Hello, first question I've posted here though it may be simple.
So, normally I wouldn't care so much about this because I've normally used a SLURM arrays to automatically submit but recently I've moved to a school with a cluster that is very difficult to work with (constant bus errors, partitions being called incorrectly, missing dependencies which I have to manually install and which may not be compatible with the R version available, etc.) so I've just been manually aligning my sequences one at a time or with a loop script.
This is of course VERY tedious and I have to ensure I don't turn off my computer etc. But it has shown me the need for some sort of progress bar in a number of bioinformatic tools and I was wondering if anybody has developed any simple code or if there's some option hidden in the documentation that I've missed. Thank you for any help anyone has!
I really would appreciate anyone's ideas on this. This is my command:
hisat2 -p 4 -k 1 --min-intronlen 50 --max-intronlen 500000 -x Homo_sapiens.GRCh38.dna.toplevel.fa -U SRR12816722.fastq.gz -S SRR12816722.fastq.gz.hisat.sam
I loop it through everything or, if SLURM isn't working that day, open up consecutive windows and do each manually -_-