I'm working on Cloudman doing RNASeq analysis. I am trying to use htseq-count tool for gene quantification, but I have this error:
Fatal error: Unknown error occured 100000 GFF lines processed. 200000 GFF lines processed. [.....] 105500000 SAM alignment record pairs processed. Error occured when processing SAM input (record #214145509 in file /mnt/galaxy/files/000/dataset_227.dat): Maximum alignment buffer size exceeded while pairing SAM alignments. [Exception type: ValueError, raised in __init__.py:671]
The input are a BAM file obtained by using HTSAT2 and the GFT file from https://www.gencodegenes.org/releases/current.html.
Did I miss something? Thanks