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T2T-CHM13_v2.0 request #408

Closed 21tesla closed 11 months ago

21tesla commented 2 years ago

Database requests

My genome is available in the Canadian Personal Genome Project as PGPC_0004. I am in the process of reprocessing the dataset against T2T-CHM13_v2.0 at [https://ftp.ncbi.nlm.nih.gov/genomes/all/annotation_releases/9606/110/GCF_009914755.1_T2T-CHM13v2.0/]. The mapping was done with bwa and variant analysis with Google DeepVariant.

Does anyone have a database completed for the T2T-CHM13_v2.0 reference genome ?

GCF_009914755.1_T2T-CHM13v2.0_genomic.gtf ----> snpEff/data/T2T-CHM13/genes.gtf GCF_009914755.1_T2T-CHM13v2.0_genomic.fa ----> snpEff/data/T2T-CHM13/sequences.fa GCF_009914755.1_T2T-CHM13v2.0_protein.faa ----> snpEff/data/T2T-CHM13/protein.fa GCF_009914755.1_T2T-CHM13v2.0_cds_from_genomic.fna ----> snpEff/data/T2T-CHM13/cds.fa

java -Xmx20g -jar snpEff.jar build -v T2T-CHM13

The error seems to be at the CDS phase of the build

CDS check: T2T-CHM13 OK: 0 Warnings: 0 Not found: 112905 Errors: 0 Error percentage: NaN% FATAL ERRORNo CDS checked. This is might be caused by differences in FASTA file transcript IDs respect to database's transcript's IDs.

jamesdalg commented 1 year ago

So, I am trying to do this right now:

/ceph/project/Wellcome_Discovery/jdalglei/reference/snpEff$ java -jar snpEff.jar build -gff3 -v chm13v2  
00:00:00 SnpEff version SnpEff 5.1d (build 2022-04-19 15:49), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'chm13v2'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'chm13v2'
00:00:00 Reading config file: /ceph/project/Wellcome_Discovery/jdalglei/reference/snpEff/snpEff.config
00:00:01 done
00:00:01 Reading GFF3 data file  : '/ceph/project/Wellcome_Discovery/jdalglei/reference/snpEff/./data/chm13v2/genes.gff'
00:00:01 Reading file '/ceph/project/Wellcome_Discovery/jdalglei/reference/snpEff/./data/chm13v2/genes.gff'
WARNING_GENE_NOT_FOUND: Gene 'CHM13_G0000003' (1:138271-151217) does not include 'CHM13_T0000005' (1:148604-151415). Created new gene 'CHM13_G0000003.2' (1:148604-151415). File '/ceph/project/Wellcome_Discovery/jdalglei/reference/snpEff/./data/chm13v2/genes.gff' line 25  'chr1   CAT transcript  148604  151415  9640    -   .   source_transcript=ENST00000406017.3;source_transcript_name=CICP18-201;source_gene=ENSG00000217929.4;transcript_modes=transMap;gene_biotype=transcribed_processed_pseudogene;transcript_biotype=transcribed_processed_pseudogene;alignment_id=ENST00000406017.3-1;frameshift=nan;exon_annotation_support=1;intron_annotation_support=nan;transcript_class=ortholog;valid_start=True;valid_stop=True;adj_start=nan;adj_stop=nan;proper_orf=True;level=2;transcript_support_level=NA;hgnc_id=HGNC:48828;ont=PGO:0000004,PGO:0000019;tag=basic;havana_gene=OTTHUMG00000014108.4;havana_transcript=OTTHUMT00000039616.3;paralogy=nan;unfiltered_paralogy=nan;gene_alternate_contigs=chr5:181892407-181905553;source_gene_common_name=CICP18;transcript_id=CHM13_T0000005;gene_id=CHM13_G0000003;Parent=CHM13_G0000003;transcript_name=CICP18-201;ID=CHM13_T0000005;Name=CICP18;gene_name=CICP18;alternative_source_transcripts=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;extra_paralog=False'
WARNING_GENE_NOT_FOUND: Gene 'CHM13_G0000012' (1:254110-288378) does not include 'CHM13_T0000019' (1:256570-288416). Created new gene 'CHM13_G0000012.2' (1:256570-288416). File '/ceph/project/Wellcome_Discovery/jdalglei/reference/snpEff/./data/chm13v2/genes.gff' line 123 'chr1   CAT transcript  256570  288416  9890    +   .   source_transcript=ENST00000445118.7;source_transcript_name=LINC01128-205;source_gene=ENSG00000228794.10;transcript_modes=transMap;gene_biotype=lncRNA;transcript_biotype=lncRNA;alignment_id=ENST00000445118.7-0;frameshift=nan;exon_annotation_support=1,1,1,1,1;intron_annotation_support=1,1,1,1;transcript_class=ortholog;valid_start=True;valid_stop=True;adj_start=nan;adj_stop=nan;proper_orf=True;level=2;transcript_support_level=1;hgnc_id=HGNC:49377;tag=basic,TAGENE;havana_gene=OTTHUMG00000196004.1;havana_transcript=OTTHUMT00000007015.4;paralogy=nan;unfiltered_paralogy=nan;source_gene_common_name=LINC01128;transcript_id=CHM13_T0000019;gene_id=CHM13_G0000012;Parent=CHM13_G0000012;transcript_name=LINC01128-205;ID=CHM13_T0000019;Name=LINC01128;gene_name=LINC01128;alternative_source_transcripts=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;extra_paralog=False'
..WARNING_GENE_NOT_FOUND: Gene 'CHM13_G0000021' (1:346509-349336) does not include 'CHM13_T0000054' (1:346509-350660). Created new gene 'CHM13_G0000021.2' (1:346509-350660). File '/ceph/project/Wellcome_Discovery/jdalglei/reference/snpEff/./data/chm13v2/genes.gff' line 434   'chr1   CAT transcript  346509  350660  9840    -   .   source_transcript=ENST00000609207.1;source_transcript_name=LINC02593-203;source_gene=ENSG00000223764.2;transcript_modes=transMap;gene_biotype=lncRNA;transcript_biotype=retained_intron;alignment_id=ENST00000609207.1-0;frameshift=nan;exon_annotation_support=1;intron_annotation_support=nan;transcript_class=ortholog;valid_start=True;valid_stop=True;adj_start=nan;adj_stop=nan;proper_orf=True;level=2;transcript_support_level=NA;hgnc_id=HGNC:53933;havana_gene=OTTHUMG00000040718.2;havana_transcript=OTTHUMT00000473217.1;paralogy=nan;unfiltered_paralogy=nan;source_gene_common_name=LINC02593;transcript_id=CHM13_T0000054;gene_id=CHM13_G0000021;Parent=CHM13_G0000021;transcript_name=LINC02593-203;ID=CHM13_T0000054;Name=LINC02593;gene_name=LINC02593;alternative_source_transcripts=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;extra_paralog=False'
....WARNING_GENE_NOT_FOUND: Gene 'CHM13_G0000028' (1:429117-430252) does not include 'CHM13_T0000094' (1:429117-430327). Created new gene 'CHM13_G0000028.2' (1:429117-430327). File '/ceph/project/Wellcome_Discovery/jdalglei/reference/snpEff/./data/chm13v2/genes.gff' line 1307    'chr1   CAT transcript  429117  430327  9970    -   .   source_transcript=ENST00000428771.6;source_transcript_name=HES4-202;source_gene=ENSG00000188290.11;transcript_modes=transMap;gene_biotype=protein_coding;transcript_biotype=protein_coding;alignment_id=ENST00000428771.6-0;frameshift=nan;exon_annotation_support=1,1,1;intron_annotation_support=2,1;transcript_class=ortholog;valid_start=True;valid_stop=True;adj_start=429382;adj_stop=430297;proper_orf=True;level=2;protein_id=ENSP00000393198.2;transcript_support_level=2;hgnc_id=HGNC:24149;tag=basic,appris_alternative_2,CCDS;ccdsid=CCDS44034.1;havana_gene=OTTHUMG00000040758.2;havana_transcript=OTTHUMT00000097945.2;paralogy=nan;unfiltered_paralogy=nan;source_gene_common_name=HES4;transcript_id=CHM13_T0000094;gene_id=CHM13_G0000028;Parent=CHM13_G0000028;transcript_name=HES4-202;ID=CHM13_T0000094;Name=HES4;gene_name=HES4;alternative_source_transcripts=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;extra_paralog=False'
......................WARNING_GENE_NOT_FOUND: Gene 'CHM13_G0000084' (1:1008608-1010385) does not include 'CHM13_T0000389' (1:1009481-1011581). Created new gene 'CHM13_G0000084.2' (1:1009481-1011581). File '/ceph/project/Wellcome_Discovery/jdalglei/reference/snpEff/./data/chm13v2/genes.gff' line 6427    'chr1   CAT transcript  1009481 1011581 9720    +   .   source_transcript=ENST00000366221.3;source_transcript_name=AL645728.1-202;source_gene=ENSG00000215014.5;transcript_modes=transMap;gene_biotype=lncRNA;transcript_biotype=retained_intron;alignment_id=ENST00000366221.3-0;frameshift=nan;exon_annotation_support=1;intron_annotation_support=nan;transcript_class=ortholog;valid_start=True;valid_stop=True;adj_start=nan;adj_stop=nan;proper_orf=True;level=2;transcript_support_level=NA;tag=RNA_Seq_supported_partial;havana_gene=OTTHUMG00000186983.2;havana_transcript=OTTHUMT00000474166.1;paralogy=nan;unfiltered_paralogy=nan;source_gene_common_name=AL645728.1;transcript_id=CHM13_T0000389;gene_id=CHM13_G0000084;Parent=CHM13_G0000084;transcript_name=AL645728.1-202;ID=CHM13_T0000389;Name=AL645728.1;gene_name=AL645728.1;alternative_source_transcripts=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;extra_paralog=False'
....................WARNING_GENE_NOT_FOUND: Gene 'CHM13_G0000118' (1:1789671-1791115) does not include 'CHM13_T0000618' (1:1789671-1792078). Created new gene 'CHM13_G0000118.2' (1:1789671-1792078). File '/ceph/project/Wellcome_Discovery/jdalglei/reference/snpEff/./data/chm13v2/genes.gff' line 11096 'chr1   CAT transcript  1789671 1792078 9710    -   .   source_transcript=ENST00000602865.1;source_transcript_name=AL513477.1-201;source_gene=ENSG00000269896.2;transcript_modes=transMap;gene_biotype=transcribed_processed_pseudogene;transcript_biotype=processed_transcript;alignment_id=ENST00000602865.1-0;frameshift=nan;exon_annotation_support=1;intron_annotation_support=nan;transcript_class=ortholog;valid_start=True;valid_stop=True;adj_start=nan;adj_stop=nan;proper_orf=True;level=2;transcript_support_level=NA;tag=basic;havana_gene=OTTHUMG00000057495.3;havana_transcript=OTTHUMT00000468095.1;paralogy=nan;unfiltered_paralogy=nan;source_gene_common_name=AL513477.1;transcript_id=CHM13_T0000618;gene_id=CHM13_G0000118;Parent=CHM13_G0000118;transcript_name=AL513477.1-201;ID=CHM13_T0000618;Name=AL513477.1;gene_name=AL513477.1;alternative_source_transcripts=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;extra_paralog=False'
........WARNING_GENE_NOT_FOUND: Gene 'CHM13_G0000144' (1:2571209-2940224) does not include 'CHM13_T0000745' (1:2571244-2943423). Created new gene 'CHM13_G0000144.2' (1:2571244-2943423). File '/ceph/project/Wellcome_Discovery/jdalglei/reference/snpEff/./data/chm13v2/genes.gff' line 12946'chr1    CAT transcript  2571244 2943423 9980    +   .   source_transcript=ENST00000270722.10;source_transcript_name=PRDM16-201;source_gene=ENSG00000142611.17;transcript_modes=transMap;gene_biotype=protein_coding;transcript_biotype=protein_coding;alignment_id=ENST00000270722.10-0;frameshift=False;exon_annotation_support=1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1;intron_annotation_support=2,1,2,2,2,2,2,2,2,2,2,2,2,2,2,2;transcript_class=ortholog;valid_start=True;valid_stop=True;adj_start=2571469;adj_stop=2938783;proper_orf=True;level=2;protein_id=ENSP00000270722.5;transcript_support_level=1;hgnc_id=HGNC:14000;tag=basic,MANE_Select,appris_principal_3,CCDS;ccdsid=CCDS41236.2;havana_gene=OTTHUMG00000000581.10;havana_transcript=OTTHUMT00000001382.4;paralogy=nan;unfiltered_paralogy=nan;source_gene_common_name=PRDM16;transcript_id=CHM13_T0000745;gene_id=CHM13_G0000144;Parent=CHM13_G0000144;transcript_name=PRDM16-201;ID=CHM13_T0000745;Name=PRDM16;gene_name=PRDM16;alternative_source_transcripts=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;extra_paralog=False'
......WARNING_GENE_NOT_FOUND: Gene 'CHM13_G0000161' (1:3247112-3258343) does not include 'CHM13_T0000805' (1:3247212-3258372). Created new gene 'CHM13_G0000161.2' (1:3247212-3258372). File '/ceph/project/Wellcome_Discovery/jdalglei/reference/snpEff/./data/chm13v2/genes.gff' line 14471   'chr1   CAT transcript  3247212 3258372 9830    -   .   source_transcript=ENST00000418088.6;source_transcript_name=TP73-AS1-201;source_gene=ENSG00000227372.12;transcript_modes=transMap;gene_biotype=transcribed_unitary_pseudogene;transcript_biotype=processed_transcript;alignment_id=ENST00000418088.6-0;frameshift=nan;exon_annotation_support=1,1,1,1,1,1;intron_annotation_support=1,1,1,1,1;transcript_class=ortholog;valid_start=True;valid_stop=True;adj_start=nan;adj_stop=nan;proper_orf=True;level=2;transcript_support_level=1;hgnc_id=HGNC:29052;havana_gene=OTTHUMG00000003414.6;havana_transcript=OTTHUMT00000009557.2;paralogy=nan;unfiltered_paralogy=nan;source_gene_common_name=TP73-AS1;transcript_id=CHM13_T0000805;gene_id=CHM13_G0000161;Parent=CHM13_G0000161;transcript_name=TP73-AS1-201;ID=CHM13_T0000805;Name=TP73-AS1;gene_name=TP73-AS1;alternative_source_transcripts=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;extra_paralog=False'
WARNING_GENE_NOT_FOUND: Gene 'CHM13_G0000161' (1:3247112-3258343) does not include 'CHM13_T0000806' (1:3247251-3258543). Created new gene 'CHM13_G0000161.3' (1:3247251-3258543). File '/ceph/project/Wellcome_Discovery/jdalglei/reference/snpEff/./data/chm13v2/genes.gff' line 14473 'chr1   CAT transcript  3247251 3258543 9790    -   .   source_transcript=ENST00000648432.1;source_transcript_name=TP73-AS1-215;source_gene=ENSG00000227372.12;transcript_modes=transMap;gene_biotype=transcribed_unitary_pseudogene;transcript_biotype=processed_transcript;alignment_id=ENST00000648432.1-0;frameshift=nan;exon_annotation_support=1,1,1,1,1,1;intron_annotation_support=1,1,1,1,1;transcript_class=ortholog;valid_start=True;valid_stop=True;adj_start=nan;adj_stop=nan;proper_orf=True;level=2;hgnc_id=HGNC:29052;tag=RNA_Seq_supported_only;havana_gene=OTTHUMG00000003414.6;havana_transcript=OTTHUMT00000501331.1;paralogy=nan;unfiltered_paralogy=nan;source_gene_common_name=TP73-AS1;transcript_id=CHM13_T0000806;gene_id=CHM13_G0000161;Parent=CHM13_G0000161;transcript_name=TP73-AS1-215;ID=CHM13_T0000806;Name=TP73-AS1;gene_name=TP73-AS1;alternative_source_transcripts=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;extra_paralog=False'
WARNING_GENE_NOT_FOUND: Gene 'CHM13_G0000161' (1:3247112-3258343) does not include 'CHM13_T0000808' (1:3247585-3258923). Created new gene 'CHM13_G0000161.4' (1:3247585-3258923). File '/ceph/project/Wellcome_Discovery/jdalglei/reference/snpEff/./data/chm13v2/genes.gff' line 14477 'chr1   CAT transcript  3247585 3258923 9900    -   .   source_transcript=ENST00000452079.5;source_transcript_name=TP73-AS1-204;source_gene=ENSG00000227372.12;transcript_modes=transMap;gene_biotype=transcribed_unitary_pseudogene;transcript_biotype=processed_transcript;alignment_id=ENST00000452079.5-0;frameshift=nan;exon_annotation_support=1,1,1,1;intron_annotation_support=1,1,1;transcript_class=ortholog;valid_start=True;valid_stop=True;adj_start=nan;adj_stop=nan;proper_orf=True;level=2;transcript_support_level=1;hgnc_id=HGNC:29052;havana_gene=OTTHUMG00000003414.6;havana_transcript=OTTHUMT00000009558.1;paralogy=nan;unfiltered_paralogy=nan;source_gene_common_name=TP73-AS1;transcript_id=CHM13_T0000808;gene_id=CHM13_G0000161;Parent=CHM13_G0000161;transcript_name=TP73-AS1-204;ID=CHM13_T0000808;Name=TP73-AS1;gene_name=TP73-AS1;alternative_source_transcripts=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;extra_paralog=False'
WARNING_GENE_NOT_FOUND: Gene 'CHM13_G0000161' (1:3247112-3258343) does not include 'CHM13_T0000811' (1:3247794-3258937). Created new gene 'CHM13_G0000161.5' (1:3247794-3258937). File '/ceph/project/Wellcome_Discovery/jdalglei/reference/snpEff/./data/chm13v2/genes.gff' line 14483 'chr1   CAT transcript  3247794 3258937 9830    -   .   source_transcript=ENST00000647831.1;source_transcript_name=TP73-AS1-213;source_gene=ENSG00000227372.12;transcript_modes=transMap;gene_biotype=transcribed_unitary_pseudogene;transcript_biotype=processed_transcript;alignment_id=ENST00000647831.1-0;frameshift=nan;exon_annotation_support=1,1,1,1,1;intron_annotation_support=1,1,1,1;transcript_class=ortholog;valid_start=True;valid_stop=True;adj_start=nan;adj_stop=nan;proper_orf=True;level=2;hgnc_id=HGNC:29052;tag=NAGNAG_splice_site;havana_gene=OTTHUMG00000003414.6;havana_transcript=OTTHUMT00000009556.2;paralogy=nan;unfiltered_paralogy=nan;source_gene_common_name=TP73-AS1;transcript_id=CHM13_T0000811;gene_id=CHM13_G0000161;Parent=CHM13_G0000161;transcript_name=TP73-AS1-213;ID=CHM13_T0000811;Name=TP73-AS1;gene_name=TP73-AS1;alternative_source_transcripts=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;extra_paralog=False'
.WARNING_GENE_NOT_FOUND: Gene 'CHM13_G0000161' (1:3247112-3258343) does not include 'CHM13_T0000814' (1:3248744-3258485). Created new gene 'CHM13_G0000161.6' (1:3248744-3258485). File '/ceph/project/Wellcome_Discovery/jdalglei/reference/snpEff/./data/chm13v2/genes.gff' line 14500    'chr1   CAT transcript  3248744 3258485 9800    -   .   source_transcript=ENST00000648600.1;source_transcript_name=TP73-AS1-219;source_gene=ENSG00000227372.12;transcript_modes=transMap;gene_biotype=transcribed_unitary_pseudogene;transcript_biotype=processed_transcript;alignment_id=ENST00000648600.1-0;frameshift=nan;exon_annotation_support=1,1,1,1,1;intron_annotation_support=1,1,1,1;transcript_class=ortholog;valid_start=True;valid_stop=True;adj_start=nan;adj_stop=nan;proper_orf=True;level=2;hgnc_id=HGNC:29052;tag=NAGNAG_splice_site,RNA_Seq_supported_only;havana_gene=OTTHUMG00000003414.6;havana_transcript=OTTHUMT00000501335.1;paralogy=nan;unfiltered_paralogy=nan;source_gene_common_name=TP73-AS1;transcript_id=CHM13_T0000814;gene_id=CHM13_G0000161;Parent=CHM13_G0000161;transcript_name=TP73-AS1-219;ID=CHM13_T0000814;Name=TP73-AS1;gene_name=TP73-AS1;alternative_source_transcripts=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;extra_paralog=False'
WARNING_GENE_NOT_FOUND: Gene 'CHM13_G0000161' (1:3247112-3258343) does not include 'CHM13_T0000815' (1:3248750-3258974). Created new gene 'CHM13_G0000161.7' (1:3248750-3258974). File '/ceph/project/Wellcome_Discovery/jdalglei/reference/snpEff/./data/chm13v2/genes.gff' line 14502 'chr1   CAT transcript  3248750 3258974 9830    -   .   source_transcript=ENST00000423764.6;source_transcript_name=TP73-AS1-203;source_gene=ENSG00000227372.12;transcript_modes=transMap;gene_biotype=transcribed_unitary_pseudogene;transcript_biotype=processed_transcript;alignment_id=ENST00000423764.6-0;frameshift=nan;exon_annotation_support=1,1,1,1,1;intron_annotation_support=1,1,1,1;transcript_class=ortholog;valid_start=True;valid_stop=True;adj_start=nan;adj_stop=nan;proper_orf=True;level=2;transcript_support_level=1;hgnc_id=HGNC:29052;tag=basic;havana_gene=OTTHUMG00000003414.6;havana_transcript=OTTHUMT00000501336.1;paralogy=nan;unfiltered_paralogy=nan;source_gene_common_name=TP73-AS1;transcript_id=CHM13_T0000815;gene_id=CHM13_G0000161;Parent=CHM13_G0000161;transcript_name=TP73-AS1-203;ID=CHM13_T0000815;Name=TP73-AS1;gene_name=TP73-AS1;alternative_source_transcripts=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;extra_paralog=False'
WARNING_GENE_NOT_FOUND: Gene 'CHM13_G0000161' (1:3247112-3258343) does not include 'CHM13_T0000816' (1:3248767-3258499). Created new gene 'CHM13_G0000161.8' (1:3248767-3258499). File '/ceph/project/Wellcome_Discovery/jdalglei/reference/snpEff/./data/chm13v2/genes.gff' line 14504 'chr1   CAT transcript  3248767 3258499 9860    -   .   source_transcript=ENST00000647817.1;source_transcript_name=TP73-AS1-212;source_gene=ENSG00000227372.12;transcript_modes=transMap;gene_biotype=transcribed_unitary_pseudogene;transcript_biotype=processed_transcript;alignment_id=ENST00000647817.1-0;frameshift=nan;exon_annotation_support=1,1,1,1,1,1;intron_annotation_support=1,1,1,1,1;transcript_class=ortholog;valid_start=True;valid_stop=True;adj_start=nan;adj_stop=nan;proper_orf=True;level=2;hgnc_id=HGNC:29052;tag=RNA_Seq_supported_only;havana_gene=OTTHUMG00000003414.6;havana_transcript=OTTHUMT00000501337.1;paralogy=nan;unfiltered_paralogy=nan;source_gene_common_name=TP73-AS1;transcript_id=CHM13_T0000816;gene_id=CHM13_G0000161;Parent=CHM13_G0000161;transcript_name=TP73-AS1-212;ID=CHM13_T0000816;Name=TP73-AS1;gene_name=TP73-AS1;alternative_source_transcripts=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;extra_paralog=False'
WARNING_GENE_NOT_FOUND: Gene 'CHM13_G0000161' (1:3247112-3258343) does not include 'CHM13_T0000817' (1:3248794-3258392). Created new gene 'CHM13_G0000161.9' (1:3248794-3258392). File '/ceph/project/Wellcome_Discovery/jdalglei/reference/snpEff/./data/chm13v2/genes.gff' line 14506 'chr1   CAT transcript  3248794 3258392 9850    -   .   source_transcript=ENST00000649123.1;source_transcript_name=TP73-AS1-222;source_gene=ENSG00000227372.12;transcript_modes=transMap;gene_biotype=transcribed_unitary_pseudogene;transcript_biotype=processed_transcript;alignment_id=ENST00000649123.1-0;frameshift=nan;exon_annotation_support=1,1,1,1,1;intron_annotation_support=1,1,1,1;transcript_class=ortholog;valid_start=True;valid_stop=True;adj_start=nan;adj_stop=nan;proper_orf=True;level=2;hgnc_id=HGNC:29052;tag=RNA_Seq_supported_only,NAGNAG_splice_site;havana_gene=OTTHUMG00000003414.6;havana_transcript=OTTHUMT00000501338.1;paralogy=nan;unfiltered_paralogy=nan;source_gene_common_name=TP73-AS1;transcript_id=CHM13_T0000817;gene_id=CHM13_G0000161;Parent=CHM13_G0000161;transcript_name=TP73-AS1-222;ID=CHM13_T0000817;Name=TP73-AS1;gene_name=TP73-AS1;alternative_source_transcripts=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;extra_paralog=False'
WARNING_GENE_NOT_FOUND: Gene 'CHM13_G0000161' (1:3247112-3258343) does not include 'CHM13_T0000820' (1:3248813-3258478). Created new gene 'CHM13_G0000161.10' (1:3248813-3258478). File '/ceph/project/Wellcome_Discovery/jdalglei/reference/snpEff/./data/chm13v2/genes.gff' line 14512    'chr1   CAT transcript  3248813 3258478 9740    -   .   source_transcript=ENST00000650039.1;source_transcript_name=TP73-AS1-228;source_gene=ENSG00000227372.12;transcript_modes=transMap;gene_biotype=transcribed_unitary_pseudogene;transcript_biotype=processed_transcript;alignment_id=ENST00000650039.1-0;frameshift=nan;exon_annotation_support=1,1,1,1,1;intron_annotation_support=1,1,1,1;transcript_class=ortholog;valid_start=True;valid_stop=True;adj_start=nan;adj_stop=nan;proper_orf=True;level=2;hgnc_id=HGNC:29052;tag=RNA_Seq_supported_only;havana_gene=OTTHUMG00000003414.6;havana_transcript=OTTHUMT00000501341.1;paralogy=nan;unfiltered_paralogy=nan;source_gene_common_name=TP73-AS1;transcript_id=CHM13_T0000820;gene_id=CHM13_G0000161;Parent=CHM13_G0000161;transcript_name=TP73-AS1-228;ID=CHM13_T0000820;Name=TP73-AS1;gene_name=TP73-AS1;alternative_source_transcripts=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;extra_paralog=False'
WARNING_GENE_NOT_FOUND: Gene 'CHM13_G0000161' (1:3247112-3258343) does not include 'CHM13_T0000821' (1:3248939-3258572). Created new gene 'CHM13_G0000161.11' (1:3248939-3258572). File '/ceph/project/Wellcome_Discovery/jdalglei/reference/snpEff/./data/chm13v2/genes.gff' line 14514    'chr1   CAT transcript  3248939 3258572 9750    -   .   source_transcript=ENST00000649468.1;source_transcript_name=TP73-AS1-226;source_gene=ENSG00000227372.12;transcript_modes=transMap;gene_biotype=transcribed_unitary_pseudogene;transcript_biotype=processed_transcript;alignment_id=ENST00000649468.1-0;frameshift=nan;exon_annotation_support=1,1,1,1,1,1;intron_annotation_support=1,1,1,1,1;transcript_class=ortholog;valid_start=True;valid_stop=True;adj_start=nan;adj_stop=nan;proper_orf=True;level=2;hgnc_id=HGNC:29052;tag=RNA_Seq_supported_only;havana_gene=OTTHUMG00000003414.6;havana_transcript=OTTHUMT00000501342.1;paralogy=nan;unfiltered_paralogy=nan;source_gene_common_name=TP73-AS1;transcript_id=CHM13_T0000821;gene_id=CHM13_G0000161;Parent=CHM13_G0000161;transcript_name=TP73-AS1-226;ID=CHM13_T0000821;Name=TP73-AS1;gene_name=TP73-AS1;alternative_source_transcripts=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;extra_paralog=False'
WARNING_GENE_NOT_FOUND: Gene 'CHM13_G0000161' (1:3247112-3258343) does not include 'CHM13_T0000823' (1:3249140-3258392). Created new gene 'CHM13_G0000161.12' (1:3249140-3258392). File '/ceph/project/Wellcome_Discovery/jdalglei/reference/snpEff/./data/chm13v2/genes.gff' line 14518    'chr1   CAT transcript  3249140 3258392 9840    -   .   source_transcript=ENST00000649348.1;source_transcript_name=TP73-AS1-224;source_gene=ENSG00000227372.12;transcript_modes=transMap;gene_biotype=transcribed_unitary_pseudogene;transcript_biotype=processed_transcript;alignment_id=ENST00000649348.1-0;frameshift=nan;exon_annotation_support=1,1,0,1;intron_annotation_support=1,1,1;transcript_class=ortholog;valid_start=True;valid_stop=True;adj_start=nan;adj_stop=nan;proper_orf=True;level=2;hgnc_id=HGNC:29052;tag=RNA_Seq_supported_only;havana_gene=OTTHUMG00000003414.6;havana_transcript=OTTHUMT00000501344.1;paralogy=nan;unfiltered_paralogy=nan;source_gene_common_name=TP73-AS1;transcript_id=CHM13_T0000823;gene_id=CHM13_G0000161;Parent=CHM13_G0000161;transcript_name=TP73-AS1-224;ID=CHM13_T0000823;Name=TP73-AS1;gene_name=TP73-AS1;alternative_source_transcripts=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;extra_paralog=False'
WARNING_GENE_NOT_FOUND: Gene 'CHM13_G0000161' (1:3247112-3258343) does not include 'CHM13_T0000824' (1:3249195-3258624). Created new gene 'CHM13_G0000161.13' (1:3249195-3258624). File '/ceph/project/Wellcome_Discovery/jdalglei/reference/snpEff/./data/chm13v2/genes.gff' line 14520    'chr1   CAT transcript  3249195 3258624 9760    -   .   source_transcript=ENST00000636630.1;source_transcript_name=TP73-AS1-209;source_gene=ENSG00000227372.12;transcript_modes=transMap;gene_biotype=transcribed_unitary_pseudogene;transcript_biotype=processed_transcript;alignment_id=ENST00000636630.1-0;frameshift=nan;exon_annotation_support=1,1,1,1,1,1;intron_annotation_support=1,1,1,1,1;transcript_class=ortholog;valid_start=True;valid_stop=True;adj_start=nan;adj_stop=nan;proper_orf=True;level=2;transcript_support_level=5;hgnc_id=HGNC:29052;tag=RNA_Seq_supported_only;havana_gene=OTTHUMG00000003414.6;havana_transcript=OTTHUMT00000489044.2;paralogy=nan;unfiltered_paralogy=nan;source_gene_common_name=TP73-AS1;transcript_id=CHM13_T0000824;gene_id=CHM13_G0000161;Parent=CHM13_G0000161;transcript_name=TP73-AS1-209;ID=CHM13_T0000824;Name=TP73-AS1;gene_name=TP73-AS1;alternative_source_transcripts=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;extra_paralog=False'
WARNING_GENE_NOT_FOUND: Gene 'CHM13_G0000161' (1:3247112-3258343) does not include 'CHM13_T0000828' (1:3251059-3258557). Created new gene 'CHM13_G0000161.14' (1:3251059-3258557). File '/ceph/project/Wellcome_Discovery/jdalglei/reference/snpEff/./data/chm13v2/genes.gff' line 14553    'chr1   CAT transcript  3251059 3258557 9770    -   .   source_transcript=ENST00000649290.1;source_transcript_name=TP73-AS1-223;source_gene=ENSG00000227372.12;transcript_modes=transMap;gene_biotype=transcribed_unitary_pseudogene;transcript_biotype=processed_transcript;alignment_id=ENST00000649290.1-0;frameshift=nan;exon_annotation_support=1,1,1,1,1;intron_annotation_support=1,1,1,1;transcript_class=ortholog;valid_start=True;valid_stop=True;adj_start=nan;adj_stop=nan;proper_orf=True;level=2;hgnc_id=HGNC:29052;tag=RNA_Seq_supported_only,NAGNAG_splice_site;havana_gene=OTTHUMG00000003414.6;havana_transcript=OTTHUMT00000501345.1;paralogy=nan;unfiltered_paralogy=nan;source_gene_common_name=TP73-AS1;transcript_id=CHM13_T0000828;gene_id=CHM13_G0000161;Parent=CHM13_G0000161;transcript_name=TP73-AS1-223;ID=CHM13_T0000828;Name=TP73-AS1;gene_name=TP73-AS1;alternative_source_transcripts=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;extra_paralog=False'
WARNING_GENE_NOT_FOUND: Gene 'CHM13_G0000161' (1:3247112-3258343) does not include 'CHM13_T0000829' (1:3251306-3258508). Created new gene 'CHM13_G0000161.15' (1:3251306-3258508). File '/ceph/project/Wellcome_Discovery/jdalglei/reference/snpEff/./data/chm13v2/genes.gff' line 14558    'chr1   CAT transcript  3251306 3258508 9760    -   .   source_transcript=ENST00000647686.1;source_transcript_name=TP73-AS1-211;source_gene=ENSG00000227372.12;transcript_modes=transMap;gene_biotype=transcribed_unitary_pseudogene;transcript_biotype=processed_transcript;alignment_id=ENST00000647686.1-0;frameshift=nan;exon_annotation_support=1,1,1,1;intron_annotation_support=1,1,1;transcript_class=ortholog;valid_start=True;valid_stop=True;adj_start=nan;adj_stop=nan;proper_orf=True;level=2;hgnc_id=HGNC:29052;tag=RNA_Seq_supported_only,NAGNAG_splice_site;havana_gene=OTTHUMG00000003414.6;havana_transcript=OTTHUMT00000501346.1;paralogy=nan;unfiltered_paralogy=nan;source_gene_common_name=TP73-AS1;transcript_id=CHM13_T0000829;gene_id=CHM13_G0000161;Parent=CHM13_G0000161;transcript_name=TP73-AS1-211;ID=CHM13_T0000829;Name=TP73-AS1;gene_name=TP73-AS1;alternative_source_transcripts=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;extra_paralog=False'
WARNING_GENE_NOT_FOUND: Gene 'CHM13_G0000161' (1:3247112-3258343) does not include 'CHM13_T0000831' (1:3251590-3258488). Created new gene 'CHM13_G0000161.16' (1:3251590-3258488). File '/ceph/project/Wellcome_Discovery/jdalglei/reference/snpEff/./data/chm13v2/genes.gff' line 14563    'chr1   CAT transcript  3251590 3258488 9700    -   .   source_transcript=ENST00000649413.1;source_transcript_name=TP73-AS1-225;source_gene=ENSG00000227372.12;transcript_modes=transMap;gene_biotype=transcribed_unitary_pseudogene;transcript_biotype=processed_transcript;alignment_id=ENST00000649413.1-0;frameshift=nan;exon_annotation_support=1,1,1,1;intron_annotation_support=1,1,1;transcript_class=ortholog;valid_start=True;valid_stop=True;adj_start=nan;adj_stop=nan;proper_orf=True;level=2;hgnc_id=HGNC:29052;tag=RNA_Seq_supported_only;havana_gene=OTTHUMG00000003414.6;havana_transcript=OTTHUMT00000501348.1;paralogy=nan;unfiltered_paralogy=nan;source_gene_common_name=TP73-AS1;transcript_id=CHM13_T0000831;gene_id=CHM13_G0000161;Parent=CHM13_G0000161;transcript_name=TP73-AS1-225;ID=CHM13_T0000831;Name=TP73-AS1;gene_name=TP73-AS1;alternative_source_transcripts=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;extra_paralog=False'
.........WARNING_GENE_NOT_FOUND: Gene 'CHM13_G0000180' (1:4085208-4107712) does not include 'CHM13_T0000918' (1:4085226-4107719). Created new gene 'CHM13_G0000180.2' (1:4085226-4107719). File '/ceph/project/Wellcome_Discovery/jdalglei/reference/snpEff/./data/chm13v2/genes.gff' line 16568'chr1   CAT transcript  4085226 4107719 9460    +   .   source_transcript=ENST00000666685.1;source_transcript_name=LINC01646-207;source_gene=ENSG00000232596.3;transcript_modes=transMap;gene_biotype=lncRNA;transcript_biotype=lncRNA;alignment_id=ENST00000666685.1-0;frameshift=nan;exon_annotation_support=1,1;intron_annotation_support=1;transcript_class=ortholog;valid_start=True;valid_stop=True;adj_start=nan;adj_stop=nan;proper_orf=True;level=2;hgnc_id=HGNC:52433;tag=TAGENE;havana_gene=OTTHUMG00000000647.7;havana_transcript=OTTHUMT00000521616.1;paralogy=nan;unfiltered_paralogy=nan;source_gene_common_name=LINC01646;transcript_id=CHM13_T0000918;gene_id=CHM13_G0000180;Parent=CHM13_G0000180;transcript_name=LINC01646-207;ID=CHM13_T0000918;Name=LINC01646;gene_name=LINC01646;alternative_source_transcripts=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;extra_paralog=False'
WARNING_GENE_NOT_FOUND: Gene 'CHM13_G0000180' (1:4085208-4107712) does not include 'CHM13_T0000921' (1:4085240-4107719). Created new gene 'CHM13_G0000180.3' (1:4085240-4107719). File '/ceph/project/Wellcome_Discovery/jdalglei/reference/snpEff/./data/chm13v2/genes.gff' line 16574 'chr1   CAT transcript  4085240 4107719 9510    +   .   source_transcript=ENST00000659059.1;source_transcript_name=LINC01646-204;source_gene=ENSG00000232596.3;transcript_modes=transMap;gene_biotype=lncRNA;transcript_biotype=lncRNA;alignment_id=ENST00000659059.1-0;frameshift=nan;exon_annotation_support=1,1,1;intron_annotation_support=1,1;transcript_class=ortholog;valid_start=True;valid_stop=True;adj_start=nan;adj_stop=nan;proper_orf=True;level=2;hgnc_id=HGNC:52433;tag=TAGENE;havana_gene=OTTHUMG00000000647.7;havana_transcript=OTTHUMT00000513190.1;paralogy=nan;unfiltered_paralogy=nan;source_gene_common_name=LINC01646;transcript_id=CHM13_T0000921;gene_id=CHM13_G0000180;Parent=CHM13_G0000180;transcript_name=LINC01646-204;ID=CHM13_T0000921;Name=LINC01646;gene_name=LINC01646;alternative_source_transcripts=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;extra_paralog=False'
.....................WARNING_GENE_NOT_FOUND: Gene 'CHM13_G0000216' (1:6080965-6105090) does not include 'CHM13_T0001136' (1:6080965-6105419). Created new gene 'CHM13_G0000216.2' (1:6080965-6105419). File '/ceph/project/Wellcome_Discovery/jdalglei/reference/snpEff/./data/chm13v2/genes.gff' line 21544    'chr1   CAT transcript  6080965 6105419 9990    +   .   source_transcript=ENST00000333172.11;source_transcript_name=TAS1R1-201;source_gene=ENSG00000173662.21;transcript_modes=transMap;gene_biotype=protein_coding;transcript_biotype=protein_coding;alignment_id=ENST00000333172.11-0;frameshift=nan;exon_annotation_support=1,1,1,1,1,1;intron_annotation_support=1,1,1,1,1;transcript_class=ortholog;valid_start=True;valid_stop=True;adj_start=6081200;adj_stop=6105417;proper_orf=True;level=2;protein_id=ENSP00000331867.6;transcript_support_level=1;hgnc_id=HGNC:14448;tag=basic,MANE_Select,appris_principal_1,CCDS;ccdsid=CCDS81.1;havana_gene=OTTHUMG00000001441.4;havana_transcript=OTTHUMT00000004211.2;paralogy=nan;unfiltered_paralogy=nan;source_gene_common_name=TAS1R1;transcript_id=CHM13_T0001136;gene_id=CHM13_G0000216;Parent=CHM13_G0000216;transcript_name=TAS1R1-201;ID=CHM13_T0001136;Name=TAS1R1;gene_name=TAS1R1;alternative_source_transcripts=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;extra_paralog=False'
WARNING_GENE_NOT_FOUND: Gene 'CHM13_G0000216' (1:6080965-6105090) does not include 'CHM13_T0001137' (1:6080967-6105290). Created new gene 'CHM13_G0000216.3' (1:6080967-6105290). File '/ceph/project/Wellcome_Discovery/jdalglei/reference/snpEff/./data/chm13v2/genes.gff' line 21546 'chr1   CAT transcript  6080967 6105290 10000   +   .   source_transcript=ENST00000351136.7;source_transcript_name=TAS1R1-202;source_gene=ENSG00000173662.21;transcript_modes=transMap;gene_biotype=protein_coding;transcript_biotype=protein_coding;alignment_id=ENST00000351136.7-0;frameshift=nan;exon_annotation_support=1,1,1,1,1;intron_annotation_support=1,1,1,1;transcript_class=ortholog;valid_start=True;valid_stop=True;adj_start=6081200;adj_stop=6105417;proper_orf=True;level=2;protein_id=ENSP00000312558.5;transcript_support_level=2;hgnc_id=HGNC:14448;tag=basic,CCDS;ccdsid=CCDS82.1;havana_gene=OTTHUMG00000001441.4;havana_transcript=OTTHUMT00000004214.2;paralogy=nan;unfiltered_paralogy=nan;source_gene_common_name=TAS1R1;transcript_id=CHM13_T0001137;gene_id=CHM13_G0000216;Parent=CHM13_G0000216;transcript_name=TAS1R1-202;ID=CHM13_T0001137;Name=TAS1R1;gene_name=TAS1R1;alternative_source_transcripts=N/A;collapsed_gene_ids=N/A;collapsed_gene_names=N/A;extra_paralog=False'
WARNING_GENE_NOT_FOUND: Too many 'WARNING_GENE_NOT_FOUND' warnings, no further warnings will be shown.
.......
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        1050000 ....................................................................................................
        1060000 ....................................................................................................
        1070000 ....................................................................................................
        1080000 ....................................................................................................
        1090000 ....................................................................................................
        1100000 ....................................................................................................
        1110000 ....................................................................................................
        1120000 ....................................................................................................
        1130000 ....................................................................................................
        1140000 ....................................................................................................
        1150000 ....................................................................................................
        1160000 ....................................................................................................
        1170000 ....................................................................................................
        1180000 ....................................................................................................
        1190000 ....................................................................................................
        1200000 ....................................................................................................
        1210000 ....................................................................................................
        1220000 ....................................................................................................
        1230000 ....................................................................................................
        1240000 ....................................................................................................
        1250000 ....................................................................................................
        1260000 ....................................................................................................
        1270000 ....................................................................................................
        1280000 ....................................................................................................
        1290000 ....................................................................................................
        1300000 ....................................................................................................
        1310000 ....................................................................................................
        1320000 ....................................................................................................
        1330000 ....................................................................................................
        1340000 ....................................................................................................
        1350000 ....................................................................................................
        1360000 ....................................................................................................
        1370000 ....................................................................................................
        1380000 ....................................................................................................
        1390000 ....................................................................................................
        1400000 ....................................................................................................
        1410000 ....................................................................................................
        1420000 ....................................................................................................
        1430000 ....................................................................................................
        1440000 ....................................................................................................
        1450000 ....................................................................................................
        1460000 ....................................................................................................
        1470000 ....................................................................................................
        1480000 ....................................................................................................
        1490000 ....................................................................................................
        1500000 ....................................................................................................
        1510000 ....................................................................................................
        1520000 ....................................................................................................
        1530000 ....................................................................................................
        1540000 ....................................................................................................
        1550000 ....................................................................................................
        1560000 ....................................................................................................
        1570000 ....................................................................................................
        1580000 ....................................................................................................
        1590000 ....................................................................................................
        1600000 ....................................................................................................
        1610000 ....................................................................................................
        1620000 ....................................................................................................
        1630000 ....................................................................................................
        1640000 ....................................................................................................
        1650000 ....................................................................................................
        1660000 ....................................................................................................
        1670000 ....................................................................................................
        1680000 ....................................................................................................
        1690000 ....................................................................................................
        1700000 ....................................................................................................
        1710000 ....................................................................................................
        1720000 ....................................................................................................
        1730000 ....................................................................................................
        1740000 ...........................................00:00:48 
    Total: 1744302 markers added.
00:00:48 Create exons from CDS (if needed): 
00:00:49 Exons created for 0 transcripts.
00:00:49 Deleting redundant exons (if needed): 
.
        0   ....................................................................................................
        10000   ....................................................................................................
        20000   ....................................................................................................
        30000   ....................................................................................................
        40000   ....................................................................................................
        50000   ....................................................................................................
        60000   ....................................................................................................
        70000   ....................................................................................................
        80000   ....................................................................................................
        90000   ...................................................................................00:00:50     Total transcripts with deleted exons: 98393
00:00:50 Collapsing zero length introns (if needed): 
.
        0   .00:00:51   Total collapsed transcripts: 190
00:00:51    Reading sequences   :
00:00:51    FASTA file: '/ceph/project/Wellcome_Discovery/jdalglei/reference/snpEff/./data/genomes/chm13v2.fa' not found.
00:00:51    Reading FASTA file: '/ceph/project/Wellcome_Discovery/jdalglei/reference/snpEff/./data/chm13v2/sequences.fa'
00:00:53        Reading sequence '1', length: 248387328
00:00:53        Adding genomic sequences to genes: 
00:00:56    Done (3320 sequences added).
00:00:56        Adding genomic sequences to exons: 
00:00:57    Done (133250 sequences added, 0 ignored).
00:00:58        Reading sequence '2', length: 242696752
00:00:58        Adding genomic sequences to genes: 
00:01:01    Done (2398 sequences added).
00:01:01        Adding genomic sequences to exons: 
00:01:02    Done (111559 sequences added, 0 ignored).
00:01:03        Reading sequence '3', length: 201105948
00:01:03        Adding genomic sequences to genes: 
00:01:05    Done (1584 sequences added).
00:01:05        Adding genomic sequences to exons: 
00:01:06    Done (94468 sequences added, 0 ignored).
00:01:06        Reading sequence '4', length: 193574945
00:01:06        Adding genomic sequences to genes: 
00:01:09    Done (1626 sequences added).
00:01:09        Adding genomic sequences to exons: 
00:01:09    Done (61529 sequences added, 0 ignored).
00:01:10        Reading sequence '5', length: 182045439
00:01:10        Adding genomic sequences to genes: 
00:01:12    Done (1654 sequences added).
00:01:12        Adding genomic sequences to exons: 
00:01:13    Done (65462 sequences added, 0 ignored).
00:01:14        Reading sequence '6', length: 172126628
00:01:14        Adding genomic sequences to genes: 
00:01:16    Done (1753 sequences added).
00:01:16        Adding genomic sequences to exons: 
00:01:16    Done (66178 sequences added, 0 ignored).
00:01:17        Reading sequence '7', length: 160567428
00:01:17        Adding genomic sequences to genes: 
00:01:18    Done (1823 sequences added).
00:01:18        Adding genomic sequences to exons: 
00:01:19    Done (68209 sequences added, 0 ignored).
00:01:19        Reading sequence '8', length: 146259331
00:01:19        Adding genomic sequences to genes: 
00:01:21    Done (1472 sequences added).
00:01:21        Adding genomic sequences to exons: 
00:01:21    Done (53229 sequences added, 0 ignored).
00:01:22        Reading sequence '9', length: 150617247
00:01:22        Adding genomic sequences to genes: 
00:01:23    Done (1515 sequences added).
00:01:23        Adding genomic sequences to exons: 
00:01:23    Done (53379 sequences added, 0 ignored).
00:01:24        Reading sequence '10', length: 134758134
00:01:24        Adding genomic sequences to genes: 
00:01:26    Done (1354 sequences added).
00:01:26        Adding genomic sequences to exons: 
00:01:26    Done (54620 sequences added, 0 ignored).
00:01:27        Reading sequence '11', length: 135127769
00:01:27        Adding genomic sequences to genes: 
00:01:28    Done (1880 sequences added).
00:01:28        Adding genomic sequences to exons: 
00:01:29    Done (82364 sequences added, 0 ignored).
00:01:29        Reading sequence '12', length: 133324548
00:01:29        Adding genomic sequences to genes: 
00:01:31    Done (1485 sequences added).
00:01:31        Adding genomic sequences to exons: 
00:01:31    Done (81341 sequences added, 0 ignored).
00:01:31        Reading sequence '13', length: 113566686
00:01:31        Adding genomic sequences to genes: 
00:01:32    Done (998 sequences added).
00:01:32        Adding genomic sequences to exons: 
00:01:32    Done (26574 sequences added, 0 ignored).
00:01:33        Reading sequence '14', length: 101161492
00:01:33        Adding genomic sequences to genes: 
00:01:34    Done (1373 sequences added).
00:01:34        Adding genomic sequences to exons: 
00:01:34    Done (49379 sequences added, 0 ignored).
00:01:35        Reading sequence '15', length: 99753195
00:01:35        Adding genomic sequences to genes: 
00:01:35    Done (1126 sequences added).
00:01:35        Adding genomic sequences to exons: 
00:01:36    Done (56337 sequences added, 0 ignored).
00:01:36        Reading sequence '16', length: 96330374
00:01:36        Adding genomic sequences to genes: 
00:01:37    Done (1280 sequences added).
00:01:37        Adding genomic sequences to exons: 
00:01:38    Done (66323 sequences added, 0 ignored).
00:01:38        Reading sequence '17', length: 84276897
00:01:38        Adding genomic sequences to genes: 
00:01:39    Done (1522 sequences added).
00:01:39        Adding genomic sequences to exons: 
00:01:39    Done (82710 sequences added, 0 ignored).
00:01:40        Reading sequence '18', length: 80542538
00:01:40        Adding genomic sequences to genes: 
00:01:40    Done (651 sequences added).
00:01:40        Adding genomic sequences to exons: 
00:01:40    Done (26712 sequences added, 0 ignored).
00:01:41        Reading sequence '19', length: 61707364
00:01:41        Adding genomic sequences to genes: 
00:01:41    Done (1593 sequences added).
00:01:41        Adding genomic sequences to exons: 
00:01:42    Done (77206 sequences added, 0 ignored).
00:01:42        Reading sequence '20', length: 66210255
00:01:42        Adding genomic sequences to genes: 
00:01:42    Done (900 sequences added).
00:01:42        Adding genomic sequences to exons: 
00:01:43    Done (33760 sequences added, 0 ignored).
00:01:43        Reading sequence '21', length: 45090682
00:01:43        Adding genomic sequences to genes: 
00:01:43    Done (592 sequences added).
00:01:43        Adding genomic sequences to exons: 
00:01:43    Done (17121 sequences added, 0 ignored).
00:01:44        Reading sequence '22', length: 51324926
00:01:44        Adding genomic sequences to genes: 
00:01:44    Done (925 sequences added).
00:01:44        Adding genomic sequences to exons: 
00:01:44    Done (31099 sequences added, 0 ignored).
00:01:45        Reading sequence 'X', length: 154259566
00:01:45        Adding genomic sequences to genes: 
00:01:46    Done (1638 sequences added).
00:01:46        Adding genomic sequences to exons: 
00:01:47    Done (45403 sequences added, 0 ignored).
00:01:47        Reading sequence 'Y', length: 62460029
00:01:47        Adding genomic sequences to genes: 
00:01:47    Done (514 sequences added).
00:01:47        Adding genomic sequences to exons: 
00:01:47    Done (6049 sequences added, 0 ignored).
00:01:47        Reading sequence 'M', length: 16569
00:01:47        Adding genomic sequences to genes: 
00:01:47    Done (32 sequences added).
00:01:47        Adding genomic sequences to exons: 
00:01:47    Done (43 sequences added, 0 ignored).
00:01:47    Total: 1444304 sequences added, 0 sequences ignored.
00:01:47 Finishing up genome
00:01:47 Adjusting transcripts: 
00:01:48 Adjusting genes: 
WARNING_GENE_COORDINATES: Gene 'CHM13_G0042557' (name:'COL25A1'), adjusting start coordinate from 112110610 to 112112602
WARNING_GENE_COORDINATES: Gene 'CHM13_G0042578' (name:'EGF'), adjusting start coordinate from 113214974 to 113214975
WARNING_GENE_COORDINATES: Gene 'CHM13_G0042648' (name:'MSTRG.4335'), adjusting start coordinate from 117205970 to 117208999
WARNING_GENE_COORDINATES: Gene 'CHM13_G0003073' (name:'OTUD7B'), adjusting start coordinate from 149062295 to 149071782
WARNING_GENE_COORDINATES: Gene 'CHM13_G0003060' (name:'H2BC19P'), adjusting start coordinate from 148967014 to 148967180
WARNING_GENE_COORDINATES: Gene 'CHM13_G0003061' (name:'H2BC20P'), adjusting start coordinate from 148968637 to 148974332
WARNING_GENE_COORDINATES: Gene 'CHM13_G0003050' (name:'AC243772.3'), adjusting start coordinate from 148800986 to 148844673
WARNING_GENE_COORDINATES: Gene 'CHM13_G0042600' (name:'AC083795.2'), adjusting start coordinate from 114933817 to 114933818
WARNING_GENE_COORDINATES: Gene 'CHM13_G0017620' (name:'TNFAIP2'), adjusting start coordinate from 97357391 to 97359357
WARNING_GENE_COORDINATES: Gene 'CHM13_G0052041' (name:'AC087071.1'), adjusting start coordinate from 131455103 to 131455127
WARNING_GENE_COORDINATES: Gene 'CHM13_G0052026' (name:'SMKR1'), adjusting start coordinate from 130815595 to 130815856
WARNING_GENE_COORDINATES: Gene 'CHM13_G0027097' (name:'CSNK1G2'), adjusting start coordinate from 1912500 to 1913788
WARNING_GENE_COORDINATES: Gene 'CHM13_G0003080' (name:'ANP32E'), adjusting start coordinate from 149343212 to 149343350
WARNING_GENE_COORDINATES: Gene 'CHM13_G0027041' (name:'GPX4'), adjusting start coordinate from 1068591 to 1068659
WARNING_GENE_COORDINATES: Gene 'CHM13_G0042681' (name:'NT5C3AP1'), adjusting start coordinate from 120877790 to 120878376
WARNING_GENE_COORDINATES: Gene 'CHM13_G0052010' (name:'TPI1P2'), adjusting start coordinate from 130368092 to 130368888
WARNING_GENE_COORDINATES: Gene 'CHM13_G0052016' (name:'TSPAN33'), adjusting start coordinate from 130457612 to 130475354
WARNING_GENE_COORDINATES: Gene 'CHM13_G0027061' (name:'GAMT'), adjusting start coordinate from 1367023 to 1367265
WARNING_GENE_COORDINATES: Gene 'CHM13_G0027126' (name:'TIMM13'), adjusting start coordinate from 2401415 to 2402355
WARNING_GENE_COORDINATES: Gene 'CHM13_G0003153' (name:'TUFT1'), adjusting start coordinate from 150663974 to 150663992
WARNING_GENE_COORDINATES: Gene 'CHM13_G0003139' (name:'ZNF687-AS1'), adjusting start coordinate from 150403370 to 150403716
WARNING_GENE_COORDINATES: Gene 'CHM13_G0027146' (name:'THOP1'), adjusting start coordinate from 2760789 to 2760800
WARNING_GENE_COORDINATES: Gene 'CHM13_G0003160' (name:'CELF3'), adjusting start coordinate from 150823441 to 150825787
WARNING_GENE_COORDINATES: Gene 'CHM13_G0027162' (name:'GNA11'), adjusting start coordinate from 3068113 to 3068400
WARNING_GENE_COORDINATES: Gene 'CHM13_G0027187' (name:'GIPC3'), adjusting start coordinate from 3563634 to 3563754
WARNING_GENE_COORDINATES: Gene 'CHM13_G0027213' (name:'MAP2K2'), adjusting start coordinate from 4073479 to 4073482
WARNING_GENE_COORDINATES: Too many 'WARNING_GENE_COORDINATES' warnings, no further warnings will be shown.
.........00:01:48 Adjusting chromosomes lengths: 
00:01:48 Ranking exons: 
....................................................................................................
        10000   ....................................................................................................
        20000   ....................................................................................................
        30000   ....................................................................................................
        40000   ....................................................................................................
        50000   ....................................................................................................
        60000   ....................................................................................................
        70000   ....................................................................................................
        80000   ....................................................................................................
        90000   ....................................................................................................
        100000  ....................................................................................................
        110000  ....................................................................................................
        120000  ....................................................................................................
        130000  ....................................................................................................
        140000  ....................................................................................................
        150000  ....................................................................................................
        160000  ....................................................................................................
        170000  ....................................................................................................
        180000  ....................................................................................................
        190000  ....................................................................................................
        200000  ....................................................................................................
        210000  ....................................................................................................
        220000  ....................................................................................................
        230000  .................................................00:01:48 Create UTRs from CDS (if needed): 
....................................................................................................
        10000   ....................................................................................................
        20000   ....................................................................................................
        30000   ....................................................................................................
        40000   ....................................................................................................
        50000   ....................................................................................................
        60000   ....................................................................................................
        70000   ....................................................................................................
        80000   ....................................................................................................
        90000   ...............................................................00:01:49 Correcting exons based on frame information.

........................................................................WARNING_CDS_TOO_SHORT: CDS too short, cannot correct frame: frame size 1, frame correction 1, CDS: 14   97756354-97756354 CDS 'STOP_CODON_stop_codon:CHM13_T0066787', frame: 0
WARNING_CDS_TOO_SHORT: CDS too short, cannot correct frame: frame size 1, frame correction 1, CDS: 14   97756354-97756354 CDS 'STOP_CODON_stop_codon:CHM13_T0066787', frame: 0
............................
100 ................................................WARNING_CDS_TOO_SHORT: CDS too short, cannot correct frame: frame size 1, frame correction 1, CDS: 4    122603880-122603880 CDS 'STOP_CODON_stop_codon:CHM13_T0169377', frame: 0
WARNING_CDS_TOO_SHORT: CDS too short, cannot correct frame: frame size 1, frame correction 1, CDS: 4    122603880-122603880 CDS 'STOP_CODON_stop_codon:CHM13_T0169377', frame: 0
.WARNING_CDS_TOO_SHORT: CDS too short, cannot correct frame: frame size 1, frame correction 1, CDS: 4   122603880-122603880 CDS 'STOP_CODON_stop_codon:CHM13_T0169376', frame: 0
WARNING_CDS_TOO_SHORT: CDS too short, cannot correct frame: frame size 1, frame correction 1, CDS: 4    122603880-122603880 CDS 'STOP_CODON_stop_codon:CHM13_T0169376', frame: 0
...................................................
200 .........................................................................................WARNING_CDS_TOO_SHORT: CDS too short, cannot correct frame: frame size 1, frame correction 1, CDS: 19  6465126-6465126 CDS 'STOP_CODON_stop_codon:CHM13_T0106768', frame: 0
WARNING_CDS_TOO_SHORT: CDS too short, cannot correct frame: frame size 1, frame correction 1, CDS: 19   6465126-6465126 CDS 'STOP_CODON_stop_codon:CHM13_T0106768', frame: 0
...........
300 ........................................................WARNING_CDS_TOO_SHORT: CDS too short, cannot correct frame: frame size 1, frame correction 1, CDS: 1    155150345-155150345 CDS 'STOP_CODON_stop_codon:CHM13_T0013272', frame: 0
WARNING_CDS_TOO_SHORT: CDS too short, cannot correct frame: frame size 1, frame correction 1, CDS: 1    155150345-155150345 CDS 'STOP_CODON_stop_codon:CHM13_T0013272', frame: 0
............................................
400 ....................................................................................................
500 ....................................................................................................
600 ......................................................................................WARNING_CDS_TOO_SHORT: CDS too short, cannot correct frame: frame size 1, frame correction 1, CDS: 1  175556615-175556615 CDS 'STOP_CODON_stop_codon:CHM13_T0015350', frame: 0
WARNING_CDS_TOO_SHORT: CDS too short, cannot correct frame: frame size 1, frame correction 1, CDS: 1    175556615-175556615 CDS 'STOP_CODON_stop_codon:CHM13_T0015350', frame: 0
..............
700 ........................................................................................WARNING_CDS_TOO_SHORT: CDS too short, cannot correct frame: frame size 1, frame correction 1, CDS: 12   109256780-109256780 CDS 'STOP_CODON_stop_codon:CHM13_T0051884', frame: 0
WARNING_CDS_TOO_SHORT: CDS too short, cannot correct frame: frame size 1, frame correction 1, CDS: 12   109256780-109256780 CDS 'STOP_CODON_stop_codon:CHM13_T0051884', frame: 0
............
800 ................WARNING_CDS_TOO_SHORT: CDS too short, cannot correct frame: frame size 1, frame correction 1, CDS: 22   42159340-42159340 CDS 'STOP_CODON_stop_codon:CHM13_T0147724', frame: 0
WARNING_CDS_TOO_SHORT: CDS too short, cannot correct frame: frame size 1, frame correction 1, CDS: 22   42159340-42159340 CDS 'STOP_CODON_stop_codon:CHM13_T0147724', frame: 0
..................................................WARNING_CDS_TOO_SHORT: CDS too short, cannot correct frame: frame size 1, frame correction 1, CDS: 22 44733504-44733504 CDS 'STOP_CODON_stop_codon:CHM13_T0148050', frame: 0
WARNING_CDS_TOO_SHORT: CDS too short, cannot correct frame: frame size 1, frame correction 1, CDS: 22   44733504-44733504 CDS 'STOP_CODON_stop_codon:CHM13_T0148050', frame: 0
..................................
900 .................................................WARNING_CDS_TOO_SHORT: CDS too short, cannot correct frame: frame size 1, frame correction 1, CDS: 12  121421898-121421898 CDS 'STOP_CODON_stop_codon:CHM13_T0053267', frame: 0
WARNING_CDS_TOO_SHORT: CDS too short, cannot correct frame: frame size 1, frame correction 1, CDS: 12   121421898-121421898 CDS 'STOP_CODON_stop_codon:CHM13_T0053267', frame: 0
...................................................
1000    ....................................................................................................
1100    ....................................................................................................
1200    ...................................................WARNING_CDS_TOO_SHORT: CDS too short, cannot correct frame: frame size 1, frame correction 1, CDS: 5 176554824-176554824 CDS 'STOP_CODON_stop_codon:CHM13_T0182528', frame: 0
WARNING_CDS_TOO_SHORT: CDS too short, cannot correct frame: frame size 1, frame correction 1, CDS: 5    176554824-176554824 CDS 'STOP_CODON_stop_codon:CHM13_T0182528', frame: 0
...............WARNING_CDS_TOO_SHORT: CDS too short, cannot correct frame: frame size 1, frame correction 1, CDS: 5 178292174-178292174 CDS 'STOP_CODON_stop_codon:CHM13_T0182946', frame: 0
WARNING_CDS_TOO_SHORT: CDS too short, cannot correct frame: frame size 1, frame correction 1, CDS: 5    178292174-178292174 CDS 'STOP_CODON_stop_codon:CHM13_T0182946', frame: 0
.............WARNING_CDS_TOO_SHORT: CDS too short, cannot correct frame: frame size 1, frame correction 1, CDS: 5   179174431-179174431 CDS 'STOP_CODON_stop_codon:CHM13_T0183092', frame: 0
WARNING_CDS_TOO_SHORT: CDS too short, cannot correct frame: frame size 1, frame correction 1, CDS: 5    179174431-179174431 CDS 'STOP_CODON_stop_codon:CHM13_T0183092', frame: 0
WARNING_CDS_TOO_SHORT: Too many 'WARNING_CDS_TOO_SHORT' warnings, no further warnings will be shown.
.....................
1300    ....................................................................................................
1400    ....................................................................................................
1500    ....................................................................................................
1600    ....................................................................................................
1700    ....................................................................................................
1800    ....................................................................................................
1900    ....................................................................................................
2000    ....................................................................................................
2100    ....................................................................................................
2200    ....................................................................................................
2300    ....................................................................................................
2400    ....................................................................................................
2500    ....................................................................................................
2600    ....................................................................................................
2700    ....................................................................................................
2800    ....................................................................................................
2900    ....................................................................................................
3000    ....................................................................................................
3100    ....................................................................................................
3200    ....................................................................................................
3300    ....................................................................................................
3400    ....................................................................................................
3500    ....................................................................................................
3600    ....................................................................................................
3700    ....................................................................................................
3800    ....................................................................................................
3900    ....................................................................................................
4000    ....................................................................................................
4100    ....................................................................................................
4200    ....................................................................................................
4300    ....................................................................................................
4400    ....................................................................................................
4500    ....................................................................................................
4600    ....................................................................................................
4700    ....................................................................................................
4800    ....................................................................................................
4900    ....................................................................................................
5000    ....................................................................................................
5100    ....................................................................................................
5200    ....................................................................................................
5300    ....................................................................................................
5400    ....................................................................................................
5500    ....................................................................................................
5600    ....................................................................................................
5700    ....................................................................................................
5800    ....................................................................................................
5900    ....................................................................................................
6000    ....................................................................................................
6100    ....................................................................................................
6200    ....................................................................................................
6300    ....................................................................................................
6400    ....................................................................................................
6500    ....................................................................................................
6600    ....................................................................................................
6700    ....................................................................................................
6800    ....................................................................................................
6900    ....................................................................................................
7000    ....................................................................................................
7100    ....................................................................................................
7200    ....................................................................................................
7300    ....................................................................................................
7400    ....................................................................................................
7500    ....................................................................................................
7600    ....................................................................................................
7700    ....................................................................................................
7800    ....................................................................................................
7900    ......................................WARNING_EXON_NOT_FOUND: WARNING: Cannot find first exonic position after 146569221 for transcript 'LOFF_T0000224'
WARNING_EXON_NOT_FOUND: WARNING: Cannot find first exonic position after 146569221 for transcript 'LOFF_T0000225'
WARNING_EXON_NOT_FOUND: WARNING: Cannot find first exonic position after 146569221 for transcript 'LOFF_T0000223'
..............................................................
8000    ....................................................................................................
8100    ....................................................................................................
8200    ....................................................................................................
8300    .................................................................................................00:01:52 
00:01:52 Remove empty chromosomes: 
00:01:52 Marking as 'coding' from CDS information: 
00:01:52 Done: 20 transcripts marked
00:01:52 
00:01:58 #-----------------------------------------------
# Genome name                : 'Human'
# Genome version             : 'chm13v2'
# Genome ID                  : 'chm13v2[0]'
# Has protein coding info    : true
# Has Tr. Support Level info : true
# Genes                      : 69002
# Protein coding genes       : 22909
#-----------------------------------------------
# Transcripts                : 234903
# Avg. transcripts per gene  : 3.40
# TSL transcripts            : 167490
#-----------------------------------------------
# Checked transcripts        : 
#               AA sequences :      0 ( 0.00% )
#              DNA sequences :      0 ( 0.00% )
#-----------------------------------------------
# Protein coding transcripts : 87017
#              Length errors :  15035 ( 17.28% )
#  STOP codons in CDS errors :   2732 ( 3.14% )
#         START codon errors :  10725 ( 12.33% )
#        STOP codon warnings :   7934 ( 9.12% )
#              UTR sequences :  81679 ( 34.77% )
#               Total Errors :  22599 ( 25.97% )
#-----------------------------------------------
# Cds                        : 772902
# Exons                      : 1444304
# Exons with sequence        : 1444304
# Exons without sequence     : 0
# Avg. exons per transcript  : 6.15
# WARNING!                   : Mitochondrion chromosome 'M' does not have a mitochondrion codon table (codon table = 'Standard'). You should update the config file.
#-----------------------------------------------
# Number of chromosomes      : 25
# Chromosomes                : Format 'chromo_name size codon_table'
#       '1' 248387328   Standard
#       '2' 242696752   Standard
#       '3' 201105948   Standard
#       '4' 193574945   Standard
#       '5' 182045439   Standard
#       '6' 172126628   Standard
#       '7' 160567428   Standard
#       'X' 154259566   Standard
#       '9' 150617247   Standard
#       '8' 146259331   Standard
#       '11'    135127769   Standard
#       '10'    134758134   Standard
#       '12'    133324548   Standard
#       '13'    113566686   Standard
#       '14'    101161492   Standard
#       '15'    99753195    Standard
#       '16'    96330374    Standard
#       '17'    84276897    Standard
#       '18'    80542538    Standard
#       '20'    66210255    Standard
#       'Y' 62460029    Standard
#       '19'    61707364    Standard
#       '22'    51324926    Standard
#       '21'    45090682    Standard
#       'M' 16569   Standard
#-----------------------------------------------

00:01:58 Caracterizing exons by splicing (stage 1) : 
    ....................................................................................................
    100000  ....................................................................................................
    200000  ....................................................................................................
    300000  ....................................................................................................
    400000  ....................................................................................................
    500000  ....................................................................................................
    600000  ....................................................................................................
    700000  ....................................................................................................
    800000  ....................................................................................................
    900000  ....................................................................................................
    1000000 ....................................................................................................
    1100000 ....................................................................................................
    1200000 ....................................................................................................
    1300000 ....................................................................................................
    1400000 ............................................
00:02:07 Caracterizing exons by splicing (stage 2) : 
    ....................................................................................................
    100000  ....................................................................................................
    200000  ....................................................................................................
    300000  ....................................................................................................
    400000  ....................................................................................................
    500000  ....................................................................................................
    600000  ....................................................................................................
    700000  ....................................................................................................
    800000  ....................................................................................................
    900000  ....................................................................................................
    1000000 ....................................................................................................
    1100000 ....................................................................................................
    1200000 ....................................................................................................
    1300000 ....................................................................................................
    1400000 ............................................00:03:17 done.
00:03:17 [Optional] Rare amino acid annotations
WARNING_FILE_NOT_FOUND: Rare Amino Acid analysis: Cannot read protein sequence file '/ceph/project/Wellcome_Discovery/jdalglei/reference/snpEff/./data/chm13v2/protein.fa', nothing done.
ERROR: CDS check file '/ceph/project/Wellcome_Discovery/jdalglei/reference/snpEff/./data/chm13v2/cds.fa' not found.
ERROR: Protein check file '/ceph/project/Wellcome_Discovery/jdalglei/reference/snpEff/./data/chm13v2/protein.fa' not found.
ERROR: Database check failed.
00:03:17 Logging
00:03:18 Checking for updates...
00:03:19 Done.

Then when I actually try to run it, I get the following:

        module load java/17.0.1; mkdir -p /ceph/project/Wellcome_Discovery/jdalglei/results/sm_pacbio/m64176e_230421_144242.hifi_reads/snpeff_snp_dv/; cd /ceph/project/Wellcome_Discovery/jdalglei/results/sm_pacbio/m64176e_230421_144242.hifi_reads/snpeff_snp_dv/;
        export SNPEFF_JAR=/ceph/project/Wellcome_Discovery/jdalglei/reference/snpEff/snpEff.jar;
        export SNPEFF_HOME=/ceph/project/Wellcome_Discovery/jdalglei/reference/snpEff;
        java -Djava.io.tmpdir=$TMPDIR -Xmx32g -jar $SNPEFF_JAR -v -lof -motif -hgvs -nextProt chm13v2 /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230421_144242.hifi_reads/deepvariant/m64176e_230421_144242.hifi_reads_deepvariant_dbsnp_anno.vcf > /ceph/project/Wellcome_Discovery/jdalglei/results/sm_pacbio/m64176e_230421_144242.hifi_reads/snpeff_snp_dv/m64176e_230421_144242.hifi_reads_dv_dbsnp_anno_snpeff.vcf.gz;
        java -Djava.io.tmpdir=$TMPDIR -Xmx32g -jar $SNPEFF_JAR -v -lof -motif -hgvs -nextProt chm13v2 /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230421_144242.hifi_reads/deepvariant/m64176e_230421_144242.hifi_reads_deepvariant_dbsnp_anno.vcf > /ceph/project/Wellcome_Discovery/jdalglei/results/sm_pacbio/m64176e_230421_144242.hifi_reads/snpeff_snp_dv/m64176e_230421_144242.hifi_reads_dv_dbsnp_anno_snpeff.vcf.gz;
        cp snpEff_genes.txt m64176e_230421_144242.hifi_reads_snpEff_genes.txt;

00:00:00 SnpEff version SnpEff 5.1d (build 2022-04-19 15:49), by Pablo Cingolani
00:00:00 Command: 'ann'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'chm13v2'
00:00:00 Reading config file: /ceph/project/Wellcome_Discovery/jdalglei/results/sm_pacbio/m64176e_230421_144242.hifi_reads/snpeff_snp_dv/snpEff.config
00:00:00 Reading config file: /ceph/project/Wellcome_Discovery/jdalglei/reference/snpEff/snpEff.config
00:00:01 done
00:00:01 Reading database for genome version 'chm13v2' from file '/ceph/project/Wellcome_Discovery/jdalglei/reference/snpEff/./data/chm13v2/snpEffectPredictor.bin' (this might take a while)
00:00:01 Database not installed
    Attempting to download and install database 'chm13v2'
00:00:01 Reading configuration file 'snpEff.config'. Genome: 'chm13v2'
00:00:01 Reading config file: /ceph/project/Wellcome_Discovery/jdalglei/results/sm_pacbio/m64176e_230421_144242.hifi_reads/snpeff_snp_dv/snpEff.config
00:00:01 Reading config file: /ceph/project/Wellcome_Discovery/jdalglei/reference/snpEff/snpEff.config
00:00:01 done
00:00:01 Downloading database for 'chm13v2'
00:00:01 Downloading from 'https://snpeff.blob.core.windows.net/databases/v5_1/snpEff_v5_1_chm13v2.zip' to local file '/var/scratch/jdalglei/16954/snpEff_v5_1_chm13v2.zip'
00:00:02 Connecting to https://snpeff.blob.core.windows.net/databases/v5_1/snpEff_v5_1_chm13v2.zip
00:00:02 Connecting to https://snpeff.blob.core.windows.net/databases/v5_1/snpEff_v5_1_chm13v2.zip, using proxy: false
00:00:02 ERROR while connecting to https://snpeff.blob.core.windows.net/databases/v5_1/snpEff_v5_1_chm13v2.zip
00:00:02 Downloading from 'https://snpeff.blob.core.windows.net/databases/v5_0/snpEff_v5_0_chm13v2.zip' to local file '/var/scratch/jdalglei/16954/snpEff_v5_0_chm13v2.zip'
00:00:02 Connecting to https://snpeff.blob.core.windows.net/databases/v5_0/snpEff_v5_0_chm13v2.zip
00:00:02 Connecting to https://snpeff.blob.core.windows.net/databases/v5_0/snpEff_v5_0_chm13v2.zip, using proxy: false
00:00:03 ERROR while connecting to https://snpeff.blob.core.windows.net/databases/v5_0/snpEff_v5_0_chm13v2.zip
FATAL ERROR: Failed to download database from [https://snpeff.blob.core.windows.net/databases/v5_1/snpEff_v5_1_chm13v2.zip, https://snpeff.blob.core.windows.net/databases/v5_0/snpEff_v5_0_chm13v2.zip]
[Tue Jul  4 13:09:56 2023]
Error in rule snpeff_snp_dv:
    jobid: 21
    input: /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230421_144242.hifi_reads/deepvariant/m64176e_230421_144242.hifi_reads_deepvariant_dbsnp_anno.vcf
    output: /ceph/project/Wellcome_Discovery/jdalglei/results/sm_pacbio/m64176e_230421_144242.hifi_reads/snpeff_snp_dv/m64176e_230421_144242.hifi_reads_dv_dbsnp_anno_snpeff.vcf.gz
    shell:

        module load java/17.0.1; mkdir -p /ceph/project/Wellcome_Discovery/jdalglei/results/sm_pacbio/m64176e_230421_144242.hifi_reads/snpeff_snp_dv/; cd /ceph/project/Wellcome_Discovery/jdalglei/results/sm_pacbio/m64176e_230421_144242.hifi_reads/snpeff_snp_dv/;
        export SNPEFF_JAR=/ceph/project/Wellcome_Discovery/jdalglei/reference/snpEff/snpEff.jar;
        export SNPEFF_HOME=/ceph/project/Wellcome_Discovery/jdalglei/reference/snpEff;
        java -Djava.io.tmpdir=$TMPDIR -Xmx32g -jar $SNPEFF_JAR -v -lof -motif -hgvs -nextProt chm13v2 /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230421_144242.hifi_reads/deepvariant/m64176e_230421_144242.hifi_reads_deepvariant_dbsnp_anno.vcf > /ceph/project/Wellcome_Discovery/jdalglei/results/sm_pacbio/m64176e_230421_144242.hifi_reads/snpeff_snp_dv/m64176e_230421_144242.hifi_reads_dv_dbsnp_anno_snpeff.vcf.gz;
        java -Djava.io.tmpdir=$TMPDIR -Xmx32g -jar $SNPEFF_JAR -v -lof -motif -hgvs -nextProt chm13v2 /ceph/project/davieslab/jdalglei/results/sm_pacbio/m64176e_230421_144242.hifi_reads/deepvariant/m64176e_230421_144242.hifi_reads_deepvariant_dbsnp_anno.vcf > /ceph/project/Wellcome_Discovery/jdalglei/results/sm_pacbio/m64176e_230421_144242.hifi_reads/snpeff_snp_dv/m64176e_230421_144242.hifi_reads_dv_dbsnp_anno_snpeff.vcf.gz;
        cp snpEff_genes.txt m64176e_230421_144242.hifi_reads_snpEff_genes.txt;

My config file looks like this:

# Human genome, version chm13v2
chm13v2.genome : Human

I'm not sure why it tries to download it.

I used the chm13v2 from https://github.com/marbl/CHM13 and this gff3 from the same page: https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/CHM13/assemblies/annotation/chm13.draft_v2.0.gene_annotation.gff3

ymcki commented 1 year ago

I find that you need to change protein id for protein.fa and cds.fa to transcript id (ie NM, XM, etc).

However, even after I did that, I still get 1175 not found and 13883 errors.

tomgutman commented 3 months ago

Hello

I tried to create the chm13v2 DB but still came to the same issue as @21tesla and @ymcki I'm sorry I didn't understand your last answer.

Is there any update on this or is there an already built DB somewhere ? I couldn't find one using the command snpeff databases