[suhaib58]

Hi Wei,

Since yesterday an error message in thrown when running featureCount program on RNA-seq data.

Run1
//================================= Running ==================================\\
|| ||
|| Load annotation file ../Homo_sapiens.GRCh38.78.gtf ... ||
|| Features : 1232660 ||
|| Meta-features : 64253 ||
|| Chromosomes : 270 ||
|| ||
|| Process BAM file 36B_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) ||
Segmentation fault (core dumped)

Run2
//================================= Running ==================================\\
|| ||
|| Load annotation file ../Homo_sapiens.GRCh38.78.gtf ... ||
|| Features : 1232660 ||
|| Meta-features : 64253 ||
|| Chromosomes : 270 ||
|| ||
|| Process BAM file 36B1_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.


//================================= Running ==================================\\
|| ||
|| Load annotation file ../Homo_sapiens.GRCh38.78.gtf ... ||
|| Features : 1232660 ||
|| Meta-features : 64253 ||
|| Chromosomes : 270 ||
|| ||
|| Process BAM file 39B_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 (core dumped)



Every different run a different error is flagged.Additionally about 225 files are dumped in working directory named

temp-core-002882-6B8B4567.sam temp-sort-002882-327B23C6-CHK00000000-BLK119.bin temp-sort-004072-327B23C6-CHK00000000-BLK007.bin temp-sort-004072-327B23C6-CHK00000000-BLK124.bin
temp-core-004072-6B8B4567.sam temp-sort-002882-327B23C6-CHK00000000-BLK120.bin temp-sort-004072-327B23C6-CHK00000000-BLK008.bin temp-sort-004072-327B23C6-CHK00000000-BLK125.bin
temp-sort-002882-327B23C6-CHK00000000-BLK004.bin

Parameters used in the program. With the same parameters I ran 40 Paired End reads aligned on bam files without any error.

featureCounts -p -s 2 -M -O \
-a ../Homo_sapiens.GRCh38.78.gtf -o ../../../Counts_overlap/${sampNo}_counts.txt -t exon -g gene_id -T 10 *accepted_hits.bam


Could you please let me know how do I troubleshoot this error.

[shi]

Have you checked if there is enough disk space in your working directory?

[suhaib58]

Hi Wei,

Well, that was the problem, the HD was almost full.

Thanks again