[Cg-pipeline-users] gene prediction

[kokwei <kok...@gm...>]

Hello,

I was trying to run the prediction module to get the ORF predicted from 
a bacterial genome and encountered the following error:

run_prediction: AKUtils::getBLASTGenePredictions: Reading blast results
run_prediction: Thread::Queue::enqueue: Invalid value for shared scalar 
at /usr/lib/perl5/5.8.8/Thread/Queue.pm line 90, <BLSOUT> line 78.
A thread exited while 17 threads were running at 
/usr/lib/perl5/5.8.8/Thread/Queue.pm line 90, <BLSOUT> line 78.

Can anyone help me to get through this, also included the command I used 
and part of <BLSOUT> around line 78 (labelled with bold),

run_pipeline predict  -p project1
==========================================
# BLASTP 2.2.26+
# Query: 
scaffold477.size2524_1995_1138_-_2028_891_1138_1995_ATGCGGGGCGCGGGTTGGCGCAACCCGACCCCATGCGCTAATCTTCTCCGCTGC
# Database: /share/apps/cg_pipeline/data/uniprot_sprot
# Fields: query id, subject id, % identity, alignment length, 
mismatches, gap opens, q. start, q. end, s. start, s.
# 28 hits found
scaffold477.size2524_1995_1138_-_2028_891_1138_1995_ATGCGGGGCGCGGGTTGGCGCAACCCGACCCCATGCGCTAATCTTCTCCGCTGCACATCATTT
scaffold477.size2524_1995_1138_-_2028_891_1138_1995_ATGCGGGGCGCGGGTTGGCGCAACCCGACCCCATGCGCTAATCTTCTCCGCTGCACATCATTT
scaffold477.size2524_1995_1138_-_2028_891_1138_1995_ATGCGGGGCGCGGGTTGGCGCAACCCGACCCCATGCGCTAATCTTCTCCGCTGCACATCATTT
scaffold477.size2524_1995_1138_-_2028_891_1138_1995_ATGCGGGGCGCGGGTTGGCGCAACCCGACCCCATGCGCTAATCTTCTCCGCTGCACATCATTT
scaffold477.size2524_1995_1138_-_2028_891_1138_1995_ATGCGGGGCGCGGGTTGGCGCAACCCGACCCCATGCGCTAATCTTCTCCGCTGCACATCATTT
scaffold477.size2524_1995_1138_-_2028_891_1138_1995_ATGCGGGGCGCGGGTTGGCGCAACCCGACCCCATGCGCTAATCTTCTCCGCTGCACATCATTT
scaffold477.size2524_1995_1138_-_2028_891_1138_1995_ATGCGGGGCGCGGGTTGGCGCAACCCGACCCCATGCGCTAATCTTCTCCGCTGCACATCATTT
scaffold477.size2524_1995_1138_-_2028_891_1138_1995_ATGCGGGGCGCGGGTTGGCGCAACCCGACCCCATGCGCTAATCTTCTCCGCTGCACATCATTT
scaffold477.size2524_1995_1138_-_2028_891_1138_1995_ATGCGGGGCGCGGGTTGGCGCAACCCGACCCCATGCGCTAATCTTCTCCGCTGCACATCATTT
scaffold477.size2524_1995_1138_-_2028_891_1138_1995_ATGCGGGGCGCGGGTTGGCGCAACCCGACCCCATGCGCTAATCTTCTCCGCTGCACATCATTT
scaffold477.size2524_1995_1138_-_2028_891_1138_1995_ATGCGGGGCGCGGGTTGGCGCAACCCGACCCCATGCGCTAATCTTCTCCGCTGCACATCATTT
scaffold477.size2524_1995_1138_-_2028_891_1138_1995_ATGCGGGGCGCGGGTTGGCGCAACCCGACCCCATGCGCTAATCTTCTCCGCTGCACATCATTT
scaffold477.size2524_1995_1138_-_2028_891_1138_1995_ATGCGGGGCGCGGGTTGGCGCAACCCGACCCCATGCGCTAATCTTCTCCGCTGCACATCATTT
scaffold477.size2524_1995_1138_-_2028_891_1138_1995_ATGCGGGGCGCGGGTTGGCGCAACCCGACCCCATGCGCTAATCTTCTCCGCTGCACATCATTT
scaffold477.size2524_1995_1138_-_2028_891_1138_1995_ATGCGGGGCGCGGGTTGGCGCAACCCGACCCCATGCGCTAATCTTCTCCGCTGCACATCATTT
scaffold477.size2524_1995_1138_-_2028_891_1138_1995_ATGCGGGGCGCGGGTTGGCGCAACCCGACCCCATGCGCTAATCTTCTCCGCTGCACATCATTT
scaffold477.size2524_1995_1138_-_2028_891_1138_1995_ATGCGGGGCGCGGGTTGGCGCAACCCGACCCCATGCGCTAATCTTCTCCGCTGCACATCATTT
scaffold477.size2524_1995_1138_-_2028_891_1138_1995_ATGCGGGGCGCGGGTTGGCGCAACCCGACCCCATGCGCTAATCTTCTCCGCTGCACATCATTT
scaffold477.size2524_1995_1138_-_2028_891_1138_1995_ATGCGGGGCGCGGGTTGGCGCAACCCGACCCCATGCGCTAATCTTCTCCGCTGCACATCATTT
scaffold477.size2524_1995_1138_-_2028_891_1138_1995_ATGCGGGGCGCGGGTTGGCGCAACCCGACCCCATGCGCTAATCTTCTCCGCTGCACATCATTT
scaffold477.size2524_1995_1138_-_2028_891_1138_1995_ATGCGGGGCGCGGGTTGGCGCAACCCGACCCCATGCGCTAATCTTCTCCGCTGCACATCATTT
scaffold477.size2524_1995_1138_-_2028_891_1138_1995_ATGCGGGGCGCGGGTTGGCGCAACCCGACCCCATGCGCTAATCTTCTCCGCTGCACATCATTT
scaffold477.size2524_1995_1138_-_2028_891_1138_1995_ATGCGGGGCGCGGGTTGGCGCAACCCGACCCCATGCGCTAATCTTCTCCGCTGCACATCATTT
scaffold477.size2524_1995_1138_-_2028_891_1138_1995_ATGCGGGGCGCGGGTTGGCGCAACCCGACCCCATGCGCTAATCTTCTCCGCTGCACATCATTT
scaffold477.size2524_1995_1138_-_2028_891_1138_1995_ATGCGGGGCGCGGGTTGGCGCAACCCGACCCCATGCGCTAATCTTCTCCGCTGCACATCATTT
scaffold477.size2524_1995_1138_-_2028_891_1138_1995_ATGCGGGGCGCGGGTTGGCGCAACCCGACCCCATGCGCTAATCTTCTCCGCTGCACATCATTT
scaffold477.size2524_1995_1138_-_2028_891_1138_1995_ATGCGGGGCGCGGGTTGGCGCAACCCGACCCCATGCGCTAATCTTCTCCGCTGCACATCATTT
scaffold477.size2524_1995_1138_-_2028_891_1138_1995_ATGCGGGGCGCGGGTTGGCGCAACCCGACCCCATGCGCTAATCTTCTCCGCTGCACATCATTT
*# BLASTP 2.2.26+**(line 78)*
# Query: 
scaffold477.size2524_816_58_-_915_858_58_816_ATGACGGCCTCCGATTGCCGCCCTCCACGAGCGCACGCGATGCCACACGACGATCCGACGA
# Database: /share/apps/cg_pipeline/data/uniprot_sprot
# Fields: query id, subject id, % identity, alignment length, 
mismatches, gap opens, q. start, q. end, s. start, s.
# 4 hits found
=================================

Thanks.