Error in correction pacbio data using pacBioToCA
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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?

next-gen Assembly genome sequence • 1.8k views
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