Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/83/0c870e2a2227a10d86d83776e1845b/fi_workdir/tih_rna_sample_00090_23H5VFLT4_s32.gtf
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d7/bd70638b27b631ed2ef660ef888db0/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d7/bd70638b27b631ed2ef660ef888db0/.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: 1907
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 1907
=> 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:1907
=> 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:
ABHD12--NINL HAVANA gene 24206 52269 . + . FI_gene_label "NINL^ENSG00000101004.15" ; ID "ABHD12--NINL^NINL^ENSG00000101004.15" ; ccdsid "CCDS33452.1" ; exon_id "ENSE00001358809.1" ; exon_number 2 ; gene_id "ABHD12--NINL^NINL^ENSG00000101004.15" ; gene_name NINL ; gene_type protein_coding ; havana_gene "OTTHUMG00000032127.5" ; havana_transcript "OTTHUMT00000078445.4" ; hgnc_id "HGNC:29163" ; level 2 ; orig_coord_info "chr20,25526408,25526587,-" ; protein_id "ENSP00000278886.6" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "ABHD12--NINL^ENST00000278886.11" ; transcript_name "NINL-201" ; transcript_support_level 1 ; transcript_type protein_coding
ABHD12--NINL HAVANA mRNA 24206 52269 . + . FI_gene_label "NINL^ENSG00000101004.15" ; ID "ABHD12--NINL^ENST00000278886.11" ; Parent "ABHD12--NINL^NINL^ENSG00000101004.15" ; ccdsid "CCDS33452.1" ; exon_id "ENSE00001358809.1" ; exon_number 2 ; gene_id "ABHD12--NINL^NINL^ENSG00000101004.15" ; gene_name NINL ; gene_type protein_coding ; havana_gene "OTTHUMG00000032127.5" ; havana_transcript "OTTHUMT00000078445.4" ; hgnc_id "HGNC:29163" ; level 2 ; orig_coord_info "chr20,25526408,25526587,-" ; protein_id "ENSP00000278886.6" ; tag basic MANE_Select appris_principal_2 CCDS ; transcript_id "ABHD12--NINL^ENST00000278886.11" ; transcript_name "NINL-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ABHD12--NINL HAVANA gene 1001 19915 . + . FI_gene_label "ABHD12^ENSG00000100997.20" ; ID "ABHD12--NINL^ABHD12^ENSG00000100997.20" ; ccdsid "CCDS42857.1" ; exon_id "ENSE00001955112.2" ; exon_number 1 ; gene_id "ABHD12--NINL^ABHD12^ENSG00000100997.20" ; gene_name ABHD12 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032121.7" ; havana_transcript "OTTHUMT00000078423.4" ; hgnc_id "HGNC:15868" ; level 2 ; orig_coord_info "chr20,25390513,25390703,-" ; protein_id "ENSP00000341408.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ABHD12--NINL^ENST00000339157.10" ; transcript_name "ABHD12-201" ; transcript_support_level 2 ; transcript_type protein_coding
ABHD12--NINL HAVANA mRNA 1001 19915 . + . FI_gene_label "ABHD12^ENSG00000100997.20" ; ID "ABHD12--NINL^ENST00000339157.10" ; Parent "ABHD12--NINL^ABHD12^ENSG00000100997.20" ; ccdsid "CCDS42857.1" ; exon_id "ENSE00001955112.2" ; exon_number 1 ; gene_id "ABHD12--NINL^ABHD12^ENSG00000100997.20" ; gene_name ABHD12 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032121.7" ; havana_transcript "OTTHUMT00000078423.4" ; hgnc_id "HGNC:15868" ; level 2 ; orig_coord_info "chr20,25390513,25390703,-" ; protein_id "ENSP00000341408.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ABHD12--NINL^ENST00000339157.10" ; transcript_name "ABHD12-201" ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created:
CDH1--TANGO6 HAVANA gene 1001 23257 . + . FI_gene_label "CDH1^ENSG00000039068.20" ; ID "CDH1--TANGO6^CDH1^ENSG00000039068.20" ; ccdsid "CCDS10869.1" ; exon_id "ENSE00003713181.1" ; exon_number 1 ; gene_id "CDH1--TANGO6^CDH1^ENSG00000039068.20" ; gene_name CDH1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000137561.6" ; havana_transcript "OTTHUMT00000268897.3" ; hgnc_id "HGNC:1748" ; level 2 ; orig_coord_info "chr16,68737416,68737463,+" ; protein_id "ENSP00000261769.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CDH1--TANGO6^ENST00000261769.10" ; transcript_name "CDH1-201" ; transcript_support_level 1 ; transcript_type protein_coding
CDH1--TANGO6 HAVANA mRNA 1001 23257 . + . FI_gene_label "CDH1^ENSG00000039068.20" ; ID "CDH1--TANGO6^ENST00000261769.10" ; Parent "CDH1--TANGO6^CDH1^ENSG00000039068.20" ; ccdsid "CCDS10869.1" ; exon_id "ENSE00003713181.1" ; exon_number 1 ; gene_id "CDH1--TANGO6^CDH1^ENSG00000039068.20" ; gene_name CDH1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000137561.6" ; havana_transcript "OTTHUMT00000268897.3" ; hgnc_id "HGNC:1748" ; level 2 ; orig_coord_info "chr16,68737416,68737463,+" ; protein_id "ENSP00000261769.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CDH1--TANGO6^ENST00000261769.10" ; transcript_name "CDH1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
CDH1--TANGO6 HAVANA gene 26258 52899 . + . FI_gene_label "TANGO6^ENSG00000103047.8" ; ID "CDH1--TANGO6^TANGO6^ENSG00000103047.8" ; ccdsid "CCDS45516.1" ; exon_id "ENSE00001111652.2" ; exon_number 1 ; gene_id "CDH1--TANGO6^TANGO6^ENSG00000103047.8" ; gene_name TANGO6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000176743.4" ; havana_transcript "OTTHUMT00000433471.3" ; hgnc_id "HGNC:25749" ; level 2 ; orig_coord_info "chr16,68843618,68843711,+" ; protein_id "ENSP00000261778.1" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CDH1--TANGO6^ENST00000261778.2" ; transcript_name "TANGO6-201" ; transcript_support_level 1 ; transcript_type protein_coding
CDH1--TANGO6 HAVANA mRNA 26258 52899 . + . FI_gene_label "TANGO6^ENSG00000103047.8" ; ID "CDH1--TANGO6^ENST00000261778.2" ; Parent "CDH1--TANGO6^TANGO6^ENSG00000103047.8" ; ccdsid "CCDS45516.1" ; exon_id "ENSE00001111652.2" ; exon_number 1 ; gene_id "CDH1--TANGO6^TANGO6^ENSG00000103047.8" ; gene_name TANGO6 ; gene_type protein_coding ; havana_gene "OTTHUMG00000176743.4" ; havana_transcript "OTTHUMT00000433471.3" ; hgnc_id "HGNC:25749" ; level 2 ; orig_coord_info "chr16,68843618,68843711,+" ; protein_id "ENSP00000261778.1" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "CDH1--TANGO6^ENST00000261778.2" ; transcript_name "TANGO6-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PCDHA11--PCDHA13 HAVANA gene 7419 15859 . + . FI_gene_label "PCDHA13^ENSG00000239389.8" ; ID "PCDHA11--PCDHA13^PCDHA13^ENSG00000239389.8" ; ccdsid "CCDS4240.1" ; exon_id "ENSE00001038419.2" ; exon_number 1 ; gene_id "PCDHA11--PCDHA13^PCDHA13^ENSG00000239389.8" ; gene_name PCDHA13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129614.4" ; havana_transcript "OTTHUMT00000335000.2" ; hgnc_id "HGNC:8667" ; level 2 ; orig_coord_info "chr5,140882269,140884662,+" ; protein_id "ENSP00000289272.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA11--PCDHA13^ENST00000289272.3" ; transcript_name "PCDHA13-201" ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA11--PCDHA13 HAVANA mRNA 7419 15859 . + . FI_gene_label "PCDHA13^ENSG00000239389.8" ; ID "PCDHA11--PCDHA13^ENST00000289272.3" ; Parent "PCDHA11--PCDHA13^PCDHA13^ENSG00000239389.8" ; ccdsid "CCDS4240.1" ; exon_id "ENSE00001038419.2" ; exon_number 1 ; gene_id "PCDHA11--PCDHA13^PCDHA13^ENSG00000239389.8" ; gene_name PCDHA13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129614.4" ; havana_transcript "OTTHUMT00000335000.2" ; hgnc_id "HGNC:8667" ; level 2 ; orig_coord_info "chr5,140882269,140884662,+" ; protein_id "ENSP00000289272.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA11--PCDHA13^ENST00000289272.3" ; transcript_name "PCDHA13-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PCDHA11--PCDHA13 HAVANA gene 1001 4418 . + . FI_gene_label "PCDHA11^ENSG00000249158.7" ; ID "PCDHA11--PCDHA13^PCDHA11^ENSG00000249158.7" ; ccdsid "CCDS75326.1" ; exon_id "ENSE00003719125.1" ; exon_number 1 ; gene_id "PCDHA11--PCDHA13^PCDHA11^ENSG00000249158.7" ; gene_name PCDHA11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163369.3" ; havana_transcript "OTTHUMT00000477577.1" ; hgnc_id "HGNC:8665" ; level 2 ; orig_coord_info "chr5,140869104,140871533,+" ; protein_id "ENSP00000482503.1" ; tag basic CCDS ; transcript_id "PCDHA11--PCDHA13^ENST00000616325.1" ; transcript_name "PCDHA11-202" ; transcript_support_level NA ; transcript_type protein_coding
PCDHA11--PCDHA13 HAVANA mRNA 1001 4418 . + . FI_gene_label "PCDHA11^ENSG00000249158.7" ; ID "PCDHA11--PCDHA13^ENST00000616325.1" ; Parent "PCDHA11--PCDHA13^PCDHA11^ENSG00000249158.7" ; ccdsid "CCDS75326.1" ; exon_id "ENSE00003719125.1" ; exon_number 1 ; gene_id "PCDHA11--PCDHA13^PCDHA11^ENSG00000249158.7" ; gene_name PCDHA11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163369.3" ; havana_transcript "OTTHUMT00000477577.1" ; hgnc_id "HGNC:8665" ; level 2 ; orig_coord_info "chr5,140869104,140871533,+" ; protein_id "ENSP00000482503.1" ; tag basic CCDS ; transcript_id "PCDHA11--PCDHA13^ENST00000616325.1" ; transcript_name "PCDHA11-202" ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created:
PCDHA11--PCDHAC1 HAVANA gene 7419 17434 . + . FI_gene_label "PCDHAC1^ENSG00000248383.5" ; ID "PCDHA11--PCDHAC1^PCDHAC1^ENSG00000248383.5" ; ccdsid "CCDS4241.1" ; exon_id "ENSE00001085780.5" ; exon_number 1 ; gene_id "PCDHA11--PCDHAC1^PCDHAC1^ENSG00000248383.5" ; gene_name PCDHAC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129603.3" ; havana_transcript "OTTHUMT00000251798.1" ; hgnc_id "HGNC:8676" ; level 2 ; orig_coord_info "chr5,140926893,140929325,+" ; protein_id "ENSP00000253807.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA11--PCDHAC1^ENST00000253807.3" ; transcript_name "PCDHAC1-201" ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA11--PCDHAC1 HAVANA mRNA 7419 17434 . + . FI_gene_label "PCDHAC1^ENSG00000248383.5" ; ID "PCDHA11--PCDHAC1^ENST00000253807.3" ; Parent "PCDHA11--PCDHAC1^PCDHAC1^ENSG00000248383.5" ; ccdsid "CCDS4241.1" ; exon_id "ENSE00001085780.5" ; exon_number 1 ; gene_id "PCDHA11--PCDHAC1^PCDHAC1^ENSG00000248383.5" ; gene_name PCDHAC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129603.3" ; havana_transcript "OTTHUMT00000251798.1" ; hgnc_id "HGNC:8676" ; level 2 ; orig_coord_info "chr5,140926893,140929325,+" ; protein_id "ENSP00000253807.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA11--PCDHAC1^ENST00000253807.3" ; transcript_name "PCDHAC1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PCDHA11--PCDHAC1 HAVANA gene 1001 4418 . + . FI_gene_label "PCDHA11^ENSG00000249158.7" ; ID "PCDHA11--PCDHAC1^PCDHA11^ENSG00000249158.7" ; ccdsid "CCDS75326.1" ; exon_id "ENSE00003719125.1" ; exon_number 1 ; gene_id "PCDHA11--PCDHAC1^PCDHA11^ENSG00000249158.7" ; gene_name PCDHA11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163369.3" ; havana_transcript "OTTHUMT00000477577.1" ; hgnc_id "HGNC:8665" ; level 2 ; orig_coord_info "chr5,140869104,140871533,+" ; protein_id "ENSP00000482503.1" ; tag basic CCDS ; transcript_id "PCDHA11--PCDHAC1^ENST00000616325.1" ; transcript_name "PCDHA11-202" ; transcript_support_level NA ; transcript_type protein_coding
PCDHA11--PCDHAC1 HAVANA mRNA 1001 4418 . + . FI_gene_label "PCDHA11^ENSG00000249158.7" ; ID "PCDHA11--PCDHAC1^ENST00000616325.1" ; Parent "PCDHA11--PCDHAC1^PCDHA11^ENSG00000249158.7" ; ccdsid "CCDS75326.1" ; exon_id "ENSE00003719125.1" ; exon_number 1 ; gene_id "PCDHA11--PCDHAC1^PCDHA11^ENSG00000249158.7" ; gene_name PCDHA11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163369.3" ; havana_transcript "OTTHUMT00000477577.1" ; hgnc_id "HGNC:8665" ; level 2 ; orig_coord_info "chr5,140869104,140871533,+" ; protein_id "ENSP00000482503.1" ; tag basic CCDS ; transcript_id "PCDHA11--PCDHAC1^ENST00000616325.1" ; transcript_name "PCDHA11-202" ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created:
PCDHA11--PCDHAC2 HAVANA gene 7425 18160 . + . FI_gene_label "PCDHAC2^ENSG00000243232.6" ; ID "PCDHA11--PCDHAC2^PCDHAC2^ENSG00000243232.6" ; ccdsid "CCDS4242.1" ; exon_id "ENSE00001038414.4" ; exon_number 1 ; gene_id "PCDHA11--PCDHAC2^PCDHAC2^ENSG00000243232.6" ; gene_name PCDHAC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129607.7" ; havana_transcript "OTTHUMT00000251802.4" ; hgnc_id "HGNC:8677" ; level 2 ; orig_coord_info "chr5,140966767,140969331,+" ; protein_id "ENSP00000289269.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA11--PCDHAC2^ENST00000289269.7" ; transcript_name "PCDHAC2-201" ; transcript_support_level 1 ; transcript_type protein_coding
PCDHA11--PCDHAC2 HAVANA mRNA 7425 18160 . + . FI_gene_label "PCDHAC2^ENSG00000243232.6" ; ID "PCDHA11--PCDHAC2^ENST00000289269.7" ; Parent "PCDHA11--PCDHAC2^PCDHAC2^ENSG00000243232.6" ; ccdsid "CCDS4242.1" ; exon_id "ENSE00001038414.4" ; exon_number 1 ; gene_id "PCDHA11--PCDHAC2^PCDHAC2^ENSG00000243232.6" ; gene_name PCDHAC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129607.7" ; havana_transcript "OTTHUMT00000251802.4" ; hgnc_id "HGNC:8677" ; level 2 ; orig_coord_info "chr5,140966767,140969331,+" ; protein_id "ENSP00000289269.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PCDHA11--PCDHAC2^ENST00000289269.7" ; transcript_name "PCDHAC2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
PCDHA11--PCDHAC2 HAVANA gene 1001 4418 . + . FI_gene_label "PCDHA11^ENSG00000249158.7" ; ID "PCDHA11--PCDHAC2^PCDHA11^ENSG00000249158.7" ; ccdsid "CCDS75326.1" ; exon_id "ENSE00003719125.1" ; exon_number 1 ; gene_id "PCDHA11--PCDHAC2^PCDHA11^ENSG00000249158.7" ; gene_name PCDHA11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163369.3" ; havana_transcript "OTTHUMT00000477577.1" ; hgnc_id "HGNC:8665" ; level 2 ; orig_coord_info "chr5,140869104,140871533,+" ; protein_id "ENSP00000482503.1" ; tag basic CCDS ; transcript_id "PCDHA11--PCDHAC2^ENST00000616325.1" ; transcript_name "PCDHA11-202" ; transcript_support_level NA ; transcript_type protein_coding
PCDHA11--PCDHAC2 HAVANA mRNA 1001 4418 . + . FI_gene_label "PCDHA11^ENSG00000249158.7" ; ID "PCDHA11--PCDHAC2^ENST00000616325.1" ; Parent "PCDHA11--PCDHAC2^PCDHA11^ENSG00000249158.7" ; ccdsid "CCDS75326.1" ; exon_id "ENSE00003719125.1" ; exon_number 1 ; gene_id "PCDHA11--PCDHAC2^PCDHA11^ENSG00000249158.7" ; gene_name PCDHA11 ; gene_type protein_coding ; havana_gene "OTTHUMG00000163369.3" ; havana_transcript "OTTHUMT00000477577.1" ; hgnc_id "HGNC:8665" ; level 2 ; orig_coord_info "chr5,140869104,140871533,+" ; protein_id "ENSP00000482503.1" ; tag basic CCDS ; transcript_id "PCDHA11--PCDHAC2^ENST00000616325.1" ; transcript_name "PCDHA11-202" ; transcript_support_level NA ; transcript_type protein_coding
L1 and L2 created:
SH3YL1--AC079779.1 HAVANA gene 2940 27933 . + . FI_gene_label "SH3YL1^ENSG00000035115.22" ; ID "SH3YL1--AC079779.1^SH3YL1^ENSG00000035115.22" ; ccdsid "CCDS42646.2" ; exon_id "ENSE00002148326.1" ; exon_number 1 ; gene_id "SH3YL1--AC079779.1^SH3YL1^ENSG00000035115.22" ; gene_name SH3YL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000151359.9" ; havana_transcript "OTTHUMT00000322350.2" ; hgnc_id "HGNC:29546" ; level 2 ; orig_coord_info "chr2,263984,263984,-" ; protein_id "ENSP00000348471.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SH3YL1--AC079779.1^ENST00000356150.10" ; transcript_name "SH3YL1-201" ; transcript_support_level 1 ; transcript_type protein_coding
SH3YL1--AC079779.1 HAVANA mRNA 2940 27933 . + . FI_gene_label "SH3YL1^ENSG00000035115.22" ; ID "SH3YL1--AC079779.1^ENST00000356150.10" ; Parent "SH3YL1--AC079779.1^SH3YL1^ENSG00000035115.22" ; ccdsid "CCDS42646.2" ; exon_id "ENSE00002148326.1" ; exon_number 1 ; gene_id "SH3YL1--AC079779.1^SH3YL1^ENSG00000035115.22" ; gene_name SH3YL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000151359.9" ; havana_transcript "OTTHUMT00000322350.2" ; hgnc_id "HGNC:29546" ; level 2 ; orig_coord_info "chr2,263984,263984,-" ; protein_id "ENSP00000348471.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SH3YL1--AC079779.1^ENST00000356150.10" ; transcript_name "SH3YL1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SH3YL1--FAM110C HAVANA gene 31713 37736 . + . FI_gene_label "FAM110C^ENSG00000184731.6" ; ID "SH3YL1--FAM110C^FAM110C^ENSG00000184731.6" ; ccdsid "CCDS42645.1" ; exon_id "ENSE00001292553.4" ; exon_number 1 ; gene_id "SH3YL1--FAM110C^FAM110C^ENSG00000184731.6" ; gene_name FAM110C ; gene_type protein_coding ; havana_gene "OTTHUMG00000151321.2" ; havana_transcript "OTTHUMT00000322220.2" ; hgnc_id "HGNC:33340" ; level 2 ; orig_coord_info "chr2,45440,46385,-" ; protein_id "ENSP00000328347.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SH3YL1--FAM110C^ENST00000327669.5" ; transcript_name "FAM110C-201" ; transcript_support_level 1 ; transcript_type protein_coding
SH3YL1--FAM110C HAVANA mRNA 31713 37736 . + . FI_gene_label "FAM110C^ENSG00000184731.6" ; ID "SH3YL1--FAM110C^ENST00000327669.5" ; Parent "SH3YL1--FAM110C^FAM110C^ENSG00000184731.6" ; ccdsid "CCDS42645.1" ; exon_id "ENSE00001292553.4" ; exon_number 1 ; gene_id "SH3YL1--FAM110C^FAM110C^ENSG00000184731.6" ; gene_name FAM110C ; gene_type protein_coding ; havana_gene "OTTHUMG00000151321.2" ; havana_transcript "OTTHUMT00000322220.2" ; hgnc_id "HGNC:33340" ; level 2 ; orig_coord_info "chr2,45440,46385,-" ; protein_id "ENSP00000328347.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SH3YL1--FAM110C^ENST00000327669.5" ; transcript_name "FAM110C-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
SH3YL1--FAM110C HAVANA gene 2940 27933 . + . FI_gene_label "SH3YL1^ENSG00000035115.22" ; ID "SH3YL1--FAM110C^SH3YL1^ENSG00000035115.22" ; ccdsid "CCDS42646.2" ; exon_id "ENSE00002148326.1" ; exon_number 1 ; gene_id "SH3YL1--FAM110C^SH3YL1^ENSG00000035115.22" ; gene_name SH3YL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000151359.9" ; havana_transcript "OTTHUMT00000322350.2" ; hgnc_id "HGNC:29546" ; level 2 ; orig_coord_info "chr2,263984,263984,-" ; protein_id "ENSP00000348471.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SH3YL1--FAM110C^ENST00000356150.10" ; transcript_name "SH3YL1-201" ; transcript_support_level 1 ; transcript_type protein_coding
SH3YL1--FAM110C HAVANA mRNA 2940 27933 . + . FI_gene_label "SH3YL1^ENSG00000035115.22" ; ID "SH3YL1--FAM110C^ENST00000356150.10" ; Parent "SH3YL1--FAM110C^SH3YL1^ENSG00000035115.22" ; ccdsid "CCDS42646.2" ; exon_id "ENSE00002148326.1" ; exon_number 1 ; gene_id "SH3YL1--FAM110C^SH3YL1^ENSG00000035115.22" ; gene_name SH3YL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000151359.9" ; havana_transcript "OTTHUMT00000322350.2" ; hgnc_id "HGNC:29546" ; level 2 ; orig_coord_info "chr2,263984,263984,-" ; protein_id "ENSP00000348471.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SH3YL1--FAM110C^ENST00000356150.10" ; transcript_name "SH3YL1-201" ; 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:
SUMF1--AC087857.1 HAVANA gene 1005 10918 . + . FI_gene_label "SUMF1^ENSG00000144455.14" ; ID "SUMF1--AC087857.1^SUMF1^ENSG00000144455.14" ; ccdsid "CCDS2564.1" ; exon_id "ENSE00001939829.1" ; exon_number 1 ; gene_id "SUMF1--AC087857.1^SUMF1^ENSG00000144455.14" ; gene_name SUMF1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000090269.6" ; havana_transcript "OTTHUMT00000206591.3" ; hgnc_id "HGNC:20376" ; level 2 ; orig_coord_info "chr3,4466976,4467245,-" ; protein_id "ENSP00000272902.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SUMF1--AC087857.1^ENST00000272902.10" ; transcript_name "SUMF1-201" ; transcript_support_level 1 ; transcript_type protein_coding
SUMF1--AC087857.1 HAVANA mRNA 1005 10918 . + . FI_gene_label "SUMF1^ENSG00000144455.14" ; ID "SUMF1--AC087857.1^ENST00000272902.10" ; Parent "SUMF1--AC087857.1^SUMF1^ENSG00000144455.14" ; ccdsid "CCDS2564.1" ; exon_id "ENSE00001939829.1" ; exon_number 1 ; gene_id "SUMF1--AC087857.1^SUMF1^ENSG00000144455.14" ; gene_name SUMF1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000090269.6" ; havana_transcript "OTTHUMT00000206591.3" ; hgnc_id "HGNC:20376" ; level 2 ; orig_coord_info "chr3,4466976,4467245,-" ; protein_id "ENSP00000272902.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "SUMF1--AC087857.1^ENST00000272902.10" ; transcript_name "SUMF1-201" ; 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:
SH3YL1--AC079779.1 HAVANA gene 31348 36384 . + . FI_gene_label "AC079779.1^ENSG00000227061.2" ; ID "SH3YL1--AC079779.1^AC079779.1^ENSG00000227061.2" ; exon_id "ENSE00001772056.1" ; exon_number 1 ; gene_id "SH3YL1--AC079779.1^AC079779.1^ENSG00000227061.2" ; gene_name "AC079779.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000151377.3" ; havana_transcript "OTTHUMT00000322421.1" ; level 2 ; orig_coord_info "chr2,197569,199901,+" ; tag basic ; transcript_id "SH3YL1--AC079779.1^ENST00000437798.1" ; transcript_name "AC079779.1-201" ; transcript_support_level 1 ; transcript_type lncRNA
SH3YL1--AC079779.1 HAVANA RNA 31348 36384 . + . FI_gene_label "AC079779.1^ENSG00000227061.2" ; ID "SH3YL1--AC079779.1^ENST00000437798.1" ; Parent "SH3YL1--AC079779.1^AC079779.1^ENSG00000227061.2" ; exon_id "ENSE00001772056.1" ; exon_number 1 ; gene_id "SH3YL1--AC079779.1^AC079779.1^ENSG00000227061.2" ; gene_name "AC079779.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000151377.3" ; havana_transcript "OTTHUMT00000322421.1" ; level 2 ; orig_coord_info "chr2,197569,199901,+" ; tag basic ; transcript_id "SH3YL1--AC079779.1^ENST00000437798.1" ; transcript_name "AC079779.1-201" ; transcript_support_level 1 ; transcript_type lncRNA
L1 and L2 created:
SUMF1--AC087857.1 HAVANA gene 30516 32334 . + . FI_gene_label "AC087857.1^ENSG00000229642.1" ; ID "SUMF1--AC087857.1^AC087857.1^ENSG00000229642.1" ; exon_id "ENSE00001625232.1" ; exon_number 1 ; gene_id "SUMF1--AC087857.1^AC087857.1^ENSG00000229642.1" ; gene_name "AC087857.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000154907.1" ; havana_transcript "OTTHUMT00000337609.1" ; level 2 ; orig_coord_info "chr3,5962842,5963081,+" ; tag basic ; transcript_id "SUMF1--AC087857.1^ENST00000425894.1" ; transcript_name "AC087857.1-201" ; transcript_support_level 3 ; transcript_type lncRNA
SUMF1--AC087857.1 HAVANA RNA 30516 32334 . + . FI_gene_label "AC087857.1^ENSG00000229642.1" ; ID "SUMF1--AC087857.1^ENST00000425894.1" ; Parent "SUMF1--AC087857.1^AC087857.1^ENSG00000229642.1" ; exon_id "ENSE00001625232.1" ; exon_number 1 ; gene_id "SUMF1--AC087857.1^AC087857.1^ENSG00000229642.1" ; gene_name "AC087857.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000154907.1" ; havana_transcript "OTTHUMT00000337609.1" ; level 2 ; orig_coord_info "chr3,5962842,5963081,+" ; tag basic ; transcript_id "SUMF1--AC087857.1^ENST00000425894.1" ; transcript_name "AC087857.1-201" ; transcript_support_level 3 ; transcript_type lncRNA
180 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 ------------------------------
345 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