<div dir="ltr">Thanks, you're right. I had to recompile blast from src with this flag: <span style="color:rgb(36,39,41);font-family:arial,"helvetica neue",helvetica,sans-serif;font-size:13px">-std=c++0x </span></div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Mar 14, 2017 at 10:36 AM, Carson Holt <span dir="ltr"><<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">The error itself is coming from BLAST. MAKER does provide the command used, so you can try it outside of MAKER. You can submit the files used as well as command used to the BLAST developers for them to test with.<div><br></div><div>MAKER deletes files on failure, but if you edit the …/maker/lib/GI.pm, you can stop it from deleting files.</div><div><br></div><div>Edit line 58 by setting CLEANUP => 0</div><div><br></div><div>Then you should be able to grab whatever files maker used to run blast, and copy the blast command used from STDERR.</div><span class="HOEnZb"><font color="#888888"><div><br></div><div>—Carson</div></font></span><div><div class="h5"><div><br></div><div><div><br></div><div><br><div><blockquote type="cite"><div>On Mar 14, 2017, at 11:29 AM, Marcus Naymik <<a href="mailto:mnaymik@tgen.org" target="_blank">mnaymik@tgen.org</a>> wrote:</div><br class="m_-511870372278323445Apple-interchange-newline"><div><div dir="ltr">I have now tried with multiple versions of blast (2.6 and 2.28 binaries and built from source) and get the same error:<div><br></div><div><p class="m_-511870372278323445gmail-p1"><span class="m_-511870372278323445gmail-s1">setting up GFF3 output and fasta chunks</span></p><p class="m_-511870372278323445gmail-p1"><span class="m_-511870372278323445gmail-s1">doing blastn of ESTs</span></p><p class="m_-511870372278323445gmail-p1"><span class="m_-511870372278323445gmail-s1">running blast search.</span></p><p class="m_-511870372278323445gmail-p1"><span class="m_-511870372278323445gmail-s1">#--------- command -------------#</span></p><p class="m_-511870372278323445gmail-p1"><span class="m_-511870372278323445gmail-s1">Widget::blastn:</span></p><p class="m_-511870372278323445gmail-p1"><span class="m_-511870372278323445gmail-s1">/home/mnaymik/TOOLS/ncbi-<wbr>blast-2.2.28+/bin/blastn -db /scratch/mnaymik/maker/tmp/<wbr>maker_cah</span></p><p class="m_-511870372278323445gmail-p1"><span class="m_-511870372278323445gmail-s1">#-----------------------------<wbr>--#</span></p><p class="m_-511870372278323445gmail-p1"><span class="m_-511870372278323445gmail-s1">Error: NCBI C++ Exception:</span></p><p class="m_-511870372278323445gmail-p1"><span class="m_-511870372278323445gmail-s1"> "/home/mnaymik/TOOLS/ncbi-<wbr>blast-2.2.28+-src/c++/src/<wbr>corelib/ncbiobj.cpp", line 925: Cr</span></p><p class="m_-511870372278323445gmail-p2"><span class="m_-511870372278323445gmail-s1"></span><br></p><p class="m_-511870372278323445gmail-p1"><span class="m_-511870372278323445gmail-s1">Error: NCBI C++ Exception:</span></p><p class="m_-511870372278323445gmail-p1"><span class="m_-511870372278323445gmail-s1"> "/home/mnaymik/TOOLS/ncbi-<wbr>blast-2.2.28+-src/c++/src/<wbr>corelib/ncbiobj.cpp", line 925: Cr</span></p><p class="m_-511870372278323445gmail-p2"><span class="m_-511870372278323445gmail-s1"></span><br></p><p class="m_-511870372278323445gmail-p1"><span class="m_-511870372278323445gmail-s1">examining contents of the fasta file and run log</span></p><p class="m_-511870372278323445gmail-p1"><span class="m_-511870372278323445gmail-s1">ERROR: BLASTN failed</span></p><p class="m_-511870372278323445gmail-p1"><span class="m_-511870372278323445gmail-s1">--> rank=87, hostname=pnap-pe7-s09</span></p><p class="m_-511870372278323445gmail-p1"><span class="m_-511870372278323445gmail-s1">ERROR: Failed while doing blastn of ESTs</span></p><p class="m_-511870372278323445gmail-p1"><span class="m_-511870372278323445gmail-s1">ERROR: Chunk failed at level:0, tier_type:3</span></p><p class="m_-511870372278323445gmail-p1"><span class="m_-511870372278323445gmail-s1">FAILED CONTIG:6537645</span></p><p class="m_-511870372278323445gmail-p2"><span class="m_-511870372278323445gmail-s1"></span><br></p><p class="m_-511870372278323445gmail-p1"><span class="m_-511870372278323445gmail-s1">ERROR: BLASTN failed</span></p><p class="m_-511870372278323445gmail-p1"><span class="m_-511870372278323445gmail-s1">--> rank=88, hostname=pnap-pe7-s09</span></p><p class="m_-511870372278323445gmail-p1"><span class="m_-511870372278323445gmail-s1">ERROR: Failed while doing blastn of ESTs</span></p><p class="m_-511870372278323445gmail-p1"><span class="m_-511870372278323445gmail-s1">ERROR: Chunk failed at level:0, tier_type:3</span></p><p class="m_-511870372278323445gmail-p1"><span class="m_-511870372278323445gmail-s1">FAILED CONTIG:6537659</span></p><p class="m_-511870372278323445gmail-p2"><span class="m_-511870372278323445gmail-s1"></span><br></p><p class="m_-511870372278323445gmail-p1"><span class="m_-511870372278323445gmail-s1">ERROR: Chunk failed at level:4, tier_type:0</span></p><p class="m_-511870372278323445gmail-p1"><span class="m_-511870372278323445gmail-s1">FAILED CONTIG:6537645</span></p><p class="m_-511870372278323445gmail-p2"><span class="m_-511870372278323445gmail-s1"></span><br></p><p class="m_-511870372278323445gmail-p1"><span class="m_-511870372278323445gmail-s1">ERROR: Chunk failed at level:4, tier_type:0</span></p><p class="m_-511870372278323445gmail-p1"><span class="m_-511870372278323445gmail-s1">FAILED CONTIG:6537659</span></p><p class="m_-511870372278323445gmail-p2"><span class="m_-511870372278323445gmail-s1"></span><br></p></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Mar 2, 2017 at 1:25 PM, Carson Holt <span dir="ltr"><<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">Try reinstalling blast, or upgrade to a newer version of blast.<div><br></div><div>—Carson</div><div><br></div><div><br><div><blockquote type="cite"><div><div class="m_-511870372278323445h5"><div>On Mar 2, 2017, at 1:05 PM, Marcus Naymik <<a href="mailto:mnaymik@tgen.org" target="_blank">mnaymik@tgen.org</a>> wrote:</div><br class="m_-511870372278323445m_-3896368484793307179Apple-interchange-newline"></div></div><div><div><div class="m_-511870372278323445h5"><div dir="ltr"><div>
<br class="m_-511870372278323445m_-3896368484793307179webkit-block-placeholder"></div><p class="m_-511870372278323445m_-3896368484793307179gmail-p1"><span class="m_-511870372278323445m_-3896368484793307179gmail-s1">I have maker running with MPI and I get this error over and over again for every contig. Any Ideas?</span></p><p class="m_-511870372278323445m_-3896368484793307179gmail-p1"><span class="m_-511870372278323445m_-3896368484793307179gmail-s1"><br></span></p><p class="m_-511870372278323445m_-3896368484793307179gmail-p1"><span class="m_-511870372278323445m_-3896368484793307179gmail-s1">MAKER WARNING: All old files will be erased before continuing</span></p><p class="m_-511870372278323445m_-3896368484793307179gmail-p1"><span class="m_-511870372278323445m_-3896368484793307179gmail-s1">#-----------------------------<wbr>------------------------------<wbr>----------</span></p><p class="m_-511870372278323445m_-3896368484793307179gmail-p1"><span class="m_-511870372278323445m_-3896368484793307179gmail-s1">Now starting the contig!!</span></p><p class="m_-511870372278323445m_-3896368484793307179gmail-p1"><span class="m_-511870372278323445m_-3896368484793307179gmail-s1">SeqID: 5239</span></p><p class="m_-511870372278323445m_-3896368484793307179gmail-p1"><span class="m_-511870372278323445m_-3896368484793307179gmail-s1">Length: 1395</span></p><p class="m_-511870372278323445m_-3896368484793307179gmail-p1"><span class="m_-511870372278323445m_-3896368484793307179gmail-s1">#-----------------------------<wbr>------------------------------<wbr>----------</span></p><p class="m_-511870372278323445m_-3896368484793307179gmail-p2"><span class="m_-511870372278323445m_-3896368484793307179gmail-s1"></span><br></p><p class="m_-511870372278323445m_-3896368484793307179gmail-p2"><span class="m_-511870372278323445m_-3896368484793307179gmail-s1"></span><br></p><p class="m_-511870372278323445m_-3896368484793307179gmail-p1"><span class="m_-511870372278323445m_-3896368484793307179gmail-s1">Error: NCBI C++ Exception:</span></p><p class="m_-511870372278323445m_-3896368484793307179gmail-p1"><span class="m_-511870372278323445m_-3896368484793307179gmail-s1"> "/packages/BUILDS/ncbi-blast-2<wbr>.2.28+-src/c++/src/corelib/ncb<wbr>iobj.cpp", line 925: Criti</span></p><div>
<br class="m_-511870372278323445m_-3896368484793307179webkit-block-placeholder"></div><p class="m_-511870372278323445m_-3896368484793307179gmail-p2"><span class="m_-511870372278323445m_-3896368484793307179gmail-s1"></span><br></p></div>
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