BS-Seeker2

BS-Seeker2在运行过程中会产生大量中间临时文件，默认写入的位置为系统目录/tmp，很容易将/tmp写满。

$ lsload c07n01
HOST_NAME       status  r15s   r1m  r15m   ut    pg  ls    it   tmp   swp   mem
c07n01              ok   4.2   4.0   7.3  11%   0.0   1     0    0M  2.4G  164G

$ du -sh /tmp/*
0   /tmp/46242617.tmpdir
37G /tmp/bs_seeker2_HP301-rep1.bsseeker2.pe.bam_-bowtie2-local-TMP-V72bZD
70G /tmp/bs_seeker2_HP301_rep3_S3.bsseeker2.pe.bam_-bowtie2-local-TMP-exeKfc
33G /tmp/bs_seeker2_IL14H_rep1_S4.bsseeker2.pe.bam_-bowtie2-local-TMP-73XO7p
69G /tmp/bs_seeker2_IL14H_rep2_S4.bsseeker2.pe.bam_-bowtie2-local-TMP-uUI9K7
29G /tmp/bs_seeker2_Ki11-rep1-reseq.bsseeker2.pe.bam_-bowtie2-local-TMP-0kc54M
38G /tmp/bs_seeker2_Ki11_rep1_S3.bsseeker2.pe.bam_-bowtie2-local-TMP-ol3mRa
57G /tmp/bs_seeker2_Ki11_rep2_S3.bsseeker2.pe.bam_-bowtie2-local-TMP-Qu2rUy
31G /tmp/bs_seeker2_Ki3_rep1_S3.bsseeker2.pe.bam_-bowtie2-local-TMP-26VhnT
71G /tmp/bs_seeker2_Ki3-rep2.bsseeker2.pe.bam_-bowtie2-local-TMP-YFwwHB

建议使用--temp_dir选项将临时文件位置改到自己的目录下。

#BSUB -J BS-Seeker2
#BSUB -n 10
#BSUB -R span[hosts=1]
#BSUB -o %J.out
#BSUB -e %J.err
#BSUB -q normal
mkdir tmp
bs_seeker2-align.py -1 sample.R1.fq -1 sample.R2.fq -o sample.bam -g genome.fa --temp_dir=./tmp

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