Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b3/d25f1016f2e1568c63c7e828f31fd2/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ad/3e2f380cc5a0ed02c16b7cf616bd73/fi_workdir/aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.gtf
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b3/d25f1016f2e1568c63c7e828f31fd2/.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: 2059
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 2059
=> 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:2059
=> 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:
BCAS1--AL133335.1 HAVANA gene 1050 15765 . + . FI_gene_label "BCAS1^ENSG00000064787.13" ; ID "BCAS1--AL133335.1^BCAS1^ENSG00000064787.13" ; ccdsid "CCDS82631.1" ; exon_id "ENSE00003714232.1" ; exon_number 2 ; gene_id "BCAS1--AL133335.1^BCAS1^ENSG00000064787.13" ; gene_name BCAS1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032772.2" ; havana_transcript "OTTHUMT00000259203.1" ; hgnc_id "HGNC:974" ; level 2 ; orig_coord_info "chr20,54058647,54058718,-" ; protein_id "ENSP00000360490.2" ; tag basic appris_alternative_2 CCDS ; transcript_id "BCAS1--AL133335.1^ENST00000371435.6" ; transcript_name "BCAS1-201" ; transcript_support_level 1 ; transcript_type protein_coding
BCAS1--AL133335.1 HAVANA mRNA 1050 15765 . + . FI_gene_label "BCAS1^ENSG00000064787.13" ; ID "BCAS1--AL133335.1^ENST00000371435.6" ; Parent "BCAS1--AL133335.1^BCAS1^ENSG00000064787.13" ; ccdsid "CCDS82631.1" ; exon_id "ENSE00003714232.1" ; exon_number 2 ; gene_id "BCAS1--AL133335.1^BCAS1^ENSG00000064787.13" ; gene_name BCAS1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032772.2" ; havana_transcript "OTTHUMT00000259203.1" ; hgnc_id "HGNC:974" ; level 2 ; orig_coord_info "chr20,54058647,54058718,-" ; protein_id "ENSP00000360490.2" ; tag basic appris_alternative_2 CCDS ; transcript_id "BCAS1--AL133335.1^ENST00000371435.6" ; transcript_name "BCAS1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
BCAS1--DOK5 HAVANA gene 24514 34439 . + . FI_gene_label "DOK5^ENSG00000101134.12" ; ID "BCAS1--DOK5^DOK5^ENSG00000101134.12" ; ccdsid "CCDS13446.1" ; exon_id "ENSE00001921899.2" ; exon_number 1 ; gene_id "BCAS1--DOK5^DOK5^ENSG00000101134.12" ; gene_name DOK5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032778.3" ; havana_transcript "OTTHUMT00000079777.3" ; hgnc_id "HGNC:16173" ; level 2 ; orig_coord_info "chr20,54475947,54476012,+" ; protein_id "ENSP00000262593.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "BCAS1--DOK5^ENST00000262593.10" ; transcript_name "DOK5-201" ; transcript_support_level 1 ; transcript_type protein_coding
BCAS1--DOK5 HAVANA mRNA 24514 34439 . + . FI_gene_label "DOK5^ENSG00000101134.12" ; ID "BCAS1--DOK5^ENST00000262593.10" ; Parent "BCAS1--DOK5^DOK5^ENSG00000101134.12" ; ccdsid "CCDS13446.1" ; exon_id "ENSE00001921899.2" ; exon_number 1 ; gene_id "BCAS1--DOK5^DOK5^ENSG00000101134.12" ; gene_name DOK5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032778.3" ; havana_transcript "OTTHUMT00000079777.3" ; hgnc_id "HGNC:16173" ; level 2 ; orig_coord_info "chr20,54475947,54476012,+" ; protein_id "ENSP00000262593.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "BCAS1--DOK5^ENST00000262593.10" ; transcript_name "DOK5-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
BCAS1--DOK5 HAVANA gene 1050 15765 . + . FI_gene_label "BCAS1^ENSG00000064787.13" ; ID "BCAS1--DOK5^BCAS1^ENSG00000064787.13" ; ccdsid "CCDS82631.1" ; exon_id "ENSE00003714232.1" ; exon_number 2 ; gene_id "BCAS1--DOK5^BCAS1^ENSG00000064787.13" ; gene_name BCAS1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032772.2" ; havana_transcript "OTTHUMT00000259203.1" ; hgnc_id "HGNC:974" ; level 2 ; orig_coord_info "chr20,54058647,54058718,-" ; protein_id "ENSP00000360490.2" ; tag basic appris_alternative_2 CCDS ; transcript_id "BCAS1--DOK5^ENST00000371435.6" ; transcript_name "BCAS1-201" ; transcript_support_level 1 ; transcript_type protein_coding
BCAS1--DOK5 HAVANA mRNA 1050 15765 . + . FI_gene_label "BCAS1^ENSG00000064787.13" ; ID "BCAS1--DOK5^ENST00000371435.6" ; Parent "BCAS1--DOK5^BCAS1^ENSG00000064787.13" ; ccdsid "CCDS82631.1" ; exon_id "ENSE00003714232.1" ; exon_number 2 ; gene_id "BCAS1--DOK5^BCAS1^ENSG00000064787.13" ; gene_name BCAS1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000032772.2" ; havana_transcript "OTTHUMT00000259203.1" ; hgnc_id "HGNC:974" ; level 2 ; orig_coord_info "chr20,54058647,54058718,-" ; protein_id "ENSP00000360490.2" ; tag basic appris_alternative_2 CCDS ; transcript_id "BCAS1--DOK5^ENST00000371435.6" ; transcript_name "BCAS1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ESR1--CCDC170 HAVANA gene 7250 25560 . + . FI_gene_label "ESR1^ENSG00000091831.24" ; ID "ESR1--CCDC170^ESR1^ENSG00000091831.24" ; ccdsid "CCDS5234.1" ; exon_id "ENSE00001877305.2" ; exon_number 1 ; gene_id "ESR1--CCDC170^ESR1^ENSG00000091831.24" ; gene_name ESR1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016103.7" ; havana_transcript "OTTHUMT00000043308.2" ; hgnc_id "HGNC:3467" ; level 2 ; orig_coord_info "chr6,151807913,151808364,+" ; protein_id "ENSP00000206249.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ESR1--CCDC170^ENST00000206249.8" ; transcript_name "ESR1-201" ; transcript_support_level 1 ; transcript_type protein_coding
ESR1--CCDC170 HAVANA mRNA 7250 25560 . + . FI_gene_label "ESR1^ENSG00000091831.24" ; ID "ESR1--CCDC170^ENST00000206249.8" ; Parent "ESR1--CCDC170^ESR1^ENSG00000091831.24" ; ccdsid "CCDS5234.1" ; exon_id "ENSE00001877305.2" ; exon_number 1 ; gene_id "ESR1--CCDC170^ESR1^ENSG00000091831.24" ; gene_name ESR1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000016103.7" ; havana_transcript "OTTHUMT00000043308.2" ; hgnc_id "HGNC:3467" ; level 2 ; orig_coord_info "chr6,151807913,151808364,+" ; protein_id "ENSP00000206249.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ESR1--CCDC170^ENST00000206249.8" ; transcript_name "ESR1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ESR1--CCDC170 HAVANA gene 35052 50483 . + . FI_gene_label "CCDC170^ENSG00000120262.10" ; ID "ESR1--CCDC170^CCDC170^ENSG00000120262.10" ; ccdsid "CCDS43515.1" ; exon_id "ENSE00001952106.3" ; exon_number 1 ; gene_id "ESR1--CCDC170^CCDC170^ENSG00000120262.10" ; gene_name CCDC170 ; gene_type protein_coding ; havana_gene "OTTHUMG00000015839.3" ; havana_transcript "OTTHUMT00000042727.3" ; hgnc_id "HGNC:21177" ; level 2 ; orig_coord_info "chr6,151494129,151494185,+" ; protein_id "ENSP00000239374.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ESR1--CCDC170^ENST00000239374.8" ; transcript_name "CCDC170-201" ; transcript_support_level 1 ; transcript_type protein_coding
ESR1--CCDC170 HAVANA mRNA 35052 50483 . + . FI_gene_label "CCDC170^ENSG00000120262.10" ; ID "ESR1--CCDC170^ENST00000239374.8" ; Parent "ESR1--CCDC170^CCDC170^ENSG00000120262.10" ; ccdsid "CCDS43515.1" ; exon_id "ENSE00001952106.3" ; exon_number 1 ; gene_id "ESR1--CCDC170^CCDC170^ENSG00000120262.10" ; gene_name CCDC170 ; gene_type protein_coding ; havana_gene "OTTHUMG00000015839.3" ; havana_transcript "OTTHUMT00000042727.3" ; hgnc_id "HGNC:21177" ; level 2 ; orig_coord_info "chr6,151494129,151494185,+" ; protein_id "ENSP00000239374.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ESR1--CCDC170^ENST00000239374.8" ; transcript_name "CCDC170-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
FSIP1--AC013652.1 HAVANA gene 1001 15962 . + . FI_gene_label "FSIP1^ENSG00000150667.8" ; ID "FSIP1--AC013652.1^FSIP1^ENSG00000150667.8" ; ccdsid "CCDS10050.1" ; exon_id "ENSE00003574039.1" ; exon_number 2 ; gene_id "FSIP1--AC013652.1^FSIP1^ENSG00000150667.8" ; gene_name FSIP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000172456.3" ; havana_transcript "OTTHUMT00000252118.4" ; hgnc_id "HGNC:21674" ; level 2 ; orig_coord_info "chr15,39776399,39776524,-" ; protein_id "ENSP00000280236.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "FSIP1--AC013652.1^ENST00000350221.4" ; transcript_name "FSIP1-201" ; transcript_support_level 1 ; transcript_type protein_coding
FSIP1--AC013652.1 HAVANA mRNA 1001 15962 . + . FI_gene_label "FSIP1^ENSG00000150667.8" ; ID "FSIP1--AC013652.1^ENST00000350221.4" ; Parent "FSIP1--AC013652.1^FSIP1^ENSG00000150667.8" ; ccdsid "CCDS10050.1" ; exon_id "ENSE00003574039.1" ; exon_number 2 ; gene_id "FSIP1--AC013652.1^FSIP1^ENSG00000150667.8" ; gene_name FSIP1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000172456.3" ; havana_transcript "OTTHUMT00000252118.4" ; hgnc_id "HGNC:21674" ; level 2 ; orig_coord_info "chr15,39776399,39776524,-" ; protein_id "ENSP00000280236.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "FSIP1--AC013652.1^ENST00000350221.4" ; transcript_name "FSIP1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
NDC1--LDLRAD1 HAVANA gene 24815 31854 . + . FI_gene_label "LDLRAD1^ENSG00000203985.11" ; ID "NDC1--LDLRAD1^LDLRAD1^ENSG00000203985.11" ; ccdsid "CCDS30725.1" ; exon_id "ENSE00003739792.1" ; exon_number 1 ; gene_id "NDC1--LDLRAD1^LDLRAD1^ENSG00000203985.11" ; gene_name LDLRAD1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000008433.2" ; havana_transcript "OTTHUMT00000023243.2" ; hgnc_id "HGNC:32069" ; level 2 ; orig_coord_info "chr1,54018092,54018112,-" ; protein_id "ENSP00000360411.1" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "NDC1--LDLRAD1^ENST00000371360.2" ; transcript_name "LDLRAD1-201" ; transcript_support_level 1 ; transcript_type protein_coding
NDC1--LDLRAD1 HAVANA mRNA 24815 31854 . + . FI_gene_label "LDLRAD1^ENSG00000203985.11" ; ID "NDC1--LDLRAD1^ENST00000371360.2" ; Parent "NDC1--LDLRAD1^LDLRAD1^ENSG00000203985.11" ; ccdsid "CCDS30725.1" ; exon_id "ENSE00003739792.1" ; exon_number 1 ; gene_id "NDC1--LDLRAD1^LDLRAD1^ENSG00000203985.11" ; gene_name LDLRAD1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000008433.2" ; havana_transcript "OTTHUMT00000023243.2" ; hgnc_id "HGNC:32069" ; level 2 ; orig_coord_info "chr1,54018092,54018112,-" ; protein_id "ENSP00000360411.1" ; tag basic MANE_Select appris_principal_4 CCDS ; transcript_id "NDC1--LDLRAD1^ENST00000371360.2" ; transcript_name "LDLRAD1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
NDC1--LDLRAD1 HAVANA gene 1168 21814 . + . FI_gene_label "NDC1^ENSG00000058804.12" ; ID "NDC1--LDLRAD1^NDC1^ENSG00000058804.12" ; ccdsid "CCDS583.1" ; exon_id "ENSE00001843774.2" ; exon_number 1 ; gene_id "NDC1--LDLRAD1^NDC1^ENSG00000058804.12" ; gene_name NDC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000008073.2" ; havana_transcript "OTTHUMT00000022101.2" ; hgnc_id "HGNC:25525" ; level 2 ; orig_coord_info "chr1,53838205,53838261,-" ; protein_id "ENSP00000360483.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NDC1--LDLRAD1^ENST00000371429.4" ; transcript_name "NDC1-201" ; transcript_support_level 1 ; transcript_type protein_coding
NDC1--LDLRAD1 HAVANA mRNA 1168 21814 . + . FI_gene_label "NDC1^ENSG00000058804.12" ; ID "NDC1--LDLRAD1^ENST00000371429.4" ; Parent "NDC1--LDLRAD1^NDC1^ENSG00000058804.12" ; ccdsid "CCDS583.1" ; exon_id "ENSE00001843774.2" ; exon_number 1 ; gene_id "NDC1--LDLRAD1^NDC1^ENSG00000058804.12" ; gene_name NDC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000008073.2" ; havana_transcript "OTTHUMT00000022101.2" ; hgnc_id "HGNC:25525" ; level 2 ; orig_coord_info "chr1,53838205,53838261,-" ; protein_id "ENSP00000360483.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NDC1--LDLRAD1^ENST00000371429.4" ; transcript_name "NDC1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
POLR2J2--FBXL13 HAVANA gene 8341 35586 . + . FI_gene_label "FBXL13^ENSG00000161040.16" ; ID "POLR2J2--FBXL13^FBXL13^ENSG00000161040.16" ; ccdsid "CCDS5726.1" ; exon_id "ENSE00003755257.1" ; exon_number 3 ; gene_id "POLR2J2--FBXL13^FBXL13^ENSG00000161040.16" ; gene_name FBXL13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000157224.3" ; havana_transcript "OTTHUMT00000348001.1" ; hgnc_id "HGNC:21658" ; level 2 ; orig_coord_info "chr7,103029351,103029418,-" ; protein_id "ENSP00000321927.4" ; tag basic appris_principal_1 CCDS ; transcript_id "POLR2J2--FBXL13^ENST00000313221.8" ; transcript_name "FBXL13-201" ; transcript_support_level 2 ; transcript_type protein_coding
POLR2J2--FBXL13 HAVANA mRNA 8341 35586 . + . FI_gene_label "FBXL13^ENSG00000161040.16" ; ID "POLR2J2--FBXL13^ENST00000313221.8" ; Parent "POLR2J2--FBXL13^FBXL13^ENSG00000161040.16" ; ccdsid "CCDS5726.1" ; exon_id "ENSE00003755257.1" ; exon_number 3 ; gene_id "POLR2J2--FBXL13^FBXL13^ENSG00000161040.16" ; gene_name FBXL13 ; gene_type protein_coding ; havana_gene "OTTHUMG00000157224.3" ; havana_transcript "OTTHUMT00000348001.1" ; hgnc_id "HGNC:21658" ; level 2 ; orig_coord_info "chr7,103029351,103029418,-" ; protein_id "ENSP00000321927.4" ; tag basic appris_principal_1 CCDS ; transcript_id "POLR2J2--FBXL13^ENST00000313221.8" ; transcript_name "FBXL13-201" ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created:
POLR2J2--FBXL13 HAVANA gene 1029 4302 . + . FI_gene_label "POLR2J2^ENSG00000228049.7" ; ID "POLR2J2--FBXL13^POLR2J2^ENSG00000228049.7" ; ccdsid "CCDS43627.1" ; exon_id "ENSE00002863681.3" ; exon_number 1 ; gene_id "POLR2J2--FBXL13^POLR2J2^ENSG00000228049.7" ; gene_name POLR2J2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150388.6" ; havana_transcript "OTTHUMT00000487870.2" ; hgnc_id "HGNC:23208" ; level 2 ; orig_coord_info "chr7,102671552,102671601,-" ; protein_id "ENSP00000330898.7" ; tag not_best_in_genome_evidence basic appris_principal_4 CCDS ; transcript_id "POLR2J2--FBXL13^ENST00000333432.8" ; transcript_name "POLR2J2-201" ; transcript_support_level 1 ; transcript_type protein_coding
POLR2J2--FBXL13 HAVANA mRNA 1029 4302 . + . FI_gene_label "POLR2J2^ENSG00000228049.7" ; ID "POLR2J2--FBXL13^ENST00000333432.8" ; Parent "POLR2J2--FBXL13^POLR2J2^ENSG00000228049.7" ; ccdsid "CCDS43627.1" ; exon_id "ENSE00002863681.3" ; exon_number 1 ; gene_id "POLR2J2--FBXL13^POLR2J2^ENSG00000228049.7" ; gene_name POLR2J2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000150388.6" ; havana_transcript "OTTHUMT00000487870.2" ; hgnc_id "HGNC:23208" ; level 2 ; orig_coord_info "chr7,102671552,102671601,-" ; protein_id "ENSP00000330898.7" ; tag not_best_in_genome_evidence basic appris_principal_4 CCDS ; transcript_id "POLR2J2--FBXL13^ENST00000333432.8" ; transcript_name "POLR2J2-201" ; 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--FAM157A HAVANA gene 4784 35054 . + . FI_gene_label "TLK2^ENSG00000146872.18" ; ID "TLK2--FAM157A^TLK2^ENSG00000146872.18" ; ccdsid "CCDS62283.1" ; exon_id "ENSE00003568961.1" ; exon_number 2 ; gene_id "TLK2--FAM157A^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--FAM157A^ENST00000326270.13" ; transcript_name "TLK2-201" ; transcript_support_level 1 ; transcript_type protein_coding
TLK2--FAM157A HAVANA mRNA 4784 35054 . + . FI_gene_label "TLK2^ENSG00000146872.18" ; ID "TLK2--FAM157A^ENST00000326270.13" ; Parent "TLK2--FAM157A^TLK2^ENSG00000146872.18" ; ccdsid "CCDS62283.1" ; exon_id "ENSE00003568961.1" ; exon_number 2 ; gene_id "TLK2--FAM157A^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--FAM157A^ENST00000326270.13" ; transcript_name "TLK2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TMEM238--BRSK1 HAVANA gene 6864 20695 . + . FI_gene_label "BRSK1^ENSG00000160469.17" ; ID "TMEM238--BRSK1^BRSK1^ENSG00000160469.17" ; ccdsid "CCDS12921.1" ; exon_id "ENSE00001355906.2" ; exon_number 1 ; gene_id "TMEM238--BRSK1^BRSK1^ENSG00000160469.17" ; gene_name BRSK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000180735.5" ; havana_transcript "OTTHUMT00000452787.2" ; hgnc_id "HGNC:18994" ; level 2 ; orig_coord_info "chr19,55284443,55284578,+" ; protein_id "ENSP00000310649.1" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TMEM238--BRSK1^ENST00000309383.6" ; transcript_name "BRSK1-201" ; transcript_support_level 1 ; transcript_type protein_coding
TMEM238--BRSK1 HAVANA mRNA 6864 20695 . + . FI_gene_label "BRSK1^ENSG00000160469.17" ; ID "TMEM238--BRSK1^ENST00000309383.6" ; Parent "TMEM238--BRSK1^BRSK1^ENSG00000160469.17" ; ccdsid "CCDS12921.1" ; exon_id "ENSE00001355906.2" ; exon_number 1 ; gene_id "TMEM238--BRSK1^BRSK1^ENSG00000160469.17" ; gene_name BRSK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000180735.5" ; havana_transcript "OTTHUMT00000452787.2" ; hgnc_id "HGNC:18994" ; level 2 ; orig_coord_info "chr19,55284443,55284578,+" ; protein_id "ENSP00000310649.1" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TMEM238--BRSK1^ENST00000309383.6" ; transcript_name "BRSK1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TMEM238--BRSK1 HAVANA gene 1001 2695 . + . FI_gene_label "TMEM238^ENSG00000233493.4" ; ID "TMEM238--BRSK1^TMEM238^ENSG00000233493.4" ; ccdsid "CCDS54323.1" ; exon_id "ENSE00001708649.4" ; exon_number 1 ; gene_id "TMEM238--BRSK1^TMEM238^ENSG00000233493.4" ; gene_name TMEM238 ; gene_type protein_coding ; havana_gene "OTTHUMG00000180795.2" ; havana_transcript "OTTHUMT00000453043.2" ; hgnc_id "HGNC:40042" ; level 2 ; orig_coord_info "chr19,55383732,55384259,-" ; protein_id "ENSP00000416154.2" ; tag upstream_ATG basic MANE_Select appris_principal_1 CCDS ; transcript_id "TMEM238--BRSK1^ENST00000444469.4" ; transcript_name "TMEM238-201" ; transcript_support_level 1 ; transcript_type protein_coding
TMEM238--BRSK1 HAVANA mRNA 1001 2695 . + . FI_gene_label "TMEM238^ENSG00000233493.4" ; ID "TMEM238--BRSK1^ENST00000444469.4" ; Parent "TMEM238--BRSK1^TMEM238^ENSG00000233493.4" ; ccdsid "CCDS54323.1" ; exon_id "ENSE00001708649.4" ; exon_number 1 ; gene_id "TMEM238--BRSK1^TMEM238^ENSG00000233493.4" ; gene_name TMEM238 ; gene_type protein_coding ; havana_gene "OTTHUMG00000180795.2" ; havana_transcript "OTTHUMT00000453043.2" ; hgnc_id "HGNC:40042" ; level 2 ; orig_coord_info "chr19,55383732,55384259,-" ; protein_id "ENSP00000416154.2" ; tag upstream_ATG basic MANE_Select appris_principal_1 CCDS ; transcript_id "TMEM238--BRSK1^ENST00000444469.4" ; transcript_name "TMEM238-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
TMEM87B--MERTK HAVANA gene 1001 23704 . + . FI_gene_label "TMEM87B^ENSG00000153214.11" ; ID "TMEM87B--MERTK^TMEM87B^ENSG00000153214.11" ; ccdsid "CCDS33275.1" ; exon_id "ENSE00001009506.5" ; exon_number 1 ; gene_id "TMEM87B--MERTK^TMEM87B^ENSG00000153214.11" ; gene_name TMEM87B ; gene_type protein_coding ; havana_gene "OTTHUMG00000153266.6" ; havana_transcript "OTTHUMT00000330500.2" ; hgnc_id "HGNC:25913" ; level 2 ; orig_coord_info "chr2,112055592,112055756,+" ; protein_id "ENSP00000283206.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TMEM87B--MERTK^ENST00000283206.9" ; transcript_name "TMEM87B-201" ; transcript_support_level 2 ; transcript_type protein_coding
TMEM87B--MERTK HAVANA mRNA 1001 23704 . + . FI_gene_label "TMEM87B^ENSG00000153214.11" ; ID "TMEM87B--MERTK^ENST00000283206.9" ; Parent "TMEM87B--MERTK^TMEM87B^ENSG00000153214.11" ; ccdsid "CCDS33275.1" ; exon_id "ENSE00001009506.5" ; exon_number 1 ; gene_id "TMEM87B--MERTK^TMEM87B^ENSG00000153214.11" ; gene_name TMEM87B ; gene_type protein_coding ; havana_gene "OTTHUMG00000153266.6" ; havana_transcript "OTTHUMT00000330500.2" ; hgnc_id "HGNC:25913" ; level 2 ; orig_coord_info "chr2,112055592,112055756,+" ; protein_id "ENSP00000283206.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TMEM87B--MERTK^ENST00000283206.9" ; transcript_name "TMEM87B-201" ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created:
TMEM87B--MERTK HAVANA gene 26709 55872 . + . FI_gene_label "MERTK^ENSG00000153208.17" ; ID "TMEM87B--MERTK^MERTK^ENSG00000153208.17" ; ccdsid "CCDS2094.1" ; exon_id "ENSE00001254759.8" ; exon_number 1 ; gene_id "TMEM87B--MERTK^MERTK^ENSG00000153208.17" ; gene_name MERTK ; gene_type protein_coding ; havana_gene "OTTHUMG00000131278.5" ; havana_transcript "OTTHUMT00000254046.3" ; hgnc_id "HGNC:7027" ; level 2 ; orig_coord_info "chr2,111898736,111898796,+" ; protein_id "ENSP00000295408.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TMEM87B--MERTK^ENST00000295408.9" ; transcript_name "MERTK-201" ; transcript_support_level 1 ; transcript_type protein_coding
TMEM87B--MERTK HAVANA mRNA 26709 55872 . + . FI_gene_label "MERTK^ENSG00000153208.17" ; ID "TMEM87B--MERTK^ENST00000295408.9" ; Parent "TMEM87B--MERTK^MERTK^ENSG00000153208.17" ; ccdsid "CCDS2094.1" ; exon_id "ENSE00001254759.8" ; exon_number 1 ; gene_id "TMEM87B--MERTK^MERTK^ENSG00000153208.17" ; gene_name MERTK ; gene_type protein_coding ; havana_gene "OTTHUMG00000131278.5" ; havana_transcript "OTTHUMT00000254046.3" ; hgnc_id "HGNC:7027" ; level 2 ; orig_coord_info "chr2,111898736,111898796,+" ; protein_id "ENSP00000295408.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TMEM87B--MERTK^ENST00000295408.9" ; transcript_name "MERTK-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:
BCAS1--AL133335.1 HAVANA gene 24514 27670 . + . FI_gene_label "AL133335.1^ENSG00000286229.1" ; ID "BCAS1--AL133335.1^AL133335.1^ENSG00000286229.1" ; exon_id "ENSE00003848160.1" ; exon_number 1 ; gene_id "BCAS1--AL133335.1^AL133335.1^ENSG00000286229.1" ; gene_name "AL133335.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000192763.1" ; havana_transcript "OTTHUMT00000499050.1" ; level 2 ; orig_coord_info "chr20,54232758,54232911,+" ; tag basic ; transcript_id "BCAS1--AL133335.1^ENST00000650710.1" ; transcript_name "AL133335.1-201" ; transcript_type lncRNA
BCAS1--AL133335.1 HAVANA RNA 24514 27670 . + . FI_gene_label "AL133335.1^ENSG00000286229.1" ; ID "BCAS1--AL133335.1^ENST00000650710.1" ; Parent "BCAS1--AL133335.1^AL133335.1^ENSG00000286229.1" ; exon_id "ENSE00003848160.1" ; exon_number 1 ; gene_id "BCAS1--AL133335.1^AL133335.1^ENSG00000286229.1" ; gene_name "AL133335.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000192763.1" ; havana_transcript "OTTHUMT00000499050.1" ; level 2 ; orig_coord_info "chr20,54232758,54232911,+" ; tag basic ; transcript_id "BCAS1--AL133335.1^ENST00000650710.1" ; transcript_name "AL133335.1-201" ; transcript_type lncRNA
L1 and L2 created:
FSIP1--AC013652.1 HAVANA gene 21835 37275 . + . FI_gene_label "AC013652.1^ENSG00000259345.7" ; ID "FSIP1--AC013652.1^AC013652.1^ENSG00000259345.7" ; exon_id "ENSE00002558629.1" ; exon_number 1 ; gene_id "FSIP1--AC013652.1^AC013652.1^ENSG00000259345.7" ; gene_name "AC013652.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000172466.4" ; havana_transcript "OTTHUMT00000418683.1" ; level 2 ; orig_coord_info "chr15,39427098,39427195,-" ; tag basic ; transcript_id "FSIP1--AC013652.1^ENST00000558209.1" ; transcript_name "AC013652.1-205" ; transcript_support_level 3 ; transcript_type lncRNA
FSIP1--AC013652.1 HAVANA RNA 21835 37275 . + . FI_gene_label "AC013652.1^ENSG00000259345.7" ; ID "FSIP1--AC013652.1^ENST00000558209.1" ; Parent "FSIP1--AC013652.1^AC013652.1^ENSG00000259345.7" ; exon_id "ENSE00002558629.1" ; exon_number 1 ; gene_id "FSIP1--AC013652.1^AC013652.1^ENSG00000259345.7" ; gene_name "AC013652.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000172466.4" ; havana_transcript "OTTHUMT00000418683.1" ; level 2 ; orig_coord_info "chr15,39427098,39427195,-" ; tag basic ; transcript_id "FSIP1--AC013652.1^ENST00000558209.1" ; transcript_name "AC013652.1-205" ; transcript_support_level 3 ; transcript_type lncRNA
L1 and L2 created:
TLK2--FAM157A HAVANA gene 40046 44186 . + . FI_gene_label "FAM157A^ENSG00000236438.7" ; ID "TLK2--FAM157A^FAM157A^ENSG00000236438.7" ; exon_id "ENSE00002579345.3" ; exon_number 1 ; gene_id "TLK2--FAM157A^FAM157A^ENSG00000236438.7" ; gene_name FAM157A ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000187506.3" ; havana_transcript "OTTHUMT00000488453.1" ; hgnc_id "HGNC:34079" ; level 2 ; orig_coord_info "chr3,198153287,198153409,+" ; tag basic ; transcript_id "TLK2--FAM157A^ENST00000437428.3" ; transcript_name "FAM157A-201" ; transcript_support_level 3 ; transcript_type processed_transcript
TLK2--FAM157A HAVANA RNA 40046 44186 . + . FI_gene_label "FAM157A^ENSG00000236438.7" ; ID "TLK2--FAM157A^ENST00000437428.3" ; Parent "TLK2--FAM157A^FAM157A^ENSG00000236438.7" ; exon_id "ENSE00002579345.3" ; exon_number 1 ; gene_id "TLK2--FAM157A^FAM157A^ENSG00000236438.7" ; gene_name FAM157A ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000187506.3" ; havana_transcript "OTTHUMT00000488453.1" ; hgnc_id "HGNC:34079" ; level 2 ; orig_coord_info "chr3,198153287,198153409,+" ; tag basic ; transcript_id "TLK2--FAM157A^ENST00000437428.3" ; transcript_name "FAM157A-201" ; transcript_support_level 3 ; transcript_type processed_transcript
151 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 ------------------------------
301 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 16 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