I am attempting to run mmquant and it keeps being killed after reading in the .gtf files. The script I am running is pasted below and the samples are all coordinate sorted bam files. Any ideas on why?
mmquant -a Reference.gtf -r 1.bam 2.bam 3.bam 4.bam 5.bam 6.bam 7.bam 8.bam 9.bam 10.bam 18.bam 19.bam -s FR -f BAM -t 13 -o GW_mmquant
An additional note: I have also added memory, allowing for 50gb and this did not seem to remedy the issue. Thanks!