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[ERROR] make_acnv_pon_config

cbaocbao Member, Broadie ✭✭

Hi,

I want build a CNV PoN by "make_acnv_pon_config". But, I got a message as following. Any suggestions? Thanks a lot! I will really appreciate your help.

Failures:
message: Task make_acnv_pon_workflow.make_acnv_pon:NA:1 failed. JES error code 10. Message: 11: Docker run failed: command failed: /cromwell_root/exec.sh: line 12: syntax error near unexpected token echo' /cromwell_root/exec.sh: line 12: echo "writing $F to agg.pcovs"' . See logs at gs://fc-b9cc3b48-69c9-4013-8eba-ff7973fc7bc9/599d74a4-5a7e-4b33-823c-0e3ad1f87f5e/make_acnv_pon_workflow/e8fd4bdb-6e0b-4003-b413-cfea7a535ec2/call-make_acnv_pon/

JES log:
2017/09/11 02:00:15 E: command failed: /cromwell_root/exec.sh: line 12: syntax error near unexpected token echo' /cromwell_root/exec.sh: line 12: echo "writing $F to agg.pcovs"'
(exit status 2)

submission id: 599d74a4-5a7e-4b33-823c-0e3ad1f87f5e
link: https://portal.firecloud.org/#workspaces/nci-cbao-bi-org/reference_hg19_cbao/monitor/599d74a4-5a7e-4b33-823c-0e3ad1f87f5e/e8fd4bdb-6e0b-4003-b413-cfea7a535ec2

Best,
Chunyang

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Best Answer

Answers

  • cbaocbao Member, Broadie ✭✭

    I solved by my self :) . I changed something as following in "make_acnv_pon" in Firecloud. It then ran successfully. I published the new one. Thanks a lot!

    Before:
    for F in ${sep =" " pcovs} do ;
    echo "writing $F to agg.pcovs"
    echo $F >> agg.pcovs
    done ;

    After:
    for F in ${sep =" " pcovs}; do
    echo "writing $F to agg.pcovs"
    echo $F >> agg.pcovs
    done

    Best,
    Chunyang

  • cbaocbao Member, Broadie ✭✭
    Accepted Answer

    I solved by myself.

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