lingjoyo

Anyone known how to solve this problem？

Dear Jack Humphrey, Thanks for your reply. The code I used to extract junc files is : regtools junctions extract -s 0 -a 8 -m 50 -M 500000 $bam -o...

This is how my junctions files look like: GL000008.2 196082 198547 JUNC00394618 74 - 196082 198547 255,0,0 2 132,72 0,2393 GL000008.2 198464 199323 JUNC00394616 76 - 198464 199323 255,0,0 2...

Hi Jonathonl, Thans for your reply. It's minimac v4.1.6. The computing resources are: > storage 16T free space > cup 32 > memory 370G It shouldn't be the problem of...

Here is the log : > minimac v4.1.6 > > Imputing 11:1-20000000 ... > Loading target haplotypes ... > Loading target haplotypes took 1 seconds > Loading reference haplotypes ......

It works well if I put everything into one folder: ``` ./minimac4 1000g_phase3_v5.chr22.with_parameter_estimates.msav \ qc_3rd-updated-chr22.vcf.gz \ -o c22.imputed.vcf.gz \ --min-r2 0.3 --min-ratio 1e-6 \ --temp-prefix c22.tmp_ ``` But it will...

I guess the problem is about the setting to temp files. What's the right way of setting --temp-prefix if I want to submit the job using SBATCH?