[maker-devel] Strange error at blastn step
Carson Holt
carsonhh at gmail.com
Fri Oct 26 16:59:30 MDT 2012
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.ma
>>>>> ker.output/maker.pdom.1.mason_datastore/scaffold_0/theVoid.scaffold_0/scaf
>>>>> fold_0.0.Amel3%2E2_Dmel5%2E47%2Efaa.blastx.temp_dir/Amel3%2E2_Dmel5%2E47%2
>>>>> Efaa.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.ma
>>>>> ker.output/maker.pdom.1.mason_datastore/scaffold_0/theVoid.scaffold_0/scaf
>>>>> fold_0.0.Amel3%2E2_Dmel5%2E47%2Efaa.blastx.temp_dir/Amel3%2E2_Dmel5%2E47%2
>>>>> Efaa.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%2Efa
>>>>>> sta.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.scaffold_866/scaffold_8
>>>>>> 66.0.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.comhttp://box290.bluehost.com/mailman/listinfo/
>>>> maker-devel_yandell-lab.org
>>>
>>
>
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