Hi,
I am using featureCounts to count reads for every gene from refSeq annotation file. But it went to error:
featureCounts -a ../refGeneReviewed.gtf -t exon -g gene_id -p -Q 10 -o ../../result/fc_accepted_hits.txt accepted_hits.bam
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.4.6
//========================== featureCounts setting ===========================\\
|| ||
|| Input files : 1 BAM file ||
|| P accepted_hits.bam ||
|| ||
|| Output file : ../../result/fc_accepted_hits.txt ||
|| Annotations : ../refGeneReviewed.gtf (GTF) ||
|| ||
|| Threads : 1 ||
|| Level : meta-feature level ||
|| Paired-end : yes ||
|| Strand specific : no ||
|| Multimapping reads : not counted ||
|| Multi-overlapping reads : not counted ||
|| ||
|| Chimeric reads : counted ||
|| Both ends mapped : not required ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
//================================= Running ==================================\\
|| ||
|| Load annotation file ../refGeneReviewed.gtf ... ||
|| Features : 304046 ||
|| Meta-features : 24154 ||
|| Chromosomes : 35 ||
|| ||
|| Process BAM file accepted_hits.bam... ||
|| Paired-end reads are included. ||
|| Assign fragments (read pairs) to features... ||
|| Found reads that are not properly paired. ||
|| (missing mate or the mate is not the next read) ||
Cannot load read part from the tmp file!
featureCounts: input-files.c:2216: sort_SAM_finalise: Assertion `0' failed.
Aborted
This bam and gtf file should be right, because I have used them to run HTSeq-count
Hi,
I found similar error:
featureCounts: input-files.c:4675: SAM_pairer_run: Assertion `0 == corrected_run' failed.
And tried the -p and -P option, but still run into this error. Can you suggestion why and what could be the solution?
Also having the same problem, and not able to fix it with -p -P ...