Long runtime with Circle Realign?

[hartlama]

Is there any way to speed up Circle Realign? I'm running with 10 processors, 15GB each, on a server, but I still have some iterations taking 1-3 hours. My sorted_read_candidates.bam file is 16GB. Any suggestions?

[iprada]

Can you share the exact command you are using and how you submit it (In case you are on cluster)?

best,

Inigo

[hartlama]

#SBATCH --job-name=realign
#SBATCH --mail-type=BEGIN,END,FAIL,REQUEUE
#SBATCH --nodes=1
#SBATCH --mem-per-cpu=15G
#SBATCH --time=14-00:00:00
#SBATCH --account=mariacas99
#SBATCH --partition=standard
#SBATCH --cpus-per-task=10

Circle-Map Realign -t 10 -v 3 -i sorted_circular_read_candidates_NPAH.bam -sbam NPAH_sorted_coord.bam -qbam NPAH_sorted_qname.bam -fasta /mm10/mm10.fa -o /NPAH_circle.bed

[iprada]

Dear hartlama,

I see. Is your data phi29 amplified?

If so, the first interations tend to be slow due to exponential amplification and then it gets faster.

On the long run, I would like to make Circle-Map a bit faster, and I have already found the lines of code that make it perform poorly. But I a afraid this can take a very long time given the amount of work I have now.

best,

Inigo

[hartlama]

Hi Inigo,

It is amplified. Would it be safe to down-sample at one of the previous steps?

Thanks,
Molly

[njaupan]

Hi,
I ran into the same problem with Circle Realign. I tested it on a plant genome with a genome size of 17G. Run the command as follows on a cluster with 96 CPUs and 496 GB of memory:

Circle-Map Realign -t 80 -i $out.bwa.qname.Circle-Map.sort.bam -qbam $out.bwa.qname.bam -sbam $out.bwa.bam -fasta $reference -o $out. bwa.qname.Circle-Map.out.bed

However, it seems to run forever at the step of 100%, any suggestions?

2021-06-27 23:28:37: Splitting clusters to to processors

32%|███▎ | 1300/4000 [04:35<08:22, 5.37it/s]
33%|███▎ | 1303/4000 [04:36<08:45, 5.13it/s]
43%|████▎ | 1713/4000 [06:02<07:24, 5.14it/s]
4000it [17:36, 3.78it/s]0 [17:36<00:00, 2.75it/s]
100%|██████████| 4000/4000 [17:36<00:00, 3.78it/s]

the best,
Panpan