Comments (5)
zhpn1024
commented on July 19, 2024
It seems to be caused by transcript annotation. We can check which transcript is causing the error. Just re-run ribotish predict adding option -v -v (verbose twice).
from ribotish.
ErinDuffyLacy
commented on July 19, 2024
I have attached the last few lines of the verbose output:
lnckb.274 lnckb.274.23 0 0
lnckb.274 lnckb.274.24 0 0
lnckb.274 lnckb.274.27 0 0
Traceback (most recent call last):
File "/home/eed13/env/lib/python2.7/site-packages/ribotish/run/predict.py", line 564, in <module>
run(p.parse_args())
File "/home/eed13/env/lib/python2.7/site-packages/ribotish/run/predict.py", line 236, in run
for result in pred_iter:
File "/home/eed13/env/lib/python2.7/site-packages/ribotish/run/predict.py", line 394, in _pred_gene
ttis = ribo.Ribo(t, bamload = tismbl, compatible = compatible, mis = compatiblemis)
File "/home/eed13/env/lib/python2.7/site-packages/ribotish/zbio/ribo.py", line 62, in __init__
self.cnts = bamload.transCounts(trans, compatible = compatible, mis = mis)
File "/home/eed13/env/lib/python2.7/site-packages/ribotish/zbio/bam.py", line 629, in transCounts
i += 1
TypeError: unsupported operand type(s) for +=: 'NoneType' and 'int'
And here are the lines in the gtf file that correspond to lnckb.274:
chr1 RefSeq gene 7693169 7704551 . - . gene_id "lnckb.274"; GENE_TYPE "lncRNA"; STATUS "known_refseq"; gene_name "LOC105376689";
chr1 Gnomon transcript 7693169 7703614 . - . transcript_id "lnckb.274.1"; gene_id "lnckb.274"; gene_name "LOC105376689"; Dbxref "GeneID:105376689,Genbank:XR_001737883.1"; Name "XR_001737883.1"; gbkey "ncRNA"; model_evidence "Supporting evidence includes similarity to: 2 ESTs, 2 long SRA reads, and 99pct coverage of the annotated genomic feature by RNAseq alignments, including 5 samples with support for all annotated introns"; ncrna_class "lncRNA"; product "uncharacterized LOC105376689, transcript variant X3"; transcript_id_alias "XR_001737883.1"; gene_biotype "lncRNA"; STATUS "known_refseq"; TYPE "non_coding"; ASSEMBLED "yes";
chr1 Gnomon exon 7693169 7694642 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.1";
chr1 Gnomon exon 7701619 7701724 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.1";
chr1 Gnomon exon 7702382 7703614 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.1";
chr1 StringTie transcript 7693170 7704018 . - . transcript_id "lnckb.274.2"; gene_id "lnckb.274"; STATUS "novel"; ASSEMBLED "yes";
chr1 StringTie exon 7693170 7701023 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.2";
chr1 StringTie exon 7701619 7701727 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.2";
chr1 StringTie exon 7702382 7702653 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.2";
chr1 StringTie exon 7703107 7703230 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.2";
chr1 StringTie exon 7703348 7704018 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.2";
chr1 StringTie transcript 7693170 7704029 . - . transcript_id "lnckb.274.3"; gene_id "lnckb.274"; STATUS "novel"; ASSEMBLED "yes";
chr1 StringTie exon 7693170 7701023 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.3";
chr1 StringTie exon 7701619 7701724 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.3";
chr1 StringTie exon 7702382 7702653 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.3";
chr1 StringTie exon 7703107 7703230 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.3";
chr1 StringTie exon 7703348 7704029 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.3";
chr1 StringTie transcript 7693170 7704031 . - . transcript_id "lnckb.274.4"; gene_id "lnckb.274"; STATUS "novel"; ASSEMBLED "yes";
chr1 StringTie exon 7693170 7701023 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.4";
chr1 StringTie exon 7701619 7701727 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.4";
chr1 StringTie exon 7702382 7702653 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.4";
chr1 StringTie exon 7703111 7703230 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.4";
chr1 StringTie exon 7703348 7704031 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.4";
chr1 StringTie transcript 7693170 7704031 . - . transcript_id "lnckb.274.5"; gene_id "lnckb.274"; STATUS "novel"; ASSEMBLED "yes";
chr1 StringTie exon 7693170 7701023 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.5";
chr1 StringTie exon 7701619 7701724 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.5";
chr1 StringTie exon 7702382 7702653 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.5";
chr1 StringTie exon 7703111 7703230 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.5";
chr1 StringTie exon 7703348 7704031 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.5";
chr1 StringTie transcript 7693170 7704031 . - . transcript_id "lnckb.274.6"; gene_id "lnckb.274"; STATUS "novel"; ASSEMBLED "yes";
chr1 StringTie exon 7693170 7701023 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.6";
chr1 StringTie exon 7701619 7701727 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.6";
chr1 StringTie exon 7702382 7702658 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.6";
chr1 StringTie exon 7703107 7703230 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.6";
chr1 StringTie exon 7703348 7704031 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.6";
chr1 StringTie transcript 7693170 7704031 . - . transcript_id "lnckb.274.7"; gene_id "lnckb.274"; STATUS "novel"; ASSEMBLED "yes";
chr1 StringTie exon 7693170 7701023 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.7";
chr1 StringTie exon 7701619 7701727 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.7";
chr1 StringTie exon 7702382 7702658 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.7";
chr1 StringTie exon 7703111 7703230 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.7";
chr1 StringTie exon 7703348 7704031 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.7";
chr1 StringTie transcript 7693170 7704031 . - . transcript_id "lnckb.274.8"; gene_id "lnckb.274"; STATUS "novel"; ASSEMBLED "yes";
chr1 StringTie exon 7693170 7701023 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.8";
chr1 StringTie exon 7701619 7701724 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.8";
chr1 StringTie exon 7702382 7702658 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.8";
chr1 StringTie exon 7703111 7703230 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.8";
chr1 StringTie exon 7703348 7704031 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.8";
chr1 lncipedia.org transcript 7693182 7694730 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.16"; gene_id_alias "lnc-UTS2-8:2"; gene_id_alias "lnc-UTS2-8"; transcript_id_alias "lnc-UTS2-8:2"; transcript_alias_1 "NONHSAT000711";
chr1 lncipedia.org exon 7693182 7693438 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.16"; transcript_id_alias "lnc-UTS2-8:2"; gene_id_alias "lnc-UTS2-8"; transcript_id_alias "lnc-UTS2-8:2"; transcript_alias_1 "NONHSAT000711";
chr1 lncipedia.org exon 7694521 7694730 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.16"; transcript_id_alias "lnc-UTS2-8:2"; gene_id_alias "lnc-UTS2-8"; transcript_id_alias "lnc-UTS2-8:2"; transcript_alias_1 "NONHSAT000711";
chr1 Cufflinks transcript 7698299 7699274 0 - . gene_id "lnckb.274"; transcript_id "lnckb.274.26"; gene_id_alias "NONHSAG000270.3"; transcript_id_alias "NONHSAT226326.1"; FPKM "0"; exon_number "1";
chr1 Cufflinks exon 7698299 7699274 0 - . gene_id "lnckb.274"; transcript_id "lnckb.274.26"; gene_id_alias "NONHSAG000270.3"; transcript_id_alias "NONHSAT226326.1"; FPKM "0"; exon_number "1";
chr1 lncipedia.org transcript 7698303 7698872 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.17"; gene_id_alias "lnc-UTS2-7:1"; gene_id_alias "lnc-UTS2-7"; transcript_id_alias "lnc-UTS2-7:1"; gene_alias_1 "ENSG00000270035.1"; gene_alias_2 "RP11-338N10.2"; gene_alias_3 "AL359881.2"; transcript_alias_1 "NONHSAT000712"; transcript_alias_2 "ENST00000602973.1";
chr1 lncipedia.org exon 7698303 7698872 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.17"; transcript_id_alias "lnc-UTS2-7:1"; gene_id_alias "lnc-UTS2-7"; transcript_id_alias "lnc-UTS2-7:1"; gene_alias_1 "ENSG00000270035.1"; gene_alias_2 "RP11-338N10.2"; gene_alias_3 "AL359881.2"; transcript_alias_1 "NONHSAT000712"; transcript_alias_2 "ENST00000602973.1";
chr1 lncipedia.org transcript 7700704 7700970 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.18"; gene_id_alias "lnc-UTS2-6:1"; gene_id_alias "lnc-UTS2-6"; transcript_id_alias "lnc-UTS2-6:1"; gene_alias_1 "ENSG00000269978.1"; gene_alias_2 "RP11-338N10.3"; gene_alias_3 "AL359881.1"; transcript_alias_1 "NONHSAT000713"; transcript_alias_2 "ENST00000602916.1";
chr1 lncipedia.org exon 7700704 7700970 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.18"; transcript_id_alias "lnc-UTS2-6:1"; gene_id_alias "lnc-UTS2-6"; transcript_id_alias "lnc-UTS2-6:1"; gene_alias_1 "ENSG00000269978.1"; gene_alias_2 "RP11-338N10.3"; gene_alias_3 "AL359881.1"; transcript_alias_1 "NONHSAT000713"; transcript_alias_2 "ENST00000602916.1";
chr1 lncipedia.org transcript 7701645 7703991 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.19"; gene_id_alias "lnc-UTS2-5:7"; gene_id_alias "lnc-UTS2-5"; transcript_id_alias "lnc-UTS2-5:7"; transcript_alias_1 "LncRNA1500:1";
chr1 lncipedia.org exon 7701645 7701724 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.19"; transcript_id_alias "lnc-UTS2-5:7"; gene_id_alias "lnc-UTS2-5"; transcript_id_alias "lnc-UTS2-5:7"; transcript_alias_1 "LncRNA1500:1";
chr1 lncipedia.org exon 7702382 7703230 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.19"; transcript_id_alias "lnc-UTS2-5:7"; gene_id_alias "lnc-UTS2-5"; transcript_id_alias "lnc-UTS2-5:7"; transcript_alias_1 "LncRNA1500:1";
chr1 lncipedia.org exon 7703348 7703991 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.19"; transcript_id_alias "lnc-UTS2-5:7"; gene_id_alias "lnc-UTS2-5"; transcript_id_alias "lnc-UTS2-5:7"; transcript_alias_1 "LncRNA1500:1";
chr1 lncipedia.org transcript 7701645 7703991 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.20"; gene_id_alias "lnc-UTS2-5:8"; gene_id_alias "lnc-UTS2-5"; transcript_id_alias "lnc-UTS2-5:8"; transcript_alias_1 "LncRNA1500:2";
chr1 lncipedia.org exon 7701645 7701727 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.20"; transcript_id_alias "lnc-UTS2-5:8"; gene_id_alias "lnc-UTS2-5"; transcript_id_alias "lnc-UTS2-5:8"; transcript_alias_1 "LncRNA1500:2";
chr1 lncipedia.org exon 7702382 7703991 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.20"; transcript_id_alias "lnc-UTS2-5:8"; gene_id_alias "lnc-UTS2-5"; transcript_id_alias "lnc-UTS2-5:8"; transcript_alias_1 "LncRNA1500:2";
chr1 lncipedia.org transcript 7701645 7704020 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.21"; gene_id_alias "lnc-UTS2-5:6"; gene_id_alias "lnc-UTS2-5"; transcript_id_alias "lnc-UTS2-5:6"; transcript_alias_1 "LncRNA1500:3";
chr1 lncipedia.org exon 7701645 7701727 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.21"; transcript_id_alias "lnc-UTS2-5:6"; gene_id_alias "lnc-UTS2-5"; transcript_id_alias "lnc-UTS2-5:6"; transcript_alias_1 "LncRNA1500:3";
chr1 lncipedia.org exon 7702382 7702468 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.21"; transcript_id_alias "lnc-UTS2-5:6"; gene_id_alias "lnc-UTS2-5"; transcript_id_alias "lnc-UTS2-5:6"; transcript_alias_1 "LncRNA1500:3";
chr1 lncipedia.org exon 7703111 7703230 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.21"; transcript_id_alias "lnc-UTS2-5:6"; gene_id_alias "lnc-UTS2-5"; transcript_id_alias "lnc-UTS2-5:6"; transcript_alias_1 "LncRNA1500:3";
chr1 lncipedia.org exon 7703348 7704020 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.21"; transcript_id_alias "lnc-UTS2-5:6"; gene_id_alias "lnc-UTS2-5"; transcript_id_alias "lnc-UTS2-5:6"; transcript_alias_1 "LncRNA1500:3";
chr1 Gnomon transcript 7701685 7704032 . - . transcript_id "lnckb.274.11"; gene_id "lnckb.274"; gene_name "LOC105376689"; Dbxref "GeneID:105376689,Genbank:XR_946915.2"; Name "XR_946915.2"; gbkey "ncRNA"; model_evidence "Supporting evidence includes similarity to: 1 EST, and 100pct coverage of the annotated genomic feature by RNAseq alignments, including 37 samples with support for all annotated introns"; ncrna_class "lncRNA"; product "uncharacterized LOC105376689, transcript variant X2"; transcript_id_alias "XR_946915.2"; gene_biotype "lncRNA"; STATUS "known_refseq"; TYPE "non_coding"; ASSEMBLED "yes";
chr1 Gnomon exon 7701685 7701724 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.11";
chr1 Gnomon exon 7702382 7703230 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.11";
chr1 Gnomon exon 7703348 7704032 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.11";
chr1 Gnomon transcript 7701688 7704032 . - . transcript_id "lnckb.274.12"; gene_id "lnckb.274"; gene_name "LOC105376689"; Dbxref "GeneID:105376689,Genbank:XR_946914.2"; Name "XR_946914.2"; gbkey "ncRNA"; model_evidence "Supporting evidence includes similarity to: 1 EST, and 100pct coverage of the annotated genomic feature by RNAseq alignments, including 54 samples with support for all annotated introns"; ncrna_class "lncRNA"; product "uncharacterized LOC105376689, transcript variant X1"; transcript_id_alias "XR_946914.2"; gene_biotype "lncRNA"; STATUS "known_refseq"; TYPE "non_coding"; ASSEMBLED "yes";
chr1 Gnomon exon 7701688 7701727 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.12";
chr1 Gnomon exon 7702382 7703230 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.12";
chr1 Gnomon exon 7703348 7704032 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.12";
chr1 Gnomon transcript 7701688 7704032 . - . transcript_id "lnckb.274.13"; gene_id "lnckb.274"; gene_name "LOC105376689"; Dbxref "GeneID:105376689,Genbank:XR_946916.2"; Name "XR_946916.2"; gbkey "ncRNA"; model_evidence "Supporting evidence includes similarity to: 100pct coverage of the annotated genomic feature by RNAseq alignments, including 27 samples with support for all annotated introns"; ncrna_class "lncRNA"; product "uncharacterized LOC105376689, transcript variant X4"; transcript_id_alias "XR_946916.2"; gene_biotype "lncRNA"; STATUS "known_refseq"; TYPE "non_coding"; ASSEMBLED "yes";
chr1 Gnomon exon 7701688 7701727 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.13";
chr1 Gnomon exon 7702382 7702653 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.13";
chr1 Gnomon exon 7703111 7703230 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.13";
chr1 Gnomon exon 7703348 7704032 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.13";
chr1 Gnomon transcript 7701688 7704032 . - . transcript_id "lnckb.274.14"; gene_id "lnckb.274"; gene_name "LOC105376689"; Dbxref "GeneID:105376689,Genbank:XR_946917.2"; Name "XR_946917.2"; gbkey "ncRNA"; model_evidence "Supporting evidence includes similarity to: 100pct coverage of the annotated genomic feature by RNAseq alignments, including 27 samples with support for all annotated introns"; ncrna_class "lncRNA"; product "uncharacterized LOC105376689, transcript variant X5"; transcript_id_alias "XR_946917.2"; gene_biotype "lncRNA"; STATUS "known_refseq"; TYPE "non_coding"; ASSEMBLED "yes";
chr1 Gnomon exon 7701688 7701727 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.14";
chr1 Gnomon exon 7702382 7702658 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.14";
chr1 Gnomon exon 7703111 7703230 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.14";
chr1 Gnomon exon 7703348 7704032 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.14";
chr1 Gnomon transcript 7701688 7704032 . - . transcript_id "lnckb.274.15"; gene_id "lnckb.274"; gene_name "LOC105376689"; Dbxref "GeneID:105376689,Genbank:XR_946918.2"; Name "XR_946918.2"; gbkey "ncRNA"; model_evidence "Supporting evidence includes similarity to: 100pct coverage of the annotated genomic feature by RNAseq alignments, including 11 samples with support for all annotated introns"; ncrna_class "lncRNA"; product "uncharacterized LOC105376689, transcript variant X6"; transcript_id_alias "XR_946918.2"; gene_biotype "lncRNA"; STATUS "known_refseq"; TYPE "non_coding"; ASSEMBLED "yes";
chr1 Gnomon exon 7701688 7701727 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.15";
chr1 Gnomon exon 7702382 7702653 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.15";
chr1 Gnomon exon 7703107 7703230 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.15";
chr1 Gnomon exon 7703348 7704032 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.15";
chr1 lncipedia.org transcript 7701705 7703990 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.22"; gene_id_alias "lnc-UTS2-5:2"; gene_id_alias "lnc-UTS2-5"; transcript_id_alias "lnc-UTS2-5:2"; transcript_alias_1 "NONHSAT000716";
chr1 lncipedia.org exon 7701705 7701724 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.22"; transcript_id_alias "lnc-UTS2-5:2"; gene_id_alias "lnc-UTS2-5"; transcript_id_alias "lnc-UTS2-5:2"; transcript_alias_1 "NONHSAT000716";
chr1 lncipedia.org exon 7702382 7702658 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.22"; transcript_id_alias "lnc-UTS2-5:2"; gene_id_alias "lnc-UTS2-5"; transcript_id_alias "lnc-UTS2-5:2"; transcript_alias_1 "NONHSAT000716";
chr1 lncipedia.org exon 7703107 7703990 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.22"; transcript_id_alias "lnc-UTS2-5:2"; gene_id_alias "lnc-UTS2-5"; transcript_id_alias "lnc-UTS2-5:2"; transcript_alias_1 "NONHSAT000716";
chr1 lncipedia.org transcript 7701705 7703990 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.23"; gene_id_alias "lnc-UTS2-5:3"; gene_id_alias "lnc-UTS2-5"; transcript_id_alias "lnc-UTS2-5:3"; transcript_alias_1 "NONHSAT000715";
chr1 lncipedia.org exon 7701705 7701724 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.23"; transcript_id_alias "lnc-UTS2-5:3"; gene_id_alias "lnc-UTS2-5"; transcript_id_alias "lnc-UTS2-5:3"; transcript_alias_1 "NONHSAT000715";
chr1 lncipedia.org exon 7702382 7702653 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.23"; transcript_id_alias "lnc-UTS2-5:3"; gene_id_alias "lnc-UTS2-5"; transcript_id_alias "lnc-UTS2-5:3"; transcript_alias_1 "NONHSAT000715";
chr1 lncipedia.org exon 7703111 7703990 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.23"; transcript_id_alias "lnc-UTS2-5:3"; gene_id_alias "lnc-UTS2-5"; transcript_id_alias "lnc-UTS2-5:3"; transcript_alias_1 "NONHSAT000715";
chr1 lncipedia.org transcript 7701705 7703990 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.24"; gene_id_alias "lnc-UTS2-5:4"; gene_id_alias "lnc-UTS2-5"; transcript_id_alias "lnc-UTS2-5:4"; transcript_alias_1 "NONHSAT000714";
chr1 lncipedia.org exon 7701705 7701724 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.24"; transcript_id_alias "lnc-UTS2-5:4"; gene_id_alias "lnc-UTS2-5"; transcript_id_alias "lnc-UTS2-5:4"; transcript_alias_1 "NONHSAT000714";
chr1 lncipedia.org exon 7702382 7703230 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.24"; transcript_id_alias "lnc-UTS2-5:4"; gene_id_alias "lnc-UTS2-5"; transcript_id_alias "lnc-UTS2-5:4"; transcript_alias_1 "NONHSAT000714";
chr1 lncipedia.org exon 7703348 7703990 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.24"; transcript_id_alias "lnc-UTS2-5:4"; gene_id_alias "lnc-UTS2-5"; transcript_id_alias "lnc-UTS2-5:4"; transcript_alias_1 "NONHSAT000714";
chr1 Cufflinks transcript 7701844 7703145 0 - . gene_id "lnckb.274"; transcript_id "lnckb.274.27"; gene_id_alias "NONHSAG000270.3"; transcript_id_alias "NONHSAT226329.1"; FPKM "0"; exon_number "2";
chr1 Cufflinks exon 7701844 7702653 0 - . gene_id "lnckb.274"; transcript_id "lnckb.274.27"; gene_id_alias "NONHSAG000270.3"; transcript_id_alias "NONHSAT226329.1"; FPKM "0"; exon_number "2";
chr1 Cufflinks exon 7703107 7703145 0 - . gene_id "lnckb.274"; transcript_id "lnckb.274.27"; gene_id_alias "NONHSAG000270.3"; transcript_id_alias "NONHSAT226329.1"; FPKM "0"; exon_number "2";
chr1 mitranscriptome transcript 7702382 7704235 1000.0 - . gene_id "lnckb.274"; transcript_id "lnckb.274.28"; tcat "lncrna"; gene_id_alias "G000374"; tss_id "TSS000853"; uce "FALSE"; transcript_id_alias "T002463"; tstatus "unannotated"; tgenic "intragenic"; func_name_final "NA";
chr1 mitranscriptome exon 7702382 7702468 1000.0 - . gene_id "lnckb.274"; transcript_id "lnckb.274.28"; exon_number "0"; tcat "lncrna"; gene_id_alias "G000374"; tss_id "TSS000853"; uce "FALSE"; transcript_id_alias "T002463"; tstatus "unannotated"; tgenic "intragenic"; func_name_final "NA";
chr1 mitranscriptome exon 7702382 7702653 1000.0 - . gene_id "lnckb.274"; transcript_id "lnckb.274.28"; exon_number "2"; tcat "lncrna"; gene_id_alias "G000374"; tss_id "TSS000854"; uce "FALSE"; transcript_id_alias "T002434"; tstatus "annotated"; tgenic "intergenic"; func_name_final "NA";
chr1 mitranscriptome exon 7702382 7702658 1000.0 - . gene_id "lnckb.274"; transcript_id "lnckb.274.28"; exon_number "1"; tcat "lncrna"; gene_id_alias "G000374"; tss_id "TSS000853"; uce "FALSE"; transcript_id_alias "T002430"; tstatus "annotated"; tgenic "intergenic"; func_name_final "NA";
chr1 mitranscriptome exon 7702382 7702658 1000.0 - . gene_id "lnckb.274"; transcript_id "lnckb.274.28"; exon_number "2"; tcat "lncrna"; gene_id_alias "G000374"; tss_id "TSS000853"; uce "FALSE"; transcript_id_alias "T002432"; tstatus "annotated"; tgenic "intergenic"; func_name_final "NA";
chr1 mitranscriptome exon 7702382 7702658 1000.0 - . gene_id "lnckb.274"; transcript_id "lnckb.274.28"; exon_number "4"; tcat "lncrna"; gene_id_alias "G000374"; tss_id "TSS000853"; uce "FALSE"; transcript_id_alias "T002431"; tstatus "annotated"; tgenic "intergenic"; func_name_final "NA";
chr1 mitranscriptome exon 7702382 7703231 1000.0 - . gene_id "lnckb.274"; transcript_id "lnckb.274.28"; exon_number "2"; tcat "lncrna"; gene_id_alias "G000374"; tss_id "TSS000853"; uce "FALSE"; transcript_id_alias "T002429"; tstatus "annotated"; tgenic "intergenic"; func_name_final "NA";
chr1 mitranscriptome exon 7702382 7703235 1000.0 - . gene_id "lnckb.274"; transcript_id "lnckb.274.28"; exon_number "4"; tcat "lncrna"; gene_id_alias "G000374"; tss_id "TSS000853"; uce "FALSE"; transcript_id_alias "T002428"; tstatus "annotated"; tgenic "intergenic"; func_name_final "NA";
chr1 mitranscriptome exon 7703111 7703230 1000.0 - . gene_id "lnckb.274"; transcript_id "lnckb.274.28"; exon_number "1"; tcat "lncrna"; gene_id_alias "G000374"; tss_id "TSS000853"; uce "FALSE"; transcript_id_alias "T002463"; tstatus "unannotated"; tgenic "intragenic"; func_name_final "NA";
chr1 mitranscriptome exon 7703111 7703230 1000.0 - . gene_id "lnckb.274"; transcript_id "lnckb.274.28"; exon_number "2"; tcat "lncrna"; gene_id_alias "G000374"; tss_id "TSS000853"; uce "FALSE"; transcript_id_alias "T002430"; tstatus "annotated"; tgenic "intergenic"; func_name_final "NA";
chr1 mitranscriptome exon 7703111 7703230 1000.0 - . gene_id "lnckb.274"; transcript_id "lnckb.274.28"; exon_number "2"; tcat "lncrna"; gene_id_alias "G000374"; tss_id "TSS000853"; uce "FALSE"; transcript_id_alias "T002433"; tstatus "annotated"; tgenic "intergenic"; func_name_final "NA";
chr1 mitranscriptome exon 7703111 7703230 1000.0 - . gene_id "lnckb.274"; transcript_id "lnckb.274.28"; exon_number "3"; tcat "lncrna"; gene_id_alias "G000374"; tss_id "TSS000853"; uce "FALSE"; transcript_id_alias "T002432"; tstatus "annotated"; tgenic "intergenic"; func_name_final "NA";
chr1 mitranscriptome exon 7703111 7703230 1000.0 - . gene_id "lnckb.274"; transcript_id "lnckb.274.28"; exon_number "5"; tcat "lncrna"; gene_id_alias "G000374"; tss_id "TSS000853"; uce "FALSE"; transcript_id_alias "T002431"; tstatus "annotated"; tgenic "intergenic"; func_name_final "NA";
chr1 mitranscriptome exon 7703111 7703237 1000.0 - . gene_id "lnckb.274"; transcript_id "lnckb.274.28"; exon_number "3"; tcat "lncrna"; gene_id_alias "G000374"; tss_id "TSS000854"; uce "FALSE"; transcript_id_alias "T002434"; tstatus "annotated"; tgenic "intergenic"; func_name_final "NA";
chr1 mitranscriptome exon 7703348 7704010 1000.0 - . gene_id "lnckb.274"; transcript_id "lnckb.274.28"; exon_number "2"; tcat "lncrna"; gene_id_alias "G000374"; tss_id "TSS000853"; uce "FALSE"; transcript_id_alias "T002463"; tstatus "unannotated"; tgenic "intragenic"; func_name_final "NA";
chr1 mitranscriptome exon 7703348 7704019 1000.0 - . gene_id "lnckb.274"; transcript_id "lnckb.274.28"; exon_number "5"; tcat "lncrna"; gene_id_alias "G000374"; tss_id "TSS000853"; uce "FALSE"; transcript_id_alias "T002428"; tstatus "annotated"; tgenic "intergenic"; func_name_final "NA";
chr1 mitranscriptome exon 7703348 7704028 1000.0 - . gene_id "lnckb.274"; transcript_id "lnckb.274.28"; exon_number "3"; tcat "lncrna"; gene_id_alias "G000374"; tss_id "TSS000853"; uce "FALSE"; transcript_id_alias "T002429"; tstatus "annotated"; tgenic "intergenic"; func_name_final "NA";
chr1 mitranscriptome exon 7703348 7704047 1000.0 - . gene_id "lnckb.274"; transcript_id "lnckb.274.28"; exon_number "3"; tcat "lncrna"; gene_id_alias "G000374"; tss_id "TSS000853"; uce "FALSE"; transcript_id_alias "T002430"; tstatus "annotated"; tgenic "intergenic"; func_name_final "NA";
chr1 mitranscriptome exon 7703348 7704047 1000.0 - . gene_id "lnckb.274"; transcript_id "lnckb.274.28"; exon_number "6"; tcat "lncrna"; gene_id_alias "G000374"; tss_id "TSS000853"; uce "FALSE"; transcript_id_alias "T002431"; tstatus "annotated"; tgenic "intergenic"; func_name_final "NA";
chr1 mitranscriptome exon 7703348 7704121 1000.0 - . gene_id "lnckb.274"; transcript_id "lnckb.274.28"; exon_number "4"; tcat "lncrna"; gene_id_alias "G000374"; tss_id "TSS000853"; uce "FALSE"; transcript_id_alias "T002432"; tstatus "annotated"; tgenic "intergenic"; func_name_final "NA";
chr1 mitranscriptome exon 7703348 7704205 1000.0 - . gene_id "lnckb.274"; transcript_id "lnckb.274.28"; exon_number "3"; tcat "lncrna"; gene_id_alias "G000374"; tss_id "TSS000853"; uce "FALSE"; transcript_id_alias "T002433"; tstatus "annotated"; tgenic "intergenic"; func_name_final "NA";
chr1 mitranscriptome exon 7703348 7704479 1000.0 - . gene_id "lnckb.274"; transcript_id "lnckb.274.28"; exon_number "4"; tcat "lncrna"; gene_id_alias "G000374"; tss_id "TSS000854"; uce "FALSE"; transcript_id_alias "T002434"; tstatus "annotated"; tgenic "intergenic"; func_name_final "NA";
chr1 mitranscriptome exon 7704036 7704235 1000.0 - . gene_id "lnckb.274"; transcript_id "lnckb.274.28"; exon_number "3"; tcat "lncrna"; gene_id_alias "G000374"; tss_id "TSS000853"; uce "FALSE"; transcript_id_alias "T002463"; tstatus "unannotated"; tgenic "intragenic"; func_name_final "NA";
chr1 lncipedia.org transcript 7702423 7703527 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.25"; gene_id_alias "lnc-UTS2-5:5"; gene_id_alias "lnc-UTS2-5"; transcript_id_alias "lnc-UTS2-5:5"; transcript_alias_1 "NONHSAT000717";
chr1 lncipedia.org exon 7702423 7702680 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.25"; transcript_id_alias "lnc-UTS2-5:5"; gene_id_alias "lnc-UTS2-5"; transcript_id_alias "lnc-UTS2-5:5"; transcript_alias_1 "NONHSAT000717";
chr1 lncipedia.org exon 7703111 7703527 . - . gene_id "lnckb.274"; transcript_id "lnckb.274.25"; transcript_id_alias "lnc-UTS2-5:5"; gene_id_alias "lnc-UTS2-5"; transcript_id_alias "lnc-UTS2-5:5"; transcript_alias_1 "NONHSAT000717";
from ribotish.
zhpn1024
commented on July 19, 2024
The transcript "lnckb.274.28" has multiple overlapping exons. This may be the problem. Remove/correct such records and try again.
from ribotish.
zhpn1024
commented on July 19, 2024
In addition, if your gtf does not contain protein coding transcripts, the TIS background estimation would be incorrect. If so, another protein coding gtf annotation file can be provided with -a option, and remove the '.bgest.txt' file for re-estimating.
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ErinDuffyLacy
commented on July 19, 2024
Excellent, I removed transcripts with overlapping exons (there were unfortunately several in this annotation file) and the script runs without errors. Thank you for your help!
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Related Issues (20)
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