[ensembl-dev] VEP error: Forked process failed.
Will McLaren
wm2 at ebi.ac.uk
Tue May 14 13:05:29 BST 2013
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.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> Dev mailing list Dev at ensembl.org
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>>>>>>>>>
>>>>>>> _______________________________________________
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>>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
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>>>>>>
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>>>>>
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