Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/37/60e6c03f85da40ea88d55c0f054fa9/fi_workdir/659_bCu-T1-TRNA-1_B23WHTKLT4_1.gtf
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a4/d4144f942c2c749856e93e02e65f1b/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a4/d4144f942c2c749856e93e02e65f1b/.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: 3442
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 3442
=> 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:3442
=> 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 2 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:
ADAM23--HDAC4 HAVANA gene 1001 32824 . + . FI_gene_label "ADAM23^ENSG00000114948.13" ; ID "ADAM23--HDAC4^ADAM23^ENSG00000114948.13" ; ccdsid "CCDS2369.1" ; exon_id "ENSE00001950784.2" ; exon_number 1 ; gene_id "ADAM23--HDAC4^ADAM23^ENSG00000114948.13" ; gene_name ADAM23 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132919.5" ; havana_transcript "OTTHUMT00000256431.4" ; hgnc_id "HGNC:202" ; level 2 ; orig_coord_info "chr2,206443867,206444080,+" ; protein_id "ENSP00000264377.3" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "ADAM23--HDAC4^ENST00000264377.8" ; transcript_name "ADAM23-201" ; transcript_support_level 1 ; transcript_type protein_coding
ADAM23--HDAC4 HAVANA mRNA 1001 32824 . + . FI_gene_label "ADAM23^ENSG00000114948.13" ; ID "ADAM23--HDAC4^ENST00000264377.8" ; Parent "ADAM23--HDAC4^ADAM23^ENSG00000114948.13" ; ccdsid "CCDS2369.1" ; exon_id "ENSE00001950784.2" ; exon_number 1 ; gene_id "ADAM23--HDAC4^ADAM23^ENSG00000114948.13" ; gene_name ADAM23 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132919.5" ; havana_transcript "OTTHUMT00000256431.4" ; hgnc_id "HGNC:202" ; level 2 ; orig_coord_info "chr2,206443867,206444080,+" ; protein_id "ENSP00000264377.3" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "ADAM23--HDAC4^ENST00000264377.8" ; transcript_name "ADAM23-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ADAM23--HDAC4 HAVANA gene 36530 81643 . + . FI_gene_label "HDAC4^ENSG00000068024.17" ; ID "ADAM23--HDAC4^HDAC4^ENSG00000068024.17" ; ccdsid "CCDS2529.1" ; exon_id "ENSE00003664840.1" ; exon_number 2 ; gene_id "ADAM23--HDAC4^HDAC4^ENSG00000068024.17" ; gene_name HDAC4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133344.7" ; havana_transcript "OTTHUMT00000257174.2" ; hgnc_id "HGNC:14063" ; level 2 ; orig_coord_info "chr2,239352678,239352699,-" ; protein_id "ENSP00000264606.3" ; tag basic appris_principal_2 CCDS ; transcript_id "ADAM23--HDAC4^ENST00000345617.7" ; transcript_name "HDAC4-201" ; transcript_support_level 1 ; transcript_type protein_coding
ADAM23--HDAC4 HAVANA mRNA 36530 81643 . + . FI_gene_label "HDAC4^ENSG00000068024.17" ; ID "ADAM23--HDAC4^ENST00000345617.7" ; Parent "ADAM23--HDAC4^HDAC4^ENSG00000068024.17" ; ccdsid "CCDS2529.1" ; exon_id "ENSE00003664840.1" ; exon_number 2 ; gene_id "ADAM23--HDAC4^HDAC4^ENSG00000068024.17" ; gene_name HDAC4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133344.7" ; havana_transcript "OTTHUMT00000257174.2" ; hgnc_id "HGNC:14063" ; level 2 ; orig_coord_info "chr2,239352678,239352699,-" ; protein_id "ENSP00000264606.3" ; tag basic appris_principal_2 CCDS ; transcript_id "ADAM23--HDAC4^ENST00000345617.7" ; transcript_name "HDAC4-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
IRAG1--ZNF143 HAVANA gene 33464 53054 . + . FI_gene_label "ZNF143^ENSG00000166478.10" ; ID "IRAG1--ZNF143^ZNF143^ENSG00000166478.10" ; exon_id "ENSE00002140238.1" ; exon_number 2 ; gene_id "IRAG1--ZNF143^ZNF143^ENSG00000166478.10" ; gene_name ZNF143 ; gene_type protein_coding ; havana_gene "OTTHUMG00000149922.5" ; havana_transcript "OTTHUMT00000313923.1" ; hgnc_id "HGNC:12928" ; level 1 ; orig_coord_info "chr11,9471309,9471420,+" ; protein_id "ENSP00000299606.2" ; tag dotter_confirmed not_organism_supported basic exp_conf ; transcript_id "IRAG1--ZNF143^ENST00000299606.6" ; transcript_name "ZNF143-201" ; transcript_support_level 5 ; transcript_type protein_coding
IRAG1--ZNF143 HAVANA mRNA 33464 53054 . + . FI_gene_label "ZNF143^ENSG00000166478.10" ; ID "IRAG1--ZNF143^ENST00000299606.6" ; Parent "IRAG1--ZNF143^ZNF143^ENSG00000166478.10" ; exon_id "ENSE00002140238.1" ; exon_number 2 ; gene_id "IRAG1--ZNF143^ZNF143^ENSG00000166478.10" ; gene_name ZNF143 ; gene_type protein_coding ; havana_gene "OTTHUMG00000149922.5" ; havana_transcript "OTTHUMT00000313923.1" ; hgnc_id "HGNC:12928" ; level 1 ; orig_coord_info "chr11,9471309,9471420,+" ; protein_id "ENSP00000299606.2" ; tag dotter_confirmed not_organism_supported basic exp_conf ; transcript_id "IRAG1--ZNF143^ENST00000299606.6" ; transcript_name "ZNF143-201" ; transcript_support_level 5 ; transcript_type protein_coding
L1 and L2 created:
IRAG1--ZNF143 HAVANA gene 1237 29755 . + . FI_gene_label "IRAG1^ENSG00000072952.19" ; ID "IRAG1--ZNF143^IRAG1^ENSG00000072952.19" ; ccdsid "CCDS55746.1" ; exon_id "ENSE00002197128.1" ; exon_number 1 ; gene_id "IRAG1--ZNF143^IRAG1^ENSG00000072952.19" ; gene_name IRAG1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165773.7" ; havana_transcript "OTTHUMT00000386137.2" ; hgnc_id "HGNC:7237" ; level 2 ; orig_coord_info "chr11,10693536,10693602,-" ; protein_id "ENSP00000412130.2" ; tag basic appris_alternative_2 CCDS ; transcript_id "IRAG1--ZNF143^ENST00000423302.6" ; transcript_name "IRAG1-201" ; transcript_support_level 2 ; transcript_type protein_coding
IRAG1--ZNF143 HAVANA mRNA 1237 29755 . + . FI_gene_label "IRAG1^ENSG00000072952.19" ; ID "IRAG1--ZNF143^ENST00000423302.6" ; Parent "IRAG1--ZNF143^IRAG1^ENSG00000072952.19" ; ccdsid "CCDS55746.1" ; exon_id "ENSE00002197128.1" ; exon_number 1 ; gene_id "IRAG1--ZNF143^IRAG1^ENSG00000072952.19" ; gene_name IRAG1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165773.7" ; havana_transcript "OTTHUMT00000386137.2" ; hgnc_id "HGNC:7237" ; level 2 ; orig_coord_info "chr11,10693536,10693602,-" ; protein_id "ENSP00000412130.2" ; tag basic appris_alternative_2 CCDS ; transcript_id "IRAG1--ZNF143^ENST00000423302.6" ; transcript_name "IRAG1-201" ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created:
NAV2--NELL1 HAVANA gene 60558 91777 . + . FI_gene_label "NELL1^ENSG00000165973.19" ; ID "NAV2--NELL1^NELL1^ENSG00000165973.19" ; ccdsid "CCDS73267.1" ; exon_id "ENSE00001311201.5" ; exon_number 1 ; gene_id "NAV2--NELL1^NELL1^ENSG00000165973.19" ; gene_name NELL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000166042.3" ; havana_transcript "OTTHUMT00000387587.1" ; hgnc_id "HGNC:7750" ; level 1 ; orig_coord_info "chr11,20669724,20669778,+" ; protein_id "ENSP00000298925.5" ; tag basic exp_conf CCDS ; transcript_id "NAV2--NELL1^ENST00000298925.9" ; transcript_name "NELL1-201" ; transcript_support_level 2 ; transcript_type protein_coding
NAV2--NELL1 HAVANA mRNA 60558 91777 . + . FI_gene_label "NELL1^ENSG00000165973.19" ; ID "NAV2--NELL1^ENST00000298925.9" ; Parent "NAV2--NELL1^NELL1^ENSG00000165973.19" ; ccdsid "CCDS73267.1" ; exon_id "ENSE00001311201.5" ; exon_number 1 ; gene_id "NAV2--NELL1^NELL1^ENSG00000165973.19" ; gene_name NELL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000166042.3" ; havana_transcript "OTTHUMT00000387587.1" ; hgnc_id "HGNC:7750" ; level 1 ; orig_coord_info "chr11,20669724,20669778,+" ; protein_id "ENSP00000298925.5" ; tag basic exp_conf CCDS ; transcript_id "NAV2--NELL1^ENST00000298925.9" ; transcript_name "NELL1-201" ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created:
NAV2--NELL1 HAVANA gene 2305 57537 . + . FI_gene_label "NAV2^ENSG00000166833.22" ; ID "NAV2--NELL1^NAV2^ENSG00000166833.22" ; ccdsid "CCDS7850.1" ; exon_id "ENSE00003846126.1" ; exon_number 1 ; gene_id "NAV2--NELL1^NAV2^ENSG00000166833.22" ; gene_name NAV2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000151837.7" ; havana_transcript "OTTHUMT00000324114.1" ; hgnc_id "HGNC:15997" ; level 2 ; orig_coord_info "chr11,19713696,19713962,+" ; protein_id "ENSP00000309577.6" ; tag basic MANE_Select CCDS ; transcript_id "NAV2--NELL1^ENST00000349880.9" ; transcript_name "NAV2-201" ; transcript_support_level 1 ; transcript_type protein_coding
NAV2--NELL1 HAVANA mRNA 2305 57537 . + . FI_gene_label "NAV2^ENSG00000166833.22" ; ID "NAV2--NELL1^ENST00000349880.9" ; Parent "NAV2--NELL1^NAV2^ENSG00000166833.22" ; ccdsid "CCDS7850.1" ; exon_id "ENSE00003846126.1" ; exon_number 1 ; gene_id "NAV2--NELL1^NAV2^ENSG00000166833.22" ; gene_name NAV2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000151837.7" ; havana_transcript "OTTHUMT00000324114.1" ; hgnc_id "HGNC:15997" ; level 2 ; orig_coord_info "chr11,19713696,19713962,+" ; protein_id "ENSP00000309577.6" ; tag basic MANE_Select CCDS ; transcript_id "NAV2--NELL1^ENST00000349880.9" ; transcript_name "NAV2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
NELL1--INSC HAVANA gene 1021 32240 . + . FI_gene_label "NELL1^ENSG00000165973.19" ; ID "NELL1--INSC^NELL1^ENSG00000165973.19" ; ccdsid "CCDS73267.1" ; exon_id "ENSE00001311201.5" ; exon_number 1 ; gene_id "NELL1--INSC^NELL1^ENSG00000165973.19" ; gene_name NELL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000166042.3" ; havana_transcript "OTTHUMT00000387587.1" ; hgnc_id "HGNC:7750" ; level 1 ; orig_coord_info "chr11,20669724,20669778,+" ; protein_id "ENSP00000298925.5" ; tag basic exp_conf CCDS ; transcript_id "NELL1--INSC^ENST00000298925.9" ; transcript_name "NELL1-201" ; transcript_support_level 2 ; transcript_type protein_coding
NELL1--INSC HAVANA mRNA 1021 32240 . + . FI_gene_label "NELL1^ENSG00000165973.19" ; ID "NELL1--INSC^ENST00000298925.9" ; Parent "NELL1--INSC^NELL1^ENSG00000165973.19" ; ccdsid "CCDS73267.1" ; exon_id "ENSE00001311201.5" ; exon_number 1 ; gene_id "NELL1--INSC^NELL1^ENSG00000165973.19" ; gene_name NELL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000166042.3" ; havana_transcript "OTTHUMT00000387587.1" ; hgnc_id "HGNC:7750" ; level 1 ; orig_coord_info "chr11,20669724,20669778,+" ; protein_id "ENSP00000298925.5" ; tag basic exp_conf CCDS ; transcript_id "NELL1--INSC^ENST00000298925.9" ; transcript_name "NELL1-201" ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created:
NELL1--INSC HAVANA gene 35246 55096 . + . FI_gene_label "INSC^ENSG00000188487.12" ; ID "NELL1--INSC^INSC^ENSG00000188487.12" ; ccdsid "CCDS41621.1" ; exon_id "ENSE00001538117.1" ; exon_number 1 ; gene_id "NELL1--INSC^INSC^ENSG00000188487.12" ; gene_name INSC ; gene_type protein_coding ; havana_gene "OTTHUMG00000165838.3" ; havana_transcript "OTTHUMT00000386590.1" ; hgnc_id "HGNC:33116" ; level 2 ; orig_coord_info "chr11,15112470,15112565,+" ; protein_id "ENSP00000368872.3" ; tag basic appris_principal_4 CCDS ; transcript_id "NELL1--INSC^ENST00000379554.7" ; transcript_name "INSC-201" ; transcript_support_level 1 ; transcript_type protein_coding
NELL1--INSC HAVANA mRNA 35246 55096 . + . FI_gene_label "INSC^ENSG00000188487.12" ; ID "NELL1--INSC^ENST00000379554.7" ; Parent "NELL1--INSC^INSC^ENSG00000188487.12" ; ccdsid "CCDS41621.1" ; exon_id "ENSE00001538117.1" ; exon_number 1 ; gene_id "NELL1--INSC^INSC^ENSG00000188487.12" ; gene_name INSC ; gene_type protein_coding ; havana_gene "OTTHUMG00000165838.3" ; havana_transcript "OTTHUMT00000386590.1" ; hgnc_id "HGNC:33116" ; level 2 ; orig_coord_info "chr11,15112470,15112565,+" ; protein_id "ENSP00000368872.3" ; tag basic appris_principal_4 CCDS ; transcript_id "NELL1--INSC^ENST00000379554.7" ; transcript_name "INSC-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PPFIBP2--PARVA HAVANA gene 1702 37120 . + . FI_gene_label "PPFIBP2^ENSG00000166387.13" ; ID "PPFIBP2--PARVA^PPFIBP2^ENSG00000166387.13" ; ccdsid "CCDS31419.1" ; exon_id "ENSE00001278528.6" ; exon_number 2 ; gene_id "PPFIBP2--PARVA^PPFIBP2^ENSG00000166387.13" ; gene_name PPFIBP2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165617.10" ; havana_transcript "OTTHUMT00000385345.3" ; hgnc_id "HGNC:9250" ; level 2 ; orig_coord_info "chr11,7549476,7549539,+" ; protein_id "ENSP00000299492.4" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "PPFIBP2--PARVA^ENST00000299492.9" ; transcript_name "PPFIBP2-201" ; transcript_support_level 1 ; transcript_type protein_coding
PPFIBP2--PARVA HAVANA mRNA 1702 37120 . + . FI_gene_label "PPFIBP2^ENSG00000166387.13" ; ID "PPFIBP2--PARVA^ENST00000299492.9" ; Parent "PPFIBP2--PARVA^PPFIBP2^ENSG00000166387.13" ; ccdsid "CCDS31419.1" ; exon_id "ENSE00001278528.6" ; exon_number 2 ; gene_id "PPFIBP2--PARVA^PPFIBP2^ENSG00000166387.13" ; gene_name PPFIBP2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165617.10" ; havana_transcript "OTTHUMT00000385345.3" ; hgnc_id "HGNC:9250" ; level 2 ; orig_coord_info "chr11,7549476,7549539,+" ; protein_id "ENSP00000299492.4" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "PPFIBP2--PARVA^ENST00000299492.9" ; transcript_name "PPFIBP2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PPFIBP2--PARVA HAVANA gene 42627 67717 . + . FI_gene_label "PARVA^ENSG00000197702.14" ; ID "PPFIBP2--PARVA^PARVA^ENSG00000197702.14" ; exon_id "ENSE00003840507.2" ; exon_number 1 ; gene_id "PPFIBP2--PARVA^PARVA^ENSG00000197702.14" ; gene_name PARVA ; gene_type protein_coding ; havana_gene "OTTHUMG00000165778.6" ; havana_transcript "OTTHUMT00000386165.5" ; hgnc_id "HGNC:14652" ; level 2 ; orig_coord_info "chr11,12377648,12377783,+" ; protein_id "ENSP00000334008.9" ; tag upstream_ATG basic MANE_Select appris_principal_1 ; transcript_id "PPFIBP2--PARVA^ENST00000334956.15" ; transcript_name "PARVA-201" ; transcript_support_level 1 ; transcript_type protein_coding
PPFIBP2--PARVA HAVANA mRNA 42627 67717 . + . FI_gene_label "PARVA^ENSG00000197702.14" ; ID "PPFIBP2--PARVA^ENST00000334956.15" ; Parent "PPFIBP2--PARVA^PARVA^ENSG00000197702.14" ; exon_id "ENSE00003840507.2" ; exon_number 1 ; gene_id "PPFIBP2--PARVA^PARVA^ENSG00000197702.14" ; gene_name PARVA ; gene_type protein_coding ; havana_gene "OTTHUMG00000165778.6" ; havana_transcript "OTTHUMT00000386165.5" ; hgnc_id "HGNC:14652" ; level 2 ; orig_coord_info "chr11,12377648,12377783,+" ; protein_id "ENSP00000334008.9" ; tag upstream_ATG basic MANE_Select appris_principal_1 ; transcript_id "PPFIBP2--PARVA^ENST00000334956.15" ; transcript_name "PARVA-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TNS1--ALK HAVANA gene 8232 56093 . + . FI_gene_label "TNS1^ENSG00000079308.19" ; ID "TNS1--ALK^TNS1^ENSG00000079308.19" ; ccdsid "CCDS2407.1" ; exon_id "ENSE00003622889.1" ; exon_number 6 ; gene_id "TNS1--ALK^TNS1^ENSG00000079308.19" ; gene_name TNS1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133056.10" ; havana_transcript "OTTHUMT00000256672.2" ; hgnc_id "HGNC:11973" ; level 2 ; orig_coord_info "chr2,217897798,217897965,-" ; protein_id "ENSP00000171887.4" ; tag basic CCDS ; transcript_id "TNS1--ALK^ENST00000171887.8" ; transcript_name "TNS1-201" ; transcript_support_level 1 ; transcript_type protein_coding
TNS1--ALK HAVANA mRNA 8232 56093 . + . FI_gene_label "TNS1^ENSG00000079308.19" ; ID "TNS1--ALK^ENST00000171887.8" ; Parent "TNS1--ALK^TNS1^ENSG00000079308.19" ; ccdsid "CCDS2407.1" ; exon_id "ENSE00003622889.1" ; exon_number 6 ; gene_id "TNS1--ALK^TNS1^ENSG00000079308.19" ; gene_name TNS1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000133056.10" ; havana_transcript "OTTHUMT00000256672.2" ; hgnc_id "HGNC:11973" ; level 2 ; orig_coord_info "chr2,217897798,217897965,-" ; protein_id "ENSP00000171887.4" ; tag basic CCDS ; transcript_id "TNS1--ALK^ENST00000171887.8" ; transcript_name "TNS1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TNS1--ALK HAVANA gene 59295 94299 . + . FI_gene_label "ALK^ENSG00000171094.18" ; ID "TNS1--ALK^ALK^ENSG00000171094.18" ; ccdsid "CCDS33172.1" ; exon_id "ENSE00001794937.2" ; exon_number 1 ; gene_id "TNS1--ALK^ALK^ENSG00000171094.18" ; gene_name ALK ; gene_type protein_coding ; havana_gene "OTTHUMG00000152034.4" ; havana_transcript "OTTHUMT00000324994.2" ; hgnc_id "HGNC:427" ; level 2 ; orig_coord_info "chr2,29919993,29920659,-" ; protein_id "ENSP00000373700.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TNS1--ALK^ENST00000389048.8" ; transcript_name "ALK-201" ; transcript_support_level 1 ; transcript_type protein_coding
TNS1--ALK HAVANA mRNA 59295 94299 . + . FI_gene_label "ALK^ENSG00000171094.18" ; ID "TNS1--ALK^ENST00000389048.8" ; Parent "TNS1--ALK^ALK^ENSG00000171094.18" ; ccdsid "CCDS33172.1" ; exon_id "ENSE00001794937.2" ; exon_number 1 ; gene_id "TNS1--ALK^ALK^ENSG00000171094.18" ; gene_name ALK ; gene_type protein_coding ; havana_gene "OTTHUMG00000152034.4" ; havana_transcript "OTTHUMT00000324994.2" ; hgnc_id "HGNC:427" ; level 2 ; orig_coord_info "chr2,29919993,29920659,-" ; protein_id "ENSP00000373700.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TNS1--ALK^ENST00000389048.8" ; transcript_name "ALK-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TRPC2--WEE1 HAVANA gene 21081 33282 . + . FI_gene_label "WEE1^ENSG00000166483.12" ; ID "TRPC2--WEE1^WEE1^ENSG00000166483.12" ; ccdsid "CCDS44536.1" ; exon_id "ENSE00003609415.1" ; exon_number 2 ; gene_id "TRPC2--WEE1^WEE1^ENSG00000166483.12" ; gene_name WEE1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165863.4" ; havana_transcript "OTTHUMT00000386758.2" ; hgnc_id "HGNC:12761" ; level 2 ; orig_coord_info "chr11,9575954,9576093,+" ; protein_id "ENSP00000299613.5" ; tag basic appris_principal_1 CCDS ; transcript_id "TRPC2--WEE1^ENST00000299613.10" ; transcript_name "WEE1-201" ; transcript_support_level 2 ; transcript_type protein_coding
TRPC2--WEE1 HAVANA mRNA 21081 33282 . + . FI_gene_label "WEE1^ENSG00000166483.12" ; ID "TRPC2--WEE1^ENST00000299613.10" ; Parent "TRPC2--WEE1^WEE1^ENSG00000166483.12" ; ccdsid "CCDS44536.1" ; exon_id "ENSE00003609415.1" ; exon_number 2 ; gene_id "TRPC2--WEE1^WEE1^ENSG00000166483.12" ; gene_name WEE1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165863.4" ; havana_transcript "OTTHUMT00000386758.2" ; hgnc_id "HGNC:12761" ; level 2 ; orig_coord_info "chr11,9575954,9576093,+" ; protein_id "ENSP00000299613.5" ; tag basic appris_principal_1 CCDS ; transcript_id "TRPC2--WEE1^ENST00000299613.10" ; transcript_name "WEE1-201" ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created:
TRPC2--WEE1 HAVANA gene 1001 17053 . + . FI_gene_label "TRPC2^ENSG00000182048.11" ; ID "TRPC2--WEE1^TRPC2^ENSG00000182048.11" ; exon_id "ENSE00001745449.1" ; exon_number 1 ; gene_id "TRPC2--WEE1^TRPC2^ENSG00000182048.11" ; gene_name TRPC2 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000011712.2" ; havana_transcript "OTTHUMT00000032350.2" ; hgnc_id "HGNC:12334" ; level 2 ; ont "PGO:0000005" "PGO:0000019" ; orig_coord_info "chr11,3609901,3609989,+" ; tag basic ; transcript_id "TRPC2--WEE1^ENST00000451043.6" ; transcript_name "TRPC2-201" ; transcript_support_level NA ; transcript_type transcribed_unprocessed_pseudogene
TRPC2--WEE1 HAVANA RNA 1001 17053 . + . FI_gene_label "TRPC2^ENSG00000182048.11" ; ID "TRPC2--WEE1^ENST00000451043.6" ; Parent "TRPC2--WEE1^TRPC2^ENSG00000182048.11" ; exon_id "ENSE00001745449.1" ; exon_number 1 ; gene_id "TRPC2--WEE1^TRPC2^ENSG00000182048.11" ; gene_name TRPC2 ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000011712.2" ; havana_transcript "OTTHUMT00000032350.2" ; hgnc_id "HGNC:12334" ; level 2 ; ont "PGO:0000005" "PGO:0000019" ; orig_coord_info "chr11,3609901,3609989,+" ; tag basic ; transcript_id "TRPC2--WEE1^ENST00000451043.6" ; transcript_name "TRPC2-201" ; transcript_support_level NA ; transcript_type transcribed_unprocessed_pseudogene
179 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 ------------------------------
324 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 11 wrong level1 location cases
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---------------------- Check13: remove identical isoforms ----------------------
None found
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------ End checks (done in 0 second) ------
GFF3 file parsed