Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9c/8c79adf017d821bd08bea68a584abe/fi_workdir/659_eHw-T1-TRNA-1_B23MHV2LT4_1.gtf
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b2/9fb7806d420d3a21c50b3a68eaf109/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b2/9fb7806d420d3a21c50b3a68eaf109/.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: 2187
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 2187
=> Number of feature type (3rd column): 2
* Level1: 0 =>
* level2: 0 =>
* level3: 2 => exon CDS
* unknown: 0 =>
=>Check because only level3 features:
* Number of feature with Parent attribute:0
* Number of feature with a common attribute:2187
=> 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 1 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:
AC092807.3--DDAH1 HAVANA gene 13647 23704 . + . FI_gene_label "DDAH1^ENSG00000153904.21" ; ID "AC092807.3--DDAH1^DDAH1^ENSG00000153904.21" ; ccdsid "CCDS705.1" ; exon_id "ENSE00001013010.7" ; exon_number 1 ; gene_id "AC092807.3--DDAH1^DDAH1^ENSG00000153904.21" ; gene_name DDAH1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000191181.3" ; havana_transcript "OTTHUMT00000029189.3" ; hgnc_id "HGNC:2715" ; level 2 ; orig_coord_info "chr1,85464743,85465045,-" ; protein_id "ENSP00000284031.8" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AC092807.3--DDAH1^ENST00000284031.13" ; transcript_name "DDAH1-201" ; transcript_support_level 1 ; transcript_type protein_coding
AC092807.3--DDAH1 HAVANA mRNA 13647 23704 . + . FI_gene_label "DDAH1^ENSG00000153904.21" ; ID "AC092807.3--DDAH1^ENST00000284031.13" ; Parent "AC092807.3--DDAH1^DDAH1^ENSG00000153904.21" ; ccdsid "CCDS705.1" ; exon_id "ENSE00001013010.7" ; exon_number 1 ; gene_id "AC092807.3--DDAH1^DDAH1^ENSG00000153904.21" ; gene_name DDAH1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000191181.3" ; havana_transcript "OTTHUMT00000029189.3" ; hgnc_id "HGNC:2715" ; level 2 ; orig_coord_info "chr1,85464743,85465045,-" ; protein_id "ENSP00000284031.8" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AC092807.3--DDAH1^ENST00000284031.13" ; transcript_name "DDAH1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ARMH3--ASPH HAVANA gene 1001 5026 . + . FI_gene_label "ARMH3^ENSG00000120029.13" ; ID "ARMH3--ASPH^ARMH3^ENSG00000120029.13" ; exon_id "ENSE00001193247.2" ; exon_number 2 ; gene_id "ARMH3--ASPH^ARMH3^ENSG00000120029.13" ; gene_name ARMH3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000018943.2" ; havana_transcript "OTTHUMT00000050010.1" ; hgnc_id "HGNC:25788" ; level 2 ; orig_coord_info "chr10,102040013,102040114,-" ; protein_id "ENSP00000312408.4" ; tag basic ; transcript_id "ARMH3--ASPH^ENST00000311122.5" ; transcript_name "ARMH3-201" ; transcript_support_level 1 ; transcript_type protein_coding
ARMH3--ASPH HAVANA mRNA 1001 5026 . + . FI_gene_label "ARMH3^ENSG00000120029.13" ; ID "ARMH3--ASPH^ENST00000311122.5" ; Parent "ARMH3--ASPH^ARMH3^ENSG00000120029.13" ; exon_id "ENSE00001193247.2" ; exon_number 2 ; gene_id "ARMH3--ASPH^ARMH3^ENSG00000120029.13" ; gene_name ARMH3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000018943.2" ; havana_transcript "OTTHUMT00000050010.1" ; hgnc_id "HGNC:25788" ; level 2 ; orig_coord_info "chr10,102040013,102040114,-" ; protein_id "ENSP00000312408.4" ; tag basic ; transcript_id "ARMH3--ASPH^ENST00000311122.5" ; transcript_name "ARMH3-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ARMH3--ASPH HAVANA gene 31466 63686 . + . FI_gene_label "ASPH^ENSG00000198363.18" ; ID "ARMH3--ASPH^ASPH^ENSG00000198363.18" ; ccdsid "CCDS43742.1" ; exon_id "ENSE00002130497.1" ; exon_number 1 ; gene_id "ARMH3--ASPH^ASPH^ENSG00000198363.18" ; gene_name ASPH ; gene_type protein_coding ; havana_gene "OTTHUMG00000164375.13" ; havana_transcript "OTTHUMT00000378511.2" ; hgnc_id "HGNC:757" ; level 2 ; orig_coord_info "chr8,61714269,61714371,-" ; protein_id "ENSP00000348841.5" ; tag basic CCDS ; transcript_id "ARMH3--ASPH^ENST00000356457.9" ; transcript_name "ASPH-201" ; transcript_support_level 1 ; transcript_type protein_coding
ARMH3--ASPH HAVANA mRNA 31466 63686 . + . FI_gene_label "ASPH^ENSG00000198363.18" ; ID "ARMH3--ASPH^ENST00000356457.9" ; Parent "ARMH3--ASPH^ASPH^ENSG00000198363.18" ; ccdsid "CCDS43742.1" ; exon_id "ENSE00002130497.1" ; exon_number 1 ; gene_id "ARMH3--ASPH^ASPH^ENSG00000198363.18" ; gene_name ASPH ; gene_type protein_coding ; havana_gene "OTTHUMG00000164375.13" ; havana_transcript "OTTHUMT00000378511.2" ; hgnc_id "HGNC:757" ; level 2 ; orig_coord_info "chr8,61714269,61714371,-" ; protein_id "ENSP00000348841.5" ; tag basic CCDS ; transcript_id "ARMH3--ASPH^ENST00000356457.9" ; transcript_name "ASPH-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
MYC--CREB3L3 HAVANA gene 11143 21055 . + . FI_gene_label "CREB3L3^ENSG00000060566.14" ; ID "MYC--CREB3L3^CREB3L3^ENSG00000060566.14" ; ccdsid "CCDS12121.1" ; exon_id "ENSE00003222636.2" ; exon_number 1 ; gene_id "MYC--CREB3L3^CREB3L3^ENSG00000060566.14" ; gene_name CREB3L3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000181846.4" ; havana_transcript "OTTHUMT00000457922.2" ; hgnc_id "HGNC:18855" ; level 2 ; orig_coord_info "chr19,4153748,4153774,+" ; protein_id "ENSP00000078445.1" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "MYC--CREB3L3^ENST00000078445.7" ; transcript_name "CREB3L3-201" ; transcript_support_level 1 ; transcript_type protein_coding
MYC--CREB3L3 HAVANA mRNA 11143 21055 . + . FI_gene_label "CREB3L3^ENSG00000060566.14" ; ID "MYC--CREB3L3^ENST00000078445.7" ; Parent "MYC--CREB3L3^CREB3L3^ENSG00000060566.14" ; ccdsid "CCDS12121.1" ; exon_id "ENSE00003222636.2" ; exon_number 1 ; gene_id "MYC--CREB3L3^CREB3L3^ENSG00000060566.14" ; gene_name CREB3L3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000181846.4" ; havana_transcript "OTTHUMT00000457922.2" ; hgnc_id "HGNC:18855" ; level 2 ; orig_coord_info "chr19,4153748,4153774,+" ; protein_id "ENSP00000078445.1" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "MYC--CREB3L3^ENST00000078445.7" ; transcript_name "CREB3L3-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
MYC--CREB3L3 HAVANA gene 1001 5668 . + . FI_gene_label "MYC^ENSG00000136997.21" ; ID "MYC--CREB3L3^MYC^ENSG00000136997.21" ; exon_id "ENSE00003540079.1" ; exon_number 2 ; gene_id "MYC--CREB3L3^MYC^ENSG00000136997.21" ; gene_name MYC ; gene_type protein_coding ; havana_gene "OTTHUMG00000128475.10" ; havana_transcript "OTTHUMT00000250278.1" ; hgnc_id "HGNC:7553" ; level 1 ; orig_coord_info "chr8,127738263,127739019,+" ; protein_id "ENSP00000259523.6" ; tag basic exp_conf ; transcript_id "MYC--CREB3L3^ENST00000259523.10" ; transcript_name "MYC-201" ; transcript_support_level 1 ; transcript_type protein_coding
MYC--CREB3L3 HAVANA mRNA 1001 5668 . + . FI_gene_label "MYC^ENSG00000136997.21" ; ID "MYC--CREB3L3^ENST00000259523.10" ; Parent "MYC--CREB3L3^MYC^ENSG00000136997.21" ; exon_id "ENSE00003540079.1" ; exon_number 2 ; gene_id "MYC--CREB3L3^MYC^ENSG00000136997.21" ; gene_name MYC ; gene_type protein_coding ; havana_gene "OTTHUMG00000128475.10" ; havana_transcript "OTTHUMT00000250278.1" ; hgnc_id "HGNC:7553" ; level 1 ; orig_coord_info "chr8,127738263,127739019,+" ; protein_id "ENSP00000259523.6" ; tag basic exp_conf ; transcript_id "MYC--CREB3L3^ENST00000259523.10" ; transcript_name "MYC-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
RNF207--ARMH3 HAVANA gene 15721 19746 . + . FI_gene_label "ARMH3^ENSG00000120029.13" ; ID "RNF207--ARMH3^ARMH3^ENSG00000120029.13" ; exon_id "ENSE00001193247.2" ; exon_number 2 ; gene_id "RNF207--ARMH3^ARMH3^ENSG00000120029.13" ; gene_name ARMH3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000018943.2" ; havana_transcript "OTTHUMT00000050010.1" ; hgnc_id "HGNC:25788" ; level 2 ; orig_coord_info "chr10,102040013,102040114,-" ; protein_id "ENSP00000312408.4" ; tag basic ; transcript_id "RNF207--ARMH3^ENST00000311122.5" ; transcript_name "ARMH3-201" ; transcript_support_level 1 ; transcript_type protein_coding
RNF207--ARMH3 HAVANA mRNA 15721 19746 . + . FI_gene_label "ARMH3^ENSG00000120029.13" ; ID "RNF207--ARMH3^ENST00000311122.5" ; Parent "RNF207--ARMH3^ARMH3^ENSG00000120029.13" ; exon_id "ENSE00001193247.2" ; exon_number 2 ; gene_id "RNF207--ARMH3^ARMH3^ENSG00000120029.13" ; gene_name ARMH3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000018943.2" ; havana_transcript "OTTHUMT00000050010.1" ; hgnc_id "HGNC:25788" ; level 2 ; orig_coord_info "chr10,102040013,102040114,-" ; protein_id "ENSP00000312408.4" ; tag basic ; transcript_id "RNF207--ARMH3^ENST00000311122.5" ; transcript_name "ARMH3-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
RNF207--ARMH3 HAVANA gene 1645 12720 . + . FI_gene_label "RNF207^ENSG00000158286.13" ; ID "RNF207--ARMH3^RNF207^ENSG00000158286.13" ; ccdsid "CCDS59.2" ; exon_id "ENSE00003677151.1" ; exon_number 2 ; gene_id "RNF207--ARMH3^RNF207^ENSG00000158286.13" ; gene_name RNF207 ; gene_type protein_coding ; havana_gene "OTTHUMG00000001089.5" ; havana_transcript "OTTHUMT00000003669.3" ; hgnc_id "HGNC:32947" ; level 2 ; orig_coord_info "chr1,6206536,6206726,+" ; protein_id "ENSP00000367173.4" ; tag not_organism_supported basic MANE_Select appris_principal_1 CCDS ; transcript_id "RNF207--ARMH3^ENST00000377939.5" ; transcript_name "RNF207-201" ; transcript_support_level 5 ; transcript_type protein_coding
RNF207--ARMH3 HAVANA mRNA 1645 12720 . + . FI_gene_label "RNF207^ENSG00000158286.13" ; ID "RNF207--ARMH3^ENST00000377939.5" ; Parent "RNF207--ARMH3^RNF207^ENSG00000158286.13" ; ccdsid "CCDS59.2" ; exon_id "ENSE00003677151.1" ; exon_number 2 ; gene_id "RNF207--ARMH3^RNF207^ENSG00000158286.13" ; gene_name RNF207 ; gene_type protein_coding ; havana_gene "OTTHUMG00000001089.5" ; havana_transcript "OTTHUMT00000003669.3" ; hgnc_id "HGNC:32947" ; level 2 ; orig_coord_info "chr1,6206536,6206726,+" ; protein_id "ENSP00000367173.4" ; tag not_organism_supported basic MANE_Select appris_principal_1 CCDS ; transcript_id "RNF207--ARMH3^ENST00000377939.5" ; transcript_name "RNF207-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
TBP--ATXN3 HAVANA gene 1078 10356 . + . FI_gene_label "TBP^ENSG00000112592.14" ; ID "TBP--ATXN3^TBP^ENSG00000112592.14" ; ccdsid "CCDS5315.1" ; exon_id "ENSE00000854356.1" ; exon_number 2 ; gene_id "TBP--ATXN3^TBP^ENSG00000112592.14" ; gene_name TBP ; gene_type protein_coding ; havana_gene "OTTHUMG00000016084.6" ; havana_transcript "OTTHUMT00000043271.2" ; hgnc_id "HGNC:11588" ; level 2 ; orig_coord_info "chr6,170557030,170557083,+" ; protein_id "ENSP00000230354.5" ; tag basic appris_principal_2 CCDS ; transcript_id "TBP--ATXN3^ENST00000230354.10" ; transcript_name "TBP-201" ; transcript_support_level 1 ; transcript_type protein_coding
TBP--ATXN3 HAVANA mRNA 1078 10356 . + . FI_gene_label "TBP^ENSG00000112592.14" ; ID "TBP--ATXN3^ENST00000230354.10" ; Parent "TBP--ATXN3^TBP^ENSG00000112592.14" ; ccdsid "CCDS5315.1" ; exon_id "ENSE00000854356.1" ; exon_number 2 ; gene_id "TBP--ATXN3^TBP^ENSG00000112592.14" ; gene_name TBP ; gene_type protein_coding ; havana_gene "OTTHUMG00000016084.6" ; havana_transcript "OTTHUMT00000043271.2" ; hgnc_id "HGNC:11588" ; level 2 ; orig_coord_info "chr6,170557030,170557083,+" ; protein_id "ENSP00000230354.5" ; tag basic appris_principal_2 CCDS ; transcript_id "TBP--ATXN3^ENST00000230354.10" ; transcript_name "TBP-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TBP--ATXN3 HAVANA gene 13368 28517 . + . FI_gene_label "ATXN3^ENSG00000066427.24" ; ID "TBP--ATXN3^ATXN3^ENSG00000066427.24" ; ccdsid "CCDS32143.1" ; exon_id "ENSE00002073369.1" ; exon_number 1 ; gene_id "TBP--ATXN3^ATXN3^ENSG00000066427.24" ; gene_name ATXN3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000162212.16" ; havana_transcript "OTTHUMT00000367924.2" ; hgnc_id "HGNC:7106" ; level 2 ; orig_coord_info "chr14,92106529,92106552,-" ; protein_id "ENSP00000339110.6" ; tag basic CCDS ; transcript_id "TBP--ATXN3^ENST00000340660.10" ; transcript_name "ATXN3-201" ; transcript_support_level 1 ; transcript_type protein_coding
TBP--ATXN3 HAVANA mRNA 13368 28517 . + . FI_gene_label "ATXN3^ENSG00000066427.24" ; ID "TBP--ATXN3^ENST00000340660.10" ; Parent "TBP--ATXN3^ATXN3^ENSG00000066427.24" ; ccdsid "CCDS32143.1" ; exon_id "ENSE00002073369.1" ; exon_number 1 ; gene_id "TBP--ATXN3^ATXN3^ENSG00000066427.24" ; gene_name ATXN3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000162212.16" ; havana_transcript "OTTHUMT00000367924.2" ; hgnc_id "HGNC:7106" ; level 2 ; orig_coord_info "chr14,92106529,92106552,-" ; protein_id "ENSP00000339110.6" ; tag basic CCDS ; transcript_id "TBP--ATXN3^ENST00000340660.10" ; transcript_name "ATXN3-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TLK2--AC240565.1 HAVANA gene 4784 35054 . + . FI_gene_label "TLK2^ENSG00000146872.18" ; ID "TLK2--AC240565.1^TLK2^ENSG00000146872.18" ; ccdsid "CCDS62283.1" ; exon_id "ENSE00003568961.1" ; exon_number 2 ; gene_id "TLK2--AC240565.1^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--AC240565.1^ENST00000326270.13" ; transcript_name "TLK2-201" ; transcript_support_level 1 ; transcript_type protein_coding
TLK2--AC240565.1 HAVANA mRNA 4784 35054 . + . FI_gene_label "TLK2^ENSG00000146872.18" ; ID "TLK2--AC240565.1^ENST00000326270.13" ; Parent "TLK2--AC240565.1^TLK2^ENSG00000146872.18" ; ccdsid "CCDS62283.1" ; exon_id "ENSE00003568961.1" ; exon_number 2 ; gene_id "TLK2--AC240565.1^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--AC240565.1^ENST00000326270.13" ; transcript_name "TLK2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TMX2--OR9Q1 HAVANA gene 1001 5581 . + . FI_gene_label "TMX2^ENSG00000213593.10" ; ID "TMX2--OR9Q1^TMX2^ENSG00000213593.10" ; ccdsid "CCDS7967.1" ; exon_id "ENSE00003846837.1" ; exon_number 1 ; gene_id "TMX2--OR9Q1^TMX2^ENSG00000213593.10" ; gene_name TMX2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000167200.3" ; havana_transcript "OTTHUMT00000393708.2" ; hgnc_id "HGNC:30739" ; level 2 ; orig_coord_info "chr11,57712619,57712807,+" ; protein_id "ENSP00000278422.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TMX2--OR9Q1^ENST00000278422.9" ; transcript_name "TMX2-201" ; transcript_support_level 1 ; transcript_type protein_coding
TMX2--OR9Q1 HAVANA mRNA 1001 5581 . + . FI_gene_label "TMX2^ENSG00000213593.10" ; ID "TMX2--OR9Q1^ENST00000278422.9" ; Parent "TMX2--OR9Q1^TMX2^ENSG00000213593.10" ; ccdsid "CCDS7967.1" ; exon_id "ENSE00003846837.1" ; exon_number 1 ; gene_id "TMX2--OR9Q1^TMX2^ENSG00000213593.10" ; gene_name TMX2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000167200.3" ; havana_transcript "OTTHUMT00000393708.2" ; hgnc_id "HGNC:30739" ; level 2 ; orig_coord_info "chr11,57712619,57712807,+" ; protein_id "ENSP00000278422.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TMX2--OR9Q1^ENST00000278422.9" ; transcript_name "TMX2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TMX2--OR9Q1 HAVANA gene 8582 13069 . + . FI_gene_label "OR9Q1^ENSG00000186509.4" ; ID "TMX2--OR9Q1^OR9Q1^ENSG00000186509.4" ; ccdsid "CCDS31543.1" ; exon_id "ENSE00001107353.5" ; exon_number 3 ; gene_id "TMX2--OR9Q1^OR9Q1^ENSG00000186509.4" ; gene_name OR9Q1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000167413.2" ; havana_transcript "OTTHUMT00000394538.2" ; hgnc_id "HGNC:14724" ; level 2 ; orig_coord_info "chr11,58179445,58180374,+" ; protein_id "ENSP00000334934.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TMX2--OR9Q1^ENST00000335397.3" ; transcript_name "OR9Q1-201" ; transcript_support_level NA ; transcript_type protein_coding
TMX2--OR9Q1 HAVANA mRNA 8582 13069 . + . FI_gene_label "OR9Q1^ENSG00000186509.4" ; ID "TMX2--OR9Q1^ENST00000335397.3" ; Parent "TMX2--OR9Q1^OR9Q1^ENSG00000186509.4" ; ccdsid "CCDS31543.1" ; exon_id "ENSE00001107353.5" ; exon_number 3 ; gene_id "TMX2--OR9Q1^OR9Q1^ENSG00000186509.4" ; gene_name OR9Q1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000167413.2" ; havana_transcript "OTTHUMT00000394538.2" ; hgnc_id "HGNC:14724" ; level 2 ; orig_coord_info "chr11,58179445,58180374,+" ; protein_id "ENSP00000334934.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TMX2--OR9Q1^ENST00000335397.3" ; transcript_name "OR9Q1-201" ; transcript_support_level NA ; 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:
AC092807.3--DDAH1 HAVANA gene 1101 8302 . + . FI_gene_label "AC092807.3^ENSG00000282057.1" ; ID "AC092807.3--DDAH1^AC092807.3^ENSG00000282057.1" ; exon_id "ENSE00001891111.1" ; exon_number 1 ; gene_id "AC092807.3--DDAH1^AC092807.3^ENSG00000282057.1" ; gene_name "AC092807.3" ; gene_type lncRNA ; havana_gene "OTTHUMG00000010578.6" ; havana_transcript "OTTHUMT00000029193.2" ; level 2 ; orig_coord_info "chr1,85577984,85578150,-" ; tag basic ; transcript_id "AC092807.3--DDAH1^ENST00000467530.5" ; transcript_name "AC092807.3-203" ; transcript_support_level 2 ; transcript_type lncRNA
AC092807.3--DDAH1 HAVANA RNA 1101 8302 . + . FI_gene_label "AC092807.3^ENSG00000282057.1" ; ID "AC092807.3--DDAH1^ENST00000467530.5" ; Parent "AC092807.3--DDAH1^AC092807.3^ENSG00000282057.1" ; exon_id "ENSE00001891111.1" ; exon_number 1 ; gene_id "AC092807.3--DDAH1^AC092807.3^ENSG00000282057.1" ; gene_name "AC092807.3" ; gene_type lncRNA ; havana_gene "OTTHUMG00000010578.6" ; havana_transcript "OTTHUMT00000029193.2" ; level 2 ; orig_coord_info "chr1,85577984,85578150,-" ; tag basic ; transcript_id "AC092807.3--DDAH1^ENST00000467530.5" ; transcript_name "AC092807.3-203" ; transcript_support_level 2 ; transcript_type lncRNA
L1 and L2 created:
TLK2--AC240565.1 HAVANA gene 40046 48301 . + . FI_gene_label "AC240565.1^ENSG00000280136.2" ; ID "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2" ; exon_id "ENSE00003756821.1" ; exon_number 1 ; gene_id "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2" ; gene_name "AC240565.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000189256.2" ; havana_transcript "OTTHUMT00000479189.2" ; level 2 ; orig_coord_info "chr17,118383,118578,-" ; tag not_best_in_genome_evidence basic ; transcript_id "TLK2--AC240565.1^ENST00000624936.2" ; transcript_name "AC240565.1-201" ; transcript_support_level 5 ; transcript_type lncRNA
TLK2--AC240565.1 HAVANA RNA 40046 48301 . + . FI_gene_label "AC240565.1^ENSG00000280136.2" ; ID "TLK2--AC240565.1^ENST00000624936.2" ; Parent "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2" ; exon_id "ENSE00003756821.1" ; exon_number 1 ; gene_id "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2" ; gene_name "AC240565.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000189256.2" ; havana_transcript "OTTHUMT00000479189.2" ; level 2 ; orig_coord_info "chr17,118383,118578,-" ; tag not_best_in_genome_evidence basic ; transcript_id "TLK2--AC240565.1^ENST00000624936.2" ; transcript_name "AC240565.1-201" ; transcript_support_level 5 ; transcript_type lncRNA
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
182 cases fixed where L3 features have parent feature(s) missing
------------------------------ done in 0 seconds -------------------------------
--------------------------- Check5: l1 linked to l2 ----------------------------
No problem found
------------------------------ done in 0 seconds -------------------------------
--------------------------- Check6: remove orphan l1 ---------------------------
We remove only those not supposed to be orphan
None found
------------------------------ done in 0 seconds -------------------------------
------------------------- Check7: all level3 locations -------------------------
------------------------------ done in 0 seconds -------------------------------
------------------------------ Check8: check cds -------------------------------
No problem found
------------------------------ done in 0 seconds -------------------------------
----------------------------- Check9: check exons ------------------------------
No exons created
No exons locations modified
No supernumerary exons removed
No level2 locations modified
------------------------------ done in 0 seconds -------------------------------
----------------------------- Check10: check utrs ------------------------------
357 UTRs created that were missing
No UTRs locations modified
No supernumerary UTRs removed
------------------------------ done in 0 seconds -------------------------------
------------------------ Check11: all level2 locations -------------------------
No problem found
------------------------------ done in 0 seconds -------------------------------
------------------------ Check12: all level1 locations -------------------------
We fixed 11 wrong level1 location cases
------------------------------ done in 0 seconds -------------------------------
---------------------- Check13: remove identical isoforms ----------------------
None found
------------------------------ done in 0 seconds -------------------------------
------ End checks (done in 0 second) ------
GFF3 file parsed