Question: MaSuRCA error: can't find 'gatekeeper' program
0
gravatar for cristamont1995
4 months ago by
cristamont19950 wrote:

Hi, im using MaSuRCA assembler and when I try to generate the assemble.sh shell script it says that runCA failed because "can't find 'gatekeeper' program":

/opt/bioinf/MaSuRCA-3.2.2/global-1/CA/bin/runCA config.txt
================================================================================

runCA failed.

----------------------------------------
Stack trace:

 at /opt/bioinf/MaSuRCA-3.2.2/global-1/CA/bin/runCA line 1121.
    main::caFailure('can\'t find \'gatekeeper\' program in /opt/bioinf/MaSuRCA-3.2...', undef) called at /opt/bioinf/MaSuRCA-3.2.2/global-1/CA/bin/runCA line 795
    main::setParameters() called at /opt/bioinf/MaSuRCA-3.2.2/global-1/CA/bin/runCA line 5314

----------------------------------------
Failure message:

can't find 'gatekeeper' program in /opt/bioinf/MaSuRCA-3.2.2/global-1/Linux-amd64/bin.  Possibly incomplete installation

Would you help me to get through this error please

assembly • 235 views
ADD COMMENTlink modified 9 weeks ago by colindaven1.7k • written 4 months ago by cristamont19950

Relevant part of the error message (Always read the error message carefully):

can't find 'gatekeeper' program in /opt/bioinf/MaSuRCA-3.2.2/global-1/Linux-amd64/bin.  Possibly incomplete installation
  
ADD REPLYlink written 4 months ago by RamRS24k

Thanks! Actually I did it, but I don't know how to solve it. I already google it and still can't do it. If you have any idea please tell me

ADD REPLYlink modified 4 months ago • written 4 months ago by cristamont19950

You may have to reinstall the package since your current installation may be incomplete.

Can you show us what you get if you do ls -lh /opt/bioinf/MaSuRCA-3.2.2/global-1/Linux-amd64/bin/gatekeeper?

ADD REPLYlink written 4 months ago by genomax71k

It says "No such file or directory"

ADD REPLYlink written 4 months ago by cristamont19950
1

It looks like the error message is correct and your install must be incomplete. If this was something you installed then do the install over. If an admin did the install let them know about the error message and ask them to correct.

ADD REPLYlink written 4 months ago by genomax71k
3
gravatar for colindaven
9 weeks ago by
colindaven1.7k
Hannover Medical School
colindaven1.7k wrote:

Looks like masurca is now available via bioconda. This might save you some time and trouble if you still have issues.

https://anaconda.org/bioconda/masurca

ADD COMMENTlink written 9 weeks ago by colindaven1.7k
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