gkudla
commented
4 years ago I have not come across an out-of-memory error with make_hyb_db. If you can't get this to work, try modifying make_hyb_db by replacing the line:
makeblastdb -in $1 -dbtype nucl -input_type fasta -hash_index -out ${1/.fasta/} -logfile ${1/.fasta/.log}
with:
formatdb -i $1 -p F -o T
This will make the blast database using the original blast package, rather than the blast+ package.
Alternatively, remove the makeblastdb line altogether. You will still be able to run hyb with blat or bowtie as the mapping program, but not with blast.
hope that helps. Greg
On Wed, Mar 4, 2020 at 1:44 PM divnand notifications@github.com wrote:
I have been trying to generate a genome database using the mouse transcriptome. I downloaded the cDNA sequences from here ( ftp://ftp.ensembl.org/pub/release-99/fasta/mus_musculus/cdna/). After a few hours of running, i get a out-of -memory error. How much memory would I need to build the db?
This is the error I see. /clusterfs/vector/scratch/dnandaku/hyb/bin/make_hyb_db: line 14: 8863 Killed makeblastdb -in $1 -dbtype nucl -input_type fasta -hash_index -out ${1/.fasta/} -logfile ${1/.fasta/.log} expandFaFastBuf: integer overflow when trying to increase buffer size from 2147483648 to a min of 10499. Building a LARGE index slurmstepd: error: Detected 2 oom-kill event(s) in step 5651184.batch cgroup. Some of your processes may have been killed by the cgroup out-of-memory handler.
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divyanandu
I have been trying to generate a genome database using the mouse transcriptome. I downloaded the cDNA sequences from here (ftp://ftp.ensembl.org/pub/release-99/fasta/mus_musculus/cdna/). After a few hours of running, i get a out-of -memory error. How much memory would I need to build the db?
This is the error I see. /clusterfs/vector/scratch/dnandaku/hyb/bin/make_hyb_db: line 14: 8863 Killed makeblastdb -in $1 -dbtype nucl -input_type fasta -hash_index -out ${1/.fasta/} -logfile ${1/.fasta/.log} expandFaFastBuf: integer overflow when trying to increase buffer size from 2147483648 to a min of 10499. Building a LARGE index slurmstepd: error: Detected 2 oom-kill event(s) in step 5651184.batch cgroup. Some of your processes may have been killed by the cgroup out-of-memory handler.