I am trying to perform a
HISAT2 indexing using a
GCF_000001405.39_GRCh38.p13_genomic.fna files downloaded from https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.39 using the procedure described in Pertea et al. (https://www.ncbi.nlm.nih.gov/pubmed/27560171), e.g. first I create
extract_exons.py and then my code looks like this
#!/bin/bash #SBATCH --time=02:30:00 #SBATCH --account=def-myusername #SBATCH --mem=160000M #SBATCH --email@example.com #SBATCH --mail-type=All module load nixpkgs/16.09 intel/2018.3 module load hisat2/2.1.0 hisat2-build --ss imam.ss --exon imam.exon GCF_000001405.39_GRCh38.p13_genomic.fna imam002
I am trying to receive a set of
imam002*.ht2 files but every time the procedure ends with a
Ran out of memory message. From here https://github.com/griffithlab/rnaseq_tutorial/wiki/Indexing I learned that I must allocate 160Gb of RAM if I want to index the entire genome. Even when I do that and submit my script via sbatch on a HPC I still got this
slurmstepd: error: Detected 1 oom-kill event(s) in step 30827017.batch cgroup.
Just in case here's the window that I have when I don't sbatch my script, I still have an error
Inactive Modules: 1) openmpi/2.1.1 The following have been reloaded with a version change: 1) gcccore/.5.4.0 => gcccore/.7.3.0 2) icc/.2016.4.258 => icc/.2018.3.222 3) ifort/.2016.4.258 => ifort/.2018.3.222 4) imkl/22.214.171.1248 => imkl/2018.3.222 5) intel/2016.4 => intel/2018.3 Settings: Output files: "imam002.*.ht2" Line rate: 7 (line is 128 bytes) Lines per side: 1 (side is 128 bytes) Offset rate: 4 (one in 16) FTable chars: 10 Strings: unpacked Local offset rate: 3 (one in 8) Local fTable chars: 6 Local sequence length: 57344 Local sequence overlap between two consecutive indexes: 1024 Endianness: little Actual local endianness: little Sanity checking: disabled Assertions: disabled Random seed: 0 Sizeofs: void*:8, int:4, long:8, size_t:8 Input files DNA, FASTA: GCF_000001405.39_GRCh38.p13_genomic.fna Reading reference sizes Time reading reference sizes: 00:00:23 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:13 Time to read SNPs and splice sites: 00:00:15 Ran out of memory; automatically trying more memory-economical parameters. ./hisat2_index.sh: line 24: 943 Killed hisat2-build --ss imam.ss --exon imam.exon GCF_000001405.39_GRCh38.p13_genomic.fna imam002
When I use the same script for another genome (not human) - I don't have this problem.
Is it really a problem of RAM and, if it is, how is usually human genome gets indexed by HISAT2? Is it even possible?