[maker-devel] Strange error at blastn step
Carson Holt
carsonhh at gmail.com
Fri Oct 26 12:24:43 MDT 2012
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.mak
>>>> er.output/maker.pdom.1.mason_datastore/scaffold_0/theVoid.scaffold_0/scaffo
>>>> ld_0.0.Amel3%2E2_Dmel5%2E47%2Efaa.blastx.temp_dir/Amel3%2E2_Dmel5%2E47%2Efa
>>>> a.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.mak
>>>> er.output/maker.pdom.1.mason_datastore/scaffold_0/theVoid.scaffold_0/scaffo
>>>> ld_0.0.Amel3%2E2_Dmel5%2E47%2Efaa.blastx.temp_dir/Amel3%2E2_Dmel5%2E47%2Efa
>>>> a.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%2Efas
>>>>> ta.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.o
>>>>> utput/maker.bogus_datastore/scaffold_866/theVoid.scaffold_866/scaffold_866
>>>>> .0.Pdom%2ETrinity%2ETrimmomatic%2Efasta.blastn.temp_dir/Pdom%2ETrinity%2ET
>>>>> rimmomatic%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/m
>>> aker-devel_yandell-lab.org
>>
>
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