Input file:  testdb/reads_R1.fastq
[M::mm_idx_gen::0.031*1.07] collected minimizers
[M::mm_idx_gen::0.044*3.47] sorted minimizers
[M::main::0.044*3.47] loaded/built the index for 1 target sequence(s)
[M::mm_mapopt_update::0.047*3.29] mid_occ = 32
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1
[M::mm_idx_stat::0.050*3.18] distinct minimizers: 49297 (60.18% are singletons); average occurrences: 1.790; average spacing: 6.798
[M::worker_pipeline::0.064*4.10] mapped 787 sequences
[M::worker_pipeline::0.073*3.66] mapped 787 sequences
[M::main] Version: 2.15-r905
[M::main] CMD: minimap2 -x map-ont -a --split-prefix /working2/rcug_lw/we_test/Wochenende/testdb/reads_R1 -t 12 testdb/ref.fa /working2/rcug_lw/we_test/Wochenende/testdb/reads_R1.fastq
[M::main] Real time: 0.075 sec; CPU: 0.270 sec; Peak RSS: 0.012 GB
[W::sam_hdr_parse] Duplicated sequence '1'
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
[M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 30 reads
Wochenende - Whole Genome/Metagenome Sequencing Alignment Pipeline
Wochenende was created by Dr. Colin Davenport and Tobias Scheithauer with help from many further contributors
version: 1.6.2 - Mar 2020

Meta/genome selected: testdb
######  Alignment  ######
minimap2 -x map-ont -a --split-prefix /working2/rcug_lw/we_test/Wochenende/testdb/reads_R1 -t 12 testdb/ref.fa /working2/rcug_lw/we_test/Wochenende/testdb/reads_R1.fastq > /working2/rcug_lw/we_test/Wochenende/testdb/reads_R1.sam
/mnt/ngsnfs/tools/miniconda3/envs/wochenende/bin/samtools view -@ 8 -bhS /working2/rcug_lw/we_test/Wochenende/testdb/reads_R1.sam > /working2/rcug_lw/we_test/Wochenende/testdb/reads_R1.bam
######  Sort BAM  ######
######  Index BAM  ######
######  samtools flagstat  ######
/mnt/ngsnfs/tools/miniconda3/envs/wochenende/bin/samtools flagstat /working2/rcug_lw/we_test/Wochenende/testdb/reads_R1.s.bam > /working2/rcug_lw/we_test/Wochenende/testdb/reads_R1.s.bam.flagstat.txt
######  Get unmapped reads from BAM  ######
/mnt/ngsnfs/tools/miniconda3/envs/wochenende/bin/samtools view -f 4 /working2/rcug_lw/we_test/Wochenende/testdb/reads_R1.s.bam | /mnt/ngsnfs/tools/miniconda3/envs/wochenende/bin/samtools bam2fq - > /working2/rcug_lw/we_test/Wochenende/testdb/reads_R1.s.bam.unmapped.fastq
/mnt/ngsnfs/tools/miniconda3/envs/wochenende/bin/samtools view -f 4 /working2/rcug_lw/we_test/Wochenende/testdb/reads_R1.s.bam | /mnt/ngsnfs/tools/miniconda3/envs/wochenende/bin/samtools bam2fq - > /working2/rcug_lw/we_test/Wochenende/testdb/reads_R1.s.bam.unmapped.fastq
######  Index BAM  ######
######  Samtools index stats - chromosome counts  ######
Filelist item: Alignment
Filelist item: /working2/rcug_lw/we_test/Wochenende/testdb/reads_R1.fastq
Filelist item: /working2/rcug_lw/we_test/Wochenende/testdb/reads_R1.bam
Filelist item: Sort BAM
Filelist item: /working2/rcug_lw/we_test/Wochenende/testdb/reads_R1.bam
Filelist item: /working2/rcug_lw/we_test/Wochenende/testdb/reads_R1.s.bam
Filelist item: Samtools calmd
Filelist item: /working2/rcug_lw/we_test/Wochenende/testdb/reads_R1.s.bam
Filelist item: /working2/rcug_lw/we_test/Wochenende/testdb/reads_R1.s.calmd.bam
Filelist item: Samtools index stats - chromosome counts
Filelist item: /working2/rcug_lw/we_test/Wochenende/testdb/reads_R1.s.calmd.bam
Filelist item: /working2/rcug_lw/we_test/Wochenende/testdb/reads_R1.s.calmd.bam.txt