Hi Daniel,<br>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>Isabel<br><br>(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><br> (>NODE_1_length_465927_cov_94.9908<br>ACAAATCAATGTCGTTCAATTCAACATTTTCGATATGAGAACATTAAACAATTCAACATA<br>ATCGAGCAGAATTGATTTTCTCAACAATTTCTTATCAATTTTGCTCGAAAAAATCGATTT<br>CCACATGGTAAAAGCAACGCAACATCGATTCACAAACGATGAAAGACGAGTTTTCAAACA<br>AAAAACAGGTGTCCAAATATCTCAAAAACTAAGACCATATATCCAAGGTCAAAAATTAGC<br>CCCAGAACAAATTGAGTTCATTAAATTGGTGTGTGGAAAGTATGGAGAGTGTGTTTTGGC<br>AAAGCCCATACTCTCCTGACTTCAATCCCATTGAATTGCTTTTCGGATGGATGAAAACAC<br>AGTTGAAAAACTATGAACATTCGGTTGACTCTCTCGAAGAGATAATGGAGCAGGTGTTTG<br>ATCAAGTTACACCCAAGTTAATCAAATCGTTTGTTCATCATTGCAAGGAAATCTGGCATG<br>ATGAGACAAAAACTTAATAAATTTCGAGTTTGATCGAAATCGATTTTGAAGGATTTCGAT<br>GTTAATCAACATCAAGTCAAAACGACAACGCATCAATGTCGCTCATTTCGATC.....)<br><br><br>On Wednesday, 23 August 2017 12:58:21 UTC-4, Ence,daniel wrote:<blockquote class="gmail_quote" style="margin: 0;margin-left: 0.8ex;border-left: 1px #ccc solid;padding-left: 1ex;">
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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>9908”?
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<div>~Daniel<br>
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<div>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;">isabel.ma...@gmail.com</a><wbr>> wrote:</div>
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<div class="gmail_quote">---------- Forwarded message ----------<br>
From: <b class="gmail_sendername">Isabel Marcelino</b> <span dir="ltr"><<a href="javascript:" target="_blank" gdf-obfuscated-mailto="40Fw3XjPCAAJ" rel="nofollow" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;">isabel.ma...@gmail.com</a><wbr>></span><br>
Date: 23 August 2017 at 11:37<br>
Subject: Errors with Blast engine and Fasta index<br>
To: <a href="javascript:" target="_blank" gdf-obfuscated-mailto="40Fw3XjPCAAJ" rel="nofollow" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;">maker...@googlegroups.com</a><br>
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<br>
<div dir="ltr">Hello,<br>
<br>
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>
The following message was appearing:<br>
<br>
BLAST engine error: Warning: Sequence contains no data <br>
deleted:0 hits<br>
stop here: NODE_1_length_465927_cov_94.<wbr>9908<br>
ERROR: Fasta index error<br>
at /home/administrateur/results/<wbr>Isa/ANNOTATION/MAKER_running_<wbr>tools/RUN_MAKER/bin/../lib/<wbr>Process/MpiChunk.pm line 1095.<br>
Process::MpiChunk::__ANON__() called at /home/administrateur/results/<wbr>Isa/ANNOTATION/MAKER_running_<wbr>tools/RUN_MAKER/bin/../lib/<wbr>Error.pm line 415<br>
eval {...} called at /home/administrateur/results/<wbr>Isa/ANNOTATION/MAKER_running_<wbr>tools/RUN_MAKER/bin/../lib/<wbr>Error.pm line 407<br>
Error::subs::try('CODE(<wbr>0x4cd5320)', 'HASH(0x4cd53f8)') called at /home/administrateur/results/<wbr>Isa/ANNOTATION/MAKER_running_<wbr>tools/RUN_MAKER/bin/../lib/<wbr>Process/MpiChunk.pm line 4224<br>
Process::MpiChunk::_go('<wbr>Process::MpiChunk=HASH(<wbr>0x4cfae20)', 'run', 'HASH(0x4cca458)', 3, 0) called at /home/administrateur/results/<wbr>Isa/ANNOTATION/MAKER_running_<wbr>tools/RUN_MAKER/bin/../lib/<wbr>Process/MpiChunk.pm
line 341<br>
Process::MpiChunk::run('<wbr>Process::MpiChunk=HASH(<wbr>0x4cfae20)', 2) called at ../../bin/maker line 1614<br>
main::run('ARRAY(0x4af3e68)', 2) called at ../../bin/maker line 999<br>
--> rank=2, hostname=SRV-WGS<br>
ERROR: Failed while preparing masked sequence<br>
ERROR: Chunk failed at level:3, tier_type:0<br>
FAILED CONTIG:NODE_1_length_465927_<wbr>cov_94.9908<br>
<br>
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>
Could you please help me out with this? Thank you so much.<br>
<br>
Cheers,<br>
Isabel <br>
<br>
******************************<wbr>*******************<br>
Isabel MARCELINO, PhD<br>
Unité Environnement Santé<br>
Institut Pasteur de Guadeloupe<br>
Morne Jolivière - B.P. 484<br>
97183 LES ABYMES Cedex<br>
Guadeloupe, FWI<br>
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