Benchmark / test report

Container name: Singularity.Bowtie2-2.4.4-GCC-10.3.0.localimage.sif

test script

#!/bin/bash

#SBATCH -J plcr-bowtie2-cpu-test
#SBATCH -N 1
#SBATCH --ntasks-per-node=4
#SBATCH -t 1-00:00:00

PLCR=${PLCR:-/net/pr2/plcr}
CONT=${1:-Singularity.Bowtie2-2.4.4-GCC-10.3.0.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 '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 bowtie2-build 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 bowtie2 --very-sensitive -x hg38 -1 ERR2356727_1.fastq -2 ERR2356727_2.fastq -S ERR.sam -p $SLURM_NTASKS
RC=$?

echo  "Test completed, rc=$RC, "

test results

PLCR test: plcr-bowtie2-cpu-test
PLCR jobid: 400262
PLCR path: /net/pr2/scratch/people/plgklimas/bowtie
Test performed on: pią, 20 maj 2022, 15:31:59 CEST
Testing container: Singularity.Bowtie2-2.4.4-GCC-10.3.0.localimage.sif
Container checksum: f9fde009428715d4a42e5b31d2c8e27ae8fffc5d53c37ba653478067c943a3fc

2022-05-20T13:32:22 prefetch.3.0.0: Current preference is set to retrieve SRA Normalized Format files with full base quality scores.
2022-05-20T13:32:22 prefetch.3.0.0: 1) Downloading 'ERR2356727'...
2022-05-20T13:32:22 prefetch.3.0.0: SRA Normalized Format file is being retrieved, if this is different from your preference, it may be due to current file availability.
2022-05-20T13:32:22 prefetch.3.0.0:  Downloading via HTTPS...
2022-05-20T13:32:29 prefetch.3.0.0:  HTTPS download succeed
2022-05-20T13:32:30 prefetch.3.0.0:  'ERR2356727' is valid
2022-05-20T13:32:30 prefetch.3.0.0: 1) 'ERR2356727' was downloaded successfully
2022-05-20T13:32:30 prefetch.3.0.0: 'ERR2356727' has 0 unresolved dependencies
Read 1222704 spots for ERR2356727/ERR2356727.sra
Written 1222704 spots for ERR2356727/ERR2356727.sra
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
    LANGUAGE = (unset),
    LC_ALL = (unset),
    LC_MEASUREMENT = "pl_PL.UTF-8",
    LC_PAPER = "pl_PL.UTF-8",
    LC_MONETARY = "pl_PL.UTF-8",
    LC_NAME = "pl_PL.UTF-8",
    LC_ADDRESS = "pl_PL.UTF-8",
    LC_NUMERIC = "pl_PL.UTF-8",
    LC_TELEPHONE = "pl_PL.UTF-8",
    LC_IDENTIFICATION = "pl_PL.UTF-8",
    LC_TIME = "pl_PL.UTF-8",
    LANG = "en_US.UTF-8"
    are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
1222704 reads; of these:
  1222704 (100.00%) were paired; of these:
    229825 (18.80%) aligned concordantly 0 times
    893616 (73.09%) aligned concordantly exactly 1 time
    99263 (8.12%) aligned concordantly >1 times
    ----
    229825 pairs aligned concordantly 0 times; of these:
      81615 (35.51%) aligned discordantly 1 time
    ----
    148210 pairs aligned 0 times concordantly or discordantly; of these:
      296420 mates make up the pairs; of these:
        284193 (95.88%) aligned 0 times
        8725 (2.94%) aligned exactly 1 time
        3502 (1.18%) aligned >1 times
88.38% overall alignment rate

real    2m58,760s
user    11m28,259s
sys 0m8,398s
Test completed, rc=0,