<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="">Hi Sangramjit,<div class=""><br class=""></div><div class="">Where the error occured means either one of your input files is not formatted correctly (i.e. not correct fasta format or not correct GFF3 format). Or the drive with your temporary directory is full (usually /tmp), and MAKER can’t write the temporary files it needs to run. Or you set the TMP= option in the control files to an NFS mounted location. Some parts of MAKER cannot run in NFS drives because of the way they handle file locks.</div><div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Apr 7, 2015, at 8:30 AM, Scott Cain <<a href="mailto:scott@scottcain.net" class="">scott@scottcain.net</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Hi Sangramjit,<div class=""><br class=""></div><div class="">I'm cc'ing the MAKER mailing list, where they should be able to help you out.</div><div class=""><br class=""></div><div class="">Scott</div><div class=""><br class=""></div></div><div class="gmail_extra"><br class=""><div class="gmail_quote">On Tue, Apr 7, 2015 at 3:57 AM, sangramjit basu <span dir="ltr" class=""><<a href="mailto:officialsjb@gmail.com" target="_blank" class="">officialsjb@gmail.com</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr" class=""><div class=""><div class=""><b class="">Hello Sir/Madam,<br class=""><br class=""></b></div><b class="">I am Bioinformatician trainee on NGS platform. I have been trying to use Maker to annotate rice genome (Oryza sativa indica), but have been facing a error that i cannot understand:<br class=""></b><br class="">setting up GFF3 output and fasta chunks<br class="">doing repeat masking<br class="">ERROR: Not a SCALAR reference<br class=""> at /opt/maker/bin/../lib/Fasta.pm line 382.<br class=""> Fasta::_formatSeq(FastaSeq=HASH(0x4219e18), 60) called at /opt/maker/bin/../lib/Fasta.pm line 369<br class=""> Fasta::toFastaRef(">1 CHUNK number:0 size:100000 offset:0", REF(0x4207be0)) called at /opt/maker/bin/../lib/FastaChunk.pm line 217<br class=""> FastaChunk::fasta_ref(FastaChunk=HASH(0x417e968)) called at /opt/maker/bin/../lib/FastaChunk.pm line 168<br class=""> FastaChunk::write_file(FastaChunk=HASH(0x417e968), "/opt/maker/Oryza_indica.ASM465v1.25.dna.chromosome.1.maker.ou"...) called at /opt/maker/bin/../lib/GI.pm line 3138<br class=""> GI::repeatmask(FastaChunk=HASH(0x417e968), "/opt/maker/Oryza_indica.ASM465v1.25.dna.chromosome.1.maker.ou"..., 1, "simple", "/opt/RepeatMasker/RepeatMasker", "", 1, runlog=HASH(0x4207cb8)) called at /opt/maker/bin/../lib/Process/MpiChunk.pm line 769<br class=""> Process::MpiChunk::__ANON__() called at /opt/maker/bin/../lib/Error.pm line 415<br class=""> eval {...} called at /opt/maker/bin/../lib/Error.pm line 407<br class=""> Error::subs::try(CODE(0x417fce0), HASH(0x4195a48)) called at /opt/maker/bin/../lib/Process/MpiChunk.pm line 4224<br class=""> Process::MpiChunk::_go(Process::MpiChunk=HASH(0x417fc80), "run", HASH(0x4208f70), 0, 1) called at /opt/maker/bin/../lib/Process/MpiChunk.pm line 341<br class=""> Process::MpiChunk::run(Process::MpiChunk=HASH(0x417fc80), 0) called at /opt/maker/bin/../lib/Process/MpiChunk.pm line 357<br class=""> Process::MpiChunk::run_all(Process::MpiChunk=HASH(0x417fc80), 0) called at /opt/maker/bin/../lib/Process/MpiTiers.pm line 287<br class=""> Process::MpiTiers::run_all(Process::MpiTiers=HASH(0x417fc20), 0) called at /opt/maker/bin/../lib/Process/MpiTiers.pm line 287<br class=""> Process::MpiTiers::run_all(Process::MpiTiers=HASH(0x4102ba8), 0) called at /opt/maker/bin/maker line 686<br class="">--> rank=NA, hostname=nucleome01-Lenovo-H520S<br class="">ERROR: Failed while doing repeat masking<br class="">ERROR: Chunk failed at level:0, tier_type:1<br class="">FAILED CONTIG:1<br class=""><br class="">ERROR: Chunk failed at level:2, tier_type:0<br class="">FAILED CONTIG:1<br class=""><br class=""></div><b class="">P.S. : I have low hard disk space, is it because of that ??</b><br class=""></div>
</blockquote></div><br class=""><br clear="all" class=""><div class=""><br class=""></div>-- <br class=""><div class="gmail_signature">------------------------------------------------------------------------<br class="">Scott Cain, Ph. D. scott at scottcain dot net<br class="">GMOD Coordinator (<a href="http://gmod.org/" class="">http://gmod.org/</a>) 216-392-3087<br class="">Ontario Institute for Cancer Research</div>
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