hostname
+ hostname
cd /data/app/NextPolish/test_data/01_rundir/01.score_chain/03.map.ref.sh.work/map_genome2
+ cd /data/app/NextPolish/test_data/01_rundir/01.score_chain/03.map.ref.sh.work/map_genome2
(  /data/app/NextPolish/bin/bwa mem -p -t 3 /data/app/NextPolish/test_data/./01_rundir/01.score_chain/input.genome.fasta.sgs /data/app/NextPolish/test_data/./01_rundir/input.sgspart.001.fastq.gz|/data/app/NextPolish/bin/samtools view --threads 5 -F 0x4 -b - |/data/app/NextPolish/bin/samtools fixmate -m --threads 3 - - |/data/app/NextPolish/bin/samtools sort - -m 2g --threads 3 -o sgs.part001.sort.bam )
+ /data/app/NextPolish/bin/bwa mem -p -t 3 /data/app/NextPolish/test_data/./01_rundir/01.score_chain/input.genome.fasta.sgs /data/app/NextPolish/test_data/./01_rundir/input.sgspart.001.fastq.gz
+ /data/app/NextPolish/bin/samtools view --threads 5 -F 0x4 -b -
+ /data/app/NextPolish/bin/samtools fixmate -m --threads 3 - -
+ /data/app/NextPolish/bin/samtools sort - -m 2g --threads 3 -o sgs.part001.sort.bam
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 119 sequences (17764 bp)...
[M::process] 1 single-end sequences; 118 paired-end sequences
[M::mem_process_seqs] Processed 1 reads in 0.001 CPU sec, 0.000 real sec
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 57, 0, 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: (283, 330, 385)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (79, 589)
[M::mem_pestat] mean and std.dev: (326.46, 72.57)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 691)
[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 118 reads in 0.014 CPU sec, 0.005 real sec
[gzclose] buffer error