[maker-devel] questions on master_datastore_index.log file
Qihua Liang
qlian003 at ucr.edu
Sat Jan 6 16:09:55 MST 2018
Hi Carson,
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?
Thanks
Qihua
#--------- command -------------#
Widget::blastx:
/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
wly_5932%3BHRSCAF=6050.0 -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/D7/4
A/ScsGwly_5932%3BHRSCAF=6050//theVoid.ScsGwly_5932%3BHRSCAF=6050/0/ScsGwly_5932%3BHRSCAF=6050.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_
proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
preparing masked sequence
preparing ab-inits
running snap.
#--------- command -------------#
Widget::snap:
/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
/tmp/maker_nJDkCL/ScsGwly_5932%3BHRSCAF=6050.abinit_masked.0 > /tmp/maker_nJDkCL/ScsGwly_5932%3BHRSCAF=6050.abinit_masked.0.maker1%2Esnap%2Eh
mm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running augustus.
#--------- command -------------#
Widget::augustus:
/usr/local/augustus.2.7/bin/augustus --species=cowpea_new --UTR=off /tmp/maker_nJDkCL/ScsGwly_5932%3BHRSCAF=6050.abinit_masked.0 > /tmp/maker
_nJDkCL/ScsGwly_5932%3BHRSCAF=6050.abinit_masked.0.cowpea_new.augustus
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/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
#-------------------------------#
doing blastx repeats
re reading blast report.
/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
deleted:0 hits
doing blastx repeats
doing blastx repeats
doing blastx repeats
doing blastx repeats
doing blastx repeats
doing blastx repeats
doing blastx repeats
doing blastx repeats
doing blastx repeats
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
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
No such file or directory
at /24-2/home/qliang/0.soft/maker/bin/../lib/Dumper/GFF/GFFV3.pm line 199.
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
Process::MpiChunk::__ANON__() called at /24-2/home/qliang/0.soft/maker/bin/../lib/Error.pm line 415
eval {...} called at /24-2/home/qliang/0.soft/maker/bin/../lib/Error.pm line 407
Error::subs::try(CODE(0x502bbb0), HASH(0x5007788)) called at /24-2/home/qliang/0.soft/maker/bin/../lib/Process/MpiChunk.pm line 4269
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
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
Process::MpiTiers::__ANON__() called at /24-2/home/qliang/0.soft/maker/bin/../lib/Error.pm line 415
eval {...} called at /24-2/home/qliang/0.soft/maker/bin/../lib/Error.pm line 407
Error::subs::try(CODE(0x50a9348), HASH(0x4ff0ec0)) called at /24-2/home/qliang/0.soft/maker/bin/../lib/Process/MpiTiers.pm line 338
Process::MpiTiers::_next_level(Process::MpiTiers=HASH(0x4fb3350)) called at /24-2/home/qliang/0.soft/maker/bin/../lib/Process/MpiTiers.pm line 179
Process::MpiTiers::next_chunk(Process::MpiTiers=HASH(0x4fb3350)) called at /24-2/home/qliang/0.soft/maker/bin/../lib/Process/MpiTiers.pm line 286
Process::MpiTiers::run_all(Process::MpiTiers=HASH(0x4fb3350), 0) called at /home/qliang/0.soft/maker/bin/maker line 695
--> rank=NA, hostname=H4
ERROR: Failed while builing masking tiers
--> rank=NA, hostname=H4
--> rank=NA, hostname=H4
ERROR: Can not get next level
running genemark.
#--------- command -------------#
Widget::genemark:
/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
#-------------------------------#
FAILED CONTIG:ScsGwly_6124;HRSCAF=6247
examining contents of the fasta file and run log
--Next Contig--
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: ScsGwly_6140;HRSCAF=6263
Length: 1247
#---------------------------------------------------------------------
> On Jan 5, 2018, at 7:22 PM, Carson Holt <carsonhh at gmail.com> wrote:
>
> 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.
>
> —Carson
>
>> On Jan 4, 2018, at 2:36 PM, Qihua Liang <qlian003 at ucr.edu <mailto:qlian003 at ucr.edu>> wrote:
>>
>> Hi Ence,
>>
>> When I searched for “E/error” in the output file, here is what first showed up:
>> Process::MpiChunk::__ANON__() called at /24-2/home/qliang/0.soft/maker/bin/../lib/Error.pm line 415
>> eval {...} called at /24-2/home/qliang/0.soft/maker/bin/../lib/Error.pm line 407
>> Error::subs::try(CODE(0x502bbb0), HASH(0x5007788)) called at /24-2/home/qliang/0.soft/maker/bin/../lib/Process/MpiChunk.pm line 4269
>> 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
>> 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
>> Process::MpiTiers::__ANON__() called at /24-2/home/qliang/0.soft/maker/bin/../lib/Error.pm line 415
>> eval {...} called at /24-2/home/qliang/0.soft/maker/bin/../lib/Error.pm line 407
>> Error::subs::try(CODE(0x50a9348), HASH(0x4ff0ec0)) called at /24-2/home/qliang/0.soft/maker/bin/../lib/Process/MpiTiers.pm line 338
>> Process::MpiTiers::_next_level(Process::MpiTiers=HASH(0x4fb3350)) called at /24-2/home/qliang/0.soft/maker/bin/../lib/Process/MpiTiers.pm line 179
>>
>> Is this what you may need?
>>
>> Qihua
>>
>>> On Jan 4, 2018, at 6:16 AM, Ence,daniel <d.ence at ufl.edu <mailto:d.ence at ufl.edu>> wrote:
>>>
>>> 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.
>>>
>>> Thanks,
>>> Daniel
>>>
>>>
>>>> On Jan 3, 2018, at 8:52 PM, Qihua Liang <qlian003 at ucr.edu <mailto:qlian003 at ucr.edu>> wrote:
>>>>
>>>> Dear Maker Develop Team,
>>>>
>>>> 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.
>>>>
>>>> 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?
>>>>
>>>> Thank you so much
>>>> Qihua
>>>> _______________________________________________
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>>
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