[maker-devel] Errors with Blast engine and Fasta index

[Carson Holt]

It can also be that your temporary directory became full at one point or you set TMP= to a location that is not a local disk (i.e. set it to a network mounted storage location). The fasta index is based off of BerkleyDB which has issues if run of of network storage. In any case just restart, and it will probably get past the error on the retry.

—Carson



> On Aug 23, 2017, at 10:57 AM, Ence,daniel <d.ence at ufl.edu> wrote:
> 
> Hi Isabel, The warning is referring to an empty entry in one of the fasta files (“Warning: Sequence contains no data”). This is probably in the genome fasta file that you are trying to annotate. Can you check the fasta entry “NODE_1_length_465927_cov_94.9908”? 
> 
> ~Daniel
> 
> 
> 
>> On Aug 23, 2017, at 12:29 PM, Isabel Marcelino <isabel.marcelino.im at gmail.com <mailto:isabel.marcelino.im at gmail.com>> wrote:
>> 
>> 
>> ---------- Forwarded message ----------
>> From: Isabel Marcelino <isabel.marcelino.im at gmail.com <mailto:isabel.marcelino.im at gmail.com>>
>> Date: 23 August 2017 at 11:37
>> Subject: Errors with Blast engine and Fasta index
>> To: maker-devel at googlegroups.com <mailto:maker-devel at googlegroups.com>
>> 
>> 
>> Hello,
>> 
>> I am new to linux and bioinformatics but I managed to set MAKER (v2.31.9) running smoothly a few weeks ago and I could perform a de novo annotation of one of my genome. In the meantime, I worked on other topics and, yesterday, when I tried to annotate another genome, MAKER was not working. 
>> The following message was appearing:
>> 
>> BLAST engine error: Warning: Sequence contains no data 
>> deleted:0 hits
>> stop here: NODE_1_length_465927_cov_94.9908
>> ERROR: Fasta index error
>> at /home/administrateur/results/Isa/ANNOTATION/MAKER_running_tools/RUN_MAKER/bin/../lib/Process/MpiChunk.pm line 1095.
>>         Process::MpiChunk::__ANON__() called at /home/administrateur/results/Isa/ANNOTATION/MAKER_running_tools/RUN_MAKER/bin/../lib/Error.pm line 415
>>         eval {...} called at /home/administrateur/results/Isa/ANNOTATION/MAKER_running_tools/RUN_MAKER/bin/../lib/Error.pm line 407
>>         Error::subs::try('CODE(0x4cd5320)', 'HASH(0x4cd53f8)') called at /home/administrateur/results/Isa/ANNOTATION/MAKER_running_tools/RUN_MAKER/bin/../lib/Process/MpiChunk.pm line 4224
>>         Process::MpiChunk::_go('Process::MpiChunk=HASH(0x4cfae20)', 'run', 'HASH(0x4cca458)', 3, 0) called at /home/administrateur/results/Isa/ANNOTATION/MAKER_running_tools/RUN_MAKER/bin/../lib/Process/MpiChunk.pm line 341
>>         Process::MpiChunk::run('Process::MpiChunk=HASH(0x4cfae20)', 2) called at ../../bin/maker line 1614
>>         main::run('ARRAY(0x4af3e68)', 2) called at ../../bin/maker line 999
>> --> rank=2, hostname=SRV-WGS
>> ERROR: Failed while preparing masked sequence
>> ERROR: Chunk failed at level:3, tier_type:0
>> FAILED CONTIG:NODE_1_length_465927_cov_94.9908
>> 
>> I tried to solve the problem (re-install Repeatmasker and blast, check location of the several executables, check tmp folder, re-install MAKER, etc) but still, I am not able to solve the problem.
>> Could you please help me out with this? Thank you so much.
>> 
>> Cheers,
>> Isabel 
>> 
>> *************************************************
>> Isabel MARCELINO, PhD
>> Unité Environnement Santé
>> Institut Pasteur de Guadeloupe
>> Morne Jolivière - B.P. 484
>> 97183 LES ABYMES Cedex
>> Guadeloupe, FWI
>> 
>> 
>> 
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