Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/92/62efbd253941bb80579e76c824e5d9/fi_workdir/BVT_FFPE_TRNA_bst_01_03_A23WKFTLT4_3.gtf
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/65/8e4e605aab4ac2b15dd805ec09f8c0/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/65/8e4e605aab4ac2b15dd805ec09f8c0/.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: 1174
=> Number of comment lines: 0
=> Fasta included: No
=> Number of features lines: 1174
=> 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:1174
=> 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 0 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:
AC092070.2--MAN2B1 HAVANA gene 12061 27290 . + . FI_gene_label "MAN2B1^ENSG00000104774.13" ; ID "AC092070.2--MAN2B1^MAN2B1^ENSG00000104774.13" ; ccdsid "CCDS54224.1" ; exon_id "ENSE00001747592.1" ; exon_number 1 ; gene_id "AC092070.2--MAN2B1^MAN2B1^ENSG00000104774.13" ; gene_name MAN2B1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000156397.5" ; havana_transcript "OTTHUMT00000344064.1" ; hgnc_id "HGNC:6826" ; level 1 ; orig_coord_info "chr19,12666543,12666701,-" ; protein_id "ENSP00000221363.4" ; tag basic appris_alternative_2 exp_conf CCDS ; transcript_id "AC092070.2--MAN2B1^ENST00000221363.8" ; transcript_name "MAN2B1-201" ; transcript_support_level 1 ; transcript_type protein_coding
AC092070.2--MAN2B1 HAVANA mRNA 12061 27290 . + . FI_gene_label "MAN2B1^ENSG00000104774.13" ; ID "AC092070.2--MAN2B1^ENST00000221363.8" ; Parent "AC092070.2--MAN2B1^MAN2B1^ENSG00000104774.13" ; ccdsid "CCDS54224.1" ; exon_id "ENSE00001747592.1" ; exon_number 1 ; gene_id "AC092070.2--MAN2B1^MAN2B1^ENSG00000104774.13" ; gene_name MAN2B1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000156397.5" ; havana_transcript "OTTHUMT00000344064.1" ; hgnc_id "HGNC:6826" ; level 1 ; orig_coord_info "chr19,12666543,12666701,-" ; protein_id "ENSP00000221363.4" ; tag basic appris_alternative_2 exp_conf CCDS ; transcript_id "AC092070.2--MAN2B1^ENST00000221363.8" ; transcript_name "MAN2B1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
DOK7--MICB HAVANA gene 17080 22456 . + . FI_gene_label "MICB^ENSG00000204516.10" ; ID "DOK7--MICB^MICB^ENSG00000204516.10" ; ccdsid "CCDS43449.1" ; exon_id "ENSE00001842955.2" ; exon_number 1 ; gene_id "DOK7--MICB^MICB^ENSG00000204516.10" ; gene_name MICB ; gene_type protein_coding ; havana_gene "OTTHUMG00000031074.4" ; havana_transcript "OTTHUMT00000076102.4" ; hgnc_id "HGNC:7091" ; level 2 ; orig_coord_info "chr6,31498194,31498263,+" ; protein_id "ENSP00000252229.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DOK7--MICB^ENST00000252229.7" ; transcript_name "MICB-201" ; transcript_support_level 1 ; transcript_type protein_coding
DOK7--MICB HAVANA mRNA 17080 22456 . + . FI_gene_label "MICB^ENSG00000204516.10" ; ID "DOK7--MICB^ENST00000252229.7" ; Parent "DOK7--MICB^MICB^ENSG00000204516.10" ; ccdsid "CCDS43449.1" ; exon_id "ENSE00001842955.2" ; exon_number 1 ; gene_id "DOK7--MICB^MICB^ENSG00000204516.10" ; gene_name MICB ; gene_type protein_coding ; havana_gene "OTTHUMG00000031074.4" ; havana_transcript "OTTHUMT00000076102.4" ; hgnc_id "HGNC:7091" ; level 2 ; orig_coord_info "chr6,31498194,31498263,+" ; protein_id "ENSP00000252229.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DOK7--MICB^ENST00000252229.7" ; transcript_name "MICB-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
DOK7--MICB HAVANA gene 1001 9638 . + . FI_gene_label "DOK7^ENSG00000175920.18" ; ID "DOK7--MICB^DOK7^ENSG00000175920.18" ; ccdsid "CCDS3370.2" ; exon_id "ENSE00003845135.1" ; exon_number 1 ; gene_id "DOK7--MICB^DOK7^ENSG00000175920.18" ; gene_name DOK7 ; gene_type protein_coding ; havana_gene "OTTHUMG00000122087.8" ; havana_transcript "OTTHUMT00000313538.2" ; hgnc_id "HGNC:26594" ; level 2 ; orig_coord_info "chr4,3463376,3463429,+" ; protein_id "ENSP00000344432.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DOK7--MICB^ENST00000340083.6" ; transcript_name "DOK7-201" ; transcript_support_level 1 ; transcript_type protein_coding
DOK7--MICB HAVANA mRNA 1001 9638 . + . FI_gene_label "DOK7^ENSG00000175920.18" ; ID "DOK7--MICB^ENST00000340083.6" ; Parent "DOK7--MICB^DOK7^ENSG00000175920.18" ; ccdsid "CCDS3370.2" ; exon_id "ENSE00003845135.1" ; exon_number 1 ; gene_id "DOK7--MICB^DOK7^ENSG00000175920.18" ; gene_name DOK7 ; gene_type protein_coding ; havana_gene "OTTHUMG00000122087.8" ; havana_transcript "OTTHUMT00000313538.2" ; hgnc_id "HGNC:26594" ; level 2 ; orig_coord_info "chr4,3463376,3463429,+" ; protein_id "ENSP00000344432.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "DOK7--MICB^ENST00000340083.6" ; transcript_name "DOK7-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
EXOC2--EPHA5 HAVANA gene 1001 32550 . + . FI_gene_label "EXOC2^ENSG00000112685.14" ; ID "EXOC2--EPHA5^EXOC2^ENSG00000112685.14" ; ccdsid "CCDS34327.1" ; exon_id "ENSE00000679928.3" ; exon_number 2 ; gene_id "EXOC2--EPHA5^EXOC2^ENSG00000112685.14" ; gene_name EXOC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000137437.4" ; havana_transcript "OTTHUMT00000039627.2" ; hgnc_id "HGNC:24968" ; level 2 ; orig_coord_info "chr6,637701,637818,-" ; protein_id "ENSP00000230449.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "EXOC2--EPHA5^ENST00000230449.9" ; transcript_name "EXOC2-201" ; transcript_support_level 1 ; transcript_type protein_coding
EXOC2--EPHA5 HAVANA mRNA 1001 32550 . + . FI_gene_label "EXOC2^ENSG00000112685.14" ; ID "EXOC2--EPHA5^ENST00000230449.9" ; Parent "EXOC2--EPHA5^EXOC2^ENSG00000112685.14" ; ccdsid "CCDS34327.1" ; exon_id "ENSE00000679928.3" ; exon_number 2 ; gene_id "EXOC2--EPHA5^EXOC2^ENSG00000112685.14" ; gene_name EXOC2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000137437.4" ; havana_transcript "OTTHUMT00000039627.2" ; hgnc_id "HGNC:24968" ; level 2 ; orig_coord_info "chr6,637701,637818,-" ; protein_id "ENSP00000230449.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "EXOC2--EPHA5^ENST00000230449.9" ; transcript_name "EXOC2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
EXOC2--EPHA5 HAVANA gene 35703 62112 . + . FI_gene_label "EPHA5^ENSG00000145242.14" ; ID "EXOC2--EPHA5^EPHA5^ENSG00000145242.14" ; ccdsid "CCDS3513.1" ; exon_id "ENSE00001816165.1" ; exon_number 1 ; gene_id "EXOC2--EPHA5^EPHA5^ENSG00000145242.14" ; gene_name EPHA5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129273.4" ; havana_transcript "OTTHUMT00000251388.2" ; hgnc_id "HGNC:3389" ; level 2 ; orig_coord_info "chr4,65669562,65669742,-" ; protein_id "ENSP00000273854.3" ; tag basic appris_alternative_2 CCDS ; transcript_id "EXOC2--EPHA5^ENST00000273854.7" ; transcript_name "EPHA5-201" ; transcript_support_level 1 ; transcript_type protein_coding
EXOC2--EPHA5 HAVANA mRNA 35703 62112 . + . FI_gene_label "EPHA5^ENSG00000145242.14" ; ID "EXOC2--EPHA5^ENST00000273854.7" ; Parent "EXOC2--EPHA5^EPHA5^ENSG00000145242.14" ; ccdsid "CCDS3513.1" ; exon_id "ENSE00001816165.1" ; exon_number 1 ; gene_id "EXOC2--EPHA5^EPHA5^ENSG00000145242.14" ; gene_name EPHA5 ; gene_type protein_coding ; havana_gene "OTTHUMG00000129273.4" ; havana_transcript "OTTHUMT00000251388.2" ; hgnc_id "HGNC:3389" ; level 2 ; orig_coord_info "chr4,65669562,65669742,-" ; protein_id "ENSP00000273854.3" ; tag basic appris_alternative_2 CCDS ; transcript_id "EXOC2--EPHA5^ENST00000273854.7" ; transcript_name "EPHA5-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
NARS2--GAB2 HAVANA gene 1011 17072 . + . FI_gene_label "NARS2^ENSG00000137513.10" ; ID "NARS2--GAB2^NARS2^ENSG00000137513.10" ; ccdsid "CCDS8261.1" ; exon_id "ENSE00001151727.6" ; exon_number 1 ; gene_id "NARS2--GAB2^NARS2^ENSG00000137513.10" ; gene_name NARS2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000166702.4" ; havana_transcript "OTTHUMT00000391138.3" ; hgnc_id "HGNC:26274" ; level 2 ; orig_coord_info "chr11,78574348,78574488,-" ; protein_id "ENSP00000281038.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NARS2--GAB2^ENST00000281038.10" ; transcript_name "NARS2-201" ; transcript_support_level 1 ; transcript_type protein_coding
NARS2--GAB2 HAVANA mRNA 1011 17072 . + . FI_gene_label "NARS2^ENSG00000137513.10" ; ID "NARS2--GAB2^ENST00000281038.10" ; Parent "NARS2--GAB2^NARS2^ENSG00000137513.10" ; ccdsid "CCDS8261.1" ; exon_id "ENSE00001151727.6" ; exon_number 1 ; gene_id "NARS2--GAB2^NARS2^ENSG00000137513.10" ; gene_name NARS2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000166702.4" ; havana_transcript "OTTHUMT00000391138.3" ; hgnc_id "HGNC:26274" ; level 2 ; orig_coord_info "chr11,78574348,78574488,-" ; protein_id "ENSP00000281038.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NARS2--GAB2^ENST00000281038.10" ; transcript_name "NARS2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
NARS2--GAB2 HAVANA gene 22864 39485 . + . FI_gene_label "GAB2^ENSG00000033327.13" ; ID "NARS2--GAB2^GAB2^ENSG00000033327.13" ; ccdsid "CCDS8260.1" ; exon_id "ENSE00003464974.1" ; exon_number 2 ; gene_id "NARS2--GAB2^GAB2^ENSG00000033327.13" ; gene_name GAB2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000166673.3" ; havana_transcript "OTTHUMT00000391084.1" ; hgnc_id "HGNC:14458" ; level 2 ; orig_coord_info "chr11,78280601,78280862,-" ; protein_id "ENSP00000343959.2" ; tag basic CCDS ; transcript_id "NARS2--GAB2^ENST00000340149.6" ; transcript_name "GAB2-201" ; transcript_support_level 1 ; transcript_type protein_coding
NARS2--GAB2 HAVANA mRNA 22864 39485 . + . FI_gene_label "GAB2^ENSG00000033327.13" ; ID "NARS2--GAB2^ENST00000340149.6" ; Parent "NARS2--GAB2^GAB2^ENSG00000033327.13" ; ccdsid "CCDS8260.1" ; exon_id "ENSE00003464974.1" ; exon_number 2 ; gene_id "NARS2--GAB2^GAB2^ENSG00000033327.13" ; gene_name GAB2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000166673.3" ; havana_transcript "OTTHUMT00000391084.1" ; hgnc_id "HGNC:14458" ; level 2 ; orig_coord_info "chr11,78280601,78280862,-" ; protein_id "ENSP00000343959.2" ; tag basic CCDS ; transcript_id "NARS2--GAB2^ENST00000340149.6" ; transcript_name "GAB2-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
RIC1--FMNL1 HAVANA gene 1001 25077 . + . FI_gene_label "RIC1^ENSG00000107036.12" ; ID "RIC1--FMNL1^RIC1^ENSG00000107036.12" ; ccdsid "CCDS47949.2" ; exon_id "ENSE00001626901.2" ; exon_number 1 ; gene_id "RIC1--FMNL1^RIC1^ENSG00000107036.12" ; gene_name RIC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000019505.5" ; havana_transcript "OTTHUMT00000051635.3" ; hgnc_id "HGNC:17686" ; level 2 ; orig_coord_info "chr9,5629310,5629453,+" ; protein_id "ENSP00000251879.6" ; tag basic CCDS ; transcript_id "RIC1--FMNL1^ENST00000251879.10" ; transcript_name "RIC1-201" ; transcript_support_level 1 ; transcript_type protein_coding
RIC1--FMNL1 HAVANA mRNA 1001 25077 . + . FI_gene_label "RIC1^ENSG00000107036.12" ; ID "RIC1--FMNL1^ENST00000251879.10" ; Parent "RIC1--FMNL1^RIC1^ENSG00000107036.12" ; ccdsid "CCDS47949.2" ; exon_id "ENSE00001626901.2" ; exon_number 1 ; gene_id "RIC1--FMNL1^RIC1^ENSG00000107036.12" ; gene_name RIC1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000019505.5" ; havana_transcript "OTTHUMT00000051635.3" ; hgnc_id "HGNC:17686" ; level 2 ; orig_coord_info "chr9,5629310,5629453,+" ; protein_id "ENSP00000251879.6" ; tag basic CCDS ; transcript_id "RIC1--FMNL1^ENST00000251879.10" ; transcript_name "RIC1-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
RIC1--FMNL1 ENSEMBL gene 34309 51145 . + . FI_gene_label "FMNL1^ENSG00000184922.14" ; ID "RIC1--FMNL1^FMNL1^ENSG00000184922.14" ; exon_id "ENSE00001337921.3" ; exon_number 1 ; gene_id "RIC1--FMNL1^FMNL1^ENSG00000184922.14" ; gene_name FMNL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000180196.5" ; hgnc_id "HGNC:1212" ; level 3 ; orig_coord_info "chr17,45222125,45222187,+" ; protein_id "ENSP00000327442.4" ; tag basic ; transcript_id "RIC1--FMNL1^ENST00000328118.7" ; transcript_name "FMNL1-201" ; transcript_support_level 2 ; transcript_type protein_coding
RIC1--FMNL1 ENSEMBL mRNA 34309 51145 . + . FI_gene_label "FMNL1^ENSG00000184922.14" ; ID "RIC1--FMNL1^ENST00000328118.7" ; Parent "RIC1--FMNL1^FMNL1^ENSG00000184922.14" ; exon_id "ENSE00001337921.3" ; exon_number 1 ; gene_id "RIC1--FMNL1^FMNL1^ENSG00000184922.14" ; gene_name FMNL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000180196.5" ; hgnc_id "HGNC:1212" ; level 3 ; orig_coord_info "chr17,45222125,45222187,+" ; protein_id "ENSP00000327442.4" ; tag basic ; transcript_id "RIC1--FMNL1^ENST00000328118.7" ; transcript_name "FMNL1-201" ; transcript_support_level 2 ; transcript_type protein_coding
L1 and L2 created:
ZSCAN22--WWC3 HAVANA gene 1001 7654 . + . FI_gene_label "ZSCAN22^ENSG00000182318.6" ; ID "ZSCAN22--WWC3^ZSCAN22^ENSG00000182318.6" ; ccdsid "CCDS12975.1" ; exon_id "ENSE00001333334.1" ; exon_number 2 ; gene_id "ZSCAN22--WWC3^ZSCAN22^ENSG00000182318.6" ; gene_name ZSCAN22 ; gene_type protein_coding ; havana_gene "OTTHUMG00000183463.2" ; havana_transcript "OTTHUMT00000466765.2" ; hgnc_id "HGNC:4929" ; level 2 ; orig_coord_info "chr19,58334803,58335205,+" ; protein_id "ENSP00000332433.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ZSCAN22--WWC3^ENST00000329665.5" ; transcript_name "ZSCAN22-201" ; transcript_support_level 1 ; transcript_type protein_coding
ZSCAN22--WWC3 HAVANA mRNA 1001 7654 . + . FI_gene_label "ZSCAN22^ENSG00000182318.6" ; ID "ZSCAN22--WWC3^ENST00000329665.5" ; Parent "ZSCAN22--WWC3^ZSCAN22^ENSG00000182318.6" ; ccdsid "CCDS12975.1" ; exon_id "ENSE00001333334.1" ; exon_number 2 ; gene_id "ZSCAN22--WWC3^ZSCAN22^ENSG00000182318.6" ; gene_name ZSCAN22 ; gene_type protein_coding ; havana_gene "OTTHUMG00000183463.2" ; havana_transcript "OTTHUMT00000466765.2" ; hgnc_id "HGNC:4929" ; level 2 ; orig_coord_info "chr19,58334803,58335205,+" ; protein_id "ENSP00000332433.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ZSCAN22--WWC3^ENST00000329665.5" ; transcript_name "ZSCAN22-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
ZSCAN22--WWC3 HAVANA gene 10655 38629 . + . FI_gene_label "WWC3^ENSG00000047644.19" ; ID "ZSCAN22--WWC3^WWC3^ENSG00000047644.19" ; ccdsid "CCDS14136.1" ; exon_id "ENSE00001486696.1" ; exon_number 2 ; gene_id "ZSCAN22--WWC3^WWC3^ENSG00000047644.19" ; gene_name WWC3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000021123.1" ; havana_transcript "OTTHUMT00000055725.1" ; hgnc_id "HGNC:29237" ; level 2 ; orig_coord_info "chrX,10063539,10063554,+" ; protein_id "ENSP00000370242.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ZSCAN22--WWC3^ENST00000380861.9" ; transcript_name "WWC3-201" ; transcript_support_level 1 ; transcript_type protein_coding
ZSCAN22--WWC3 HAVANA mRNA 10655 38629 . + . FI_gene_label "WWC3^ENSG00000047644.19" ; ID "ZSCAN22--WWC3^ENST00000380861.9" ; Parent "ZSCAN22--WWC3^WWC3^ENSG00000047644.19" ; ccdsid "CCDS14136.1" ; exon_id "ENSE00001486696.1" ; exon_number 2 ; gene_id "ZSCAN22--WWC3^WWC3^ENSG00000047644.19" ; gene_name WWC3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000021123.1" ; havana_transcript "OTTHUMT00000055725.1" ; hgnc_id "HGNC:29237" ; level 2 ; orig_coord_info "chrX,10063539,10063554,+" ; protein_id "ENSP00000370242.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "ZSCAN22--WWC3^ENST00000380861.9" ; transcript_name "WWC3-201" ; transcript_support_level 1 ; transcript_type protein_coding
L1 and L2 created:
AC092070.2--MAN2B1 HAVANA gene 1001 5545 . + . FI_gene_label "AC092070.2^ENSG00000269001.2" ; ID "AC092070.2--MAN2B1^AC092070.2^ENSG00000269001.2" ; exon_id "ENSE00003144051.1" ; exon_number 1 ; gene_id "AC092070.2--MAN2B1^AC092070.2^ENSG00000269001.2" ; gene_name "AC092070.2" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000182887.2" ; havana_transcript "OTTHUMT00000464185.1" ; level 2 ; orig_coord_info "chr19,53197111,53197262,+" ; tag basic ; transcript_id "AC092070.2--MAN2B1^ENST00000597550.5" ; transcript_name "AC092070.2-201" ; transcript_support_level 4 ; transcript_type processed_transcript
AC092070.2--MAN2B1 HAVANA RNA 1001 5545 . + . FI_gene_label "AC092070.2^ENSG00000269001.2" ; ID "AC092070.2--MAN2B1^ENST00000597550.5" ; Parent "AC092070.2--MAN2B1^AC092070.2^ENSG00000269001.2" ; exon_id "ENSE00003144051.1" ; exon_number 1 ; gene_id "AC092070.2--MAN2B1^AC092070.2^ENSG00000269001.2" ; gene_name "AC092070.2" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000182887.2" ; havana_transcript "OTTHUMT00000464185.1" ; level 2 ; orig_coord_info "chr19,53197111,53197262,+" ; tag basic ; transcript_id "AC092070.2--MAN2B1^ENST00000597550.5" ; transcript_name "AC092070.2-201" ; transcript_support_level 4 ; transcript_type processed_transcript
76 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 1 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 ------------------------------
113 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 9 wrong level1 location cases
------------------------------ done in 0 seconds -------------------------------
---------------------- Check13: remove identical isoforms ----------------------
None found
------------------------------ done in 0 seconds -------------------------------
------ End checks (done in 1 second) ------
GFF3 file parsed