[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