[ensembl-dev] version 91 error report

Wed Jan 3 09:11:37 GMT 2018

Hi Hiram

Sorry for the delayed response, everyone was away for Christmas. The sequences you have reported have come from our non-coding RNA pipeline, we will look in to this further and fix it for future releases.

Thank you 
Leanne

> On 22 Dec 2017, at 10:16, Emily Perry <emily at ebi.ac.uk> wrote:
> 
> Hi Hiram
> 
> This does look a bit weird. I'm afraid we're on skeleton staff today, as lots of people have already left for the Christmas break, and we have no genebuilders in at all. Somebody will look at this when we're all back in the New Year.
> 
> All the best
> 
> Emily
> 
> On 21/12/2017 19:10, Hiram Clawson wrote:
>> Good Morning Ensembl Gene Fans:
>> 
>> As I transfer the Ensembl gene definitions to the UCSC genome browser,
>> there are sometimes a few difficulties with a few of the annotations.
>> Mostly in the newly released genome annotations.  Please note below
>> the anomalies I find in the version 91 release for 17 of the sequences.
>> 
>> To move forward on these, I drop these few annotations as they are
>> transferred into the UCSC genome browser.  These annotations can
>> be seen in the genome-test.soe.ucsc.ed browser for the assemblies:
>> 
>> aotNan1 felCat8 gorGor4 jacJac1 macFas5 manLeu1 mesAur1 micMur3 nanGal1
>> octDeg1 panPan2 panTro5 proCoq1 rhiBie1 rhiRox1 saiBol1 tarSyr2
>> 
>> These errors can be found from the Ensembl gtf.gz file via the process:
>>   gtfToGenePred ensembl.gtf.gz ucscGenePred.gp
>>   genePredCheck -chromSizes=chrom.sizes ucscGenePred.gp
>> 
>> Where chrom.sizes can be created from:
>>   faToTwoBit ensembl.dna.toplevel.fa.gz ensembl.2bit
>>   twoBitInfo ensembl.2bit stdout | sort -k2,2nr > chrom.sizes
>> 
>> --Hiram
>> 
>> === Aotus_nancymaae.Anan_2.0.91.gtf.gz
>> ENSANAT00000008002.1 txEnd 21157 >= chromSize 21156
>> ENSANAT00000018995.1 txEnd 11710 >= chromSize 11706
>> ENSANAT00000001044.1 txEnd 9860 >= chromSize 9850
>> ENSANAT00000005144.1 txEnd 3639 >= chromSize 3636
>> checked: 50016 failed: 4
>> ============================================
>> 
>> === Felis_catus.Felis_catus_8.0.91.gtf.gz
>> ENSFCAT00000040388.1 txEnd 851 >= chromSize 830
>> ENSFCAT00000022232.2 txEnd 778 >= chromSize 777
>> ENSFCAT00000046539.1 txEnd 618 >= chromSize 615
>> ENSFCAT00000038331.1 txEnd 621 >= chromSize 602
>> ENSFCAT00000042688.1 txEnd 616 >= chromSize 602
>> ENSFCAT00000042073.1 txEnd 561 >= chromSize 559
>> ENSFCAT00000035557.1 txEnd 538 >= chromSize 533
>> ENSFCAT00000042534.1 txEnd 536 >= chromSize 533
>> checked: 34879 failed: 8
>> ============================================
>> 
>> === Gorilla_gorilla.gorGor4.91.gtf.gz
>> ENSGGOT00000040833.2 txEnd 2008 >= chromSize 2000
>> ENSGGOT00000066834.1 txEnd 2009 >= chromSize 2000
>> ENSGGOT00000065889.1 txEnd 1325 >= chromSize 1322
>> ENSGGOT00000041741.2 txEnd 923 >= chromSize 913
>> ENSGGOT00000064312.1 txEnd 900 >= chromSize 894
>> ENSGGOT00000042831.1 txEnd 872 >= chromSize 870
>> ENSGGOT00000039360.2 txEnd 831 >= chromSize 818
>> checked: 52960 failed: 7
>> ============================================
>> 
>> === Jaculus_jaculus.JacJac1.0.91.gtf.gz
>> ENSJJAT00000007476.1 txEnd 4410 >= chromSize 4389
>> ENSJJAT00000002946.1 txEnd 1935 >= chromSize 1923
>> checked: 31768 failed: 2
>> ============================================
>> 
>> === Macaca_fascicularis.Macaca_fascicularis_5.0.91.gtf.gz
>> ENSMFAT00000049321.1 txEnd 5011 >= chromSize 5009
>> checked: 53156 failed: 1
>> ============================================
>> 
>> === Mandrillus_leucophaeus.Mleu.le_1.0.91.gtf.gz
>> ENSMLET00000030838.1 txEnd 35289 >= chromSize 35264
>> checked: 47765 failed: 1
>> ============================================
>> 
>> === Mesocricetus_auratus.MesAur1.0.91.gtf.gz
>> ENSMAUT00000008954.1 txEnd 18377 >= chromSize 18369
>> ENSMAUT00000008838.1 txEnd 1152 >= chromSize 1150
>> checked: 29936 failed: 2
>> ============================================
>> 
>> === Microcebus_murinus.Mmur_3.0.91.gtf.gz
>> ENSMICT00000068593.1 txEnd 5528 >= chromSize 5525
>> ENSMICT00000068583.1 txEnd 4860 >= chromSize 4858
>> ENSMICT00000039077.2 txEnd 4792 >= chromSize 4790
>> ENSMICT00000052172.2 txEnd 2742 >= chromSize 2739
>> ENSMICT00000049755.2 txEnd 1553 >= chromSize 1539
>> ENSMICT00000068718.1 txEnd 1264 >= chromSize 1261
>> checked: 44024 failed: 6
>> ============================================
>> 
>> === Nannospalax_galili.S.galili_v1.0.91.gtf.gz
>> ENSNGAT00000010911.1 txEnd 1279026 >= chromSize 1279023
>> ENSNGAT00000011043.1 txEnd 3095 >= chromSize 3068
>> ENSNGAT00000005613.1 txEnd 883 >= chromSize 874
>> ENSNGAT00000005469.1 txEnd 843 >= chromSize 822
>> ENSNGAT00000003195.1 txEnd 661 >= chromSize 657
>> ENSNGAT00000004333.1 txEnd 660 >= chromSize 631
>> ENSNGAT00000010598.1 txEnd 588 >= chromSize 564
>> ENSNGAT00000004053.1 txEnd 491 >= chromSize 488
>> ENSNGAT00000004795.1 txEnd 337 >= chromSize 334
>> ENSNGAT00000008686.1 txEnd 245 >= chromSize 238
>> checked: 32861 failed: 10
>> ============================================
>> 
>> === Octodon_degus.OctDeg1.0.91.gtf.gz
>> ENSODET00000030480.1 txEnd 10465 >= chromSize 10456
>> checked: 32968 failed: 1
>> ============================================
>> 
>> === Pan_paniscus.panpan1.1.91.gtf.gz
>> ENSPPAT00000007687.1 txEnd 2172 >= chromSize 2168
>> checked: 50791 failed: 1
>> ============================================
>> 
>> === Pan_troglodytes.Pan_tro_3.0.91.gtf.gz
>> ENSPTRT00000103531.1 txEnd 10764 >= chromSize 10756
>> ENSPTRT00000079867.1 txEnd 1416 >= chromSize 1400
>> ENSPTRT00000096982.1 txEnd 1326 >= chromSize 1310
>> checked: 58366 failed: 3
>> ============================================
>> 
>> === Propithecus_coquereli.Pcoq_1.0.91.gtf.gz
>> ENSPCOT00000008378.1 txEnd 14532 >= chromSize 14529
>> checked: 37912 failed: 1
>> ============================================
>> 
>> === Rhinopithecus_bieti.ASM169854v1.91.gtf.gz
>> ENSRBIT00000004729.1 txEnd 1295 >= chromSize 1287
>> ENSRBIT00000004240.1 txEnd 925 >= chromSize 896
>> ENSRBIT00000007958.1 txEnd 874 >= chromSize 870
>> ENSRBIT00000005433.1 txEnd 499 >= chromSize 496
>> ENSRBIT00000004757.1 txEnd 492 >= chromSize 474
>> checked: 50868 failed: 5
>> ============================================
>> 
>> === Rhinopithecus_roxellana.Rrox_v1.91.gtf.gz
>> ENSRROT00000015658.1 txEnd 2904 >= chromSize 2895
>> ENSRROT00000003328.1 txEnd 575 >= chromSize 551
>> ENSRROT00000003014.1 txEnd 553 >= chromSize 550
>> ENSRROT00000017963.1 txEnd 425 >= chromSize 423
>> ENSRROT00000004422.1 txEnd 409 >= chromSize 406
>> ENSRROT00000005493.1 txEnd 247 >= chromSize 235
>> ENSRROT00000010204.1 txEnd 233 >= chromSize 229
>> ENSRROT00000009486.1 txEnd 223 >= chromSize 220
>> ENSRROT00000000177.1 txEnd 217 >= chromSize 214
>> checked: 53209 failed: 9
>> ============================================
>> 
>> === Saimiri_boliviensis_boliviensis.SaiBol1.0.91.gtf.gz
>> ENSSBOT00000006176.1 txEnd 1192 >= chromSize 1189
>> checked: 48403 failed: 1
>> ============================================
>> 
>> === Carlito_syrichta.Tarsius_syrichta-2.0.1.91.gtf.gz
>> ENSTSYT00000036298.1 txEnd 9974 >= chromSize 9960
>> ENSTSYT00000025862.1 txEnd 865 >= chromSize 863
>> ENSTSYT00000041648.1 txEnd 480 >= chromSize 479
>> ENSTSYT00000046606.1 txEnd 454 >= chromSize 452
>> checked: 38314 failed: 4
>> ============================================
>> 
>> 
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> 
> -- 
> Dr Emily Perry (Pritchard)
> Ensembl Outreach Project Leader
> 
> European Bioinformatics Institute (EMBL-EBI)
> European Molecular Biology Laboratory
> Wellcome Trust Genome Campus
> Hinxton
> Cambridge
> CB10 1SD
> UK
> 
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