[ensembl-dev] VEP error: Forked process failed.
Duarte Molha
duartemolha at gmail.com
Fri May 17 16:57:06 BST 2013
That has done the trick :)
Thanks
=========================
Duarte Miguel Paulo Molha
http://about.me/duarte
=========================
On Fri, May 17, 2013 at 4:51 PM, Will McLaren <wm2 at ebi.ac.uk> wrote:
> Fixed
>
>
> On 17 May 2013 16:41, Duarte Molha <duartemolha at gmail.com> wrote:
>
>> Something is definitely something wrong with the later changes ... both
>> using the branch version and the head version of VEP throughs thousands of
>> errors of the type
>>
>> Use of uninitialized value $_ in scalar chomp at
>> /services/.array/OGTIP/duartem/workspace/VEP_dev/Bio/EnsEMBL/Variation/Utils/VEP.pm
>> line 1081, <$child> line XXXXXXX.
>>
>> Best regards
>>
>> Duarte
>>
>>
>>
>> =========================
>> Duarte Miguel Paulo Molha
>> http://about.me/duarte
>> =========================
>>
>>
>> On Fri, May 17, 2013 at 4:13 PM, Will McLaren <wm2 at ebi.ac.uk> wrote:
>>
>>> I pushed the fork changes to branch as well today as I felt they were
>>> stable enough.
>>>
>>> So, you can use branch and it should be fine.
>>>
>>> There will be more coming but they can wait for the next main release.
>>>
>>> Will
>>>
>>>
>>> On 17 May 2013 16:06, Duarte Molha <Duarte.Molha at ogt.com> wrote:
>>>
>>>> I believe you have to use the version in HEAD from the CSV repository.*
>>>> ***
>>>>
>>>> ** **
>>>>
>>>> Please correct me if I am wrong Will.****
>>>>
>>>> ** **
>>>>
>>>> Best regards****
>>>>
>>>> ** **
>>>>
>>>> Duarte****
>>>>
>>>> ** **
>>>>
>>>> ** **
>>>>
>>>> *From:* dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] *On
>>>> Behalf Of *Guillermo Marco Puche
>>>> *Sent:* 16 May 2013 12:30
>>>> *To:* Ensembl developers list
>>>> *Subject:* Re: [ensembl-dev] VEP error: Forked process failed.****
>>>>
>>>> ** **
>>>>
>>>> Hello,
>>>>
>>>> I got lost in this topic.
>>>> So if I understand well.. to fix the VEP forking issue I must can
>>>> re-download the VEP script from ensembl website?
>>>>
>>>> Thank you !
>>>>
>>>> Best regards,
>>>> Guillermo.
>>>>
>>>> On 05/15/2013 01:35 PM, Will McLaren wrote:****
>>>>
>>>> This is now fixed on branch and head too. ****
>>>>
>>>> ** **
>>>>
>>>> Will****
>>>>
>>>> ** **
>>>>
>>>> On 14 May 2013 17:30, Duarte Molha <duartemolha at gmail.com> wrote:****
>>>>
>>>> Sorry Will... today you have loads of people bugging you :-) ****
>>>>
>>>> ** **
>>>>
>>>> I just updated to the latest VEP you pointed me to ... and now the fail
>>>> in on line 1307****
>>>>
>>>> ** **
>>>>
>>>> Use of uninitialized value $line in join or string at
>>>> /NGS_Test/duarte/vep_71/Bio/EnsEMBL/Variation/Utils/VEP.pm line 1307.**
>>>> **
>>>>
>>>> ** **
>>>>
>>>> Cheers****
>>>>
>>>>
>>>> Duarte****
>>>>
>>>> ** **
>>>>
>>>>
>>>> ****
>>>>
>>>> =========================
>>>> Duarte Miguel Paulo Molha ****
>>>>
>>>> http://about.me/duarte
>>>> =========================****
>>>>
>>>> ** **
>>>>
>>>> On Tue, May 14, 2013 at 4:26 PM, Will McLaren <wm2 at ebi.ac.uk> wrote:***
>>>> *
>>>>
>>>> Hi Duarte, ****
>>>>
>>>> ** **
>>>>
>>>> You are correct, it was the --individual flag causing the problem.****
>>>>
>>>> ** **
>>>>
>>>> I have committed a fix to the 71 branch (does not include forking
>>>> fixes) and to head (does include forking fixes, download from
>>>> http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm?revision=1.94&root=ensembl
>>>> ).****
>>>>
>>>> ** **
>>>>
>>>> Regards****
>>>>
>>>> ** **
>>>>
>>>> Will****
>>>>
>>>> ** **
>>>>
>>>> On 14 May 2013 15:17, Duarte Molha <duartemolha at gmail.com> wrote:****
>>>>
>>>> However I believe it must be something related to the --individual
>>>> [all|ind list] flag ****
>>>>
>>>> And does not seem to be related to the --forks argument since it also
>>>> thoughs that error when running single threaded. ****
>>>>
>>>> ** **
>>>>
>>>> However in single thread mode it simply displays the error and keeps
>>>> going and with multiple forks the process dies entirely.****
>>>>
>>>> ****
>>>>
>>>> My vcf contains 3 samples genotypes and I have included the
>>>> --individual all option. ****
>>>>
>>>> ** **
>>>>
>>>> Best regards****
>>>>
>>>> Duarte****
>>>>
>>>> ** **
>>>>
>>>>
>>>> ****
>>>>
>>>> =========================
>>>> Duarte Miguel Paulo Molha ****
>>>>
>>>> http://about.me/duarte
>>>> =========================****
>>>>
>>>> ** **
>>>>
>>>> On Tue, May 14, 2013 at 2:00 PM, Duarte Molha <duartemolha at gmail.com>
>>>> wrote:****
>>>>
>>>> Hi Will ****
>>>>
>>>> ** **
>>>>
>>>> Unfortunately the script does not report in which line it fails and I
>>>> cannot provide you with the entire file since it is private data.****
>>>>
>>>> Is there a way of reporting the line >****
>>>>
>>>> ** **
>>>>
>>>> Thanks****
>>>>
>>>>
>>>> Duarte****
>>>>
>>>> ** **
>>>>
>>>>
>>>> ****
>>>>
>>>> =========================
>>>> Duarte Miguel Paulo Molha ****
>>>>
>>>> http://about.me/duarte
>>>> =========================****
>>>>
>>>> ** **
>>>>
>>>> On Tue, May 14, 2013 at 1:05 PM, Will McLaren <wm2 at ebi.ac.uk> wrote:***
>>>> *
>>>>
>>>> Hi Duarte, ****
>>>>
>>>>
>>>> Do you have some input that causes this error?****
>>>>
>>>> ** **
>>>>
>>>> Thanks****
>>>>
>>>> ** **
>>>>
>>>> Will****
>>>>
>>>> ** **
>>>>
>>>> On 14 May 2013 12:57, Duarte Molha <duartemolha at gmail.com> wrote:****
>>>>
>>>> Another bug using the updated version... now using the --check_alleles
>>>> and --check_existing options the script dies at line 4759 ****
>>>>
>>>> ** **
>>>>
>>>> Use of uninitialized value in string ne at
>>>> /NGS_Test/duarte/vep_71/Bio/EnsEMBL/Variation/Utils/VEP.pm line 4759.**
>>>> **
>>>>
>>>> ** **
>>>>
>>>> ** **
>>>>
>>>> Best regards****
>>>>
>>>> ** **
>>>>
>>>> Duarte****
>>>>
>>>>
>>>> ****
>>>>
>>>> =========================
>>>> Duarte Miguel Paulo Molha ****
>>>>
>>>> http://about.me/duarte
>>>> =========================****
>>>>
>>>> ** **
>>>>
>>>> On Tue, May 14, 2013 at 11:22 AM, Will McLaren <wm2 at ebi.ac.uk> wrote:**
>>>> **
>>>>
>>>> Thanks - try
>>>> http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm?revision=1.93&root=ensembl
>>>> ****
>>>>
>>>> ** **
>>>>
>>>> Will****
>>>>
>>>> ** **
>>>>
>>>> On 14 May 2013 11:09, Duarte Molha <duartemolha at gmail.com> wrote:****
>>>>
>>>> It seems the problems are still there : ****
>>>>
>>>> ** **
>>>>
>>>> Here is my output:****
>>>>
>>>> ** **
>>>>
>>>> perl variant_effect_predictor.pl --config vep_human.ini -i INPUT.vcf
>>>> --fork 16****
>>>>
>>>> ** **
>>>>
>>>> 2013-05-14 10:33:38 - Read configuration from vep_human.ini****
>>>>
>>>> #----------------------------------#****
>>>>
>>>> # ENSEMBL VARIANT EFFECT PREDICTOR #****
>>>>
>>>> #----------------------------------#****
>>>>
>>>> ** **
>>>>
>>>> version 71****
>>>>
>>>> ** **
>>>>
>>>> By Will McLaren (wm2 at ebi.ac.uk)****
>>>>
>>>> ** **
>>>>
>>>> Configuration options:****
>>>>
>>>> ** **
>>>>
>>>> ###****
>>>>
>>>> allow_non_variant 1****
>>>>
>>>> buffer_size 500000****
>>>>
>>>> cache 1****
>>>>
>>>> canonical 1****
>>>>
>>>> ccds 1****
>>>>
>>>> check_alleles 1****
>>>>
>>>> check_existing 1****
>>>>
>>>> config vep_human.ini****
>>>>
>>>> core_type core****
>>>>
>>>> custom
>>>> /ReferenceData/vep_additional_annotations/Somatic_variation_phenotypes.bed.gz,Somatic,bed,exact
>>>> ****
>>>>
>>>>
>>>> /ReferenceData/vep_additional_annotations/dbsnp135_ensembl_variation_phenotype.bed.gz,dbsnp135,bed,exact
>>>> ****
>>>>
>>>> dir /ReferenceData/vep_cache/****
>>>>
>>>> domains 1****
>>>>
>>>> force_overwrite 1****
>>>>
>>>> fork 16****
>>>>
>>>> gmaf 1****
>>>>
>>>> hgnc 1****
>>>>
>>>> host ensembldb.ensembl.org****
>>>>
>>>> individual all****
>>>>
>>>> input_file INPUT.vcf****
>>>>
>>>> numbers 1****
>>>>
>>>> plugin Blosum62
>>>> Condel,/ReferenceData/vep_cache/Plugins/config/Condel/config,b Carol**
>>>> **
>>>>
>>>> polyphen b****
>>>>
>>>> port 5306****
>>>>
>>>> protein 1****
>>>>
>>>> regulatory 1****
>>>>
>>>> sift b****
>>>>
>>>> species homo_sapiens****
>>>>
>>>> stats HASH(0x35a8000)****
>>>>
>>>> terms SO****
>>>>
>>>> toplevel_dir /ReferenceData/vep_cache/****
>>>>
>>>> verbose 1****
>>>>
>>>> xref_refseq 1****
>>>>
>>>> ** **
>>>>
>>>> --------------------****
>>>>
>>>> ** **
>>>>
>>>> Will only load v71 databases****
>>>>
>>>> Species 'homo_sapiens' loaded from database 'homo_sapiens_core_71_37'**
>>>> **
>>>>
>>>> Species 'homo_sapiens' loaded from database 'homo_sapiens_cdna_71_37'**
>>>> **
>>>>
>>>> Species 'homo_sapiens' loaded from database 'homo_sapiens_vega_71_37'**
>>>> **
>>>>
>>>> Species 'homo_sapiens' loaded from database
>>>> 'homo_sapiens_otherfeatures_71_37'****
>>>>
>>>> Species 'homo_sapiens' loaded from database 'homo_sapiens_rnaseq_71_37'
>>>> ****
>>>>
>>>> homo_sapiens_variation_71_37 loaded****
>>>>
>>>> homo_sapiens_funcgen_71_37 loaded****
>>>>
>>>> Bio::EnsEMBL::Compara::DBSQL::DBAdaptor not found so the following
>>>> compara databases will be ignored: ensembl_compara_71****
>>>>
>>>> ensembl_ancestral_71 loaded****
>>>>
>>>> ensembl_ontology_71 loaded****
>>>>
>>>> 2013-05-14 10:33:39 - Connected to core version 71 database and
>>>> variation version 71 database****
>>>>
>>>> 2013-05-14 10:33:39 - Read existing cache info****
>>>>
>>>> 2013-05-14 10:33:39 - Loaded plugin: Blosum62****
>>>>
>>>> 2013-05-14 10:33:39 - Loaded plugin: Condel****
>>>>
>>>> 2013-05-14 10:33:39 - Loaded plugin: Carol****
>>>>
>>>> 2013-05-14 10:33:40 - Starting...****
>>>>
>>>> 2013-05-14 10:33:40 - Detected format of input file as vcf****
>>>>
>>>> 2013-05-14 10:33:46 - Read 195789 variants into buffer****
>>>>
>>>> 2013-05-14 10:33:46 - Skipping 67552 non-variant loci****
>>>>
>>>> 2013-05-14 10:33:46 - Reading transcript data from cache and/or database
>>>> ****
>>>>
>>>> [======================================================================================================]
>>>> [ 100% ]****
>>>>
>>>> 2013-05-14 10:40:19 - Retrieved 189344 transcripts (0 mem, 202901
>>>> cached, 0 DB, 13557 duplicates)****
>>>>
>>>> 2013-05-14 10:40:19 - Reading regulatory data from cache and/or database
>>>> ****
>>>>
>>>> [======================================================================================================]
>>>> [ 100% ]****
>>>>
>>>> 2013-05-14 10:50:09 - Retrieved 872092 regulatory features (0 mem,
>>>> 872351 cached, 0 DB, 259 duplicates)****
>>>>
>>>> 2013-05-14 10:50:12 - Calculating consequences****
>>>>
>>>> Use of uninitialized value $_ in pattern match (m//) at
>>>> /NGS_Test/duarte/vep_71/Bio/EnsEMBL/Variation/Utils/VEP.pm line 1022.**
>>>> **
>>>>
>>>> Use of uninitialized value $_ in pattern match (m//) at
>>>> /NGS_Test/duarte/vep_71/Bio/EnsEMBL/Variation/Utils/VEP.pm line 1030.**
>>>> **
>>>>
>>>> Use of uninitialized value $_ in pattern match (m//) at
>>>> /NGS_Test/duarte/vep_71/Bio/EnsEMBL/Variation/Utils/VEP.pm line 1037.**
>>>> **
>>>>
>>>> Use of uninitialized value $_ in pattern match (m//) at
>>>> /NGS_Test/duarte/vep_71/Bio/EnsEMBL/Variation/Utils/VEP.pm line 1089.**
>>>> **
>>>>
>>>> Use of uninitialized value $_ in concatenation (.) or string at
>>>> /NGS_Test/duarte/vep_71/Bio/EnsEMBL/Variation/Utils/VEP.pm line 1097.**
>>>> **
>>>>
>>>> ** **
>>>>
>>>> ERROR: Forked process failed****
>>>>
>>>> ** **
>>>>
>>>> ** **
>>>>
>>>> ** **
>>>>
>>>>
>>>> ****
>>>>
>>>> =========================
>>>> Duarte Miguel Paulo Molha ****
>>>>
>>>> http://about.me/duarte
>>>> =========================****
>>>>
>>>> ** **
>>>>
>>>> On Tue, May 14, 2013 at 10:42 AM, Duarte Molha <duartemolha at gmail.com>
>>>> wrote:****
>>>>
>>>> Thanks ****
>>>>
>>>> ** **
>>>>
>>>> Running a annotation using 16 forks... lets see how it handles :)****
>>>>
>>>> I'll report back any issues.****
>>>>
>>>> ** **
>>>>
>>>> Thanks for the update****
>>>>
>>>> ** **
>>>>
>>>> Duarte****
>>>>
>>>> ** **
>>>>
>>>>
>>>> ****
>>>>
>>>> =========================
>>>> Duarte Miguel Paulo Molha ****
>>>>
>>>> http://about.me/duarte
>>>> =========================****
>>>>
>>>> ** **
>>>>
>>>> On Tue, May 14, 2013 at 10:16 AM, Will McLaren <wm2 at ebi.ac.uk> wrote:**
>>>> **
>>>>
>>>> Stuart, Guillermo, Duarte, ****
>>>>
>>>> ** **
>>>>
>>>> I'm currently working on some code as I stated above to improve
>>>> stability and performance under forking.****
>>>>
>>>> ** **
>>>>
>>>> I've committed some code to the HEAD of our CVS tree which should help
>>>> the problems you are encountering. You'd all be welcome to test this out,
>>>> with the obvious proviso that this is development code and may contain bugs!
>>>> ****
>>>>
>>>> ** **
>>>>
>>>> To use this, you should download the copy of VEP.pm from:****
>>>>
>>>> ** **
>>>>
>>>>
>>>> http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm?revision=1.92&root=ensembl
>>>> ****
>>>>
>>>> ** **
>>>>
>>>> and replace the VEP.pm under
>>>> ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils (or just
>>>> Bio/EnsEMBL/Variation/Utils if you use INSTALL.pl) with this one.****
>>>>
>>>> ** **
>>>>
>>>> This code will appear in production in the next proper release of
>>>> Ensembl.****
>>>>
>>>> ** **
>>>>
>>>> Regards****
>>>>
>>>> ** **
>>>>
>>>> Will****
>>>>
>>>> ** **
>>>>
>>>> On 14 May 2013 09:55, Stuart Meacham <sm766 at cam.ac.uk> wrote:****
>>>>
>>>> Hi,
>>>>
>>>> I certainly don't want to hijack this thread but it seemed daft to
>>>> start another. I am also getting forking errors. I don't use any custom
>>>> plugins and am using a validated VCF as input (with about 600,000
>>>> variants). Trying to fork more than 4 threads is unstable even on my
>>>> machine which has 64 cores and half a TB of RAM.
>>>>
>>>> I haven't found anything reproducible, however if I do I'll report back
>>>> to the list.
>>>>
>>>> Thanks
>>>>
>>>> Stuart ****
>>>>
>>>>
>>>>
>>>> On 14/05/2013 09:42, Will McLaren wrote:****
>>>>
>>>> Hello, ****
>>>>
>>>> ** **
>>>>
>>>> Your aa_grantham_distance plugin is somewhat inefficient - it retrieves
>>>> the peptide alleles from the HGVS annotation, which itself requires some
>>>> database fetching and processing to produce. This is why it is slow.***
>>>> *
>>>>
>>>> ** **
>>>>
>>>> You can get the peptides from the transcript variation object:****
>>>>
>>>> ** **
>>>>
>>>> my @peps = split "/", $tva->transcript_variation->pep_allele_string();*
>>>> ***
>>>>
>>>> ** **
>>>>
>>>> This will give you single-letter AA codes, but you could either modify
>>>> your hash or use BioPerl to convert:****
>>>>
>>>> ** **
>>>>
>>>> $seqobj = Bio::PrimarySeq->new ( -seq => $single_letter_aa);
>>>> $three_letter_aa = Bio::SeqUtils->seq3($seqobj); ****
>>>>
>>>> ** **
>>>>
>>>> You should also declare your distances hash in the new() sub and store
>>>> it on $self; this will also marginally speed up your plugin.****
>>>>
>>>> ** **
>>>>
>>>> Regarding the forking issues, we are working on improving stability
>>>> under forking.****
>>>>
>>>> ** **
>>>>
>>>> Thanks for your patience****
>>>>
>>>> ** **
>>>>
>>>> Will****
>>>>
>>>> ** **
>>>>
>>>> On 14 May 2013 07:37, Guillermo Marco Puche <
>>>> guillermo.marco at sistemasgenomicos.com> wrote:****
>>>>
>>>> Hello,
>>>>
>>>> I'm not really sure which one of those plugins is causing the fork
>>>> error. I cannot recreate it now running each one of them separately.
>>>>
>>>> Here are both:
>>>>
>>>> https://github.com/guillermomarco/vep_plugins_71
>>>>
>>>> They also slow the calculating consequences process a lot.
>>>> aa_grantham_distance.pm is just a hardcoded plugin from one of the
>>>> biologists in my work. It was just a pure copy paste and adaptation to make
>>>> it work as a VEP plugin. Maybe the problem is in the matrix definition
>>>> every time the sub routine is called. I'm not running out of memory nor
>>>> CPU. I'm currently using it with 2 threads and buffersize of 500 for a 5000
>>>> variant vcf file.
>>>>
>>>> I'm my honest opinion, I think one (or even both) of those plugins are
>>>> slowing so much the calculating process that sometimes the fork just dies.
>>>> Like when you have a timeout during to heavy network traffic. So when you
>>>> use them together with lot of other plugins like Condel, Consequence, etc..
>>>> they may be causing the process to handle and die.
>>>>
>>>> Best regards,
>>>> Guillermo. ****
>>>>
>>>>
>>>>
>>>> On 05/13/2013 03:55 PM, Duarte Molha wrote:****
>>>>
>>>> I also get this error... it is so prevalent and so difficult to
>>>> pinpoint what is causing it that I have given up on forking my annotation
>>>> process. ****
>>>>
>>>> ** **
>>>>
>>>> I do think it is related to the number of forks. It seems to crash less
>>>> often if you use a low number of forks... anything above 5
>>>> will undoubtedly crash the script at least in my experience.****
>>>>
>>>> ** **
>>>>
>>>> Cheers****
>>>>
>>>>
>>>> Duarte****
>>>>
>>>>
>>>> ****
>>>>
>>>> =========================
>>>> Duarte Miguel Paulo Molha ****
>>>>
>>>> http://about.me/duarte
>>>> =========================****
>>>>
>>>> ** **
>>>>
>>>> On Mon, May 13, 2013 at 2:50 PM, Will McLaren <wm2 at ebi.ac.uk> wrote:***
>>>> *
>>>>
>>>> Hi Guillermo, ****
>>>>
>>>> ** **
>>>>
>>>> Test each plugin individually until you find the one that causes the
>>>> error. It is highly unlikely that a particular combination of plugins is
>>>> causing the crash.****
>>>>
>>>> ** **
>>>>
>>>> Check that there are no "print" (to STDOUT or STDERR) statements in
>>>> your plugin - forking assumes that code remains silent otherwise it will
>>>> throw errors like this.****
>>>>
>>>> ** **
>>>>
>>>> Also, check what, if anything, is cached between runs of your plugin.
>>>> If you are caching things (for example to avoid re-querying a database),
>>>> you may need to write storable hooks to ensure the data is getting cached
>>>> between forks - see
>>>> https://github.com/ensembl-variation/VEP_plugins/blob/master/ProteinSeqs.pmfor an example.
>>>> ****
>>>>
>>>> ** **
>>>>
>>>> If you still have no luck, send me the code and an input file that
>>>> recreates the problem.****
>>>>
>>>> ** **
>>>>
>>>> Regards****
>>>>
>>>> ** **
>>>>
>>>> Will****
>>>>
>>>> ** **
>>>>
>>>> On 13 May 2013 13:18, Guillermo Marco Puche <
>>>> guillermo.marco at sistemasgenomicos.com> wrote:****
>>>>
>>>> Hello,
>>>>
>>>> I've started to recently having problems with VEP script while using
>>>> different plugins (most of them own plugins).****
>>>>
>>>> 2013-05-13 13:59:44 - Connected to core version 71 database and variation version 71 database****
>>>>
>>>> 2013-05-13 13:59:44 - Loaded plugin: vcf_input****
>>>>
>>>> 2013-05-13 13:59:44 - Loaded plugin: biobase****
>>>>
>>>> 2013-05-13 13:59:44 - Loaded plugin: aa_grantham_distance****
>>>>
>>>> 2013-05-13 13:59:44 - Loaded plugin: flanking_sequence****
>>>>
>>>> 2013-05-13 13:59:44 - Loaded plugin: Condel****
>>>>
>>>> 2013-05-13 13:59:44 - Output fields redefined (37 defined)****
>>>>
>>>> 2013-05-13 13:59:44 - Starting...****
>>>>
>>>> 2013-05-13 13:59:45 - Read 3888 variants into buffer****
>>>>
>>>>
>>>>
>>>> 2013-05-13 13:59:54 - Reading transcript data from cache and/or database****
>>>>
>>>> [===============================================] [ 100% ]****
>>>>
>>>> 2013-05-13 14:02:38 - Retrieved 6463 transcripts (0 mem, 0 cached, 13743 DB, 7280 duplicates)****
>>>>
>>>> 2013-05-13 14:02:38 - Calculating consequences****
>>>>
>>>> [===================================> ] [ 78% ]****
>>>>
>>>> ERROR: Forked process failed****
>>>>
>>>> ** **
>>>>
>>>> ** **
>>>>
>>>> I'm not getting any other error message. So I cannot debug properly. I
>>>> thought my plugins were OK but it's seems they don't. I think the problem
>>>> occurs when I use "aa_grantham_distance plugin" together with
>>>> "flanking_sequence". I've no idea what could be causing this.
>>>>
>>>> I'm running VEP on verbose mode but I can't get any usefull
>>>> information. How could I debug that?
>>>>
>>>> Best regards,
>>>> Guillermo.****
>>>>
>>>> ** **
>>>>
>>>> _______________________________________________
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>>>>
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>>>>
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