[maker-devel] maker problem

[Fields, Christopher J]

On Jul 18, 2016, at 10:03 AM, Carson Holt <carsonhh at gmail.com<mailto:carsonhh at gmail.com>> wrote:

1. Make sure you are using the current CPAN version of BioPerl, and not BioPerl live.

Just curious, is there anything broken w/ bioperl-live we need to know about?  We’re about to release BioPerl v1.7.0 (I’m already on RC5), it would be nice to know if we’re missing anything that would potentially break downstream applications.

chris

2. Try installing a different version of BLAST incase the BLAST report is somehow not created correctly.
3. Make sure  TMP= in the maker_opts.ctl file is not set to a network mounted disk

—Carson


On Jul 18, 2016, at 9:00 AM, Chuanlin Yin <yincl2013 at 126.com<mailto:yincl2013 at 126.com>> wrote:

Thank you very much!

I know the error is saying that there is a hit with no HSPs, but why other scaffolds are all OK except that one. I have checked that scaffold for many times and the format is correct.

Thanks!

Best wishes!
Ian

2016-07-18
________________________________
Chuanlin Yin
________________________________
发件人：Carson Holt <carsonhh at gmail.com<mailto:carsonhh at gmail.com>>
发送时间：2016-07-18 22:53
主题：Re: [maker-devel] maker problem
收件人："Chuanlin Yin"<yincl2013 at 126.com<mailto:yincl2013 at 126.com>>
抄送："maker-devel"<maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>>

The error is saying that there is a hit with no HSPs. Make sure you are using the current CPAN version of BioPerl, and not BioPerl live. Also you can try a different version of BLAST if the BLAST report is somehow not created correctly.  Finally do not set your TMP= location to a network mounted disk (on many clusters your home directory is network mounted). This will cause IO errors and partial result files. I can’t tell what your temporary directory is set to because your STDERR is truncated.

Thanks,
Carson


On Jul 13, 2016, at 4:10 AM, Chuanlin Yin <yincl2013 at 126.com<mailto:yincl2013 at 126.com>> wrote:

Hello,

When I use the maker for geomic annotation pipeline, I met a very big problem. My genome has 7282 scaffolds, all is success but for one scaffold is failed. I don‘t konw why and I have check the log, but I still can't fix the problem. So I need you help, and I will appreciate it very much.

Here is a part of main error log:
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Can't get HSPs: data not collected.
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:449
STACK: Bio::Search::Hit::PhatHit::Base::hsps /disk/home/yincl/software/maker/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm:552
STACK: Widget::blastx::keepers /disk/home/yincl/software/maker/maker/bin/../lib/Widget/blastx.pm:190
STACK: Widget::blastx::parse /disk/home/yincl/software/maker/maker/bin/../lib/Widget/blastx.pm:132
STACK: GI::blastx /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:2622
STACK: GI::blastx /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:2631
STACK: GI::reblast_merged_hits /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:445
STACK: GI::merge_resolve_hits /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:289
STACK: Process::MpiChunk::_go /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:2821
STACK: Process::MpiChunk::run /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:341
STACK: Process::MpiChunk::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:357
STACK: Process::MpiTiers::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiTiers.pm:287
STACK: Process::MpiTiers::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiTiers.pm:287
STACK: /disk/home/yincl/software/maker/maker/bin/maker:686
-----------------------------------------------------------
--> rank=NA, hostname=localhost.localdomain
--> rank=NA, hostname=localhost.localdomain
--> rank=NA, hostname=localhost.localdomain
ERROR: Failed while collecting blastx reports
ERROR: Chunk failed at level:9, tier_type:3
FAILED CONTIG:QPacbio.Hiseq_683

ERROR: Chunk failed at level:4, tier_type:0
FAILED CONTIG:QPacbio.Hiseq_683

examining contents of the fasta file and run log
Thanks!

Best regards,
Ian
Department of Entomology, College of Plant Protection, Nanjing Agricultural University
No. 1, Weigang Road, Xuanwu District, Nanjing, Jiangsu 210095, China


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