Entering edit mode
Hello everyone,
I'm having this problem with subread 2.0.3 featureCounts in Linux OS. This gtf file is converted with gff3 file using gffread.
This is my using code.
featureCounts -T 10 -p -a aPleWal.anno.v2.20220926.gtf -o regeneration.readscount 3M-1L_Aligned.sorted.bam
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v2.0.1
//========================== featureCounts setting ===========================\\
Input files : 1 BAM file
o Aligned.sorted.bam
Output file : reg.readscount
Summary : reg.readscount.summary
Annotation : aPleWal.anno.v2.20220926.gtf (GTF)
Dir for temp files : ./
Threads : 10
Level : meta-feature level
Paired-end : yes
Multimapping reads : not counted
Multi-overlapping reads : not counted
Min overlapping bases : 1
Chimeric reads : counted
Both ends mapped : not required
\\============================================================================//
//================================= Running ==================================\\
Load annotation file aPleWal.anno.v2.20220926.gtf ...
Segmentation fault
Top 10 line in my GTF.
manual_scaffold_10 transdecoder transcript 1148581 1151013 . - . transcript_id "mRNA1"; gene_id "gene1"
manual_scaffold_10 transdecoder exon 1148581 1148829 . - . transcript_id "mRNA1"; gene_id "gene1";
manual_scaffold_10 transdecoder exon 1149153 1151013 . - . transcript_id "mRNA1"; gene_id "gene1";
manual_scaffold_10 transdecoder CDS 1149262 1149741 . - 0 transcript_id "mRNA1"; gene_id "gene1";
manual_scaffold_10 transdecoder transcript 1148581 1151013 . - . transcript_id "mRNA2"; gene_id "gene1"
manual_scaffold_10 transdecoder exon 1148581 1148829 . - . transcript_id "mRNA2"; gene_id "gene1";
manual_scaffold_10 transdecoder exon 1149153 1151013 . - . transcript_id "mRNA2"; gene_id "gene1";
manual_scaffold_10 transdecoder CDS 1150522 1150932 . - 0 transcript_id "mRNA2"; gene_id "gene1";
manual_scaffold_10 transdecoder transcript 1157949 1301565 . - . transcript_id "mRNA3"; gene_id "gene2"
manual_scaffold_10 transdecoder exon 1157949 1158665 . - . transcript_id "mRNA3"; gene_id "gene2";
This is GFF3
manual_scaffold_10 transdecoder gene 1148581 1151013 . - . ID=gene1;Name=POL
manual_scaffold_10 transdecoder mRNA 1148581 1151013 . - . ID=mRNA1;Parent=gene1;Name=POL
manual_scaffold_10 transdecoder exon 1148581 1148829 . - . Parent=mRNA1
manual_scaffold_10 transdecoder three_prime_UTR 1148581 1148829 . - . Parent=mRNA1
manual_scaffold_10 transdecoder three_prime_UTR 1149153 1149261 . - . Parent=mRNA1
manual_scaffold_10 transdecoder exon 1149153 1151013 . - . Parent=mRNA1
manual_scaffold_10 transdecoder CDS 1149262 1149741 . - 0 Parent=mRNA1
manual_scaffold_10 transdecoder five_prime_UTR 1149742 1151013 . - . Parent=mRNA1
manual_scaffold_10 transdecoder mRNA 1148581 1151013 . - . ID=mRNA2;Parent=gene1;Name=POL
manual_scaffold_10 transdecoder exon 1148581 1148829 . - . Parent=mRNA2
manual_scaffold_10 transdecoder three_prime_UTR 1148581 1148829 . - . Parent=mRNA2
manual_scaffold_10 transdecoder three_prime_UTR 1149153 1150521 . - . Parent=mRNA2
manual_scaffold_10 transdecoder exon 1149153 1151013 . - . Parent=mRNA2
manual_scaffold_10 transdecoder CDS 1150522 1150932 . - 0 Parent=mRNA2
manual_scaffold_10 transdecoder five_prime_UTR 1150933 1151013 . - . Parent=mRNA2
###
manual_scaffold_10 transdecoder gene 1157949 1301565 . - . ID=gene2;Name=WIPI4
manual_scaffold_10 transdecoder mRNA 1157949 1301565 . - . ID=mRNA3;Parent=gene2;Name=WIPI4
manual_scaffold_10 transdecoder three_prime_UTR 1157949 1158555 . - . Parent=mRNA3
manual_scaffold_10 transdecoder exon 1157949 1158665 . - . Parent=mRNA3
manual_scaffold_10 transdecoder CDS 1158556 1158665 . - 2 ID=CDS1;Parent=mRNA3
manual_scaffold_10 transdecoder exon 1175229 1175374 . - . Parent=mRNA3
manual_scaffold_10 transdecoder CDS 1175229 1175374 . - 1 ID=CDS1;Parent=mRNA3
manual_scaffold_10 transdecoder exon 1222565 1222666 . - . Parent=mRNA3
manual_scaffold_10 transdecoder CDS 1222565 1222666 . - 1 ID=CDS1;Parent=mRNA3
manual_scaffold_10 transdecoder exon 1223663 1223871 . - . Parent=mRNA3
manual_scaffold_10 transdecoder CDS 1223663 1223871 . - 0 ID=CDS1;Parent=mRNA3
manual_scaffold_10 transdecoder exon 1227060 1227139 . - . Parent=mRNA3
manual_scaffold_10 transdecoder CDS 1227060 1227139 . - 2 ID=CDS1;Parent=mRNA3
manual_scaffold_10 transdecoder exon 1242421 1242515 . - . Parent=mRNA3
manual_scaffold_10 transdecoder CDS 1242421 1242515 . - 1 ID=CDS1;Parent=mRNA3
manual_scaffold_10 transdecoder exon 1244923 1245028 . - . Parent=mRNA3
manual_scaffold_10 transdecoder CDS 1244923 1245028 . - 2 ID=CDS1;Parent=mRNA3
manual_scaffold_10 transdecoder exon 1247050 1247154 . - . Parent=mRNA3
manual_scaffold_10 transdecoder CDS 1247050 1247154 . - 2 ID=CDS1;Parent=mRNA3
manual_scaffold_10 transdecoder exon 1251898 1251972 . - . Parent=mRNA3
manual_scaffold_10 transdecoder CDS 1251898 1251972 . - 2 ID=CDS1;Parent=mRNA3
manual_scaffold_10 transdecoder CDS 1301401 1301449 . - 0 ID=CDS1;Parent=mRNA3
manual_scaffold_10 transdecoder exon 1301401 1301565 . - . Parent=mRNA3
manual_scaffold_10 transdecoder five_prime_UTR 1301450 1301565 . - . Parent=mRNA3
I'm not sure if this happens in Rsubread, but I've searched every way I can find and still no solution. Any help would be greatly appreciated!
