Question: Sample ORTHOMCL run on my Fasta file.
1
gravatar for Nari
5.2 years ago by
Nari880
United States
Nari880 wrote:

I wish to process orthomcl output clusters with perl.

I have general idea about how the output looks like. but have no Linux resources right now.

Can anybody kindly run orthomcl on my data. (I will keep the input as small as possible just for testing purpose) and deliver the cluster file?

Default parameters (identity, coverage) will do.

Even results for this small input will suffice:

>1|307346730|Prevotella_amnii_CRIS_21A-A|31#
MLCFANDAIKEGYHVLGGDNYLMLDGNFVLEPKRINKSSGTSHIVISFIHKSNLYAGLYHIQMDLK
>1|306346738|Prevotella_amnii_CRIS_21A-A|35#
MLCFANDAIKEGYHVLGGDNYLMLDGNFVLEPKRINKSSGTSHIVISFIHKSNLYAGLYHIQMDLK
>1|307346705|Prevotella_amnii_CRIS_21A-A|32#
MKALKKIFNWYFSANALPYWVILIIDGIICYLSGLIVFWLSCRGNFISLTNFKSISCSIIIYMIFVLIGIRAFKTYSGIVRYSSFVDIRRVFFAILLSLIIAEAMHYVIYNWRFAGIEFYPMNGKQIFVMYI
>1|307346704|Prevotella_amnii_CRIS_21A-A|32#
MFSGIIEEMATIVAIKHEKENIHLTLTCSFVNELGIDQSISHNGVCLTVVCIEGERYTVTAMRETIERSNLGLLKVGDSVNVERSMIMNGRLDGHIVQGHVDETATCVDIKDANGSTYYTFEYPFNKAMAARGYFTVDKGSITVNGVSLTVCQPTDNTFTVAIIPYTKENTNFKYIGVGTIVNIEFDILGKYIARLQSIIK
>1|307346728|Prevotella_amnii_CRIS_21A-A|34#
MKQKYILLTVLGVALFSLTGCKKEKHTHDIITKIAPKPKLPKGPIELQGFTYTKKVDWLGTQYIITIIRKADKGLPLAYDEDGKKYYDNKIIINIKREDGTKFYQKEFTKKDFIQFSDEQYGKNGALLGFMFDSVYLKTLRFGASIGSPAPSSDEYIPIDIVIDNLGHLSMTKAQTLDTDGDQQKDKNNSKATEKAKDTEEEGV
>2|270333715|Prevotella_bergensis_DSM_17361|47#
MEIIAVESQAYQELIDRLNRIEQYVERTSRLIQDIDDELEMTTKDLIGTLNVSESTLYRWRKKQLVRYRYTEGGDVRYFFKSIVIATKCNRLRVSGMRNDEILGRLNRFKDNLIMSSCINPKNRQL
>2|270333716|Prevotella_bergensis_DSM_17361|45#
MIEKEQILLLTQGGLNVFSHFLGFEVNLHRNFRSPFYDDRRASCHIYYDRKTSSYKFYDHGDTTYSGDCFWFVATLRNLNLKTSFPEVLETIVQELGLYSLCDGEKHSSHITSAYKKTIVPTPKADITKWTEERPYSFEIQPFDDGLLNYWGHYGIHEDTLRRFRVRSLKRYESVSAEGKKFELYSSPTEPMFAYIGNGYVKIYRPHSPKIRFLYGGRMPATYCFGMEQIPAKGDMLFITGGEKDVLSLYAHGFNAICFNSETA
>2|270333717|Prevotella_bergensis_DSM_17361|42#
MPYIDYKTEDTWQKRLFDKLISVEDKLDRLLILQEQSVDTTVHPPLKPEYLDIIDVSKILKVEQKTIYNWVWAGKIPYLKANGRLLFLREEIDKMVRKRDDW
>2|270333718|Prevotella_bergensis_DSM_17361|38#
MANKESRSIQEQIDLLKHRGMIIEDEEFAHLHLSHISYYRLKGYWWDMQTDKERHIFKNDANFKDVIARYFFDKELRLILFDAIEAIEIALRTKMIYHLSQSYGGLYYMDKGLFNNEELQQQHIHDLMGEFM
ADD COMMENTlink modified 5.2 years ago • written 5.2 years ago by Nari880
4
gravatar for arnstrm
5.2 years ago by
arnstrm1.8k
Ames, IA
arnstrm1.8k wrote:

Hi,

If you are interested, you can run it yourself on you local machine. Here is the virtual box image with the pre-installed orthomcl. If you are in windows, you can get it started in less than 5 minutes. There is an accompanying guide as well. I am the author of this guide/VM, so if you have any questions, I will be glad to answer!

 

ADD COMMENTlink written 5.2 years ago by arnstrm1.8k

Thanks @arnstrm for your reply. I am having only one error after this command:

orthomclPairs mysql.config pairs.log cleanup=no

It's like:

DBD::mysql::st execute failed: Table 'BestQueryTaxonScore' already exists at /opt/orthomcl/bin/ orthomclPairs line 709, <F> line 14.

What may be the cause and solution.

ADD REPLYlink modified 5.2 years ago • written 5.2 years ago by Nari880
1

It looks like the table already existed in the database, did you run any command twice? The easiest thing to do is to drop the database and start fresh.

mysql -u purduepete -p
drop database orthomcl;
create database orthomcl;
exit

This should reset the database and you can continue from the orthomclInstallSchema step.

ADD REPLYlink modified 5.2 years ago • written 5.2 years ago by arnstrm1.8k
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