<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 Carson,<div class=""><br class=""></div><div class="">I just check with the system administrator and we think the disk space should be working fine. And actually I also ran another attempt with much fewer processors days ago and I am having the same issues.</div><div class=""><br class=""></div><div class="">Maybe I will try renaming the contig names to see how the new attempt works? Or any other suggestions?</div><div class=""><br class=""></div><div class="">Thank you!</div><div class="">Qihua</div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Jan 9, 2018, at 9:14 AM, Carson Holt <<a href="mailto:carsonhh@gmail.com" class="">carsonhh@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta http-equiv="content-type" content="text/html; charset=utf-8" class=""><div dir="auto" class="">Your contig names may create issues. Specifically the ‘;’ character, but you should also remove the ‘=‘ character. However, I believe your problem may be IO. If you are running under MPI or are running multiple jobs, the disk one of the machines may have that location unmounted, it may be full, you may have hit a system file quota limit, or the IO load is slowing it is not actually finished writing the file when MAKER tries to read it. If IO load, is the issue, then you just need to run fewer processes. The other possibilities would mean you need to make space, fix the mount, or raise any quotas on your systems.<br class=""><br class=""><div class="">Thanks,</div><div class="">Carson</div><div class=""><br class="">On Jan 6, 2018, at 4:09 PM, Qihua Liang <<a href="mailto:qlian003@ucr.edu" class="">qlian003@ucr.edu</a>> wrote:<br class=""><br class=""></div><blockquote type="cite" class=""><div class=""><meta http-equiv="Content-Type" content="text/html charset=utf-8" class="">Hi Carson,<div class=""><br class=""></div><div class="">I am pasting more lines of error messages. I notice an error of "ERROR: Can't open seq file: /24-2/home/qliang/cowpea/annotation/22.dovetail.assembly/map.maker.output/map_datastore/ED/F1/ScsGwly_6124%3BHRSCAF=6247//theVoid.ScsGwly_6124%3BHRSCAF=6247/query.masked.gff.seq”, the seq name of “ScsGwly” is ">ScsGwly_6124;HRSCAF=6247”, is it because of the seq naming that makes the temp file name weird?</div><div class=""><br class=""></div><div class="">Thanks</div><div class="">Qihua</div><div class=""><br class=""></div><div class=""><div style="margin: 0px; font-size: 14px; line-height: normal; font-family: 'Andale Mono'; color: rgb(246, 255, 249); background-color: rgb(0, 0, 0);" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">#--------- command -------------#</span></div><div style="margin: 0px; font-size: 14px; line-height: normal; font-family: 'Andale Mono'; color: rgb(246, 255, 249); background-color: rgb(0, 0, 0);" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">Widget::blastx:</span></div><div style="margin: 0px; font-size: 14px; line-height: normal; font-family: 'Andale Mono'; color: rgb(246, 255, 249); background-color: rgb(0, 0, 0);" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">/24-2/home/qliang/0.soft/maker/bin/../exe/blast/bin/blastx -db /tmp/maker_nJDkCL/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nJDkCL/0/ScsG</span></div><div style="margin: 0px; font-size: 14px; line-height: normal; font-family: 'Andale Mono'; color: rgb(246, 255, 249); background-color: rgb(0, 0, 0);" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">wly_5932%3BHRSCAF=6050.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes </span></div><div style="margin: 0px; font-size: 14px; line-height: normal; font-family: 'Andale Mono'; color: rgb(246, 255, 249); background-color: rgb(0, 0, 0);" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">-soft_masking true -lcase_masking -show_gis -out /24-2/home/qliang/cowpea/annotation/22.dovetail.assembly/map.maker.output/map_datastore/D7/4</span></div><div style="margin: 0px; font-size: 14px; line-height: normal; font-family: 'Andale Mono'; color: rgb(246, 255, 249); background-color: rgb(0, 0, 0);" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">A/ScsGwly_5932%3BHRSCAF=6050//theVoid.ScsGwly_5932%3BHRSCAF=6050/0/ScsGwly_5932%3BHRSCAF=6050.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_</span></div><div style="margin: 0px; font-size: 14px; line-height: normal; font-family: 'Andale Mono'; color: rgb(246, 255, 249); background-color: rgb(0, 0, 0);" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">proteins%2Efasta.mpi.10.9.repeatrunner</span></div><div style="margin: 0px; font-size: 14px; line-height: normal; font-family: 'Andale Mono'; color: rgb(246, 255, 249); background-color: rgb(0, 0, 0);" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">#-------------------------------#</span></div><div style="margin: 0px; font-size: 14px; line-height: normal; font-family: 'Andale Mono'; color: rgb(246, 255, 249); background-color: rgb(0, 0, 0);" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">deleted:0 hits</span></div><div style="margin: 0px; font-size: 14px; line-height: normal; font-family: 'Andale Mono'; color: rgb(246, 255, 249); background-color: rgb(0, 0, 0);" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">collecting blastx repeatmasking</span></div><div style="margin: 0px; font-size: 14px; line-height: normal; font-family: 'Andale Mono'; color: rgb(246, 255, 249); background-color: rgb(0, 0, 0);" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">processing all repeats</span></div><div style="margin: 0px; font-size: 14px; line-height: normal; font-family: 'Andale Mono'; color: rgb(246, 255, 249); background-color: rgb(0, 0, 0);" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">in cluster::shadow_cluster...</span></div><div style="margin: 0px; font-size: 14px; line-height: normal; font-family: 'Andale Mono'; color: rgb(246, 255, 249); background-color: rgb(0, 0, 0);" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">...finished clustering.</span></div><div style="margin: 0px; font-size: 14px; line-height: normal; font-family: 'Andale Mono'; color: rgb(246, 255, 249); background-color: rgb(0, 0, 0);" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">preparing masked sequence</span></div><div style="margin: 0px; font-size: 14px; line-height: normal; font-family: 'Andale Mono'; color: rgb(246, 255, 249); background-color: rgb(0, 0, 0);" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">preparing ab-inits</span></div><div style="margin: 0px; font-size: 14px; line-height: normal; font-family: 'Andale Mono'; color: rgb(246, 255, 249); background-color: rgb(0, 0, 0);" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">running snap.</span></div><div style="margin: 0px; font-size: 14px; line-height: normal; font-family: 'Andale Mono'; color: rgb(246, 255, 249); background-color: rgb(0, 0, 0);" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">#--------- command -------------#</span></div><div style="margin: 0px; font-size: 14px; line-height: normal; font-family: 'Andale Mono'; color: rgb(246, 255, 249); background-color: rgb(0, 0, 0);" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">Widget::snap:</span></div><div style="margin: 0px; font-size: 14px; line-height: normal; font-family: 'Andale Mono'; color: rgb(246, 255, 249); background-color: rgb(0, 0, 0);" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">/24-2/home/qliang/0.soft/maker/exe/snap/snap /home/qliang/cowpea/annotation/09.tingting/4.Abintio/2.CEGMA/3.maker/maker1.hmm/maker1.snap.hmm </span></div><div style="margin: 0px; font-size: 14px; line-height: normal; font-family: 'Andale Mono'; color: rgb(246, 255, 249); background-color: rgb(0, 0, 0);" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">/tmp/maker_nJDkCL/ScsGwly_5932%3BHRSCAF=6050.abinit_masked.0 > /tmp/maker_nJDkCL/ScsGwly_5932%3BHRSCAF=6050.abinit_masked.0.maker1%2Esnap%2Eh</span></div><div style="margin: 0px; font-size: 14px; line-height: normal; font-family: 'Andale Mono'; color: rgb(246, 255, 249); background-color: rgb(0, 0, 0);" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">mm.snap</span></div><div style="margin: 0px; font-size: 14px; line-height: normal; font-family: 'Andale Mono'; color: rgb(246, 255, 249); background-color: rgb(0, 0, 0);" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">#-------------------------------#</span></div><div style="margin: 0px; font-size: 14px; line-height: normal; font-family: 'Andale Mono'; color: rgb(246, 255, 249); background-color: rgb(0, 0, 0);" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">scoring....decoding.10.20.30.40.50.60.70.80.90.100 done</span></div><div style="margin: 0px; font-size: 14px; line-height: normal; font-family: 'Andale Mono'; color: rgb(246, 255, 249); background-color: rgb(0, 0, 0);" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">scoring....decoding.10.20.30.40.50.60.70.80.90.100 done</span></div><div style="margin: 0px; font-size: 14px; line-height: normal; font-family: 'Andale Mono'; color: rgb(246, 255, 249); background-color: rgb(0, 0, 0);" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">running augustus.</span></div><div style="margin: 0px; font-size: 14px; line-height: normal; font-family: 'Andale Mono'; color: rgb(246, 255, 249); background-color: rgb(0, 0, 0);" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">#--------- command -------------#</span></div><div style="margin: 0px; font-size: 14px; line-height: normal; font-family: 'Andale Mono'; color: rgb(246, 255, 249); background-color: rgb(0, 0, 0);" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">Widget::augustus:</span></div><div style="margin: 0px; font-size: 14px; line-height: normal; font-family: 'Andale Mono'; color: rgb(246, 255, 249); background-color: rgb(0, 0, 0);" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">/usr/local/augustus.2.7/bin/augustus --species=cowpea_new --UTR=off /tmp/maker_nJDkCL/ScsGwly_5932%3BHRSCAF=6050.abinit_masked.0 > /tmp/maker</span></div><div style="margin: 0px; font-size: 14px; line-height: normal; font-family: 'Andale Mono'; color: rgb(246, 255, 249); background-color: rgb(0, 0, 0);" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">_nJDkCL/ScsGwly_5932%3BHRSCAF=6050.abinit_masked.0.cowpea_new.augustus</span></div><div style="margin: 0px; font-size: 14px; line-height: normal; font-family: 'Andale Mono'; color: rgb(246, 255, 249); background-color: rgb(0, 0, 0);" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">#-------------------------------#</span></div><div style="margin: 0px; font-size: 14px; line-height: normal; font-family: 'Andale Mono'; color: rgb(246, 255, 249); background-color: rgb(0, 0, 0);" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">deleted:0 hits</span></div><div style="margin: 0px; font-size: 14px; line-height: normal; font-family: 'Andale Mono'; color: rgb(246, 255, 249); background-color: rgb(0, 0, 0);" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">collecting blastx repeatmasking</span></div><div style="margin: 0px; font-size: 14px; line-height: normal; font-family: 'Andale Mono'; color: rgb(246, 255, 249); background-color: rgb(0, 0, 0);" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">processing all repeats</span></div><div style="margin: 0px; font-size: 14px; line-height: normal; font-family: 'Andale Mono'; color: rgb(246, 255, 249); background-color: rgb(0, 0, 0);" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">in cluster::shadow_cluster...</span></div><div style="margin: 0px; font-size: 14px; line-height: normal; font-family: 'Andale Mono'; color: rgb(246, 255, 249); background-color: rgb(0, 0, 0);" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">...finished clustering.</span></div></div><div style="margin: 0px; font-size: 14px; line-height: normal; font-family: 'Andale Mono'; color: rgb(246, 255, 249); background-color: rgb(0, 0, 0);" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""><div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">deleted:0 hits</span></div><div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">doing blastx repeats</span></div><div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">running blast search.</span></div><div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">#--------- command -------------#</span></div><div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">Widget::blastx:</span></div><div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">/24-2/home/qliang/0.soft/maker/bin/../exe/blast/bin/blastx -db /tmp/maker_mvdRkd/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_mvdRkd/0/chr10.75 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /24-2/home/qliang/cowpea/annotation/22.dovetail.assembly/map.maker.output/map_datastore/ED/09/chr10//theVoid.chr10/7/chr10.75.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner</span></div><div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">#-------------------------------#</span></div><div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">doing blastx repeats</span></div><div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">re reading blast report.</span></div><div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">/24-2/home/qliang/cowpea/annotation/22.dovetail.assembly/map.maker.output/map_datastore/ED/F1/ScsGwly_6124%3BHRSCAF=6247//theVoid.ScsGwly_6124%3BHRSCAF=6247/0/ScsGwly_6124%3BHRSCAF=6247.0.te_proteins%2Efasta.repeatrunner</span></div><div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">deleted:0 hits</span></div><div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">doing blastx repeats</span></div><div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">doing blastx repeats</span></div><div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">doing blastx repeats</span></div><div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">doing blastx repeats</span></div><div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">doing blastx repeats</span></div><div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">doing blastx repeats</span></div><div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">doing blastx repeats</span></div><div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">doing blastx repeats</span></div><div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">doing blastx repeats</span></div><div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">collecting blastx repeatmasking</span></div><div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">processing all repeats</span></div><div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">in cluster::shadow_cluster...</span></div><div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">...finished clustering.</span></div><div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">ERROR: Can't open seq file: /24-2/home/qliang/cowpea/annotation/22.dovetail.assembly/map.maker.output/map_datastore/ED/F1/ScsGwly_6124%3BHRSCAF=6247//theVoid.ScsGwly_6124%3BHRSCAF=6247/query.masked.gff.seq</span></div><div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">No such file or directory</span></div><div style="margin: 0px; line-height: normal; min-height: 16px;" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""></span><br class=""></div><div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> at /24-2/home/qliang/0.soft/maker/bin/../lib/Dumper/GFF/GFFV3.pm line 199.</span></div><div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> Dumper::GFF::GFFV3::finalize(Dumper::GFF::GFFV3=HASH(0x5000ab8)) called at /24-2/home/qliang/0.soft/maker/bin/../lib/Process/MpiChunk.pm line 700</span></div><div class=""><span style="font-variant-ligatures: no-common-ligatures" class=""><div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> Process::MpiChunk::__ANON__() called at /24-2/home/qliang/0.soft/maker/bin/../lib/</span><span style="font-variant-ligatures: no-common-ligatures; background-color: rgb(246, 255, 249);" class="">Error</span><span style="font-variant-ligatures: no-common-ligatures" class="">.pm line 415</span></div><div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> eval {...} called at /24-2/home/qliang/0.soft/maker/bin/../lib/</span><span style="font-variant-ligatures: no-common-ligatures; background-color: rgb(246, 255, 249);" class="">Error</span><span style="font-variant-ligatures: no-common-ligatures" class="">.pm line 407</span></div><div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> </span><span style="font-variant-ligatures: no-common-ligatures; background-color: rgb(246, 255, 249);" class="">Error</span><span style="font-variant-ligatures: no-common-ligatures" class="">::subs::try(CODE(0x502bbb0), HASH(0x5007788)) called at /24-2/home/qliang/0.soft/maker/bin/../lib/Process/MpiChunk.pm line 4269</span></div><div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> Process::MpiChunk::_go(Process::MpiChunk=HASH(0x50a1a18), "flow", HASH(0x50ad0f0), 2, 0) called at /24-2/home/qliang/0.soft/maker/bin/../lib/Process/MpiChunk.pm line 378</span></div><div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> Process::MpiChunk::_flow(Process::MpiChunk=HASH(0x50a1a18), HASH(0x50ad0f0), 2, 0, Process::MpiTiers=HASH(0x4fb3350)) called at /24-2/home/qliang/0.soft/maker/bin/../lib/Process/MpiTiers.pm line 318</span></div><div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> Process::MpiTiers::__ANON__() called at /24-2/home/qliang/0.soft/maker/bin/../lib/</span><span style="font-variant-ligatures: no-common-ligatures; background-color: rgb(246, 255, 249);" class="">Error</span><span style="font-variant-ligatures: no-common-ligatures" class="">.pm line 415</span></div><div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> eval {...} called at /24-2/home/qliang/0.soft/maker/bin/../lib/</span><span style="font-variant-ligatures: no-common-ligatures; background-color: rgb(246, 255, 249);" class="">Error</span><span style="font-variant-ligatures: no-common-ligatures" class="">.pm line 407</span></div><div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> </span><span style="font-variant-ligatures: no-common-ligatures; background-color: rgb(246, 255, 249);" class="">Error</span><span style="font-variant-ligatures: no-common-ligatures" class="">::subs::try(CODE(0x50a9348), HASH(0x4ff0ec0)) called at /24-2/home/qliang/0.soft/maker/bin/../lib/Process/MpiTiers.pm line 338</span></div><div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> Process::MpiTiers::_next_level(Process::MpiTiers=HASH(0x4fb3350)) called at /24-2/home/qliang/0.soft/maker/bin/../lib/Process/MpiTiers.pm line 179</span></div><div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> Process::MpiTiers::next_chunk(Process::MpiTiers=HASH(0x4fb3350)) called at /24-2/home/qliang/0.soft/maker/bin/../lib/Process/MpiTiers.pm line 286</span></div><div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> Process::MpiTiers::run_all(Process::MpiTiers=HASH(0x4fb3350), 0) called at /home/qliang/0.soft/maker/bin/maker line 695</span></div><div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">--> rank=NA, hostname=H4</span></div><div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">ERROR: Failed while builing masking tiers</span></div><div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">--> rank=NA, hostname=H4</span></div><div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">--> rank=NA, hostname=H4</span></div><div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">ERROR: Can not get next level</span></div><div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">running genemark.</span></div><div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">#--------- command -------------#</span></div><div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">Widget::genemark:</span></div><div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">/24-2/home/qliang/0.soft/PerlPackages/ActivePerl-5.22/bin/perl-static /24-2/home/qliang/0.soft/maker/bin/../lib/Widget/genemark/gmhmm_wrap -m /home/qliang/cowpea/annotation/05.CEGMA/2.genemask/output/gmhmm.mod -g /24-2/home/qliang/0.soft/makerPackages/gm_et_linux_64/gmes_petap/gmhmme3 -p /24-2/home/qliang/0.soft/makerPackages/gm_et_linux_64/gmes_petap/probuild -o /tmp/maker_nJDkCL/ScsGwly_5932%3BHRSCAF=6050.abinit_nomask.0.gmhmm%2Emod.genemark /tmp/maker_nJDkCL/ScsGwly_5932%3BHRSCAF=6050.abinit_nomask.0</span></div><div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">#-------------------------------#</span></div><div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">FAILED CONTIG:ScsGwly_6124;HRSCAF=6247</span></div><div style="margin: 0px; line-height: normal; min-height: 16px;" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""></span><br class=""></div><div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">examining contents of the fasta file and run log</span></div><div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""><div style="margin: 0px; line-height: normal; min-height: 16px;" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""></span><br class=""></div><div style="margin: 0px; line-height: normal; min-height: 16px;" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""></span><br class=""></div><div style="margin: 0px; line-height: normal; min-height: 16px;" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""></span><br class=""></div><div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">--Next Contig--</span></div><div style="margin: 0px; line-height: normal; min-height: 16px;" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""></span><br class=""></div><div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">#---------------------------------------------------------------------</span></div><div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">Now starting the contig!!</span></div><div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">SeqID: ScsGwly_6140;HRSCAF=6263</span></div><div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">Length: 1247</span></div><div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">#---------------------------------------------------------------------</span></div><div style="margin: 0px; line-height: normal; min-height: 16px;" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""></span><br class=""></div></span></div></span></div></span></div><div class=""><span style="font-variant-ligatures: no-common-ligatures" class=""><br class=""></span></div><div class=""><br class=""></div><div class=""><br class=""><div class=""><blockquote type="cite" class=""><div class="">On Jan 5, 2018, at 7:22 PM, Carson Holt <<a href="mailto:carsonhh@gmail.com" class="">carsonhh@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta http-equiv="Content-Type" content="text/html; charset=utf-8" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">That’s the stack trace. The error is going to be a few lines further back. It would be best to get a few hundred lines right around the area you are showing.<div class=""><br class=""></div><div class="">—Carson<br class=""><div class=""><br class=""><blockquote type="cite" class=""><div class="">On Jan 4, 2018, at 2:36 PM, Qihua Liang <<a href="mailto:qlian003@ucr.edu" class="">qlian003@ucr.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta http-equiv="Content-Type" content="text/html charset=utf-8" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi Ence,<div class=""><br class=""></div><div class="">When I searched for “E/error” in the output file, here is what first showed up:</div><div class=""><div style="margin: 0px; font-size: 14px; line-height: normal; font-family: 'Andale Mono'; color: rgb(246, 255, 249); background-color: rgb(0, 0, 0);" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">Process::MpiChunk::__ANON__() called at /24-2/home/qliang/0.soft/maker/bin/../lib/E</span><span style="font-variant-ligatures: no-common-ligatures; background-color: rgb(246, 255, 249);" class="">rror</span><span style="font-variant-ligatures: no-common-ligatures" class="">.pm line 415</span></div><div style="margin: 0px; font-size: 14px; line-height: normal; font-family: 'Andale Mono'; color: rgb(246, 255, 249); background-color: rgb(0, 0, 0);" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> eval {...} called at /24-2/home/qliang/0.soft/maker/bin/../lib/E</span><span style="font-variant-ligatures: no-common-ligatures; background-color: rgb(246, 255, 249);" class="">rror</span><span style="font-variant-ligatures: no-common-ligatures" class="">.pm line 407</span></div><div style="margin: 0px; font-size: 14px; line-height: normal; font-family: 'Andale Mono'; color: rgb(246, 255, 249); background-color: rgb(0, 0, 0);" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> E</span><span style="font-variant-ligatures: no-common-ligatures; background-color: rgb(246, 255, 249);" class="">rror</span><span style="font-variant-ligatures: no-common-ligatures" class="">::subs::try(CODE(0x502bbb0), HASH(0x5007788)) called at /24-2/home/qliang/0.soft/maker/bin/../lib/Process/MpiChunk.pm line 4269</span></div><div style="margin: 0px; font-size: 14px; line-height: normal; font-family: 'Andale Mono'; color: rgb(246, 255, 249); background-color: rgb(0, 0, 0);" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> Process::MpiChunk::_go(Process::MpiChunk=HASH(0x50a1a18), "flow", HASH(0x50ad0f0), 2, 0) called at /24-2/home/qliang/0.soft/maker/bin/../lib/Process/MpiChunk.pm line 378</span></div><div style="margin: 0px; font-size: 14px; line-height: normal; font-family: 'Andale Mono'; color: rgb(246, 255, 249); background-color: rgb(0, 0, 0);" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> Process::MpiChunk::_flow(Process::MpiChunk=HASH(0x50a1a18), HASH(0x50ad0f0), 2, 0, Process::MpiTiers=HASH(0x4fb3350)) called at /24-2/home/qliang/0.soft/maker/bin/../lib/Process/MpiTiers.pm line 318</span></div><div style="margin: 0px; font-size: 14px; line-height: normal; font-family: 'Andale Mono'; color: rgb(246, 255, 249); background-color: rgb(0, 0, 0);" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> Process::MpiTiers::__ANON__() called at /24-2/home/qliang/0.soft/maker/bin/../lib/E</span><span style="font-variant-ligatures: no-common-ligatures; background-color: rgb(246, 255, 249);" class="">rror</span><span style="font-variant-ligatures: no-common-ligatures" class="">.pm line 415</span></div><div style="margin: 0px; font-size: 14px; line-height: normal; font-family: 'Andale Mono'; color: rgb(246, 255, 249); background-color: rgb(0, 0, 0);" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> eval {...} called at /24-2/home/qliang/0.soft/maker/bin/../lib/E</span><span style="font-variant-ligatures: no-common-ligatures; background-color: rgb(246, 255, 249);" class="">rror</span><span style="font-variant-ligatures: no-common-ligatures" class="">.pm line 407</span></div><div style="margin: 0px; font-size: 14px; line-height: normal; font-family: 'Andale Mono'; color: rgb(246, 255, 249); background-color: rgb(0, 0, 0);" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> E</span><span style="font-variant-ligatures: no-common-ligatures; background-color: rgb(246, 255, 249);" class="">rror</span><span style="font-variant-ligatures: no-common-ligatures" class="">::subs::try(CODE(0x50a9348), HASH(0x4ff0ec0)) called at /24-2/home/qliang/0.soft/maker/bin/../lib/Process/MpiTiers.pm line 338</span></div><div style="margin: 0px; font-size: 14px; line-height: normal; font-family: 'Andale Mono'; color: rgb(246, 255, 249); background-color: rgb(0, 0, 0);" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> Process::MpiTiers::_next_level(Process::MpiTiers=HASH(0x4fb3350)) called at /24-2/home/qliang/0.soft/maker/bin/../lib/Process/MpiTiers.pm line 179</span></div></div><div class=""><span style="font-variant-ligatures: no-common-ligatures" class=""><br class=""></span></div><div class="">Is this what you may need?</div><div class=""><br class=""></div><div class="">Qihua</div><div class=""><br class=""><div class=""><blockquote type="cite" class=""><div class="">On Jan 4, 2018, at 6:16 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=""><div class="">Hi, Before we can give any help to debug it, we need the error messages. These should be in the same file that the “maker is finished” message is in. Look for the first error message (the one closest to the top of the file) and send that to the mailing list. <br class=""><br class="">Thanks,<br class="">Daniel <br class=""><br class=""><br class=""><blockquote type="cite" class="">On Jan 3, 2018, at 8:52 PM, Qihua Liang <<a href="mailto:qlian003@ucr.edu" class="">qlian003@ucr.edu</a>> wrote:<br class=""><br class="">Dear Maker Develop Team,<br class=""><br class="">I have successfully run Maker for several times before. But I came across a strange thing days ago when I ran Maker again on a different assembly with the same input files and settings.<br class=""><br class="">I saw the message of "Maker is now finished!!!” but got empty GFF3 and no fasta files. And then I checked the master_datastore_index.log and realized that there are a lot of “failed”s and “retry”s and “failed” again. What does this mean? Since I used same inputs as previous successful runs, could you provide some instructions on how to debug and solve it?<br class=""><br class="">Thank you so much<br class="">Qihua<br class="">_______________________________________________<br class="">maker-devel mailing list<br class=""><a href="mailto:maker-devel@box290.bluehost.com" class="">maker-devel@box290.bluehost.com</a><br class=""><a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__box290.bluehost.com_mailman_listinfo_maker-2Ddevel-5Fyandell-2Dlab.org&d=DwIGaQ&c=pZJPUDQ3SB9JplYbifm4nt2lEVG5pWx2KikqINpWlZM&r=12jzlNvGVD0AlPJ4E7cTlw1Dvu6n9cb4kMCobJ28XPs&m=nUDCP_0kFOhDYlTHgOpWtf_zdL77aQFeQwYOGIQwP8c&s=9Z4T1hdtxOyIjpn6f70qhrQRuGsZxXdV-oLSJF1zGkY&e=" class="">https://urldefense.proofpoint.com/v2/url?u=http-3A__box290.bluehost.com_mailman_listinfo_maker-2Ddevel-5Fyandell-2Dlab.org&d=DwIGaQ&c=pZJPUDQ3SB9JplYbifm4nt2lEVG5pWx2KikqINpWlZM&r=12jzlNvGVD0AlPJ4E7cTlw1Dvu6n9cb4kMCobJ28XPs&m=nUDCP_0kFOhDYlTHgOpWtf_zdL77aQFeQwYOGIQwP8c&s=9Z4T1hdtxOyIjpn6f70qhrQRuGsZxXdV-oLSJF1zGkY&e=</a> <br class=""></blockquote><br class=""></div></div></blockquote></div><br class=""></div></div>_______________________________________________<br class="">maker-devel mailing list<br class=""><a href="mailto:maker-devel@box290.bluehost.com" class="">maker-devel@box290.bluehost.com</a><br class=""><a href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org" class="">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org</a><br class=""></div></blockquote></div><br class=""></div></div></div></blockquote></div><br class=""></div></div></blockquote></div></div></blockquote></div><br class=""></div></body></html>