STAR的速度为何如此诡异 / 开普饭

同样的fastq文件大小，时间完全不一样！

希望走过路过的小伙伴能检查一下自己的转录组数据，帮我测试一下你们的star，看看能不能发现这样的现象哈，欢迎发邮件跟我交流，我的邮箱是 jmzeng1314 在 163邮箱。

这个数据耗时约3个小时。

1.5G Dec 1 23:45 /MK2305-4LA_1.fq.gz 1.7G Dec 1 23:47 /MK2305-4LA_2.fq.gz MK2305-4LA /MK2305-4LA_1.fq.gz /MK2305-4LA_2.fq.gz May 23 20:22:34 ..... started STAR run May 23 20:22:35 ..... loading genome May 23 20:25:15 ..... started 1st pass mapping May 23 21:10:43 ..... finished 1st pass mapping May 23 21:10:44 ..... inserting junctions into the genome indices May 23 21:13:32 ..... started mapping May 23 23:14:01 ..... finished successfully

下面的耗时约16个小时

1.9G Dec 2 10:17 /MK2313-3RA_1.fq.gz 2.1G Dec 2 10:02 /MK2313-3RA_2.fq.gz MK2313-3RA /MK2313-3RA_1.fq.gz /MK2313-3RA_2.fq.gz May 23 23:56:03 ..... started STAR run May 23 23:56:03 ..... loading genome May 23 23:58:30 ..... started 1st pass mapping May 24 05:05:39 ..... finished 1st pass mapping May 24 05:05:41 ..... inserting junctions into the genome indices May 24 05:08:35 ..... started mapping May 24 15:42:39 ..... finished successfully

从文件大小来看，看不出区别：

2.3G May 23 23:26 MK2305-4LA.bam 2.4M May 23 23:27 MK2305-4LA.bam.bai 71M May 23 23:13 MK2305-4LA_Chimeric.out.junction 587M May 23 23:13 MK2305-4LA_Chimeric.out.sam 20M May 23 23:49 MK2305-4LA.counts.txt 332 May 23 23:49 MK2305-4LA.counts.txt.summary 439 May 23 23:28 MK2305-4LA.flagstat 1.9K May 23 23:13 MK2305-4LA_Log.final.out 24K May 23 23:13 MK2305-4LA_Log.out 15K May 23 23:13 MK2305-4LA_Log.progress.out 8.1M May 23 23:13 MK2305-4LA_SJ.out.tab 2.8G May 24 15:58 MK2313-3RA.bam 2.5M May 24 15:59 MK2313-3RA.bam.bai 108M May 24 15:42 MK2313-3RA_Chimeric.out.junction 886M May 24 15:42 MK2313-3RA_Chimeric.out.sam 20M May 24 16:27 MK2313-3RA.counts.txt 332 May 24 16:27 MK2313-3RA.counts.txt.summary 439 May 24 16:00 MK2313-3RA.flagstat 1.9K May 24 15:42 MK2313-3RA_Log.final.out 24K May 24 15:42 MK2313-3RA_Log.out 42K May 24 15:42 MK2313-3RA_Log.progress.out 8.2M May 24 15:42 MK2313-3RA_SJ.out.tab

我的star命令是：

if [ ! -f $sample.bam ]; then #$bin_star --runThreadN 5 --genomeLoad LoadAndKeep --genomeDir $star_index --readFilesCommand zcat --readFilesIn $analysis_dir/clean/${fq1_base}_val_1.fq.gz $analysis_dir/clean/${fq2_base}_val_2.fq.gz --outFileNamePrefix ${sample}_ $bin_star --runThreadN 5 \ --genomeDir $star_index \ --twopassMode Basic --outReadsUnmapped None \ --chimSegmentMin 12 \ --alignIntronMax 100000 \ --chimSegmentReadGapMax parameter 3 \ --alignSJstitchMismatchNmax 5 -1 5 5 \ --readFilesCommand zcat \ --readFilesIn $analysis_dir/clean/${fq1_base}_val_1.fq.gz \ $analysis_dir/clean/${fq2_base}_val_2.fq.gz \ --outFileNamePrefix ${sample}_ fi

STAR的速度为何如此诡异

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