > bamCoverage (1)
Sep-14 22:24:59.518 [Task submitter] DEBUG n.processor.TaskPollingMonitor - %% e
xecutor local > tasks in the submission queue: 1 -- tasks to be submitted are sh
own below
~> TaskHandler[id: 16; name: bamCoverage (2); status: NEW; exit: -; error: -; wo
rkDir: /home/centos/cipher-workflow-platform/work/d9/a0c3f7a4eb6d4a9a464518e132e
51a]
Sep-14 22:24:59.519 [Actor Thread 21] DEBUG nextflow.Session - <<< barrier arriv
e (process: estimate_fragment_size)
Sep-14 22:24:59.523 [Actor Thread 21] DEBUG nextflow.Session - <<< barrier arriv
e (process: narrow_peak_calling_NI)
Sep-14 22:25:00.167 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task c
ompleted > TaskHandler[id: 15; name: bamCoverage (1); status: COMPLETED; exit: 1
; error: -; workDir: /home/centos/cipher-workflow-platform/work/fe/2d68b3d00b4a8
215b73c4bba7a948a]
Sep-14 22:25:00.169 [Task submitter] INFO  nextflow.Session - [d9/a0c3f7] Submit
ted process > bamCoverage (2)
Sep-14 22:25:00.194 [Task monitor] ERROR nextflow.processor.TaskProcessor - Erro
r executing process > 'bamCoverage (1)'

Caused by:
  Process `bamCoverage (1)` terminated with an error exit status (1)

Command executed:

  bamCoverage -b input.1 -o Input.RPKMnorm.bw -of bigwig -bs 50 -p 1 --normalize
UsingRPKM --smoothLength 100 -e 150 --centerReads 2> Input.bamcoverage_report.tx
t
  echo 'bamCoverage -b input.1 -o Input.RPKMnorm.bw -of bigwig -bs 50 -p 1 --nor
malizeUsingRPKM --smoothLength 100 -e 150 --centerReads' > bamcoverage_parameter
s_Input.txt

Command exit status:
  1

Command output:
  (empty)

Work dir:
  /home/centos/cipher-workflow-platform/work/fe/2d68b3d00b4a8215b73c4bba7a948a

Tip: you can try to figure out what's wrong by changing to the process work dir 
and showing the script file named `.command.sh`
Sep-14 22:25:00.196 [Task monitor] DEBUG nextflow.Session - Session aborted -- C
ause: Process `bamCoverage (1)` terminated with an error exit status (1)
Sep-14 22:25:00.245 [main] DEBUG nextflow.Session - Session await > all process 
finished
Sep-14 22:25:00.246 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< ba
rrier arrives (monitor: local)
Sep-14 22:25:00.246 [main] DEBUG nextflow.Session - Session await > all barriers
 passed
Sep-14 22:25:00.288 [main] WARN  n.processor.TaskPollingMonitor - Killing pendin
g tasks (1)
Sep-14 22:25:00.317 [main] DEBUG nextflow.CacheDB - Closing CacheDB done
Sep-14 22:25:00.328 [main] DEBUG nextflow.script.ScriptRunner - > Execution comp
lete -- Goodby

What can I do?

[c-guzman]

Oh this is interesting.

Could you show me your config.txt file?

I think I know exactly where the problem is and it should be a relatively quick fix.

[bioinfo-dirty-jobs]

cat example_data/config.txt 
H3K4me3 H3K4me3_Rep1    /home/centos/cipher-workflow-platform/example_data/H3K4me3.500k_reads.fastq.gz  control1    H3K4me3
Input   Input_Rep1  /home/centos/cipher-workflow-platform/example_data/Input.500k_reads.fastq.gz    control1    input

[c-guzman]

Yes I know exactly what's going on here.

I've run into it a few times, but the error comes and goes but it appears that this problem has to do with the merging of files prior to running bamcoverage.

I'll work on this and push out a fix today or tomorrow!

Thank you!