Re: [Cg-pipeline-users] gene prediction

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

Thanks for your prompt answer.

On 10/6/2013 1:00 AM, Lee Katz wrote:
> Hi, unfortunately it looks like I added something into run_prediction 
> that isn't perl 5.8 compatible. Thank you for pointing it out. I will 
> put in some better error reporting for it.
>
> The best fix, it seems is to upgrade to something newer. I think that 
> perl 5.10 should be ok, but you will be safer with 5.12 or 5.14 (or 
> newer).
>
> Let me know if you have any other problems.
>
> On Jun 9, 2013, at 10:48, kokwei <kok...@gm... 
> <mailto:kok...@gm...>> wrote:
>
>> 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.
>>
>>
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