Entering edit mode
8.7 years ago
Medhat
9.7k
Using this command
./pacBioToCA -length 500 -partitions 200 -l rice_pacbio -t 10 -s ./pacbio.spec -fastq ~/rice/rice_pacbio.fa_0001.fastq ~/rice/rice.frg > run.log.`date +%F` 2>&1
version wgs-8.3rc2
I have this error;
ERROR: Failed with signal ABRT (6)
================================================================================
runCA failed.
----------------------------------------
Stack trace:
at /home/medhat/source/wgs-8.3rc2/wgs-8.3rc2/Linux-amd64/bin/runCA line 1628.
main::caFailure('scaffolder failed', '/data/test_data_from_server_maize/pbcr/rice/rice_pacbio/6-clo...') called at /home/medhat/source/wgs-8.3rc2/wgs-8.3rc2/Linux-amd64/bin/runCA line 5044
main::CGW('6-clonesize', undef, '/data/test_data_from_server_maize/pbcr/rice/rice_pacbio/6-clo...', 2, undef, 0) called at /home/medhat/source/wgs-8.3rc2/wgs-8.3rc2/Linux-amd64/bin/runCA line 5255
main::scaffolder() called at /home/medhat/source/wgs-8.3rc2/wgs-8.3rc2/Linux-amd64/bin/runCA line 6260`
----------------------------------------
Last few lines of the relevant log file (/data/test_data_from_server_maize/pbcr/rice/rice_pacbio/6-clonesize/cgw.out
):
ERROR: Frag 299012 has null cid or CIid. Fragment is not in an input unitig!
ERROR: Frag 299044 has null cid or CIid. Fragment is not in an input unitig!
ERROR: Frag 299095 has null cid or CIid. Fragment is not in an input unitig!
ERROR: Frag 299097 has null cid or CIid. Fragment is not in an input unitig!
..
..
..
..
GDB:
Aborted (core dumped)
----------------------------------------
Failure message:
scaffolder failed
Any idea?