需要比对的结果，在snakemake脚本里添加log

Posted on | Edited on

log名要添加{sample}，不然出现如下错误

1
2
3
4
[qizhengyang@node1 gatk_snakemake]$ snakemake -n --quiet
SyntaxError:
Not all output, log and benchmark files of rule star_1pass_align contain the same wildcards. This is crucial though, in order to avoid that two or more jobs write to the same file.
  File "/home02/qizhengyang/qizhengyang/gatk_snakemake/Snakefile", line 63, in <module>

开始跑，大概 2019-3-2 21:10

1
2
3
snakemake -n --quiet
pestat
nohup snakemake --cluster "qsub -q low" --jobs 100 &> snakemake.out &

2019-3-2 23:52:22 一切正常

打算关闭终端，查看用：

1
ps aux|grep Snakefile|grep -v grep

2019-3-3 15:34:06

1
2
3
4
150 of 255 steps (59%) done
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: /home02/qizhengyang/qizhengyang/gatk_snakemake/.snakemake/log/2019-03-02T210938.398049.snakemake.log

error picard_markduplicates

1
2
3
4
5
6
OpenJDK 64-Bit Server VM warning: INFO: os::commit_memory(0x00002b6141200000, 1882193920, 0) failed; error='无法分配内存' (errno=12)
#
# There is insufficient memory for the Java Runtime Environment to continue.
# Native memory allocation (mmap) failed to map 1882193920 bytes for committing reserved memory.
# An error report file with more information is saved as:
# /home02/qizhengyang/qizhengyang/gatk_snakemake/hs_err_pid14847.log
1
2
snakemake -n --quiet
nohup snakemake --cluster "qsub -q low" --jobs 100 &>> snakemake.out &

2019-3-5 11:37:02

用时：

开始：[Sat Mar 2 21:09:38 2019]

结束：[Sun Mar 3 08:21:52 2019]

中间出错过一次，java -Xmx40g -jar $picard MarkDuplicates，下次设置JVM最大可用内存为80g

开始：[Sun Mar 3 16:11:13 2019]

结束：[Mon Mar 4 22:12:01 2019]

总用时 ~41 小时

附运行代码

添加log没有用，比对信息有输出

HB-10-1Log.final.out