<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">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.<div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""></div><div class=""><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Aug 23, 2017, at 10:57 AM, Ence,daniel <<a href="mailto:d.ence@ufl.edu" class="">d.ence@ufl.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class="">
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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.<wbr class="">9908”?
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<div class="">~Daniel<br class="">
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<div class="">On Aug 23, 2017, at 12:29 PM, Isabel Marcelino <<a href="mailto:isabel.marcelino.im@gmail.com" class="">isabel.marcelino.im@gmail.com</a>> wrote:</div>
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<div class="gmail_quote">---------- Forwarded message ----------<br class="">
From: <b class="gmail_sendername">Isabel Marcelino</b> <span dir="ltr" class=""><<a href="mailto:isabel.marcelino.im@gmail.com" class="">isabel.marcelino.im@gmail.com</a>></span><br class="">
Date: 23 August 2017 at 11:37<br class="">
Subject: Errors with Blast engine and Fasta index<br class="">
To: <a href="mailto:maker-devel@googlegroups.com" class="">maker-devel@googlegroups.com</a><br class="">
<br class="">
<br class="">
<div dir="ltr" class="">Hello,<br class="">
<br class="">
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. <br class="">
The following message was appearing:<br class="">
<br class="">
BLAST engine error: Warning: Sequence contains no data <br class="">
deleted:0 hits<br class="">
stop here: NODE_1_length_465927_cov_94.<wbr class="">9908<br class="">
ERROR: Fasta index error<br class="">
at /home/administrateur/results/<wbr class="">Isa/ANNOTATION/MAKER_running_<wbr class="">tools/RUN_MAKER/bin/../lib/<wbr class="">Process/MpiChunk.pm line 1095.<br class="">
Process::MpiChunk::__ANON__() called at /home/administrateur/results/<wbr class="">Isa/ANNOTATION/MAKER_running_<wbr class="">tools/RUN_MAKER/bin/../lib/<wbr class="">Error.pm line 415<br class="">
eval {...} called at /home/administrateur/results/<wbr class="">Isa/ANNOTATION/MAKER_running_<wbr class="">tools/RUN_MAKER/bin/../lib/<wbr class="">Error.pm line 407<br class="">
Error::subs::try('CODE(<wbr class="">0x4cd5320)', 'HASH(0x4cd53f8)') called at /home/administrateur/results/<wbr class="">Isa/ANNOTATION/MAKER_running_<wbr class="">tools/RUN_MAKER/bin/../lib/<wbr class="">Process/MpiChunk.pm line 4224<br class="">
Process::MpiChunk::_go('<wbr class="">Process::MpiChunk=HASH(<wbr class="">0x4cfae20)', 'run', 'HASH(0x4cca458)', 3, 0) called at /home/administrateur/results/<wbr class="">Isa/ANNOTATION/MAKER_running_<wbr class="">tools/RUN_MAKER/bin/../lib/<wbr class="">Process/MpiChunk.pm
line 341<br class="">
Process::MpiChunk::run('<wbr class="">Process::MpiChunk=HASH(<wbr class="">0x4cfae20)', 2) called at ../../bin/maker line 1614<br class="">
main::run('ARRAY(0x4af3e68)', 2) called at ../../bin/maker line 999<br class="">
--> rank=2, hostname=SRV-WGS<br class="">
ERROR: Failed while preparing masked sequence<br class="">
ERROR: Chunk failed at level:3, tier_type:0<br class="">
FAILED CONTIG:NODE_1_length_465927_<wbr class="">cov_94.9908<br class="">
<br class="">
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.<br class="">
Could you please help me out with this? Thank you so much.<br class="">
<br class="">
Cheers,<br class="">
Isabel <br class="">
<br class="">
******************************<wbr class="">*******************<br class="">
Isabel MARCELINO, PhD<br class="">
Unité Environnement Santé<br class="">
Institut Pasteur de Guadeloupe<br class="">
Morne Jolivière - B.P. 484<br class="">
97183 LES ABYMES Cedex<br class="">
Guadeloupe, FWI<br class="">
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