Menu
▾
▴
Re: [wgs-assembler-users] Celera Assembly : segmentation fault
|
From: Brian W. <th...@gm...> - 2015-01-15 17:11:32
|
That's definitely NOT the 8.2 version.
Yours has: -dumpfasta[seq|qlt] dump fragment sequence or quality, as
fasta format
8.2 has: -dumpfasta <prefix> dump fragment sequence and quality
into <p.fasta> and <p.fasta.qual>
What does 'gatekeeper --version' report? (note, that's two dashes)
You should also verify that you're using the version you think you're
using: 'which gatekeeper'. There might be an older version installed in
your path. I've been stung by this a couple times.
b
On Tue, Jan 13, 2015 at 12:30 AM, Arpita Ghosh - Xcelris <
arp...@xc...> wrote:
> Dear Brain
>
> Thank you for your prompt response.
> *I want to run the following with the version 8.2 what should i use
> instead of** "-dumpfastaseq".*
>
> gatekeeper -dumpfastaseq genome.gkpStore > gatekeeper.fasta
>
>
> I tried gatekeeper -dumpfasta genome.gkpStore > gatekeeper.fasta with
> version 8.2 but it was not running. Can you please help.
>
> *The gatekeeper version is not mentioned but the help is as follows:*
>
> gatekeeper -h
> usage1: gatekeeper -o gkpStore [append/create options] <input.frg>
> <input.frg> ...
> usage2: gatekeeper -P partitionfile gkpStore
> usage3: gatekeeper [id-selection] [options] [format] gkpStore
> ----------------------------------------------------------------------
> The first usage will append to or create a GateKeeper store:
> -a append to existing store
> -o <gkpStore> append to or create gkpStore
>
> -T do not check minimum length (for OBT)
> -F fix invalid insert size estimates
>
> -E <error.frg> write errors to this file
>
> -v <vector-info> load vector clear ranges into each read.
> MUST be done on an existing, complete store.
> example: -a -v vectorfile -o that.gkpStore
> format: 'UID vec-clr-begin vec-clr-end'
>
> ----------------------------------------------------------------------
> The second usage will partition an existing store, allowing
> the entire store partition to be loaded into memory.
> -P <partitionfile> a list of (partition fragiid)
>
> ----------------------------------------------------------------------
> The third usage will dump the contents of a GateKeeper store.
> There are THREE components to a dump, what to dump, options, and format.
> The first two are optional, the last is mandatory. Examples:
>
> Dump metainfo for the first 100 fragments
> gatekeeper -b 1 -e 100 -tabular -dumpfragments my.gkpStore >
> first100.tsv
>
> Dump a random 25% of the reads in the first library
> gatekeeper -randomsubset 1 0.25 -dumpfrg my.gkpStore > random25.frg
>
> Dump fasta sequence for the UIDs in 'uidFile'
> gatekeeper -uid uidFile -dumpfastaseq -dumpfrg my.gkpStore > file.fasta
>
> -----------------------------------
> [selection of what objects to dump]
> -----------------------------------
> -b <begin-iid> dump starting at this library or read
> -e <ending-iid> dump stopping after this iid
> -uid <uid-file> dump only objects listed in 'uid-file'
> -iid <iid-file> dump only objects listed in 'iid-file'
> -randommated <lib> <n> pick n mates (2n frags) at random from library
> lib
> -randomsubset <lib> <f> dump a random fraction f of library lib
> -randomlength <lib> <l> dump a random fraction of library lib, fraction
> picked
> so that the untrimmed length is close to l
>
> ---------
> [options]
> ---------
> -tabular dump info, libraries or fragments in a tabular
> format (for -dumpinfo, -dumplibraries,
> and -dumpfragments, ignores -withsequence and
> -clear)
> -isfeatureset <libID> <X> sets exit value to 0 if feature X is set in
> library libID, 1 otherwise.
> If libID == 0, check all libraries.
> -nouid dump info without including the read UID (for
> -dumpinfo, -dumplibraries, -dumpfragments)
>
> ----------------
> [format of dump]
> ----------------
> -dumpinfo print information on the store
> -lastfragiid just print the last IID in the store
> -dumplibraries dump all library records
> -dumpfragments dump fragment info, no sequence
> -withsequence ...and include sequence
> -clear <clr> ...in clear range <clr>, default=LATEST
> -dumpfasta[seq|qlt] dump fragment sequence or quality, as fasta format
> -allreads ...all reads, regardless of deletion status
> (deleted are lowercase)
> -allbases ...all bases (lowercase for non-clear)
> -decoded ...quality as integers ('20 21 19')
> -clear <clr> ...in clear range <clr>, default=LATEST
> -dumpfrg extract LIB, FRG and LKG messages
> -allreads ...all reads, regardless of deletion status
> -donotfixmates ...only extract the fragments given, do not add
> in
> missing mated reads
> -clear <clr> ...use clear range <clr>, default=LATEST
> -format2 ...extract using frg format version 2
> -dumpnewbler <prefix> extract LIB, FRG and LKG messages, write in a
> format appropriate for Newbler. This will create
> files 'prefix.fna' and 'prefix.fna.qual'. Options
> -donotfixmates and -clear also apply.
> -dumpfastq <prefix> extract LIB, FRG and LKG messages, write in FastQ
> format. Currently
> this works only on a store with one library as
> all the mated reads
> are dumped into a single file. This will create
> files 'prefix.paired.fastq',
> 'prefix.1.fastq', 'prefix.2.fastq' and
> 'prefix.unmated.fastq' for unmated
> reads. Options -donotfixmates and -clear also
> apply.
>
> The Gatekeeper ensures that data entering the assembly system meets
> the data specification (see GateKeeper design document). It is also
> used for examining and partitioning the assembler data store.
>
> Each input message is checked for semantic consistency as described in
> the defining document for that stage. Messages containing a UID are
> converted to a UID,IID pair -- the assembler modules require
> consecutive IID beginning at 1 for efficient indexing of internal and
> disk-based data structures; gatekeeper performs this task. Finally,
> each message is inserted into the assembly data store.
>
> The GateKeeper succeeds if it consumes its entire input with less than
> a specified number of errors (the -e option). Upon successful exit,
> the store reflects all of the records that were successfully read.
> Unsuccessful records are reported to stderr, along with a brief
> explanation of the problem.
>
> If unsuccessful, the store is partially updated.
>
> Resoure Requirements
>
> The key gatekeeper data structures are in-memory copies of its store.
> This store should scale linearly with the number of fragments.
>
> No formal benchmarking of the gatekeeper has been performed to date.
> However, each LKG message requires four random disk accesses -- two to
> read the linked fragment records, and two two write the updated
> fragment records. This can cause problems when gatekeeper is run over
> low-performance or heavily used NFS mount points.
>
> 3. General Pre Conditions
>
> a) Each input UID must be unique. A new message with a duplicate UID
> will be rejected as an error.
>
> b) Any object referred to in a message must be defined:
> def-before-ref. Likewise, before an object can be deleted, all
> references to it must be removed: unref-before-undef.
>
> c) The input specification is defined elsewhere.
>
> Regards,
>
> Arpita Ghosh
>
> Scientist
>
> Xcelris Labs Limited
>
> Old Premchandnagar Road,
>
> Opp. Satyagrah Chhavani,
>
> Bodakdev, Ahmedabad-380015 India.
>
> Tel:+91-79-66197777/66311114
>
> Fax:+91-79-66309341
>
> Email: arp...@xc...
>
> www.xcelrisgenomics.com
> On 10-01-2015 20:07, Brian Walenz wrote:
>
> Hi-
>
> "-dumpfastaseq"? What version are you using? The usage for the latest
> versions (all of the 8.x series) is "gatekeeper -dumpfasta <out-prefix>
> *.gkpStore". Do any of the other dumps work?
>
> b
>
>
>
> On Sat, Jan 10, 2015 at 6:37 AM, Arpita Ghosh - Xcelris <
> arp...@xc...> wrote:
>
>> Dear User
>>
>>
>> I am using Celera assembler latest version but i am facing a problem in
>> one step as mentioned below.
>> After runCA i am running gatekeeper -dumpfastaseq genome.gkpStore >
>> gatekeeper.fasta and getting segmentation fault.
>>
>> I am user Server having specification of *64 core, 1TB RAM and AMD6378,
>> 2.4GHz processor. *The data input is Miseq PE 90 Gb, NextSeq MP 100 Gb
>> and 454 SG and PE of 2 Gb.
>>
>>
>> Can you suggest what might be the reason of the segmentation fault and
>> how can i come over it.
>>
>> --
>>
>> Regards,
>>
>> Arpita Ghosh
>>
>> Scientist
>>
>> Xcelris Labs Limited
>>
>> Old Premchandnagar Road,
>>
>> Opp. Satyagrah Chhavani,
>>
>> Bodakdev, Ahmedabad-380015 India.
>>
>> Tel:+91-79-66197777/66311114
>>
>> Fax:+91-79-66309341
>>
>> Email: arp...@xc...
>>
>> www.xcelrisgenomics.com
>>
>> "Please don't print this e-mail unless you really need to. Save Paper,
>> Save Trees"
>>
>> --------------------------------------------------------------------------------
>>
>> Disclaimer
>> The information contained in this e-mail message and / or attachments to
>> it may contain confidential or privileged information of Xcelris Labs
>> Limited and / or its group companies. If you are not the intended
>> recipient, any dissemination, use, review, distribution, printing or
>> copying of the information contained in this e-mail message and / or
>> attachments to it is strictly prohibited. If you have received this
>> communication in error, please notify us by reply e-mail or telephone and
>> immediately delete / destroy the message and / or any attachments
>> permanently.
>>
>> Any views or opinions presented in this e-mail are solely those of the
>> author and do not necessarily represent those of the company. Employees of
>> the company are expressly required not to make defamatory statements and
>> not to infringe or authorize any infringement of copyright or any other
>> legal right by e-mail communication. Any such communication is contrary to
>> company policy and outside the scope of the employment of the individual
>> concerned. The company will not accept any liability in respect of such
>> communication.
>>
>> No employee or associate is authorized to conclude any binding agreement
>> on behalf of Xcelris with another party by e-mail without expressly written
>> confirmation of the company.
>>
>> Warning-Computer viruses can be transmitted via e-mail. The recipient
>> should check this e-mail and any attachment for the presence of viruses.
>> The company has taken every reasonable precaution to minimize this risk,
>> and is not liable for any damage you may sustain as a result of any virus
>> in this e-mail. You should carry out your own virus checks before acting
>> upon the e-mail or any attachment to it.
>>
>> --------------------------------------------------------------------------------
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Dive into the World of Parallel Programming! The Go Parallel Website,
>> sponsored by Intel and developed in partnership with Slashdot Media, is
>> your
>> hub for all things parallel software development, from weekly thought
>> leadership blogs to news, videos, case studies, tutorials and more. Take a
>> look and join the conversation now. http://goparallel.sourceforge.net
>> _______________________________________________
>> wgs-assembler-users mailing list
>> wgs...@li...
>> https://lists.sourceforge.net/lists/listinfo/wgs-assembler-users
>>
>>
>
>
>
>
> --------------------------------------------------------------------------------
>
> Disclaimer
> The information contained in this e-mail message and / or attachments to
> it may contain confidential or privileged information of Xcelris Labs
> Limited and / or its group companies. If you are not the intended
> recipient, any dissemination, use, review, distribution, printing or
> copying of the information contained in this e-mail message and / or
> attachments to it is strictly prohibited. If you have received this
> communication in error, please notify us by reply e-mail or telephone and
> immediately delete / destroy the message and / or any attachments
> permanently.
>
> Any views or opinions presented in this e-mail are solely those of the
> author and do not necessarily represent those of the company. Employees of
> the company are expressly required not to make defamatory statements and
> not to infringe or authorize any infringement of copyright or any other
> legal right by e-mail communication. Any such communication is contrary to
> company policy and outside the scope of the employment of the individual
> concerned. The company will not accept any liability in respect of such
> communication.
>
> No employee or associate is authorized to conclude any binding agreement
> on behalf of Xcelris with another party by e-mail without expressly written
> confirmation of the company.
>
> Warning-Computer viruses can be transmitted via e-mail. The recipient
> should check this e-mail and any attachment for the presence of viruses.
> The company has taken every reasonable precaution to minimize this risk,
> and is not liable for any damage you may sustain as a result of any virus
> in this e-mail. You should carry out your own virus checks before acting
> upon the e-mail or any attachment to it.
>
> --------------------------------------------------------------------------------
>
>
|
