wgs-assembler-users

[wgs-assembler-users] runCA error

[Takashi K. <tak...@gm...>]

Hello.
I recently started to work with wgs-8.3rc1 and have two problems in runCA.
It would be appreciated if anyone give me solutions.

In first problem, I got an error when runCA run gatekeeper but error has
gone away if I retry runCA without any modification.
The error message is below:
----------------------------------------START Fri Mar 13 11:39:14 2015
/opt/bio/wgs-8.3rc1/Linux-amd64/bin/gatekeeper -dumpfastaseq -clear UNTRIM
/home/tkoyama/Documents/SquSex/seqs/SquSD_BACassembly/CeleraAssembler/163a23/assembly1/163a23_assembly1.gkpStore
2>
/home/tkoyama/Documents/SquSex/seqs/SquSD_BACassembly/CeleraAssembler/163a23/assembly1/0-preoverlap/gatekeeper.err
>
/home/tkoyama/Documents/SquSex/seqs/SquSD_BACassembly/CeleraAssembler/163a23/assembly1/163a23_assembly1.fasta
sh:
/home/tkoyama/Documents/SquSex/seqs/SquSD_BACassembly/CeleraAssembler/163a23/assembly1/0-preoverlap/gatekeeper.err:
そのようなファイルやディレクトリはありません
----------------------------------------END Fri Mar 13 11:39:14 2015 (0
seconds)
ERROR: Failed with signal HUP (1)
================================================================================

runCA failed.

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

 at /usr/local/genome/bin/runCA line 1649.
    main::caFailure("failed to dump gatekeeper store for figaro trimmer",
"/home/tkoyama/Documents/SquSex/seqs/SquSD_BACassembly/CeleraA"...) called
at /usr/local/genome/bin/runCA line 2971
    main::generateVectorTrim() called at /usr/local/genome/bin/runCA line
1991

main::preoverlap("/home/tkoyama/Documents/SquSex/seqs/SquSD_BACassembly/CeleraA"...,
"/home/tkoyama/Documents/SquSex/seqs/SquSD_BACassembly/CeleraA"...,
"/home/tkoyama/Documents/SquSex/seqs/SquSD_BACassembly/CeleraA"...,
"/home/tkoyama/Documents/SquSex/seqs/SquSD_BACassembly/CeleraA"...,
"/home/tkoyama/Documents/SquSex/seqs/SquSD_BACassembly/CeleraA"...,
"/home/tkoyama/Documents/SquSex/seqs/SquSD_BACassembly/CeleraA"...) called
at /usr/local/genome/bin/runCA line 6551

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

failed to dump gatekeeper store for figaro trimmer




In second problem, I got an error when runCA run overlapStoreBuild. The
error message is below:
----------------------------------------START Fri Mar 13 11:47:29 2015
/opt/bio/wgs-8.3rc1/Linux-amd64/bin/overlapStoreBuild  -o
/home/tkoyama/Documents/SquSex/seqs/SquSD_BACassembly/CeleraAssembler/163a23/assembly1/163a23_assembly1.ovlStore.BUILDING
-g
/home/tkoyama/Documents/SquSex/seqs/SquSD_BACassembly/CeleraAssembler/163a23/assembly1/163a23_assembly1.gkpStore
-i 0 -M 24000 -L
/home/tkoyama/Documents/SquSex/seqs/SquSD_BACassembly/CeleraAssembler/163a23/assembly1/163a23_assembly1.ovlStore.list
>
/home/tkoyama/Documents/SquSex/seqs/SquSD_BACassembly/CeleraAssembler/163a23/assembly1/163a23_assembly1.ovlStore.err
2>&1
----------------------------------------END Fri Mar 13 11:47:29 2015 (0
seconds)
ERROR: Failed with signal HUP (1)
================================================================================

runCA failed.

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

 at /usr/local/genome/bin/runCA line 1649, <J> line 2.
    main::caFailure("failed to create the overlap store",
"/home/tkoyama/Documents/SquSex/seqs/SquSD_BACassembly/CeleraA"...) called
at /usr/local/genome/bin/runCA line 3993
    main::createOverlapStore() called at /usr/local/genome/bin/runCA line
6556

----------------------------------------
Last few lines of the relevant log file
(/home/tkoyama/Documents/SquSex/seqs/SquSD_BACassembly/CeleraAssembler/163a23/assembly1/163a23_assembly1.ovlStore.err):

/opt/bio/wgs-8.3rc1/Linux-amd64/bin/overlapStoreBuild: unknown option '-i'.
usage: /opt/bio/wgs-8.3rc1/Linux-amd64/bin/overlapStoreBuild -o
asm.ovlStore -g asm.gkpStore [opts] [-L fileList | *.ovb.gz]
  -o asm.ovlStore       path to store to create
  -g asm.gkpStore       path to gkpStore for this assembly

  -F f                  use up to 'f' files for store creation
  -M m                  use up to 'm' MB memory for store creation

  -plc t                type of filtering for PLC fragments -- NOT SUPPORTED
  -obt                  filter overlaps for OBT
  -dup                  filter overlaps for OBT/dedupe

  -e e                  filter overlaps above e fraction error
  -L fileList           read input filenames from 'flieList'

  -big iid              handle a large number of overlaps in the last
library
                        iid is the first read iid in the last library, from
                        'gatekeeper -dumpinfo *gkpStore'

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

failed to create the overlap store

Re: [wgs-assembler-users] runCA error

[Brian W. <th...@gm...>]

Unfortunately, there is a fair bit of obsolete code in the assembler, and
it appears you're trying to use some of it.

1) Don't use option vectorTrimmer=figaro.
2) Don't use option closureOverlaps.

I'll stick these on my list for the next time I need to kill some time.
Thanks for testing them.  ;-)

b


On Thu, Mar 12, 2015 at 10:55 PM, Takashi Koyama <tak...@gm...>
wrote:

> Hello.
> I recently started to work with wgs-8.3rc1 and have two problems in runCA.
> It would be appreciated if anyone give me solutions.
>
> In first problem, I got an error when runCA run gatekeeper but error has
> gone away if I retry runCA without any modification.
> The error message is below:
> ----------------------------------------START Fri Mar 13 11:39:14 2015
> /opt/bio/wgs-8.3rc1/Linux-amd64/bin/gatekeeper -dumpfastaseq -clear UNTRIM
> /home/tkoyama/Documents/SquSex/seqs/SquSD_BACassembly/CeleraAssembler/163a23/assembly1/163a23_assembly1.gkpStore
> 2>
> /home/tkoyama/Documents/SquSex/seqs/SquSD_BACassembly/CeleraAssembler/163a23/assembly1/0-preoverlap/gatekeeper.err
> >
> /home/tkoyama/Documents/SquSex/seqs/SquSD_BACassembly/CeleraAssembler/163a23/assembly1/163a23_assembly1.fasta
> sh:
> /home/tkoyama/Documents/SquSex/seqs/SquSD_BACassembly/CeleraAssembler/163a23/assembly1/0-preoverlap/gatekeeper.err:
> そのようなファイルやディレクトリはありません
> ----------------------------------------END Fri Mar 13 11:39:14 2015 (0
> seconds)
> ERROR: Failed with signal HUP (1)
>
> ================================================================================
>
> runCA failed.
>
> ----------------------------------------
> Stack trace:
>
>  at /usr/local/genome/bin/runCA line 1649.
>     main::caFailure("failed to dump gatekeeper store for figaro trimmer",
> "/home/tkoyama/Documents/SquSex/seqs/SquSD_BACassembly/CeleraA"...) called
> at /usr/local/genome/bin/runCA line 2971
>     main::generateVectorTrim() called at /usr/local/genome/bin/runCA line
> 1991
>
> main::preoverlap("/home/tkoyama/Documents/SquSex/seqs/SquSD_BACassembly/CeleraA"...,
> "/home/tkoyama/Documents/SquSex/seqs/SquSD_BACassembly/CeleraA"...,
> "/home/tkoyama/Documents/SquSex/seqs/SquSD_BACassembly/CeleraA"...,
> "/home/tkoyama/Documents/SquSex/seqs/SquSD_BACassembly/CeleraA"...,
> "/home/tkoyama/Documents/SquSex/seqs/SquSD_BACassembly/CeleraA"...,
> "/home/tkoyama/Documents/SquSex/seqs/SquSD_BACassembly/CeleraA"...) called
> at /usr/local/genome/bin/runCA line 6551
>
> ----------------------------------------
> Failure message:
>
> failed to dump gatekeeper store for figaro trimmer
>
>
>
>
> In second problem, I got an error when runCA run overlapStoreBuild. The
> error message is below:
> ----------------------------------------START Fri Mar 13 11:47:29 2015
> /opt/bio/wgs-8.3rc1/Linux-amd64/bin/overlapStoreBuild  -o
> /home/tkoyama/Documents/SquSex/seqs/SquSD_BACassembly/CeleraAssembler/163a23/assembly1/163a23_assembly1.ovlStore.BUILDING
> -g
> /home/tkoyama/Documents/SquSex/seqs/SquSD_BACassembly/CeleraAssembler/163a23/assembly1/163a23_assembly1.gkpStore
> -i 0 -M 24000 -L
> /home/tkoyama/Documents/SquSex/seqs/SquSD_BACassembly/CeleraAssembler/163a23/assembly1/163a23_assembly1.ovlStore.list
> >
> /home/tkoyama/Documents/SquSex/seqs/SquSD_BACassembly/CeleraAssembler/163a23/assembly1/163a23_assembly1.ovlStore.err
> 2>&1
> ----------------------------------------END Fri Mar 13 11:47:29 2015 (0
> seconds)
> ERROR: Failed with signal HUP (1)
>
> ================================================================================
>
> runCA failed.
>
> ----------------------------------------
> Stack trace:
>
>  at /usr/local/genome/bin/runCA line 1649, <J> line 2.
>     main::caFailure("failed to create the overlap store",
> "/home/tkoyama/Documents/SquSex/seqs/SquSD_BACassembly/CeleraA"...) called
> at /usr/local/genome/bin/runCA line 3993
>     main::createOverlapStore() called at /usr/local/genome/bin/runCA line
> 6556
>
> ----------------------------------------
> Last few lines of the relevant log file
> (/home/tkoyama/Documents/SquSex/seqs/SquSD_BACassembly/CeleraAssembler/163a23/assembly1/163a23_assembly1.ovlStore.err):
>
> /opt/bio/wgs-8.3rc1/Linux-amd64/bin/overlapStoreBuild: unknown option '-i'.
> usage: /opt/bio/wgs-8.3rc1/Linux-amd64/bin/overlapStoreBuild -o
> asm.ovlStore -g asm.gkpStore [opts] [-L fileList | *.ovb.gz]
>   -o asm.ovlStore       path to store to create
>   -g asm.gkpStore       path to gkpStore for this assembly
>
>   -F f                  use up to 'f' files for store creation
>   -M m                  use up to 'm' MB memory for store creation
>
>   -plc t                type of filtering for PLC fragments -- NOT
> SUPPORTED
>   -obt                  filter overlaps for OBT
>   -dup                  filter overlaps for OBT/dedupe
>
>   -e e                  filter overlaps above e fraction error
>   -L fileList           read input filenames from 'flieList'
>
>   -big iid              handle a large number of overlaps in the last
> library
>                         iid is the first read iid in the last library, from
>                         'gatekeeper -dumpinfo *gkpStore'
>
> ----------------------------------------
> Failure message:
>
> failed to create the overlap store
>
>
> ------------------------------------------------------------------------------
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