Subread2.0.3 featureCounts segmentation fault when loading gtf file
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yao hua • 0
@4ef3ae2d
Last seen 7 months ago
Singapore

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!

Subread GTF featureCounts segmentationfault • 253 views
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