Closed sen1019san closed 1 year ago
I slove the problem by splitting the merge_rnaseq.bam
file into long.bam file and short.bam file and it succeed.
i was trying to get transcript file using stringtie then error occured stringtie output_sorted_bam -o transcripts_gtf -G Piper_nigrum.gff3 -A assembly.txt WARNING: no reference transcripts were found for the genomic sequences where reads were mapped! Please make sure the -G annotation file uses the same naming convention for the genome sequences.
these are first few lines of my annotation file
Pn1 EVM mRNA 10842 11267 . + . ID=evm.model.Pn1.1 Pn1 EVM exon 10842 11267 . + . ID=evm.model.Pn1.1.exon1;Parent=evm.model.Pn1.1 Pn1 EVM CDS 10842 11267 . + 0 ID=cds.evm.model.Pn1.1;Parent=evm.model.Pn1.1
Pn1 EVM mRNA 19952 20188 . + . ID=evm.model.Pn1.2 Pn1 EVM exon 19952 20188 . + . ID=evm.model.Pn1.2.exon1;Parent=evm.model.Pn1.2 Pn1 EVM CDS 19952 20188 . + 0 ID=cds.evm.model.Pn1.2;Parent=evm.model.Pn1.2
Pn1 EVM mRNA 67496 68035 . - . ID=evm.model.Pn1.3 Pn1 EVM exon 67496 68035 . - . ID=evm.model.Pn1.3.exon1;Parent=evm.model.Pn1.3 Pn1 EVM CDS 67496 68035 . - 0 ID=cds.evm.model.Pn1.3;Parent=evm.model.Pn1.3
Pn1 EVM mRNA 68921 69345 . - . ID=evm.model.Pn1.4 Pn1 EVM exon 68921 69087 . - . ID=evm.model.Pn1.4.exon2;Parent=evm.model.Pn1.4 Pn1 EVM CDS 68921 69087 . - 2 ID=cds.evm.model.Pn1.4;Parent=evm.model.Pn1.4 Pn1 EVM exon 69249 69345 . - . ID=evm.model.Pn1.4.exon1;Parent=evm.model.Pn1.4 Pn1 EVM CDS 69249 69345 . - 0 ID=cds.evm.model.Pn1.4;Parent=evm.model.Pn1.4
Pn1 EVM mRNA 73564 74589 . - . ID=evm.model.Pn1.5 Pn1 EVM exon 73564 74589 . - . ID=evm.model.Pn1.5.exon1;Parent=evm.model.Pn1.5 Pn1 EVM CDS 73564 74589 . - 0 ID=cds.evm.model.Pn1.5;Parent=evm.model.Pn1.5
Pn1 EVM mRNA 76279 78348 . - . ID=evm.model.Pn1.6 Pn1 EVM exon 76279 77882 . - . ID=evm.model.Pn1.6.exon3;Parent=evm.model.Pn1.6 Pn1 EVM CDS 76279 77882 . - 2 ID=cds.evm.model.Pn1.6;Parent=evm.model.Pn1.6 Pn1 EVM exon 77981 78152 . - . ID=evm.model.Pn1.6.exon2;Parent=evm.model.Pn1.6 Pn1 EVM CDS 77981 78152 . - 0 ID=cds.evm.model.Pn1.6;Parent=evm.model.Pn1.6 Pn1 EVM exon 78241 78348 . - . ID=evm.model.Pn1.6.exon1;Parent=evm.model.Pn1.6 Pn1 EVM CDS 78241 78348 . - 0 ID=cds.evm.model.Pn1.6;Parent=evm.model.Pn1.6
Pn1 EVM mRNA 78599 80899 . + . ID=evm.model.Pn1.7 Pn1 EVM exon 78599 80899 . + . ID=evm.model.Pn1.7.exon1;Parent=evm.model.Pn1.7 Pn1 EVM CDS 78599 80899 . + 0 ID=cds.evm.model.Pn1.7;Parent=evm.model.Pn1.7
Pn1 EVM mRNA 94000 97630 . - . ID=evm.model.Pn1.8 Pn1 EVM exon 94000 94039 . - . ID=evm.model.Pn1.8.exon6;Parent=evm.model.Pn1.8 Pn1 EVM CDS 94000 94039 . - 1 ID=cds.evm.model.Pn1.8;Parent=evm.model.Pn1.8 Pn1 EVM exon 94111 94173 . - . ID=evm.model.Pn1.8.exon5;Parent=evm.model.Pn1.8 Pn1 EVM CDS 94111 94173 . - 1 ID=cds.evm.model.Pn1.8;Parent=evm.model.Pn1.8 Pn1 EVM exon 95257 95328 . - . ID=evm.model.Pn1.8.exon4;Parent=evm.model.Pn1.8 Pn1 EVM CDS 95257 95328 . - 1 ID=cds.evm.model.Pn1.8;Parent=evm.model.Pn1.8 Pn1 EVM exon 95706 95782 . - . ID=evm.model.Pn1.8.exon3;Parent=evm.model.Pn1.8 Pn1 EVM CDS 95706 95782 . - 0 ID=cds.evm.model.Pn1.8;Parent=evm.model.Pn1.8 Pn1 EVM exon 97358 97453 . - . ID=evm.model.Pn1.8.exon2;Parent=evm.model.Pn1.8 Pn1 EVM CDS 97358 97453 . - 0 ID=cds.evm.model.Pn1.8;Parent=evm.model.Pn1.8 Pn1 EVM exon 97568 97630 . - . ID=evm.model.Pn1.8.exon1;Parent=evm.model.Pn1.8 Pn1 EVM CDS 97568 97630 . - 0 ID=cds.evm.model.Pn1.8;Parent=evm.model.Pn1.8
Pn1 EVM mRNA 99324 103009 . - . ID=evm.model.Pn1.9 Pn1 EVM exon 99324 99436 . - . ID=evm.model.Pn1.9.exon3;Parent=evm.model.Pn1.9 Pn1 EVM CDS 99324 99436 . - 1 ID=cds.evm.model.Pn1.9;Parent=evm.model.Pn1.9 Pn1 EVM exon 100641 100687 . - . ID=evm.model.Pn1.9.exon2;Parent=evm.model.Pn1.9 Pn1 EVM CDS 100641 100687 . - 0 ID=cds.evm.model.Pn1.9;Parent=evm.model.Pn1.9 Pn1 EVM exon 102917 103009 . - . ID=evm.model.Pn1.9.exon1;Parent=evm.model.Pn1.9 Pn1 EVM CDS 102917 103009 . - 0 ID=cds.evm.model.Pn1.9;Parent=evm.model.Pn1.9
Pn1 EVM mRNA 115756 116324 . - . ID=evm.model.Pn1.10 Pn1 EVM exon 115756 115776 . - . ID=evm.model.Pn1.10.exon2;Parent=evm.model.Pn1.10 Pn1 EVM CDS 115756 115776 . - 0 ID=cds.evm.model.Pn1.10;Parent=evm.model.Pn1.10 Pn1 EVM exon 116115 116324 . - . ID=evm.model.Pn1.10.exon1;Parent=evm.model.Pn1.10 Pn1 EVM CDS 116115 116324 . - 0 ID=cds.evm.model.Pn1.10;Parent=evm.model.Pn1.10
Hi, I am trying to assemble RNA-seq data for gene annotation using StringTie. But the program fails returned the "Segmentation fault" error. The program stop at the Chr1:17731527-19123574 site as followings:
The alignment bam file is a merge type with long and short RNA-seq data. The StringTie (latest version: v2.2.1) command is the following:
I have tried to get the stop bundle file using only one thread with
-p 1
following the instructions here Extracting bundle data for debugging. This is the bam file I extracted from the stop site:The extracted
bundle_c1.bam
file is about 900Mb and shared in dropbox: https://www.dropbox.com/s/efl4wnpdsokz4uj/bundle_c1.bam?dl=0I wish the problem to be solved quickly.