Menu
▾
▴
cg-pipeline-users
|
From: kokwei <kok...@gm...> - 2013-06-09 14:48:53
|
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. |
|
From: Lee K. <ls...@gm...> - 2013-06-09 17:00:41
|
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...> 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. ------------------------------------------------------------------------------ How ServiceNow helps IT people transform IT departments: 1. A cloud service to automate IT design, transition and operations 2. Dashboards that offer high-level views of enterprise services 3. A single system of record for all IT processes http://p.sf.net/sfu/servicenow-d2d-j _______________________________________________ Cg-pipeline-users mailing list Cg-...@li... https://lists.sourceforge.net/lists/listinfo/cg-pipeline-users |
|
From: kokwei <kok...@gm...> - 2013-06-10 06:24:34
|
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. >> >> >> ------------------------------------------------------------------------------ >> How ServiceNow helps IT people transform IT departments: >> 1. A cloud service to automate IT design, transition and operations >> 2. Dashboards that offer high-level views of enterprise services >> 3. A single system of record for all IT processes >> http://p.sf.net/sfu/servicenow-d2d-j >> _______________________________________________ >> Cg-pipeline-users mailing list >> Cg-...@li... >> <mailto:Cg-...@li...> >> https://lists.sourceforge.net/lists/listinfo/cg-pipeline-users |
×
Want the latest updates on software, tech news, and AI?
Get latest updates about software, tech news, and AI from SourceForge directly in your inbox once a month.
Thanks for helping keep SourceForge clean.
X