[ensembl-dev] Almost no annotation with v61 EFG Array Mapping

[Oliver, Gavin]

Hi, 

 

I have rerun my array annotations with v61.  Everything seemed fine
until I looked at the log and saw that perhaps 2 probesets per array
have actually mapped to a transcript.

Can you think of something obvious that might have gone wrong here?  The
log output is below.

 

Best, 

 

Gavin

 

 

(Nathan I'm posting here incase you didn't receive my mail)

 

 

::      ::      Running on probe2transcript.pl on:
ni-cr-svc-slv.phar-services.com   ::      :: - Mon Feb 21 09:01:02 2011

 

::      Params are:     --species homo_sapiens --transcript_dbname
homo_sapiens_core_61_37f --transcript_host ni-cr-svc-bs3
--transcript_port 3306 --transcript_user root --transcript_pass pass
--xref_host ni-cr-svc-bs3 --xref_dbname homo_sapiens_funcgen_61_37f
--xref_user root --xref_pass pass --unannotated_5_utr 0
--unannotated_3_utr 0 -annotated_5_prime_extend 0
-annotated_3_prime_extend 0 --threshold 0.000005 --mismatches 2 -vendor
AFFY -format AFFY_UTR -arrays ADXOCv1a520630 ADXBRCv2a520413
ADXECv1a520743 ADXLCv1a520538 ADXCRCG2a520319 HG-U133_Plus_2
ADXPCv1a520642 -import_edb

::      No probe DB params specified, defaulting to xref params

 

 

::      ::      Checking existing Xrefs ::      ::

 

::      You have specified -utr_multiplier and a -3|5_prime_extend,
-3|5_prime_extend will override where appropriate

::      Setting 3 unannotated UTR length to 0

::      Setting 5 unannotated UTR length to 0

::      Identified 167074 transcripts for probe mapping

::      Allowed mismatches = 2

::      Caching arrays per ProbeSet - Mon Feb 21 09:01:21 2011

::      Performing overlap analysis. % Complete:

::      0 ::    1 ::    2 ::    3 ::    4 ::    5 ::    6 ::    7 ::
8 ::    9 ::    10 ::   11 ::   12 ::   13 ::   14 ::   15 ::   16 ::
17 ::   18 ::   19 ::   20 ::   21 ::   22 ::   23 ::   24 ::   25 ::
26 ::   27 ::   28 ::   29 ::   30 ::   31 ::   32 ::   33 ::   34 ::
35 ::   36 ::   37 ::   38 ::   39 ::   40 ::   41 ::   42 ::   43 ::
44 ::   45 ::   46 ::   47 ::   48 ::   49 ::   50 ::   51 ::   52 ::
53 ::   54 ::   55 ::   56 ::   57 ::   58 ::   59 ::   60 ::   61 ::
62 ::   63 ::   64 ::   65 ::   66 ::   67 ::   68 ::   69 ::   70 ::
71 ::   72 ::   73 ::   74 ::   75 ::   76 ::   77 ::   78 ::   79 ::
80 ::   81 ::   82 ::   83 ::   84 ::   85 ::   86 ::   87 ::   88 ::
89 ::   90 ::   91 ::   92 ::   93 ::   94 ::   95 ::   96 ::   97 ::
98 ::   99 ::

::      Failed to extend 1 transcripts

::      Seen 0 5 prime UTRs with and average length of 0

::      Seen 0 3 prime UTRs with and average length of 0

 

 

::      ::      Writing ADXOCv1a520630 ADXBRCv2a520413 ADXECv1a520743
ADXLCv1a520538 ADXCRCG2a520319 HG-U133_Plus_2 ADXPCv1a520642 Xrefs
::      :: - Mon Feb 21 18:26:37 2011

 

::      Logging probesets that don't map to any transcripts - Mon Feb 21
18:26:37 2011

::      Updating 0 promiscuous probesets - Mon Feb 21 18:40:28 2011

::      UnmappedObjects loaded:                 598994

::      ADXBRCv2a520413 distinct ProbeSet xrefs mapped(total xrefs):
1/60856(1)

::      ADXOCv1a520630 distinct ProbeSet xrefs mapped(total xrefs):
4/120373(7)

::      ADXECv1a520743 distinct ProbeSet xrefs mapped(total xrefs):
4/111012(7)

::      ADXLCv1a520538 distinct ProbeSet xrefs mapped(total xrefs):
4/60416(10)

::      ADXCRCG2a520319 distinct ProbeSet xrefs mapped(total xrefs):
2/61528(2)

::      HG-U133_Plus_2 distinct ProbeSet xrefs mapped(total xrefs):
1/54675(4)

::      ADXPCv1a520642 distinct ProbeSet xrefs mapped(total xrefs):
2/121563(2)

::      Mapped 9/167074 transcripts  - Mon Feb 21 18:40:39 2011

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