Question: snpEff warning information
0
gravatar for zhengyunchaosky
3.9 years ago by
Technical University of Munich
zhengyunchaosky20 wrote:

Hi,

I try to use "ftp://ftp.ensemblgenomes.org/pub/release-30/plants/gff3/oryza_sativa/Oryza_sativa.IRGSP-1.0.30.gff3.gz" to build the database to do snp annotation. 

java -Xmx15G  -jar snpEff.jar build -gff3 -v IRGSP 

However,I got warning information below.

00:00:00.000    SnpEff version SnpEff 4.1 (build 2015-01-07), by Pablo Cingolani
00:00:00.010    Command: 'build'
00:00:00.028    Building database for 'IRGSP'
00:00:00.029    Reading configuration file 'snpEff.config'. Genome: 'IRGSP'
00:00:01.262    done
Reading GFF3 data file  : '/datacenter/disk2/zhengyunchao/snpEffnipo/snpEff/./data/IRGSP/genes.gff'
        Reading genes       : ....................................................................................................
                10000   ....................................................................................................
                20000   ....................................................................................................
                30000   ........................................................
        Total: 35679 Genes added.
        Reading transcripts :   Total: 0 Transcripts added.
        Reading exons       : WARNING: Cannot find transcript 'transcript:EPlOSAT00000003714'. Created transcript 'transcript:EPlOSAT00000003714' and gene 'Gene_transcript:EPlOSAT00000003714'
 for this exon. File '/datacenter/disk2/zhengyunchao/snpEffnipo/snpEff/./data/IRGSP/genes.gff' line 68  '1      agi     exon    2631    2760    .       -       .       Parent=transcript:EPlOS
AT00000003714;Name=EPlOSAE00000004118;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=EPlOSAE00000004118;rank=1;version=1'
WARNING: Cannot find transcript 'transcript:OS01T0100100-01'. Created transcript 'transcript:OS01T0100100-01' and gene 'Gene_transcript:OS01T0100100-01' for this exon. File '/datacenter/disk2
/zhengyunchao/snpEffnipo/snpEff/./data/IRGSP/genes.gff' line 72 '1      irgsp   exon    2983    3268    .       +       .       Parent=transcript:OS01T0100100-01;Name=OS01T0100100-01.exon1;co
nstitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=OS01T0100100-01.exon1;rank=1;version=1'
 

 

Anyway, I successfully build the database to do my annotation.

 Total: 248345 sequences added, 0 sequences ignored.

        Adjusting transcripts: 
        Adjusting genes: 
        Adjusting chromosomes lengths: 
        Ranking exons: 
        Create UTRs from CDS (if needed): 
        Correcting exons based on frame information.

        Remove empty chromosomes: 

        Marking as 'coding' from CDS information: 
        Done: 42132 transcripts marked
#-----------------------------------------------
# Genome name                : 'IRGSP'
# Genome version             : 'IRGSP'
# Has protein coding info    : true
# Genes                      : 133430
# Protein coding genes       : 42132
#-----------------------------------------------
# Transcripts                : 97751
# Avg. transcripts per gene  : 0.73
#-----------------------------------------------
# Checked transcripts        : 
#               AA sequences :      0 ( 0.00% )
#              DNA sequences :      0 ( 0.00% )
#-----------------------------------------------
# Protein coding transcripts : 42132
#              Length errors :   1261 ( 2.99% )
#  STOP codons in CDS errors :      0 ( 0.00% )
#         START codon errors :   9404 ( 22.32% )
#        STOP codon warnings :   1929 ( 4.58% )
#              UTR sequences :  38051 ( 38.93% )
#               Total Errors :  10269 ( 24.37% )
#-----------------------------------------------
# Cds                        : 163451
# Exons                      : 248345
# Exons with sequence        : 248345
# Exons without sequence     : 0
# Avg. exons per transcript  : 2.54
# WARNING                    : No mitochondrion chromosome found
#-----------------------------------------------
# Number of chromosomes      : 61
# Chromosomes names [sizes]  :
#               '1' [43270923]
#               '3' [36413819]
#               '2' [35937250]
#               '4' [35502694]
#               '6' [31248787]
#               '5' [29958434]
#               '7' [29697621]
#               '11' [29021106]
#               '8' [28443022]
#               '12' [27531856]
#               '10' [23207287]
#               '9' [23012720]
#               'AP008246' [206004]
#               'AP008247' [157458]
#               'AC160949' [128256]
#               'AC156495' [88500]
#               'AC155918' [32941]
#               'Syng_TIGR_028' [31094]
#               'Syng_TIGR_023' [24772]
#               'Syng_TIGR_045' [22545]
#               'Syng_TIGR_005' [21787]
#               'Syng_TIGR_014' [21421]
#               'Syng_TIGR_047' [20829]
#               'Syng_TIGR_026' [19971]
#               'Syng_TIGR_004' [19457]
#               'Syng_TIGR_021' [17477]
#               'Syng_TIGR_008' [16676]
#               'Syng_TIGR_012' [16417]
#               'Syng_TIGR_010' [15493]
#               'AC174930' [15426]
#               'Syng_TIGR_002' [14476]
#               'Syng_TIGR_037' [13061]
#               'Syng_TIGR_029' [12884]
#               'Syng_TIGR_016' [12792]
#               'Syng_TIGR_027' [11522]
#               'Syng_TIGR_046' [11447]
#               'Syng_TIGR_033' [11093]
#               'Syng_TIGR_011' [10901]
#               'Syng_TIGR_030' [10794]
#               'Syng_TIGR_020' [10699]
#               'Syng_TIGR_035' [10686]
#               'Syng_TIGR_015' [10595]
#               'Syng_TIGR_013' [10512]
#               'Syng_TIGR_036' [10434]
#               'Syng_TIGR_019' [10422]
#               'Syng_TIGR_034' [10311]
#               'Syng_TIGR_009' [10296]
#               'Syng_TIGR_041' [10210]
#               'Syng_TIGR_024' [10060]
#               'Syng_TIGR_022' [9889]
#               'Syng_TIGR_032' [9603]
#               'Syng_TIGR_031' [9548]
#               'Syng_TIGR_050' [8529]
#               'Syng_TIGR_038' [8197]
#               'Syng_TIGR_007' [7820]
#               'Syng_TIGR_048' [7140]
#               'Syng_TIGR_039' [6269]
#               'Syng_TIGR_049' [6261]
#               'Syng_TIGR_044' [6000]
#               'Syng_TIGR_042' [5510]
#               'Syng_TIGR_043' [4236]
#-----------------------------------------------

00:01:02.976    Caracterizing exons by splicing (stage 1) : 
        ....................................................................................................
        100000  ....................................................................................................
        200000  ................................................
00:01:03.841    Caracterizing exons by splicing (stage 2) : 
        ....................................................................................................
        100000  ....................................................................................................
        200000  ................................................00:01:04.100    done.
00:01:04.101    [Optional] Rare amino acid annotations
00:01:04.106    Warning: Cannot read optional protein sequence file '/datacenter/disk2/zhengyunchao/snpEffnipo/snpEff/./data/IRGSP/protein.fa', nothing done.
00:01:04.108    Saving database
00:01:54.212    [Optional] Reading regulation elements: GFF
00:01:54.214    Warning: Cannot read optional regulation file '/datacenter/disk2/zhengyunchao/snpEffnipo/snpEff/./data/IRGSP/regulation.gff', nothing done.
00:01:54.214    [Optional] Reading regulation elements: BED 
00:01:54.215    Cannot find optional regulation dir '/datacenter/disk2/zhengyunchao/snpEffnipo/snpEff/./data/IRGSP/regulation.bed/', nothing done.
00:01:54.216    [Optional] Reading motifs: GFF
00:01:54.217    Warning: Cannot open PWMs file /datacenter/disk2/zhengyunchao/snpEffnipo/snpEff/./data/IRGSP/pwms.bin. Nothing done
00:01:54.217    Done
00:01:54.240    Logging
00:01:55.259    Checking for updates...

 

I wonder why the warning information came up. Thanks in advance!

snp genome • 2.7k views
ADD COMMENTlink modified 3.9 years ago • written 3.9 years ago by zhengyunchaosky20

Maybe there are some 'errors' in the gff3 you've used for creating the db. Can you check if EPlOSAT00000003714 transcript has a transcript line in the gff3 file (apart from exon line)?

ADD REPLYlink written 3.9 years ago by iraun3.6k
0
gravatar for zhengyunchaosky
3.9 years ago by
Technical University of Munich
zhengyunchaosky20 wrote:

Thanks for your respond! Yes, it has the transcript line. 

1       agi     transcript      2631    2760    .       -       .       ID=transcript:EPlOSAT00000003714;Parent=gene:EPlOSAG00000002326;biotype=ncRNA;transcript_id=EPlOSAT00000003714;version=1
1       agi     exon    2631    2760    .       -       .       Parent=transcript:EPlOSAT00000003714;Name=EPlOSAE00000004118;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=EPlOSAE00000004118;rank=1;version=1

 

ADD COMMENTlink written 3.9 years ago by zhengyunchaosky20
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