Error while running DKFZ

baminou · September 21, 2017, 6:50pm

The PCAWG DKFZ workflow has some errors when I am trying to run it. I do not know what is the error, but I am sharing the output.

gist.github.com

https://gist.github.com/baminou/6688a118e746c2322634b833484eb04b

run.log

nohup: ignoring input
/usr/local/bin/cwltool 1.0.20170217172322
Resolved 'pcawg-dkfz-variant-caller.cwl' to 'file:///home/ubuntu/pcawg-dkfz-variant-caller/test-2/pcawg-dkfz-variant-caller.cwl'
[job pcawg-dkfz-variant-caller.cwl] initializing from file:///home/ubuntu/pcawg-dkfz-variant-caller/test-2/pcawg-dkfz-variant-caller.cwl
[job pcawg-dkfz-variant-caller.cwl] {
    "run-id": "run_id", 
    "tumor-bam": {
        "class": "File", 
        "location": "file:///home/ubuntu/pcawg-dkfz-variant-caller/test-2/input/HCC1143.bam", 
        "basename": "HCC1143.bam"

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