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haowenz / chromap

Fast alignment and preprocessing of chromatin profiles
https://haowenz.github.io/chromap/
MIT License
192 stars 21 forks source link

why so slow? #165

Closed zhaotao1987 closed 4 months ago

zhaotao1987 commented 5 months ago

Hi Haowen,

I used the following command for chromap mapping: chromap --preset hic -x $index -t $cpu -q $mapQ -r $asm -1 $read1 -2 $read2 --SAM -o $asm.hic.aligned.Q_"$mapQ".sam compared to bwa mem, I found it not that fast as expected, in actual, much slower even, also it generates over 400 temporary files, and it took hours to merge and combine, could you help and give instruction about how to improve? Thanks very much! Best, Tao

mourisl commented 5 months ago

The sam file is pretty large to merge and generate. How's the speed when outputting in the pairs format?

haowenz commented 5 months ago

Output in pairs format would be faster. If you use BWA, you still have to run samtools after, which should be even slower.