need help with bwa

I successfully used bwa to index chr19 using bwa index chr19.fa , but when I do index of hg38.fa, it dose not work. I have plenty of storage on my ubuntu cluster and I don't know why. Can anyone help me please? I'm new to this place.

gunzip hg38.fa.gz
[email protected]:~/wes_cancer/data$ nohup bwa index hg38.fa &
~/wes_cancer/data$ bwa index hg38.fa
[bwa_index] Pack FASTA... Killed

I used Homo_sapiens_assembly38.fasta, but it still not working. I did successfully download the files from websites and bwa is fine, but don't know why it is not working?

bwa index Homo_sapiens_assembly38.fasta
[bwa_index] Pack FASTA... Killed
time bwa index -a bwtsw -p gatk_hg38 ~/wes_cancer/data/Homo_sapiens_assembly38.fasta
[bwa_index] Pack FASTA... Killed

real    0m12.877s
user    0m4.771s
sys 0m1.196s


sequence

• 216 views

What system is that? Are you sure you have "purchased and HPC"? That does not sound likely, people don't just go around "purchasing HPCs".

What all advice here tries to uncover is whether you have sufficient resources to run the tool. When you "purchased the HPC" what kinds of resources were you given? How many CPUs and how much memory. If it is indeed a purchase, these values are usually the first listed as the cost is directly proportional to resources.

Or link to the site where you "purchased the HPC"


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