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Hi Isabel, if the issue isn’t with the fasta file itself, then I would look into the things that Carson suggested: out of memory issues on the disk where the TMP directory is located, etc.
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<div class="">~Daniel</div>
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<div class="">On Aug 23, 2017, at 1:38 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="">Hi Daniel,<br class="">
Thank you for your feedback. In fact, my fasta entry is not empty (please see below). I even tried to reprocess the genome fasta file that I already processed using MAKER and it doesn't work either...<br class="">
Isabel<br class="">
<br class="">
(PS: I do not manage to "reply" your message but only "forward" it. I was wondering if there are any settings I should change? I participate in other google groups and I can "reply" to messages. Thanks for the help)<br class="">
<br class="">
(>NODE_1_length_465927_cov_94.9908<br class="">
ACAAATCAATGTCGTTCAATTCAACATTTTCGATATGAGAACATTAAACAATTCAACATA<br class="">
ATCGAGCAGAATTGATTTTCTCAACAATTTCTTATCAATTTTGCTCGAAAAAATCGATTT<br class="">
CCACATGGTAAAAGCAACGCAACATCGATTCACAAACGATGAAAGACGAGTTTTCAAACA<br class="">
AAAAACAGGTGTCCAAATATCTCAAAAACTAAGACCATATATCCAAGGTCAAAAATTAGC<br class="">
CCCAGAACAAATTGAGTTCATTAAATTGGTGTGTGGAAAGTATGGAGAGTGTGTTTTGGC<br class="">
AAAGCCCATACTCTCCTGACTTCAATCCCATTGAATTGCTTTTCGGATGGATGAAAACAC<br class="">
AGTTGAAAAACTATGAACATTCGGTTGACTCTCTCGAAGAGATAATGGAGCAGGTGTTTG<br class="">
ATCAAGTTACACCCAAGTTAATCAAATCGTTTGTTCATCATTGCAAGGAAATCTGGCATG<br class="">
ATGAGACAAAAACTTAATAAATTTCGAGTTTGATCGAAATCGATTTTGAAGGATTTCGAT<br class="">
GTTAATCAACATCAAGTCAAAACGACAACGCATCAATGTCGCTCATTTCGATC.....)<br class="">
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<br class="">
On Wednesday, 23 August 2017 12:58:21 UTC-4, Ence,daniel wrote:
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<div style="word-wrap:break-word" class="">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="javascript:" target="_blank" gdf-obfuscated-mailto="40Fw3XjPCAAJ" rel="nofollow" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;" class="">isabel.ma...@gmail.com</a><wbr class="">>
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="javascript:" target="_blank" gdf-obfuscated-mailto="40Fw3XjPCAAJ" rel="nofollow" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;" class="">isabel.ma...@gmail.com</a><wbr class="">></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="javascript:" target="_blank" gdf-obfuscated-mailto="40Fw3XjPCAAJ" rel="nofollow" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;" class="">
maker...@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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