Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/05/4801c0c88db67b2c41f79bbdafc351/fi_workdir/aih-tih-sc-4e749e-R1_A23WJ53LT4_1.gtf
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/67/8b939504cbf656b7a7f27166aa7f72/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/67/8b939504cbf656b7a7f27166aa7f72/.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: 3563
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 3563
=> 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:3563
=> 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:
ADAM9--WRN HAVANA gene 42035 80777 . + . FI_gene_label "WRN^ENSG00000165392.11" ; ID "ADAM9--WRN^WRN^ENSG00000165392.11" ; ccdsid "CCDS6082.1" ; exon_id "ENSE00001092693.2" ; exon_number 2 ; gene_id "ADAM9--WRN^WRN^ENSG00000165392.11" ; gene_name WRN ; gene_type protein_coding ; havana_gene "OTTHUMG00000163894.4" ; havana_transcript "OTTHUMT00000376248.3" ; hgnc_id "HGNC:12791" ; level 2 ; orig_coord_info "chr8,31058448,31058543,+" ; protein_id "ENSP00000298139.5" ; tag CAGE_supported_TSS basic MANE_Select appris_principal_1 CCDS ; transcript_id "ADAM9--WRN^ENST00000298139.7" ; transcript_name "WRN-201" ; transcript_support_level 1 ; transcript_type protein_coding
ADAM9--WRN HAVANA mRNA 42035 80777 . + . FI_gene_label "WRN^ENSG00000165392.11" ; ID "ADAM9--WRN^ENST00000298139.7" ; Parent "ADAM9--WRN^WRN^ENSG00000165392.11" ; ccdsid "CCDS6082.1" ; exon_id "ENSE00001092693.2" ; exon_number 2 ; gene_id "ADAM9--WRN^WRN^ENSG00000165392.11" ; gene_name WRN ; gene_type protein_coding ; havana_gene "OTTHUMG00000163894.4" ; havana_transcript "OTTHUMT00000376248.3" ; hgnc_id "HGNC:12791" ; level 2 ; orig_coord_info "chr8,31058448,31058543,+" ; protein_id "ENSP00000298139.5" ; tag CAGE_supported_TSS basic MANE_Select appris_principal_1 CCDS ; transcript_id "ADAM9--WRN^ENST00000298139.7" ; transcript_name "WRN-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ADAM9--WRN HAVANA gene 1273 38711 . + . FI_gene_label "ADAM9^ENSG00000168615.13" ; ID "ADAM9--WRN^ADAM9^ENSG00000168615.13" ; exon_id "ENSE00001854428.1" ; exon_number 1 ; gene_id "ADAM9--WRN^ADAM9^ENSG00000168615.13" ; gene_name ADAM9 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159783.5" ; havana_transcript "OTTHUMT00000357297.1" ; hgnc_id "HGNC:216" ; level 2 ; orig_coord_info "chr8,38997064,38997160,+" ; protein_id "ENSP00000369249.3" ; transcript_id "ADAM9--WRN^ENST00000379917.7" ; transcript_name "ADAM9-201" ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay
ADAM9--WRN HAVANA mRNA 1273 38711 . + . FI_gene_label "ADAM9^ENSG00000168615.13" ; ID "ADAM9--WRN^ENST00000379917.7" ; Parent "ADAM9--WRN^ADAM9^ENSG00000168615.13" ; exon_id "ENSE00001854428.1" ; exon_number 1 ; gene_id "ADAM9--WRN^ADAM9^ENSG00000168615.13" ; gene_name ADAM9 ; gene_type protein_coding ; havana_gene "OTTHUMG00000159783.5" ; havana_transcript "OTTHUMT00000357297.1" ; hgnc_id "HGNC:216" ; level 2 ; orig_coord_info "chr8,38997064,38997160,+" ; protein_id "ENSP00000369249.3" ; transcript_id "ADAM9--WRN^ENST00000379917.7" ; transcript_name "ADAM9-201" ; transcript_support_level 1 ; transcript_type nonsense_mediated_decay
L1 and L2 created:
ADAMTS2--AC136628.4 HAVANA gene 1001 29814 . + . FI_gene_label "ADAMTS2^ENSG00000087116.16" ; ID "ADAMTS2--AC136628.4^ADAMTS2^ENSG00000087116.16" ; ccdsid "CCDS4444.1" ; exon_id "ENSE00003847948.1" ; exon_number 1 ; gene_id "ADAMTS2--AC136628.4^ADAMTS2^ENSG00000087116.16" ; gene_name ADAMTS2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130915.7" ; havana_transcript "OTTHUMT00000253507.2" ; hgnc_id "HGNC:218" ; level 2 ; orig_coord_info "chr5,179345190,179345328,-" ; protein_id "ENSP00000251582.7" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "ADAMTS2--AC136628.4^ENST00000251582.12" ; transcript_name "ADAMTS2-201" ; transcript_support_level 1 ; transcript_type protein_coding
ADAMTS2--AC136628.4 HAVANA mRNA 1001 29814 . + . FI_gene_label "ADAMTS2^ENSG00000087116.16" ; ID "ADAMTS2--AC136628.4^ENST00000251582.12" ; Parent "ADAMTS2--AC136628.4^ADAMTS2^ENSG00000087116.16" ; ccdsid "CCDS4444.1" ; exon_id "ENSE00003847948.1" ; exon_number 1 ; gene_id "ADAMTS2--AC136628.4^ADAMTS2^ENSG00000087116.16" ; gene_name ADAMTS2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000130915.7" ; havana_transcript "OTTHUMT00000253507.2" ; hgnc_id "HGNC:218" ; level 2 ; orig_coord_info "chr5,179345190,179345328,-" ; protein_id "ENSP00000251582.7" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "ADAMTS2--AC136628.4^ENST00000251582.12" ; transcript_name "ADAMTS2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
CHID1--AP2A2 HAVANA gene 2781 19775 . + . FI_gene_label "CHID1^ENSG00000177830.18" ; ID "CHID1--AP2A2^CHID1^ENSG00000177830.18" ; ccdsid "CCDS7722.1" ; exon_id "ENSE00003657827.1" ; exon_number 2 ; gene_id "CHID1--AP2A2^CHID1^ENSG00000177830.18" ; gene_name CHID1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133314.6" ; havana_transcript "OTTHUMT00000257112.3" ; hgnc_id "HGNC:28474" ; level 2 ; orig_coord_info "chr11,904706,904816,-" ; protein_id "ENSP00000325055.8" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CHID1--AP2A2^ENST00000323578.13" ; transcript_name "CHID1-201" ; transcript_support_level 1 ; transcript_type protein_coding
CHID1--AP2A2 HAVANA mRNA 2781 19775 . + . FI_gene_label "CHID1^ENSG00000177830.18" ; ID "CHID1--AP2A2^ENST00000323578.13" ; Parent "CHID1--AP2A2^CHID1^ENSG00000177830.18" ; ccdsid "CCDS7722.1" ; exon_id "ENSE00003657827.1" ; exon_number 2 ; gene_id "CHID1--AP2A2^CHID1^ENSG00000177830.18" ; gene_name CHID1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133314.6" ; havana_transcript "OTTHUMT00000257112.3" ; hgnc_id "HGNC:28474" ; level 2 ; orig_coord_info "chr11,904706,904816,-" ; protein_id "ENSP00000325055.8" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CHID1--AP2A2^ENST00000323578.13" ; transcript_name "CHID1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
CHID1--AP2A2 ENSEMBL gene 23691 55581 . + . FI_gene_label "AP2A2^ENSG00000183020.14" ; ID "CHID1--AP2A2^AP2A2^ENSG00000183020.14" ; ccdsid "CCDS73234.1" ; exon_id "ENSE00003719967.1" ; exon_number 1 ; gene_id "CHID1--AP2A2^AP2A2^ENSG00000183020.14" ; gene_name AP2A2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165627.7" ; hgnc_id "HGNC:562" ; level 3 ; orig_coord_info "chr11,926022,926088,+" ; protein_id "ENSP00000327694.5" ; tag basic appris_alternative_1 CCDS ; transcript_id "CHID1--AP2A2^ENST00000332231.9" ; transcript_name "AP2A2-201" ; transcript_support_level 1 ; transcript_type protein_coding
CHID1--AP2A2 ENSEMBL mRNA 23691 55581 . + . FI_gene_label "AP2A2^ENSG00000183020.14" ; ID "CHID1--AP2A2^ENST00000332231.9" ; Parent "CHID1--AP2A2^AP2A2^ENSG00000183020.14" ; ccdsid "CCDS73234.1" ; exon_id "ENSE00003719967.1" ; exon_number 1 ; gene_id "CHID1--AP2A2^AP2A2^ENSG00000183020.14" ; gene_name AP2A2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165627.7" ; hgnc_id "HGNC:562" ; level 3 ; orig_coord_info "chr11,926022,926088,+" ; protein_id "ENSP00000327694.5" ; tag basic appris_alternative_1 CCDS ; transcript_id "CHID1--AP2A2^ENST00000332231.9" ; transcript_name "AP2A2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
GGA3--SLC5A4 HAVANA gene 16393 32421 . + . FI_gene_label "SLC5A4^ENSG00000100191.6" ; ID "GGA3--SLC5A4^SLC5A4^ENSG00000100191.6" ; ccdsid "CCDS13903.1" ; exon_id "ENSE00000911207.5" ; exon_number 1 ; gene_id "GGA3--SLC5A4^SLC5A4^ENSG00000100191.6" ; gene_name SLC5A4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150007.2" ; havana_transcript "OTTHUMT00000315724.2" ; hgnc_id "HGNC:11039" ; level 2 ; orig_coord_info "chr22,32255195,32255329,-" ; protein_id "ENSP00000266086.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "GGA3--SLC5A4^ENST00000266086.6" ; transcript_name "SLC5A4-201" ; transcript_support_level 1 ; transcript_type protein_coding
GGA3--SLC5A4 HAVANA mRNA 16393 32421 . + . FI_gene_label "SLC5A4^ENSG00000100191.6" ; ID "GGA3--SLC5A4^ENST00000266086.6" ; Parent "GGA3--SLC5A4^SLC5A4^ENSG00000100191.6" ; ccdsid "CCDS13903.1" ; exon_id "ENSE00000911207.5" ; exon_number 1 ; gene_id "GGA3--SLC5A4^SLC5A4^ENSG00000100191.6" ; gene_name SLC5A4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150007.2" ; havana_transcript "OTTHUMT00000315724.2" ; hgnc_id "HGNC:11039" ; level 2 ; orig_coord_info "chr22,32255195,32255329,-" ; protein_id "ENSP00000266086.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "GGA3--SLC5A4^ENST00000266086.6" ; transcript_name "SLC5A4-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
GGA3--SLC5A4 HAVANA gene 1758 13392 . + . FI_gene_label "GGA3^ENSG00000125447.18" ; ID "GGA3--SLC5A4^GGA3^ENSG00000125447.18" ; ccdsid "CCDS11717.1" ; exon_id "ENSE00003741321.2" ; exon_number 1 ; gene_id "GGA3--SLC5A4^GGA3^ENSG00000125447.18" ; gene_name GGA3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179483.7" ; havana_transcript "OTTHUMT00000446645.2" ; hgnc_id "HGNC:17079" ; level 2 ; orig_coord_info "chr17,75261548,75261587,-" ; protein_id "ENSP00000438085.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "GGA3--SLC5A4^ENST00000537686.6" ; transcript_name "GGA3-201" ; transcript_support_level 1 ; transcript_type protein_coding
GGA3--SLC5A4 HAVANA mRNA 1758 13392 . + . FI_gene_label "GGA3^ENSG00000125447.18" ; ID "GGA3--SLC5A4^ENST00000537686.6" ; Parent "GGA3--SLC5A4^GGA3^ENSG00000125447.18" ; ccdsid "CCDS11717.1" ; exon_id "ENSE00003741321.2" ; exon_number 1 ; gene_id "GGA3--SLC5A4^GGA3^ENSG00000125447.18" ; gene_name GGA3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179483.7" ; havana_transcript "OTTHUMT00000446645.2" ; hgnc_id "HGNC:17079" ; level 2 ; orig_coord_info "chr17,75261548,75261587,-" ; protein_id "ENSP00000438085.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "GGA3--SLC5A4^ENST00000537686.6" ; transcript_name "GGA3-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
GPCPD1--MYO5B HAVANA gene 28831 78603 . + . FI_gene_label "MYO5B^ENSG00000167306.20" ; ID "GPCPD1--MYO5B^MYO5B^ENSG00000167306.20" ; ccdsid "CCDS42436.1" ; exon_id "ENSE00002302584.3" ; exon_number 1 ; gene_id "GPCPD1--MYO5B^MYO5B^ENSG00000167306.20" ; gene_name MYO5B ; gene_type protein_coding ; havana_gene "OTTHUMG00000179843.5" ; havana_transcript "OTTHUMT00000448515.3" ; hgnc_id "HGNC:7603" ; level 2 ; orig_coord_info "chr18,50194767,50194793,-" ; protein_id "ENSP00000285039.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "GPCPD1--MYO5B^ENST00000285039.12" ; transcript_name "MYO5B-201" ; transcript_support_level 1 ; transcript_type protein_coding
GPCPD1--MYO5B HAVANA mRNA 28831 78603 . + . FI_gene_label "MYO5B^ENSG00000167306.20" ; ID "GPCPD1--MYO5B^ENST00000285039.12" ; Parent "GPCPD1--MYO5B^MYO5B^ENSG00000167306.20" ; ccdsid "CCDS42436.1" ; exon_id "ENSE00002302584.3" ; exon_number 1 ; gene_id "GPCPD1--MYO5B^MYO5B^ENSG00000167306.20" ; gene_name MYO5B ; gene_type protein_coding ; havana_gene "OTTHUMG00000179843.5" ; havana_transcript "OTTHUMT00000448515.3" ; hgnc_id "HGNC:7603" ; level 2 ; orig_coord_info "chr18,50194767,50194793,-" ; protein_id "ENSP00000285039.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "GPCPD1--MYO5B^ENST00000285039.12" ; transcript_name "MYO5B-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
GPCPD1--MYO5B HAVANA gene 1001 25830 . + . FI_gene_label "GPCPD1^ENSG00000125772.14" ; ID "GPCPD1--MYO5B^GPCPD1^ENSG00000125772.14" ; ccdsid "CCDS13090.1" ; exon_id "ENSE00003782897.1" ; exon_number 2 ; gene_id "GPCPD1--MYO5B^GPCPD1^ENSG00000125772.14" ; gene_name GPCPD1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000031806.5" ; havana_transcript "OTTHUMT00000077869.4" ; hgnc_id "HGNC:26957" ; level 2 ; orig_coord_info "chr20,5604364,5604412,-" ; protein_id "ENSP00000368305.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "GPCPD1--MYO5B^ENST00000379019.7" ; transcript_name "GPCPD1-201" ; transcript_support_level 1 ; transcript_type protein_coding
GPCPD1--MYO5B HAVANA mRNA 1001 25830 . + . FI_gene_label "GPCPD1^ENSG00000125772.14" ; ID "GPCPD1--MYO5B^ENST00000379019.7" ; Parent "GPCPD1--MYO5B^GPCPD1^ENSG00000125772.14" ; ccdsid "CCDS13090.1" ; exon_id "ENSE00003782897.1" ; exon_number 2 ; gene_id "GPCPD1--MYO5B^GPCPD1^ENSG00000125772.14" ; gene_name GPCPD1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000031806.5" ; havana_transcript "OTTHUMT00000077869.4" ; hgnc_id "HGNC:26957" ; level 2 ; orig_coord_info "chr20,5604364,5604412,-" ; protein_id "ENSP00000368305.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "GPCPD1--MYO5B^ENST00000379019.7" ; transcript_name "GPCPD1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
JAG1--CFAP61 HAVANA gene 25854 70112 . + . FI_gene_label "CFAP61^ENSG00000089101.19" ; ID "JAG1--CFAP61^CFAP61^ENSG00000089101.19" ; ccdsid "CCDS33447.1" ; exon_id "ENSE00003670284.1" ; exon_number 2 ; gene_id "JAG1--CFAP61^CFAP61^ENSG00000089101.19" ; gene_name CFAP61 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032006.15" ; havana_transcript "OTTHUMT00000078228.4" ; hgnc_id "HGNC:15872" ; level 2 ; orig_coord_info "chr20,20056654,20056796,+" ; protein_id "ENSP00000245957.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "JAG1--CFAP61^ENST00000245957.10" ; transcript_name "CFAP61-201" ; transcript_support_level 1 ; transcript_type protein_coding
JAG1--CFAP61 HAVANA mRNA 25854 70112 . + . FI_gene_label "CFAP61^ENSG00000089101.19" ; ID "JAG1--CFAP61^ENST00000245957.10" ; Parent "JAG1--CFAP61^CFAP61^ENSG00000089101.19" ; ccdsid "CCDS33447.1" ; exon_id "ENSE00003670284.1" ; exon_number 2 ; gene_id "JAG1--CFAP61^CFAP61^ENSG00000089101.19" ; gene_name CFAP61 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032006.15" ; havana_transcript "OTTHUMT00000078228.4" ; hgnc_id "HGNC:15872" ; level 2 ; orig_coord_info "chr20,20056654,20056796,+" ; protein_id "ENSP00000245957.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "JAG1--CFAP61^ENST00000245957.10" ; transcript_name "CFAP61-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
JAG1--CFAP61 HAVANA gene 1001 22835 . + . FI_gene_label "JAG1^ENSG00000101384.12" ; ID "JAG1--CFAP61^JAG1^ENSG00000101384.12" ; ccdsid "CCDS13112.1" ; exon_id "ENSE00001871530.4" ; exon_number 1 ; gene_id "JAG1--CFAP61^JAG1^ENSG00000101384.12" ; gene_name JAG1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000031872.6" ; havana_transcript "OTTHUMT00000077998.4" ; hgnc_id "HGNC:6188" ; level 2 ; orig_coord_info "chr20,10673450,10673530,-" ; protein_id "ENSP00000254958.4" ; tag CAGE_supported_TSS basic MANE_Select appris_principal_1 CCDS ; transcript_id "JAG1--CFAP61^ENST00000254958.10" ; transcript_name "JAG1-201" ; transcript_support_level 1 ; transcript_type protein_coding
JAG1--CFAP61 HAVANA mRNA 1001 22835 . + . FI_gene_label "JAG1^ENSG00000101384.12" ; ID "JAG1--CFAP61^ENST00000254958.10" ; Parent "JAG1--CFAP61^JAG1^ENSG00000101384.12" ; ccdsid "CCDS13112.1" ; exon_id "ENSE00001871530.4" ; exon_number 1 ; gene_id "JAG1--CFAP61^JAG1^ENSG00000101384.12" ; gene_name JAG1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000031872.6" ; havana_transcript "OTTHUMT00000077998.4" ; hgnc_id "HGNC:6188" ; level 2 ; orig_coord_info "chr20,10673450,10673530,-" ; protein_id "ENSP00000254958.4" ; tag CAGE_supported_TSS basic MANE_Select appris_principal_1 CCDS ; transcript_id "JAG1--CFAP61^ENST00000254958.10" ; transcript_name "JAG1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
NDUFAF2--AC026444.1 HAVANA gene 1029 13642 . + . FI_gene_label "NDUFAF2^ENSG00000164182.12" ; ID "NDUFAF2--AC026444.1^NDUFAF2^ENSG00000164182.12" ; ccdsid "CCDS3979.1" ; exon_id "ENSE00001178522.7" ; exon_number 1 ; gene_id "NDUFAF2--AC026444.1^NDUFAF2^ENSG00000164182.12" ; gene_name NDUFAF2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000131221.4" ; havana_transcript "OTTHUMT00000253965.3" ; hgnc_id "HGNC:28086" ; level 2 ; orig_coord_info "chr5,60945256,60945382,+" ; protein_id "ENSP00000296597.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NDUFAF2--AC026444.1^ENST00000296597.10" ; transcript_name "NDUFAF2-201" ; transcript_support_level 1 ; transcript_type protein_coding
NDUFAF2--AC026444.1 HAVANA mRNA 1029 13642 . + . FI_gene_label "NDUFAF2^ENSG00000164182.12" ; ID "NDUFAF2--AC026444.1^ENST00000296597.10" ; Parent "NDUFAF2--AC026444.1^NDUFAF2^ENSG00000164182.12" ; ccdsid "CCDS3979.1" ; exon_id "ENSE00001178522.7" ; exon_number 1 ; gene_id "NDUFAF2--AC026444.1^NDUFAF2^ENSG00000164182.12" ; gene_name NDUFAF2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000131221.4" ; havana_transcript "OTTHUMT00000253965.3" ; hgnc_id "HGNC:28086" ; level 2 ; orig_coord_info "chr5,60945256,60945382,+" ; protein_id "ENSP00000296597.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NDUFAF2--AC026444.1^ENST00000296597.10" ; transcript_name "NDUFAF2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
NDUFAF2--COX7C HAVANA gene 18161 21160 . + . FI_gene_label "COX7C^ENSG00000127184.13" ; ID "NDUFAF2--COX7C^COX7C^ENSG00000127184.13" ; ccdsid "CCDS4063.1" ; exon_id "ENSE00000998734.4" ; exon_number 1 ; gene_id "NDUFAF2--COX7C^COX7C^ENSG00000127184.13" ; gene_name COX7C ; gene_type protein_coding ; havana_gene "OTTHUMG00000119049.5" ; havana_transcript "OTTHUMT00000239260.2" ; hgnc_id "HGNC:2292" ; level 2 ; orig_coord_info "chr5,86618056,86618130,+" ; protein_id "ENSP00000247655.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NDUFAF2--COX7C^ENST00000247655.4" ; transcript_name "COX7C-201" ; transcript_support_level 1 ; transcript_type protein_coding
NDUFAF2--COX7C HAVANA mRNA 18161 21160 . + . FI_gene_label "COX7C^ENSG00000127184.13" ; ID "NDUFAF2--COX7C^ENST00000247655.4" ; Parent "NDUFAF2--COX7C^COX7C^ENSG00000127184.13" ; ccdsid "CCDS4063.1" ; exon_id "ENSE00000998734.4" ; exon_number 1 ; gene_id "NDUFAF2--COX7C^COX7C^ENSG00000127184.13" ; gene_name COX7C ; gene_type protein_coding ; havana_gene "OTTHUMG00000119049.5" ; havana_transcript "OTTHUMT00000239260.2" ; hgnc_id "HGNC:2292" ; level 2 ; orig_coord_info "chr5,86618056,86618130,+" ; protein_id "ENSP00000247655.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NDUFAF2--COX7C^ENST00000247655.4" ; transcript_name "COX7C-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
NDUFAF2--COX7C HAVANA gene 1029 13642 . + . FI_gene_label "NDUFAF2^ENSG00000164182.12" ; ID "NDUFAF2--COX7C^NDUFAF2^ENSG00000164182.12" ; ccdsid "CCDS3979.1" ; exon_id "ENSE00001178522.7" ; exon_number 1 ; gene_id "NDUFAF2--COX7C^NDUFAF2^ENSG00000164182.12" ; gene_name NDUFAF2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000131221.4" ; havana_transcript "OTTHUMT00000253965.3" ; hgnc_id "HGNC:28086" ; level 2 ; orig_coord_info "chr5,60945256,60945382,+" ; protein_id "ENSP00000296597.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NDUFAF2--COX7C^ENST00000296597.10" ; transcript_name "NDUFAF2-201" ; transcript_support_level 1 ; transcript_type protein_coding
NDUFAF2--COX7C HAVANA mRNA 1029 13642 . + . FI_gene_label "NDUFAF2^ENSG00000164182.12" ; ID "NDUFAF2--COX7C^ENST00000296597.10" ; Parent "NDUFAF2--COX7C^NDUFAF2^ENSG00000164182.12" ; ccdsid "CCDS3979.1" ; exon_id "ENSE00001178522.7" ; exon_number 1 ; gene_id "NDUFAF2--COX7C^NDUFAF2^ENSG00000164182.12" ; gene_name NDUFAF2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000131221.4" ; havana_transcript "OTTHUMT00000253965.3" ; hgnc_id "HGNC:28086" ; level 2 ; orig_coord_info "chr5,60945256,60945382,+" ; protein_id "ENSP00000296597.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NDUFAF2--COX7C^ENST00000296597.10" ; transcript_name "NDUFAF2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
STX16--NPEPL1 HAVANA gene 1021 7754 . + . FI_gene_label "STX16^ENSG00000124222.22" ; ID "STX16--NPEPL1^STX16^ENSG00000124222.22" ; exon_id "ENSE00003459479.1" ; exon_number 3 ; gene_id "STX16--NPEPL1^STX16^ENSG00000124222.22" ; gene_name STX16 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033084.8" ; havana_transcript "OTTHUMT00000267911.2" ; hgnc_id "HGNC:11431" ; level 2 ; orig_coord_info "chr20,58667505,58667597,+" ; protein_id "ENSP00000312086.8" ; tag alternative_5_UTR mRNA_end_NF cds_end_NF ; transcript_id "STX16--NPEPL1^ENST00000312283.12" ; transcript_name "STX16-201" ; transcript_support_level 3 ; transcript_type protein_coding
STX16--NPEPL1 HAVANA mRNA 1021 7754 . + . FI_gene_label "STX16^ENSG00000124222.22" ; ID "STX16--NPEPL1^ENST00000312283.12" ; Parent "STX16--NPEPL1^STX16^ENSG00000124222.22" ; exon_id "ENSE00003459479.1" ; exon_number 3 ; gene_id "STX16--NPEPL1^STX16^ENSG00000124222.22" ; gene_name STX16 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033084.8" ; havana_transcript "OTTHUMT00000267911.2" ; hgnc_id "HGNC:11431" ; level 2 ; orig_coord_info "chr20,58667505,58667597,+" ; protein_id "ENSP00000312086.8" ; tag alternative_5_UTR mRNA_end_NF cds_end_NF ; transcript_id "STX16--NPEPL1^ENST00000312283.12" ; transcript_name "STX16-201" ; transcript_support_level 3 ; transcript_type protein_coding
L1 and L2 created:
STX16--NPEPL1 HAVANA gene 18353 29399 . + . FI_gene_label "NPEPL1^ENSG00000215440.12" ; ID "STX16--NPEPL1^NPEPL1^ENSG00000215440.12" ; ccdsid "CCDS46621.1" ; exon_id "ENSE00001408052.7" ; exon_number 1 ; gene_id "STX16--NPEPL1^NPEPL1^ENSG00000215440.12" ; gene_name NPEPL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033060.8" ; havana_transcript "OTTHUMT00000080402.7" ; hgnc_id "HGNC:16244" ; level 2 ; orig_coord_info "chr20,58692901,58693050,+" ; protein_id "ENSP00000348395.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "STX16--NPEPL1^ENST00000356091.11" ; transcript_name "NPEPL1-201" ; transcript_support_level 1 ; transcript_type protein_coding
STX16--NPEPL1 HAVANA mRNA 18353 29399 . + . FI_gene_label "NPEPL1^ENSG00000215440.12" ; ID "STX16--NPEPL1^ENST00000356091.11" ; Parent "STX16--NPEPL1^NPEPL1^ENSG00000215440.12" ; ccdsid "CCDS46621.1" ; exon_id "ENSE00001408052.7" ; exon_number 1 ; gene_id "STX16--NPEPL1^NPEPL1^ENSG00000215440.12" ; gene_name NPEPL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033060.8" ; havana_transcript "OTTHUMT00000080402.7" ; hgnc_id "HGNC:16244" ; level 2 ; orig_coord_info "chr20,58692901,58693050,+" ; protein_id "ENSP00000348395.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "STX16--NPEPL1^ENST00000356091.11" ; transcript_name "NPEPL1-201" ; 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:
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:
ADAMTS2--AC136628.4 HAVANA gene 32815 34349 . + . FI_gene_label "AC136628.4^ENSG00000253652.1" ; ID "ADAMTS2--AC136628.4^AC136628.4^ENSG00000253652.1" ; exon_id "ENSE00002123349.1" ; exon_number 1 ; gene_id "ADAMTS2--AC136628.4^AC136628.4^ENSG00000253652.1" ; gene_name "AC136628.4" ; gene_type lncRNA ; havana_gene "OTTHUMG00000163567.1" ; havana_transcript "OTTHUMT00000374246.1" ; level 1 ; orig_coord_info "chr5,179515464,179515579,-" ; tag basic exp_conf ; transcript_id "ADAMTS2--AC136628.4^ENST00000520758.1" ; transcript_name "AC136628.4-201" ; transcript_support_level 2 ; transcript_type lncRNA
ADAMTS2--AC136628.4 HAVANA RNA 32815 34349 . + . FI_gene_label "AC136628.4^ENSG00000253652.1" ; ID "ADAMTS2--AC136628.4^ENST00000520758.1" ; Parent "ADAMTS2--AC136628.4^AC136628.4^ENSG00000253652.1" ; exon_id "ENSE00002123349.1" ; exon_number 1 ; gene_id "ADAMTS2--AC136628.4^AC136628.4^ENSG00000253652.1" ; gene_name "AC136628.4" ; gene_type lncRNA ; havana_gene "OTTHUMG00000163567.1" ; havana_transcript "OTTHUMT00000374246.1" ; level 1 ; orig_coord_info "chr5,179515464,179515579,-" ; tag basic exp_conf ; transcript_id "ADAMTS2--AC136628.4^ENST00000520758.1" ; transcript_name "AC136628.4-201" ; transcript_support_level 2 ; transcript_type lncRNA
L1 and L2 created:
NDUFAF2--AC026444.1 HAVANA gene 18148 18643 . + . FI_gene_label "AC026444.1^ENSG00000251585.1" ; ID "NDUFAF2--AC026444.1^AC026444.1^ENSG00000251585.1" ; exon_id "ENSE00002031026.1" ; exon_number 1 ; gene_id "NDUFAF2--AC026444.1^AC026444.1^ENSG00000251585.1" ; gene_name "AC026444.1" ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000162580.2" ; havana_transcript "OTTHUMT00000369663.2" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr5,86402465,86402960,+" ; tag pseudo_consens basic ; transcript_id "NDUFAF2--AC026444.1^ENST00000502592.1" ; transcript_name "AC026444.1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
NDUFAF2--AC026444.1 HAVANA RNA 18148 18643 . + . FI_gene_label "AC026444.1^ENSG00000251585.1" ; ID "NDUFAF2--AC026444.1^ENST00000502592.1" ; Parent "NDUFAF2--AC026444.1^AC026444.1^ENSG00000251585.1" ; exon_id "ENSE00002031026.1" ; exon_number 1 ; gene_id "NDUFAF2--AC026444.1^AC026444.1^ENSG00000251585.1" ; gene_name "AC026444.1" ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000162580.2" ; havana_transcript "OTTHUMT00000369663.2" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr5,86402465,86402960,+" ; tag pseudo_consens basic ; transcript_id "NDUFAF2--AC026444.1^ENST00000502592.1" ; transcript_name "AC026444.1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene
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
242 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 ------------------------------
637 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 14 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