Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/94/dc0a44fff244214614e4042b707522/fi_workdir/659_6i-T1-TRNA-1_A23MVY2LT4_2.gtf
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fa/cb418118e339be41d667564136dbdc/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fa/cb418118e339be41d667564136dbdc/.command.run
==> STAGING COMPLETE (3 inputs)
Using standard /usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/agat_config.yaml file
------------------------------------------------------------------------------
| Another GFF Analysis Toolkit (AGAT) - Version: v1.2.0 |
| https://github.com/NBISweden/AGAT |
| National Bioinformatics Infrastructure Sweden (NBIS) - www.nbis.se |
------------------------------------------------------------------------------
------ Start parsing ------
-------------------------- parse options and metadata --------------------------
=> Accessing the feature_levels YAML file
Using standard /usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/feature_levels.yaml file
=> Attribute used to group features when no Parent/ID relationship exists (i.e common tag):
* locus_tag
* gene_id
=> merge_loci option deactivated
=> Machine information:
This script is being run by perl v5.32.1
Bioperl location being used: /usr/local/lib/perl5/site_perl/Bio/
Operating system being used: linux
=> Accessing Ontology
No ontology accessible from the gff file header!
We use the SOFA ontology distributed with AGAT:
/usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/so.obo
Read ontology /usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/so.obo:
4 root terms, and 2596 total terms, and 1516 leaf terms
Filtering ontology:
We found 1861 terms that are sequence_feature or is_a child of it.
--------------------------------- parsing file ---------------------------------
=> Number of line in file: 1717
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 1717
=> Number of feature type (3rd column): 2
* Level1: 0 =>
* level2: 0 =>
* level3: 2 => CDS exon
* unknown: 0 =>
=>Check because only level3 features:
* Number of feature with Parent attribute:0
* Number of feature with a common attribute:1717
=> Some common attributes and some Parent attributes missing.
/!\ For features where both are missing A single Level2 features (e.g. mRNA) and a single level1 (e.g. gene) will be created by AGAT, and all level3 feautres (e,g, CDS,exon) will be attached to them. This is probably not what you want...
see B. 2.2 and 3. at https://agat.readthedocs.io/en/latest/agat_how_does_it_work.html
/!\ For features where the common attribute or the parent attribute is missing, it would be fine as long as you do not expect isoforms in your annotation (Eukaryote). see B. 4. at https://agat.readthedocs.io/en/latest/agat_how_does_it_work.html
!! You might try to fix the issue by choosing a common tag attribute to use in order to group the features correctly (parameter --ct in agat_convert_sp_gxf2gxf.pl).
=> Version of the Bioperl GFF parser selected by AGAT: 2
------ End parsing (done in 0 second) ------
------ Start checks ------
---------------------------- Check1: feature types -----------------------------
----------------------------------- ontology -----------------------------------
All feature types in agreement with the Ontology.
------------------------------------- agat -------------------------------------
AGAT can deal with all the encountered feature types (3rd column)
------------------------------ done in 0 seconds -------------------------------
------------------------------ Check2: duplicates ------------------------------
None found
------------------------------ done in 0 seconds -------------------------------
-------------------------- Check3: sequential bucket ---------------------------
Nothing to check as sequential bucket!
------------------------------ done in 0 seconds -------------------------------
--------------------------- Check4: l2 linked to l3 ----------------------------
L1 and L2 created:
CPNE4--ADGRG7 HAVANA gene 32467 49835 . + . FI_gene_label "ADGRG7^ENSG00000144820.8" ; ID "CPNE4--ADGRG7^ADGRG7^ENSG00000144820.8" ; ccdsid "CCDS2938.1" ; exon_id "ENSE00001225273.6" ; exon_number 1 ; gene_id "CPNE4--ADGRG7^ADGRG7^ENSG00000144820.8" ; gene_name ADGRG7 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159083.2" ; havana_transcript "OTTHUMT00000353236.2" ; hgnc_id "HGNC:19241" ; level 2 ; orig_coord_info "chr3,100609857,100609971,+" ; protein_id "ENSP00000273352.3" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "CPNE4--ADGRG7^ENST00000273352.8" ; transcript_name "ADGRG7-201" ; transcript_support_level 1 ; transcript_type protein_coding
CPNE4--ADGRG7 HAVANA mRNA 32467 49835 . + . FI_gene_label "ADGRG7^ENSG00000144820.8" ; ID "CPNE4--ADGRG7^ENST00000273352.8" ; Parent "CPNE4--ADGRG7^ADGRG7^ENSG00000144820.8" ; ccdsid "CCDS2938.1" ; exon_id "ENSE00001225273.6" ; exon_number 1 ; gene_id "CPNE4--ADGRG7^ADGRG7^ENSG00000144820.8" ; gene_name ADGRG7 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159083.2" ; havana_transcript "OTTHUMT00000353236.2" ; hgnc_id "HGNC:19241" ; level 2 ; orig_coord_info "chr3,100609857,100609971,+" ; protein_id "ENSP00000273352.3" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "CPNE4--ADGRG7^ENST00000273352.8" ; transcript_name "ADGRG7-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
CPNE4--ADGRG7 ENSEMBL gene 6503 29459 . + . FI_gene_label "CPNE4^ENSG00000196353.11" ; ID "CPNE4--ADGRG7^CPNE4^ENSG00000196353.11" ; ccdsid "CCDS3072.1" ; exon_id "ENSE00003536115.1" ; exon_number 2 ; gene_id "CPNE4--ADGRG7^CPNE4^ENSG00000196353.11" ; gene_name CPNE4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159631.14" ; hgnc_id "HGNC:2317" ; level 3 ; orig_coord_info "chr3,131905264,131905443,-" ; protein_id "ENSP00000411904.1" ; tag basic appris_principal_1 CCDS ; transcript_id "CPNE4--ADGRG7^ENST00000429747.5" ; transcript_name "CPNE4-201" ; transcript_support_level 1 ; transcript_type protein_coding
CPNE4--ADGRG7 ENSEMBL mRNA 6503 29459 . + . FI_gene_label "CPNE4^ENSG00000196353.11" ; ID "CPNE4--ADGRG7^ENST00000429747.5" ; Parent "CPNE4--ADGRG7^CPNE4^ENSG00000196353.11" ; ccdsid "CCDS3072.1" ; exon_id "ENSE00003536115.1" ; exon_number 2 ; gene_id "CPNE4--ADGRG7^CPNE4^ENSG00000196353.11" ; gene_name CPNE4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159631.14" ; hgnc_id "HGNC:2317" ; level 3 ; orig_coord_info "chr3,131905264,131905443,-" ; protein_id "ENSP00000411904.1" ; tag basic appris_principal_1 CCDS ; transcript_id "CPNE4--ADGRG7^ENST00000429747.5" ; transcript_name "CPNE4-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
DAPK2--RAD51B ENSEMBL gene 5533 30352 . + . FI_gene_label "DAPK2^ENSG00000035664.11" ; ID "DAPK2--RAD51B^DAPK2^ENSG00000035664.11" ; ccdsid "CCDS10188.1" ; exon_id "ENSE00003473652.1" ; exon_number 1 ; gene_id "DAPK2--RAD51B^DAPK2^ENSG00000035664.11" ; gene_name DAPK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132947.5" ; hgnc_id "HGNC:2675" ; level 3 ; orig_coord_info "chr15,64040170,64040261,-" ; protein_id "ENSP00000261891.3" ; tag basic appris_principal_1 CCDS ; transcript_id "DAPK2--RAD51B^ENST00000261891.7" ; transcript_name "DAPK2-201" ; transcript_support_level 2 ; transcript_type protein_coding
DAPK2--RAD51B ENSEMBL mRNA 5533 30352 . + . FI_gene_label "DAPK2^ENSG00000035664.11" ; ID "DAPK2--RAD51B^ENST00000261891.7" ; Parent "DAPK2--RAD51B^DAPK2^ENSG00000035664.11" ; ccdsid "CCDS10188.1" ; exon_id "ENSE00003473652.1" ; exon_number 1 ; gene_id "DAPK2--RAD51B^DAPK2^ENSG00000035664.11" ; gene_name DAPK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132947.5" ; hgnc_id "HGNC:2675" ; level 3 ; orig_coord_info "chr15,64040170,64040261,-" ; protein_id "ENSP00000261891.3" ; tag basic appris_principal_1 CCDS ; transcript_id "DAPK2--RAD51B^ENST00000261891.7" ; transcript_name "DAPK2-201" ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created:
DAPK2--RAD51B ENSEMBL gene 33386 44112 . + . FI_gene_label "RAD51B^ENSG00000182185.18" ; ID "DAPK2--RAD51B^RAD51B^ENSG00000182185.18" ; exon_id "ENSE00001518458.1" ; exon_number 2 ; gene_id "DAPK2--RAD51B^RAD51B^ENSG00000182185.18" ; gene_name RAD51B ; gene_type protein_coding ; havana_gene "OTTHUMG00000157530.6" ; hgnc_id "HGNC:9822" ; level 3 ; orig_coord_info "chr14,67823544,67823627,+" ; protein_id "ENSP00000375101.4" ; tag basic ; transcript_id "DAPK2--RAD51B^ENST00000390683.7" ; transcript_name "RAD51B-201" ; transcript_support_level 1 ; transcript_type protein_coding
DAPK2--RAD51B ENSEMBL mRNA 33386 44112 . + . FI_gene_label "RAD51B^ENSG00000182185.18" ; ID "DAPK2--RAD51B^ENST00000390683.7" ; Parent "DAPK2--RAD51B^RAD51B^ENSG00000182185.18" ; exon_id "ENSE00001518458.1" ; exon_number 2 ; gene_id "DAPK2--RAD51B^RAD51B^ENSG00000182185.18" ; gene_name RAD51B ; gene_type protein_coding ; havana_gene "OTTHUMG00000157530.6" ; hgnc_id "HGNC:9822" ; level 3 ; orig_coord_info "chr14,67823544,67823627,+" ; protein_id "ENSP00000375101.4" ; tag basic ; transcript_id "DAPK2--RAD51B^ENST00000390683.7" ; transcript_name "RAD51B-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TLK2--LINC01347 HAVANA gene 4784 35054 . + . FI_gene_label "TLK2^ENSG00000146872.18" ; ID "TLK2--LINC01347^TLK2^ENSG00000146872.18" ; ccdsid "CCDS62283.1" ; exon_id "ENSE00003568961.1" ; exon_number 2 ; gene_id "TLK2--LINC01347^TLK2^ENSG00000146872.18" ; gene_name TLK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179176.3" ; havana_transcript "OTTHUMT00000445140.1" ; hgnc_id "HGNC:11842" ; level 2 ; orig_coord_info "chr17,62481126,62481206,+" ; protein_id "ENSP00000316512.9" ; tag basic CCDS ; transcript_id "TLK2--LINC01347^ENST00000326270.13" ; transcript_name "TLK2-201" ; transcript_support_level 1 ; transcript_type protein_coding
TLK2--LINC01347 HAVANA mRNA 4784 35054 . + . FI_gene_label "TLK2^ENSG00000146872.18" ; ID "TLK2--LINC01347^ENST00000326270.13" ; Parent "TLK2--LINC01347^TLK2^ENSG00000146872.18" ; ccdsid "CCDS62283.1" ; exon_id "ENSE00003568961.1" ; exon_number 2 ; gene_id "TLK2--LINC01347^TLK2^ENSG00000146872.18" ; gene_name TLK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179176.3" ; havana_transcript "OTTHUMT00000445140.1" ; hgnc_id "HGNC:11842" ; level 2 ; orig_coord_info "chr17,62481126,62481206,+" ; protein_id "ENSP00000316512.9" ; tag basic CCDS ; transcript_id "TLK2--LINC01347^ENST00000326270.13" ; transcript_name "TLK2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TMPRSS2--ERG HAVANA gene 30939 50248 . + . FI_gene_label "ERG^ENSG00000157554.19" ; ID "TMPRSS2--ERG^ERG^ENSG00000157554.19" ; ccdsid "CCDS13658.1" ; exon_id "ENSE00001931764.2" ; exon_number 1 ; gene_id "TMPRSS2--ERG^ERG^ENSG00000157554.19" ; gene_name ERG ; gene_type protein_coding ; havana_gene "OTTHUMG00000090767.4" ; havana_transcript "OTTHUMT00000207531.2" ; hgnc_id "HGNC:3446" ; level 2 ; orig_coord_info "chr21,38498363,38498380,-" ; protein_id "ENSP00000288319.7" ; tag CAGE_supported_TSS basic MANE_Select appris_principal_1 CCDS ; transcript_id "TMPRSS2--ERG^ENST00000288319.12" ; transcript_name "ERG-201" ; transcript_support_level 1 ; transcript_type protein_coding
TMPRSS2--ERG HAVANA mRNA 30939 50248 . + . FI_gene_label "ERG^ENSG00000157554.19" ; ID "TMPRSS2--ERG^ENST00000288319.12" ; Parent "TMPRSS2--ERG^ERG^ENSG00000157554.19" ; ccdsid "CCDS13658.1" ; exon_id "ENSE00001931764.2" ; exon_number 1 ; gene_id "TMPRSS2--ERG^ERG^ENSG00000157554.19" ; gene_name ERG ; gene_type protein_coding ; havana_gene "OTTHUMG00000090767.4" ; havana_transcript "OTTHUMT00000207531.2" ; hgnc_id "HGNC:3446" ; level 2 ; orig_coord_info "chr21,38498363,38498380,-" ; protein_id "ENSP00000288319.7" ; tag CAGE_supported_TSS basic MANE_Select appris_principal_1 CCDS ; transcript_id "TMPRSS2--ERG^ENST00000288319.12" ; transcript_name "ERG-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TMPRSS2--ERG HAVANA gene 4575 23486 . + . FI_gene_label "TMPRSS2^ENSG00000184012.14" ; ID "TMPRSS2--ERG^TMPRSS2^ENSG00000184012.14" ; ccdsid "CCDS33564.1" ; exon_id "ENSE00003502036.1" ; exon_number 2 ; gene_id "TMPRSS2--ERG^TMPRSS2^ENSG00000184012.14" ; gene_name TMPRSS2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000086762.7" ; havana_transcript "OTTHUMT00000195189.2" ; hgnc_id "HGNC:11876" ; level 2 ; orig_coord_info "chr21,41498119,41498133,-" ; protein_id "ENSP00000330330.5" ; tag CAGE_supported_TSS basic MANE_Select appris_principal_2 CCDS ; transcript_id "TMPRSS2--ERG^ENST00000332149.10" ; transcript_name "TMPRSS2-201" ; transcript_support_level 1 ; transcript_type protein_coding
TMPRSS2--ERG HAVANA mRNA 4575 23486 . + . FI_gene_label "TMPRSS2^ENSG00000184012.14" ; ID "TMPRSS2--ERG^ENST00000332149.10" ; Parent "TMPRSS2--ERG^TMPRSS2^ENSG00000184012.14" ; ccdsid "CCDS33564.1" ; exon_id "ENSE00003502036.1" ; exon_number 2 ; gene_id "TMPRSS2--ERG^TMPRSS2^ENSG00000184012.14" ; gene_name TMPRSS2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000086762.7" ; havana_transcript "OTTHUMT00000195189.2" ; hgnc_id "HGNC:11876" ; level 2 ; orig_coord_info "chr21,41498119,41498133,-" ; protein_id "ENSP00000330330.5" ; tag CAGE_supported_TSS basic MANE_Select appris_principal_2 CCDS ; transcript_id "TMPRSS2--ERG^ENST00000332149.10" ; transcript_name "TMPRSS2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TVP23C--CDRT4 HAVANA gene 1052 15760 . + . FI_gene_label "TVP23C^ENSG00000175106.17" ; ID "TVP23C--CDRT4^TVP23C^ENSG00000175106.17" ; ccdsid "CCDS11170.1" ; exon_id "ENSE00001105678.2" ; exon_number 1 ; gene_id "TVP23C--CDRT4^TVP23C^ENSG00000175106.17" ; gene_name TVP23C ; gene_type protein_coding ; havana_gene "OTTHUMG00000171461.10" ; havana_transcript "OTTHUMT00000130705.3" ; hgnc_id "HGNC:30453" ; level 2 ; orig_coord_info "chr17,15563437,15563448,-" ; protein_id "ENSP00000225576.3" ; tag basic CCDS ; transcript_id "TVP23C--CDRT4^ENST00000225576.7" ; transcript_name "TVP23C-201" ; transcript_support_level 1 ; transcript_type protein_coding
TVP23C--CDRT4 HAVANA mRNA 1052 15760 . + . FI_gene_label "TVP23C^ENSG00000175106.17" ; ID "TVP23C--CDRT4^ENST00000225576.7" ; Parent "TVP23C--CDRT4^TVP23C^ENSG00000175106.17" ; ccdsid "CCDS11170.1" ; exon_id "ENSE00001105678.2" ; exon_number 1 ; gene_id "TVP23C--CDRT4^TVP23C^ENSG00000175106.17" ; gene_name TVP23C ; gene_type protein_coding ; havana_gene "OTTHUMG00000171461.10" ; havana_transcript "OTTHUMT00000130705.3" ; hgnc_id "HGNC:30453" ; level 2 ; orig_coord_info "chr17,15563437,15563448,-" ; protein_id "ENSP00000225576.3" ; tag basic CCDS ; transcript_id "TVP23C--CDRT4^ENST00000225576.7" ; transcript_name "TVP23C-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TVP23C--CDRT4 HAVANA gene 19889 25887 . + . FI_gene_label "CDRT4^ENSG00000239704.11" ; ID "TVP23C--CDRT4^CDRT4^ENSG00000239704.11" ; ccdsid "CCDS73995.1" ; exon_id "ENSE00003735347.1" ; exon_number 3 ; gene_id "TVP23C--CDRT4^CDRT4^ENSG00000239704.11" ; gene_name CDRT4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059070.14" ; havana_transcript "OTTHUMT00000130383.9" ; hgnc_id "HGNC:14383" ; level 2 ; orig_coord_info "chr17,15440208,15440238,-" ; protein_id "ENSP00000482523.1" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TVP23C--CDRT4^ENST00000619038.5" ; transcript_name "CDRT4-204" ; transcript_support_level 1 ; transcript_type protein_coding
TVP23C--CDRT4 HAVANA mRNA 19889 25887 . + . FI_gene_label "CDRT4^ENSG00000239704.11" ; ID "TVP23C--CDRT4^ENST00000619038.5" ; Parent "TVP23C--CDRT4^CDRT4^ENSG00000239704.11" ; ccdsid "CCDS73995.1" ; exon_id "ENSE00003735347.1" ; exon_number 3 ; gene_id "TVP23C--CDRT4^CDRT4^ENSG00000239704.11" ; gene_name CDRT4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059070.14" ; havana_transcript "OTTHUMT00000130383.9" ; hgnc_id "HGNC:14383" ; level 2 ; orig_coord_info "chr17,15440208,15440238,-" ; protein_id "ENSP00000482523.1" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TVP23C--CDRT4^ENST00000619038.5" ; transcript_name "CDRT4-204" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
AC025884.2--IGH-@-ext HAVANA gene 1001 1711 . + . FI_gene_label "AC025884.2^ENSG00000259098.1" ; ID "AC025884.2--IGH-@-ext^AC025884.2^ENSG00000259098.1" ; exon_id "ENSE00002441536.1" ; exon_number 1 ; gene_id "AC025884.2--IGH-@-ext^AC025884.2^ENSG00000259098.1" ; gene_name "AC025884.2" ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000171790.1" ; havana_transcript "OTTHUMT00000415152.1" ; level 2 ; ont "PGO:0000004" ; orig_coord_info "chr15,22258138,22258848,+" ; tag basic ; transcript_id "AC025884.2--IGH-@-ext^ENST00000553429.1" ; transcript_name "AC025884.2-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
AC025884.2--IGH-@-ext HAVANA RNA 1001 1711 . + . FI_gene_label "AC025884.2^ENSG00000259098.1" ; ID "AC025884.2--IGH-@-ext^ENST00000553429.1" ; Parent "AC025884.2--IGH-@-ext^AC025884.2^ENSG00000259098.1" ; exon_id "ENSE00002441536.1" ; exon_number 1 ; gene_id "AC025884.2--IGH-@-ext^AC025884.2^ENSG00000259098.1" ; gene_name "AC025884.2" ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000171790.1" ; havana_transcript "OTTHUMT00000415152.1" ; level 2 ; ont "PGO:0000004" ; orig_coord_info "chr15,22258138,22258848,+" ; tag basic ; transcript_id "AC025884.2--IGH-@-ext^ENST00000553429.1" ; transcript_name "AC025884.2-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created:
AC025884.2--IGH-@-ext SuperLocus-ext gene 4712 1296052 . + . FI_gene_label "IGH-@-ext^IGH-.g@-ext" ; ID "AC025884.2--IGH-@-ext^IGH-@-ext^IGH-.g@-ext" ; gene_id "AC025884.2--IGH-@-ext^IGH-@-ext^IGH-.g@-ext" ; gene_name "IGH-@-ext" ; orig_coord_info "chr14,105583731,106875071,+" ; transcript_id "AC025884.2--IGH-@-ext^IGH-.t@-ext"
AC025884.2--IGH-@-ext SuperLocus-ext RNA 4712 1296052 . + . FI_gene_label "IGH-@-ext^IGH-.g@-ext" ; ID "AC025884.2--IGH-@-ext^IGH-.t@-ext" ; Parent "AC025884.2--IGH-@-ext^IGH-@-ext^IGH-.g@-ext" ; gene_id "AC025884.2--IGH-@-ext^IGH-@-ext^IGH-.g@-ext" ; gene_name "IGH-@-ext" ; orig_coord_info "chr14,105583731,106875071,+" ; transcript_id "AC025884.2--IGH-@-ext^IGH-.t@-ext"
L1 and L2 created:
TLK2--LINC01347 HAVANA gene 41405 47393 . + . FI_gene_label "LINC01347^ENSG00000214837.8" ; ID "TLK2--LINC01347^LINC01347^ENSG00000214837.8" ; exon_id "ENSE00002389344.1" ; exon_number 1 ; gene_id "TLK2--LINC01347^LINC01347^ENSG00000214837.8" ; gene_name LINC01347 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000039861.5" ; havana_transcript "OTTHUMT00000481524.1" ; hgnc_id "HGNC:50566" ; level 2 ; ont "PGO:0000005" "PGO:0000019" ; orig_coord_info "chr1,243097190,243097299,-" ; tag basic ; transcript_id "TLK2--LINC01347^ENST00000417964.2" ; transcript_name "LINC01347-201" ; transcript_support_level NA ; transcript_type transcribed_unprocessed_pseudogene
TLK2--LINC01347 HAVANA RNA 41405 47393 . + . FI_gene_label "LINC01347^ENSG00000214837.8" ; ID "TLK2--LINC01347^ENST00000417964.2" ; Parent "TLK2--LINC01347^LINC01347^ENSG00000214837.8" ; exon_id "ENSE00002389344.1" ; exon_number 1 ; gene_id "TLK2--LINC01347^LINC01347^ENSG00000214837.8" ; gene_name LINC01347 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000039861.5" ; havana_transcript "OTTHUMT00000481524.1" ; hgnc_id "HGNC:50566" ; level 2 ; ont "PGO:0000005" "PGO:0000019" ; orig_coord_info "chr1,243097190,243097299,-" ; tag basic ; transcript_id "TLK2--LINC01347^ENST00000417964.2" ; transcript_name "LINC01347-201" ; transcript_support_level NA ; transcript_type transcribed_unprocessed_pseudogene
L1 and L2 created:
TLK2P1--AC110079.1 HAVANA gene 1001 4192 . + . FI_gene_label "TLK2P1^ENSG00000226049.3" ; ID "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3" ; exon_id "ENSE00002174619.1" ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3" ; gene_name TLK2P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166422.1" ; havana_transcript "OTTHUMT00000389700.1" ; hgnc_id "HGNC:18048" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr17,34036681,34039872,-" ; tag pseudo_consens basic ; transcript_id "TLK2P1--AC110079.1^ENST00000530992.1" ; transcript_name "TLK2P1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
TLK2P1--AC110079.1 HAVANA RNA 1001 4192 . + . FI_gene_label "TLK2P1^ENSG00000226049.3" ; ID "TLK2P1--AC110079.1^ENST00000530992.1" ; Parent "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3" ; exon_id "ENSE00002174619.1" ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3" ; gene_name TLK2P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166422.1" ; havana_transcript "OTTHUMT00000389700.1" ; hgnc_id "HGNC:18048" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr17,34036681,34039872,-" ; tag pseudo_consens basic ; transcript_id "TLK2P1--AC110079.1^ENST00000530992.1" ; transcript_name "TLK2P1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
L1 and L2 created:
TLK2P1--AC110079.1 HAVANA gene 7193 19707 . + . FI_gene_label "AC110079.1^ENSG00000260404.3" ; ID "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3" ; exon_id "ENSE00002625896.1" ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3" ; gene_name "AC110079.1" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000161164.4" ; havana_transcript "OTTHUMT00000364170.2" ; level 2 ; orig_coord_info "chr4,118591773,118591895,+" ; tag dotter_confirmed basic ; transcript_id "TLK2P1--AC110079.1^ENST00000567913.2" ; transcript_name "AC110079.1-201" ; transcript_support_level 5 ; transcript_type processed_transcript
TLK2P1--AC110079.1 HAVANA RNA 7193 19707 . + . FI_gene_label "AC110079.1^ENSG00000260404.3" ; ID "TLK2P1--AC110079.1^ENST00000567913.2" ; Parent "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3" ; exon_id "ENSE00002625896.1" ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3" ; gene_name "AC110079.1" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000161164.4" ; havana_transcript "OTTHUMT00000364170.2" ; level 2 ; orig_coord_info "chr4,118591773,118591895,+" ; tag dotter_confirmed basic ; transcript_id "TLK2P1--AC110079.1^ENST00000567913.2" ; transcript_name "AC110079.1-201" ; transcript_support_level 5 ; transcript_type processed_transcript
130 cases fixed where L3 features have parent feature(s) missing
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--------------------------- Check5: l1 linked to l2 ----------------------------
No problem found
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--------------------------- Check6: remove orphan l1 ---------------------------
We remove only those not supposed to be orphan
None found
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------------------------- Check7: all level3 locations -------------------------
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------------------------------ Check8: check cds -------------------------------
No problem found
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----------------------------- Check9: check exons ------------------------------
No exons created
No exons locations modified
No supernumerary exons removed
No level2 locations modified
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----------------------------- Check10: check utrs ------------------------------
267 UTRs created that were missing
No UTRs locations modified
No supernumerary UTRs removed
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------------------------ Check11: all level2 locations -------------------------
No problem found
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------------------------ Check12: all level1 locations -------------------------
We fixed 9 wrong level1 location cases
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---------------------- Check13: remove identical isoforms ----------------------
None found
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------ End checks (done in 1 second) ------
GFF3 file parsed