Benchmark / test report
Container name: Singularity.BWA-0.7.17-intel-2021b.localimage.sif
test script
#!/bin/bash
#SBATCH -J plcr-bwa-cpu-test
#SBATCH -N 1
#SBATCH --ntasks-per-node=4
# SBATCH -t 1-00:00:00
PLCR=${PLCR:-/net/pr2/plcr}
CONT=${1:-Singularity.BWA-0.7.17-intel-2021b.localimage.sif}
echo "PLCR test: $SLURM_JOB_NAME"
echo "PLCR jobid: $SLURM_JOBID"
echo "PLCR path: $PLCR"
echo "Test performed on: "`date`
echo "Testing container: $CONT"
SHA=`dd bs=1M if=$PLCR/images/$CONT 2>/dev/null | sha256sum | cut -d' ' -f1`
echo "Container checksum: $SHA"
cd $TMPDIR
wget- q 'http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz'
gzip -dk hg38.fa.gz
singularity -s run -B $PWD:/host_pwd --pwd /host_pwd $PLCR/images/$CONT bwa index -a bwtsw hg38.fa hg38
singularity -s run -B $PWD:/host_pwd --pwd /host_pwd $PLCR/images/$CONT prefetch ERR2356727
singularity -s run -B $PWD:/host_pwd --pwd /host_pwd $PLCR/images/$CONT fastq-dump --split-files ERR2356727/ERR2356727.sra
time singularity -s run -B $PWD:/host_pwd --pwd /host_pwd $PLCR/images/$CONT bwa mem -t $SLURM_NTASKS hg38.fa ERR2356727_1.fastq ERR2356727_2.fastq > ERR.sam
RC=$?
echo "Test completed, rc=$RC, "
test results
PLCR test: plcr-bwa-cpu-test
PLCR jobid: 402366
PLCR path: /net/pr2/plcr
Test performed on: czw, 26 maj 2022, 10:29:08 CEST
Testing container: Singularity.BWA-0.7.17-intel-2021b.localimage.sif
Container checksum: fe96b0ffc5287ef62b8fa6c15f3c5831225cf206fdd2e2809edc9834fcccfd92
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 264902 sequences (40000202 bp)...
[M::process] read 264902 sequences (40000202 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 111072, 241, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (163, 170, 190)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (109, 244)
[M::mem_pestat] mean and std.dev: (175.56, 17.34)
[M::mem_pestat] low and high boundaries for proper pairs: (82, 271)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (16, 29, 49)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 115)
[M::mem_pestat] mean and std.dev: (33.57, 19.66)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 148)
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation RF
[M::mem_process_seqs] Processed 264902 reads in 43.941 CPU sec, 11.065 real sec
[M::process] read 264902 sequences (40000202 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 110945, 266, 3)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (163, 170, 190)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (109, 244)
[M::mem_pestat] mean and std.dev: (175.50, 17.39)
[M::mem_pestat] low and high boundaries for proper pairs: (82, 271)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (19, 32, 46)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 100)
[M::mem_pestat] mean and std.dev: (33.38, 17.94)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 127)
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation RF
[M::mem_process_seqs] Processed 264902 reads in 45.188 CPU sec, 11.362 real sec
[M::process] read 264902 sequences (40000202 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 111196, 324, 2)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (163, 170, 190)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (109, 244)
[M::mem_pestat] mean and std.dev: (175.50, 17.35)
[M::mem_pestat] low and high boundaries for proper pairs: (82, 271)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (18, 36, 48)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 108)
[M::mem_pestat] mean and std.dev: (34.71, 18.25)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 138)
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation RF
[M::mem_process_seqs] Processed 264902 reads in 44.724 CPU sec, 11.250 real sec
[M::process] read 264902 sequences (40000202 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 111692, 207, 1)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (163, 170, 190)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (109, 244)
[M::mem_pestat] mean and std.dev: (175.72, 17.36)
[M::mem_pestat] low and high boundaries for proper pairs: (82, 271)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (18, 35, 49)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 111)
[M::mem_pestat] mean and std.dev: (34.36, 18.47)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 142)
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation RF
[M::mem_process_seqs] Processed 264902 reads in 44.012 CPU sec, 11.066 real sec
[M::process] read 264902 sequences (40000202 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 111720, 244, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (163, 170, 190)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (109, 244)
[M::mem_pestat] mean and std.dev: (175.66, 17.31)
[M::mem_pestat] low and high boundaries for proper pairs: (82, 271)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (18, 38, 51)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 117)
[M::mem_pestat] mean and std.dev: (35.71, 19.34)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 150)
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation RF
[M::mem_process_seqs] Processed 264902 reads in 44.515 CPU sec, 11.181 real sec
[M::process] read 264902 sequences (40000202 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 118975, 118, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (163, 171, 196)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (97, 262)
[M::mem_pestat] mean and std.dev: (176.83, 18.18)
[M::mem_pestat] low and high boundaries for proper pairs: (64, 295)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (20, 36, 55)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 125)
[M::mem_pestat] mean and std.dev: (36.97, 19.60)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 160)
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation RF
[M::mem_process_seqs] Processed 264902 reads in 33.743 CPU sec, 8.486 real sec
[M::process] read 264902 sequences (40000202 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 122159, 32, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (163, 176, 196)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (97, 262)
[M::mem_pestat] mean and std.dev: (177.36, 18.51)
[M::mem_pestat] low and high boundaries for proper pairs: (64, 295)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (30, 45, 59)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 117)
[M::mem_pestat] mean and std.dev: (37.82, 17.85)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 146)
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation RF
[M::mem_process_seqs] Processed 264902 reads in 28.517 CPU sec, 7.176 real sec
[M::process] read 264902 sequences (40000202 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (1, 122257, 28, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (163, 176, 196)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (97, 262)
[M::mem_pestat] mean and std.dev: (177.39, 18.43)
[M::mem_pestat] low and high boundaries for proper pairs: (64, 295)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (20, 44, 64)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 152)
[M::mem_pestat] mean and std.dev: (38.52, 20.00)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 196)
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation RF
[M::mem_process_seqs] Processed 264902 reads in 28.923 CPU sec, 7.274 real sec
[M::process] read 61290 sequences (9254790 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (1, 122059, 22, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (163, 174, 196)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (97, 262)
[M::mem_pestat] mean and std.dev: (177.33, 18.49)
[M::mem_pestat] low and high boundaries for proper pairs: (64, 295)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (22, 37, 53)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 115)
[M::mem_pestat] mean and std.dev: (35.90, 16.95)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 146)
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation RF
[M::mem_process_seqs] Processed 264902 reads in 28.468 CPU sec, 7.162 real sec
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 28302, 9, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (163, 176, 196)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (97, 262)
[M::mem_pestat] mean and std.dev: (177.41, 18.42)
[M::mem_pestat] low and high boundaries for proper pairs: (64, 295)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 61290 reads in 6.819 CPU sec, 1.717 real sec
[main] Version: 0.7.17-r1188
[main] CMD: bwa mem -t 4 hg38.fa ERR2356727_1.fastq ERR2356727_2.fastq
[main] Real time: 93.168 sec; CPU: 352.470 sec
real 1m34,094s
user 5m47,074s
sys 0m5,791s
Test completed, rc=0,