diaAsm 组装
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docker run -it --rm -v $PWD/dipasm/DipAsm:/wd/dipasm/DipAsm/ -e HOSTWD=$PWD/dipasm/DipAsm -v /var/run/docker.sock:/var/run/docker.sock -v /data_raid1/gene_data/data_archive/xbgy/pig_hic_hifi:/data dipasm:latest /bin/bash
python pipeline.py --hic-path /data/bgi --pb-path /data/hifi --sample pig --prefix asm
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sudo docker pull google/deepvariant:0.8.0
依赖deepvariant
修改dv.sh gcr的无法下载升级到最新版本
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W third_party/nucleus/io/sam_reader.cc:534] Could not read base quality scores m64061_200704_010207/21954972/ccs: Not found: Could not read base quality scores
替换fasta 为fastq
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time: cannot run /tools/biobambam2/2.0.87-release-20180301132713/x86_64-etch-linux-gnu/bin/bammarkduplicates2: No such file or directory
Command exited with non-zero status 127
0.00user 0.00system 0:00.00elapsed 0%CPU (0avgtext+0avgdata 1236maxresident)k
8inputs+8outputs (0major+31minor)pagefaults 0swaps
安装
biobambam2
Dockerfile中有该安装步骤 但是不知道镜像中没有该工具 用axel下载快一些 -
bgzip没有安装 安装tabix会同时安装bgzip
apt install tabix