[maker-devel] Strange error at blastn step
Daniel Standage
daniel.standage at gmail.com
Mon Oct 29 07:39:05 MDT 2012
Carson,
I was able to run the first svn update before the test job ran, but I
didn't get the message about this second update until after it has already
executed and failed. I got about 372 lines of such.
STATUS: Parsing control files...
STATUS: Processing and indexing input FASTA files...
STATUS: Setting up database for any GFF3 input...
A data structure will be created for you at:
/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/DELETEME.maker.pdom.1.mason.maker.output/DELETEME.maker.pdom.1.mason_datastore
To access files for individual sequences use the datastore index:
/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/DELETEME.maker.pdom.1.mason.maker.output/DELETEME.maker.pdom.1.mason_master_datastore_index.log
STATUS: Now running MAKER...
WARNING: Cannot find >scaffold_0, trying to re-index the fasta.
stop here: scaffold_0
ERROR: Fasta index error
at
/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm
line 239.
Process::MpiChunk::_prepare('Process::MpiChunk=HASH(0x3c8b300)',
'HASH(0x3c80820)', 0) called at
/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm
line 73
Process::MpiTiers::__ANON__() called at
/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Error.pm line 415
eval {...} called at
/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Error.pm line 407
Error::subs::try('CODE(0x3c808b0)', 'HASH(0x3c8ec40)') called at
/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm
line 79
Process::MpiTiers::_prepare('Process::MpiTiers=HASH(0x3c71f30)')
called at
/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm
line 56
Process::MpiTiers::new('Process::MpiTiers', 'HASH(0x3c80640)', 0,
'Process::MpiChunk') called at
/N/u/dstandag/Mason/local/src/maker-dev/bin/maker line 627
--> rank=NA, hostname=c4
ERROR: Failed in tier preparation
WARNING: You must always set a rank before running MpiTiers
FATAL: argument `seq_id` does not exist in MpiTier object
at
/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm
line 86.
Process::MpiChunk::_initialize_vars('Process::MpiChunk=HASH(0x3cc93d0)',
'HASH(0x3cc9400)') called at
/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm
line 47
Process::MpiChunk::new('Process::MpiChunk', 'HASH(0x3c80820)', 0,
0) called at
/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm
line 407
Process::MpiChunk::__ANON__() called at
/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Error.pm line 415
eval {...} called at
/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Error.pm line 407
Error::subs::try('CODE(0x3c8f498)', 'HASH(0x3cc8f20)') called at
/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm
line 3811
Process::MpiChunk::_go('Process::MpiChunk=HASH(0x3c8b300)', 'load',
'HASH(0x3c80820)', 0, 0) called at
/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm
line 310
Process::MpiChunk::_loader('Process::MpiChunk=HASH(0x3c8b300)',
'HASH(0x3c80820)', 0, 0, 'Process::MpiTiers=HASH(0x3c71f30)') called at
/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm
line 364
Process::MpiTiers::__ANON__() called at
/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Error.pm line 415
eval {...} called at
/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Error.pm line 407
Error::subs::try('CODE(0x3c8f9c0)', 'HASH(0x3c8fb28)') called at
/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm
line 375
I'll try the next update and run the test again. I see a lot of references
in there to MPI, and just thought I would make it clear that although I am
running in a cluster environment, I am using the default serial version of
Maker, not the parallel MPI version.
Also, after this failed, I tried changing the TMP directory so that it was
located on the same NFS mount as the scratch disk to which the output was
written. This did not seem to have any affect, and I saw the same issues
with the EST sequences unable to be found.
--
Daniel S. Standage
Ph.D. Candidate
Bioinformatics and Computational Biology Program
Department of Genetics, Development, and Cell Biology
Iowa State University
On Fri, Oct 26, 2012 at 6:59 PM, Carson Holt <carsonhh at gmail.com> wrote:
>
>
> From: Carson Holt <carsonhh at gmail.com>
> Date: Friday, 26 October, 2012 6:10 PM
> To: Daniel Standage <daniel.standage at gmail.com>
> Cc: "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
>
> Subject: Re: [maker-devel] Strange error at blastn step
>
> I've been going over the indexing code using different scenarios and I may
> have isolated a candidate for what is causing this. Could you do one more
> 'svn update' inside the maker devel directory before running a test job?
>
> Thanks,
> Carson
>
> From: Daniel Standage <daniel.standage at gmail.com>
> Date: Friday, 26 October, 2012 2:29 PM
> To: Carson Holt <carsonhh at gmail.com>
> Cc: "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
>
> Subject: Re: [maker-devel] Strange error at blastn step
>
> Got this from the compute node. Looks like native disk space to me.
>
> [dstandag at mason ~] df /tmp
> Filesystem 1K-blocks Used Available Use% Mounted on
> /dev/sda1 478573472 12319684 441943620 3% /tmp
>
> Installing a bundle of Perl prereqs for development version, will try that
> soon.
>
> --
> Daniel S. Standage
> Ph.D. Candidate
> Bioinformatics and Computational Biology Program
> Department of Genetics, Development, and Cell Biology
> Iowa State University
>
>
>
> On Fri, Oct 26, 2012 at 2:24 PM, Carson Holt <carsonhh at gmail.com> wrote:
>
>> Ok. Try the developer release and see if it still happens.
>>
>> Thanks,
>> Carson
>>
>>
>> From: Daniel Standage <daniel.standage at gmail.com>
>> Date: Friday, 26 October, 2012 2:19 PM
>>
>> To: Carson Holt <carsonhh at gmail.com>
>> Cc: "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
>>
>> Subject: Re: [maker-devel] Strange error at blastn step
>>
>> Unfortunately, the job is no longer running and as a result I cannot
>> connect to the compute nodes as I could while it was running. On the
>> interactive node, it looks like it's real disk, although it looks like
>> there are some tmpfs mounts.
>>
>> [dstandag at mason src] df /tmp
>> Filesystem 1K-blocks Used Available Use% Mounted on
>> /dev/sdb2 462824304 180235660 259078476 42% /tmp
>> [dstandag at mason src] df
>> Filesystem 1K-blocks Used Available Use% Mounted on
>> login_x86_64 16497564 3077352 13420212 19% /
>> tmpfs 16497564 0 16497564 0% /dev/shm
>> tmpfs 10240 0 10240 0% /var/tmp
>> /dev/sdb2 462824304 180235660 259078476 42% /tmp
>> AFS 9000000 0 9000000 0% /afs
>> bl-nas1:/vol/hd00 3435973856 1775658144 1660315712 52% /N/hd00
>> bl-nas1:/vol/hd01 3435973856 1684116928 1751856928 50% /N/hd01
>> bl-nas2:/vol/hd02 3435973856 1856598656 1579375200 55% /N/hd02
>> bl-nas2:/vol/hd03 3435973856 2747626240 688347616 80% /N/hd03
>> bl-nas1:/vol/hdln 81920 3424 78496 5% /N/u
>> bl-nas2:/vol/soft 1258291200 837003424 421287776 67% /N/soft
>> bl-nas1:/vol/logs 419430400 67163328 352267072 17% /N/logs
>> ...
>> ...
>>
>> I'll see if I can launch another short job and verify this on the compute
>> nodes.
>>
>> --
>> Daniel S. Standage
>> Ph.D. Candidate
>> Bioinformatics and Computational Biology Program
>> Department of Genetics, Development, and Cell Biology
>> Iowa State University
>>
>>
>>
>> On Fri, Oct 26, 2012 at 2:14 PM, Carson Holt <carsonhh at gmail.com> wrote:
>>
>>> The command 'df /tmp' will tell you whether /tmp is a tmpfs mount
>>>
>>> Thanks,
>>> Carson
>>>
>>>
>>> From: Daniel Standage <daniel.standage at gmail.com>
>>> Date: Friday, 26 October, 2012 2:12 PM
>>> To: Carson Holt <carsonhh at gmail.com>
>>> Cc: "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
>>>
>>> Subject: Re: [maker-devel] Strange error at blastn step
>>>
>>> It looks like /tmp is indeed being used: the files I played with were
>>> under */tmp/maker_1YQF9o*.
>>>
>>> --
>>> Daniel S. Standage
>>> Ph.D. Candidate
>>> Bioinformatics and Computational Biology Program
>>> Department of Genetics, Development, and Cell Biology
>>> Iowa State University
>>>
>>>
>>>
>>> On Fri, Oct 26, 2012 at 2:09 PM, Carson Holt <carsonhh at gmail.com> wrote:
>>>
>>>> Check to see where /tmp is located? Some clusters have it set up as a
>>>> tmpfs directory and I have had problems with fasta indexes running from
>>>> tmpfs mounts in the past.
>>>>
>>>> --Carson
>>>>
>>>>
>>>> From: Daniel Standage <daniel.standage at gmail.com>
>>>> Date: Friday, 26 October, 2012 2:05 PM
>>>> To: Carson Holt <carsonhh at gmail.com>
>>>>
>>>> Subject: Re: [maker-devel] Strange error at blastn step
>>>>
>>>> The maker working directory is in a cluster environment with shared
>>>> scratch space (I'm guessing NFS-mounted). I didn't change the temp
>>>> directory setting, so it should be the local default (/tmp).
>>>>
>>>> I'll give the dev version a shot. Thanks.
>>>>
>>>> --
>>>> Daniel S. Standage
>>>> Ph.D. Candidate
>>>> Bioinformatics and Computational Biology Program
>>>> Department of Genetics, Development, and Cell Biology
>>>> Iowa State University
>>>>
>>>>
>>>>
>>>> On Fri, Oct 26, 2012 at 1:57 PM, Carson Holt <carsonhh at gmail.com>wrote:
>>>>
>>>>> Could you try this development version and tell me if the error still
>>>>> happens?
>>>>>
>>>>> Use this command to download -->
>>>>> <<blanked out from the mailing list>>
>>>>>
>>>>> Username: <<blanked out from the mailing list>>
>>>>> Password: <<blanked out from the mailing list>>
>>>>>
>>>>> Are you running in an NFS mounted directory or are you resetting TMP
>>>>> to a different location?
>>>>>
>>>>> Thanks,
>>>>> Carson
>>>>>
>>>>>
>>>>> From: Daniel Standage <daniel.standage at gmail.com>
>>>>> Date: Friday, 26 October, 2012 1:52 PM
>>>>> To: Maker Mailing List <maker-devel at yandell-lab.org>
>>>>> Subject: Re: [maker-devel] Strange error at blastn step
>>>>>
>>>>> I have since installed Maker on a different machine and tried it out.
>>>>> The test run completed successfully, but as I commenced with the full
>>>>> genome annotation, I have noticed the following error popping up frequently.
>>>>>
>>>>> formating database...
>>>>> #--------- command -------------#
>>>>> Widget::formater:
>>>>> /N/u/dstandag/Mason/local/bin/makeblastdb -dbtype prot -in
>>>>> /tmp/maker_1YQF9o/Amel3%2E2_Dmel5%2E47%2Efaa.mpi.10.8
>>>>> #-------------------------------#
>>>>> running blast search.
>>>>> #--------- command -------------#
>>>>> Widget::blastx:
>>>>> /N/u/dstandag/Mason/local/bin/blastx -db
>>>>> /tmp/maker_1YQF9o/Amel3%2E2_Dmel5%2E47%2Efaa.mpi.10.8 -query
>>>>> /tmp/maker_1YQF9o/rank0/scaffold_0.0 -num_alignments 100000
>>>>> -num_descriptions 100000 -evalue 1e-06 -dbsize 300 -searchsp 500000000
>>>>> -num_threads 16 -seg yes -soft_masking true -lcase_masking -show_gis -out
>>>>> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.1.mason.maker.output/maker.pdom.1.mason_datastore/scaffold_0/theVoid.scaffold_0/scaffold_0.0.Amel3%2E2_Dmel5%2E47%2Efaa.blastx.temp_dir/Amel3%2E2_Dmel5%2E47%2Efaa.mpi.10.8.blastx
>>>>> #-------------------------------#
>>>>> deleted:-10 hits
>>>>> formating database...
>>>>> #--------- command -------------#
>>>>> Widget::formater:
>>>>> /N/u/dstandag/Mason/local/bin/makeblastdb -dbtype prot -in
>>>>> /tmp/maker_1YQF9o/Amel3%2E2_Dmel5%2E47%2Efaa.mpi.10.9
>>>>> #-------------------------------#
>>>>> running blast search.
>>>>> #--------- command -------------#
>>>>> Widget::blastx:
>>>>> /N/u/dstandag/Mason/local/bin/blastx -db
>>>>> /tmp/maker_1YQF9o/Amel3%2E2_Dmel5%2E47%2Efaa.mpi.10.9 -query
>>>>> /tmp/maker_1YQF9o/rank0/scaffold_0.0 -num_alignments 100000
>>>>> -num_descriptions 100000 -evalue 1e-06 -dbsize 300 -searchsp 500000000
>>>>> -num_threads 16 -seg yes -soft_masking true -lcase_masking -show_gis -out
>>>>> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.1.mason.maker.output/maker.pdom.1.mason_datastore/scaffold_0/theVoid.scaffold_0/scaffold_0.0.Amel3%2E2_Dmel5%2E47%2Efaa.blastx.temp_dir/Amel3%2E2_Dmel5%2E47%2Efaa.mpi.10.9.blastx
>>>>> #-------------------------------#
>>>>> deleted:-6 hits
>>>>> WARNING: Cannot find> comp59088_c1_seq7, trying to re-index the fasta.
>>>>> stop here:comp59088_c1_seq7
>>>>> ERROR: Fasta index error
>>>>>
>>>>> FATAL ERROR
>>>>> ERROR: Failed while polishig ESTs!!
>>>>>
>>>>> ERROR: Chunk failed at level 14
>>>>> !!
>>>>> FAILED CONTIG:scaffold_0
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --Next Contig--
>>>>>
>>>>> #---------------------------------------------------------------------
>>>>> Now starting the contig!!
>>>>> SeqID: scaffold_1
>>>>> Length: 5805686
>>>>> #---------------------------------------------------------------------
>>>>>
>>>>>
>>>>> My first thought based on the message is that *blastdbcmd* could not
>>>>> find the sequence in the database. I verified this was the case--I could
>>>>> not extract sequence *comp59088_c1_seq7* from the database Maker had
>>>>> created under /tmp. However, after removing the index files and re-running
>>>>> *makeblastdb* with the *-parse_seqids* option set, *blastdbcmd* successfully
>>>>> extracted the sequence.
>>>>>
>>>>> I was initially happy with this finding, but upon closer inspection it
>>>>> looks like Maker does not use *blastdbcmd* to extract sequences, but
>>>>> rather its own internal code. Therefore I'm still not sure where the
>>>>> problem is and how I might fix it. Any insights?
>>>>>
>>>>> Thanks!
>>>>>
>>>>> --
>>>>> Daniel S. Standage
>>>>> Ph.D. Candidate
>>>>> Bioinformatics and Computational Biology Program
>>>>> Department of Genetics, Development, and Cell Biology
>>>>> Iowa State University
>>>>>
>>>>>
>>>>>
>>>>> On Thu, Oct 25, 2012 at 3:30 PM, Daniel Standage <
>>>>> daniel.standage at gmail.com> wrote:
>>>>>
>>>>>> Greetings!
>>>>>>
>>>>>> I am doing a test run of my Maker setup on a new machine, annotating
>>>>>> a pretty short contig (about 3kb). However, there seems to be a hiccup
>>>>>> during the blastn stage. This is the terminal message.
>>>>>>
>>>>>> #--------- command -------------#
>>>>>> Widget::blastn:
>>>>>> /share/home/01854/standage/local/bin/blastn -db
>>>>>> /tmp/2881473.1.development/maker_i6ZSJi/Pdom%2ETrinity%2ETrimmomatic%2Efasta.mpi.10.7
>>>>>> -query /tmp/2881473.1.development/maker_i6ZSJi/rank0/scaffold_866.0
>>>>>> -num_alignments 100000 -num_descriptions 100000 -evalue 1e-10 -gapextend 3
>>>>>> -word_size 15 -reward 1 -penalty -3 -gapopen 3 -dbsize 1000
>>>>>> -searchsp 500000000 -num_threads 16 -lcase_masking -dust yes -soft_masking
>>>>>> true -show_gis -out
>>>>>> /scratch/01854/standage/PdomGenomic/Annotation/scripts/maker.bogus.maker.output/maker.bogus_datastore/scaffold_866/theVoid.scaff
>>>>>> old_866/scaffold_866.0.Pdom%2ETrinity%2ETrimmomatic%2Efasta.blastn.temp_dir/Pdom%2ETrinity%2ETrimmomatic%2Efasta.mpi.10.7.blastn
>>>>>> #-------------------------------#
>>>>>> deleted:0 hits
>>>>>> ERROR: Could not obtain lock to format database
>>>>>>
>>>>>>
>>>>>> FATAL ERROR
>>>>>> ERROR: Failed while doing blastn of ESTs!!
>>>>>>
>>>>>> ERROR: Chunk failed at level 8
>>>>>> !!
>>>>>> FAILED CONTIG:scaffold_866
>>>>>>
>>>>>>
>>>>>> Several blastn steps appeared to have completed successfully to this
>>>>>> one failing. Any ideas what could be causing this?
>>>>>>
>>>>>> Thanks!
>>>>>>
>>>>>> --
>>>>>> Daniel S. Standage
>>>>>> Ph.D. Candidate
>>>>>> Bioinformatics and Computational Biology Program
>>>>>> Department of Genetics, Development, and Cell Biology
>>>>>> Iowa State University
>>>>>>
>>>>>>
>>>>> _______________________________________________ maker-devel mailing
>>>>> list maker-devel at box290.bluehost.com
>>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>>>
>>>>
>>>>
>>>
>>
>
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