search

biod / sambamba

Tools for working with SAM/BAM data
http://thebird.nl/blog/D_Dragon.html
GNU General Public License v2.0
555 stars 104 forks source link

conda sambamba 1.0 is running slower than conda sambamba 0.6 #503

Closed ericpanyc closed 11 months ago

ericpanyc commented 1 year ago

The bug is described as the title.

sambamba 0.6.6 from conda

`time ~/miniconda3/envs/sambamba-0.6/bin/sambamba depth region -F 'not unmapped and not secondary_alignment and not duplicate and not failed_quality_control and mapping_quality > 9' -t 4 -c 0 -T 10 -L /mnt/efs/Annotations/References/Hsapiens/GRCh38/bed/refseq_allexons_extend5_ucsc_hg38.bed -o ./test_sambamba_depth_region_one_thresh.bed ./PLM00993810-B-D_20230306_TES_Clinical1.0-dragen.hg38.bam Processing reference #1 (chr1) Processing reference #2 (chr2) Processing reference #3 (chr3) Processing reference #4 (chr4) Processing reference #5 (chr5) Processing reference #6 (chr6) Processing reference #7 (chr7) Processing reference #8 (chr8) Processing reference #9 (chr9) Processing reference #10 (chr10) Processing reference #11 (chr11) Processing reference #12 (chr12) Processing reference #13 (chr13) Processing reference #14 (chr14) Processing reference #15 (chr15) Processing reference #16 (chr16) Processing reference #17 (chr17) Processing reference #18 (chr18) Processing reference #19 (chr19) Processing reference #20 (chr20) Processing reference #21 (chr21) Processing reference #22 (chr22) Processing reference #23 (chrX) Processing reference #24 (chrY)

real 6m35.792s user 13m50.081s sys 0m14.050s`

sambamba 1.0.0 from conda

`time ~/miniconda3/envs/sambamba-1.0/bin/sambamba depth region -F 'not unmapped and not secondary_alignment and not duplicate and not failed_quality_control and mapping_quality > 9' -t 4 -c 0 -T 10 -L /mnt/efs/Annotations/References/Hsapiens/GRCh38/bed/refseq_allexons_extend5_ucsc_hg38.bed -o ./test_sambamba1.0_depth_region_one_thresh.bed ./PLM00993810-B-D_20230306_TES_Clinical1.0-dragen.hg38.bam

sambamba 1.0.0 by Artem Tarasov and Pjotr Prins (C) 2012-2022 LDC 1.28.1 / DMD v2.098.1 / LLVM12.0.0 / bootstrap LDC - the LLVM D compiler (1.28.1)

Processing reference #1 (chr1) Processing reference #2 (chr2) Processing reference #3 (chr3) Processing reference #4 (chr4) Processing reference #5 (chr5) Processing reference #6 (chr6) Processing reference #7 (chr7) Processing reference #8 (chr8) Processing reference #9 (chr9) Processing reference #10 (chr10) Processing reference #11 (chr11) Processing reference #12 (chr12) Processing reference #13 (chr13) Processing reference #14 (chr14) Processing reference #15 (chr15) Processing reference #16 (chr16) Processing reference #17 (chr17) Processing reference #18 (chr18) Processing reference #19 (chr19) Processing reference #20 (chr20) Processing reference #21 (chr21) Processing reference #22 (chr22) Processing reference #23 (chrX) Processing reference #24 (chrY)

real 40m32.600s user 46m37.605s sys 0m16.209s`

I can reproduce the issue on other x86_64 instances.

pjotrp commented 11 months ago

Please contact conda. Or try the actual releases you can download from https://github.com/biod/sambamba/releases