Commit f91f0e2d authored by Gonzalo S Nido's avatar Gonzalo S Nido
Browse files

Added pigz instead of gzip

parent 5d46a9f4
......@@ -4,7 +4,7 @@ echo "#### Updating Ubuntu dist..."
sudo apt update && sudo apt -y upgrade
echo "#### Installing some Ubuntu packages..."
sudo apt -y install unzip build-essential libncurses5-dev zlib1g-dev libbz2-dev liblzma-dev p7zip-full
sudo apt -y install unzip build-essential libncurses5-dev zlib1g-dev libbz2-dev liblzma-dev p7zip-full pigz
echo "#### Installing samtools 1.10..."
cd ~
......
......@@ -307,21 +307,21 @@ fi
echo -ne " 1.5 Extracting MT and Lambda methylation... "
CMD="cat ${output_dir}/CpG_context_b38_${sample_id}.dedup.txt | python3 ${ext_chr_srt} ${MT_chr_name} | gzip -nc > \
CMD="cat ${output_dir}/CpG_context_b38_${sample_id}.dedup.txt | python3 ${ext_chr_srt} ${MT_chr_name} | pigz -nc > \
${output_dir}/CpG_context_chrM_${sample_id}.dedup.txt.gz && \
cat ${output_dir}/CpG_context_b38_${sample_id}.dedup.txt | python3 ${ext_chr_srt} ${LAMBDA_chr_name} | gzip -nc > \
cat ${output_dir}/CpG_context_b38_${sample_id}.dedup.txt | python3 ${ext_chr_srt} ${LAMBDA_chr_name} | pigz -nc > \
${output_dir}/CpG_context_LAMBDA_${sample_id}.dedup.txt.gz && \
gzip ${output_dir}/CpG_context_b38_${sample_id}.dedup.txt \n\
cat ${output_dir}/CHH_context_b38_${sample_id}.dedup.txt | python3 ${ext_chr_srt} ${MT_chr_name} | gzip -nc > \
pigz ${output_dir}/CpG_context_b38_${sample_id}.dedup.txt \n\
cat ${output_dir}/CHH_context_b38_${sample_id}.dedup.txt | python3 ${ext_chr_srt} ${MT_chr_name} | pigz -nc > \
${output_dir}/CHH_context_chrM_${sample_id}.dedup.txt.gz && \
cat ${output_dir}/CHH_context_b38_${sample_id}.dedup.txt | python3 ${ext_chr_srt} ${LAMBDA_chr_name} | gzip -nc > \
cat ${output_dir}/CHH_context_b38_${sample_id}.dedup.txt | python3 ${ext_chr_srt} ${LAMBDA_chr_name} | pigz -nc > \
${output_dir}/CHH_context_LAMBDA_${sample_id}.dedup.txt.gz && \
gzip ${output_dir}/CHH_context_b38_${sample_id}.dedup.txt \n\
cat ${output_dir}/CHG_context_b38_${sample_id}.dedup.txt | python3 ${ext_chr_srt} ${MT_chr_name} | gzip -nc > \
pigz ${output_dir}/CHH_context_b38_${sample_id}.dedup.txt \n\
cat ${output_dir}/CHG_context_b38_${sample_id}.dedup.txt | python3 ${ext_chr_srt} ${MT_chr_name} | pigz -nc > \
${output_dir}/CHG_context_chrM_${sample_id}.dedup.txt.gz && \
cat ${output_dir}/CHG_context_b38_${sample_id}.dedup.txt | python3 ${ext_chr_srt} ${LAMBDA_chr_name} | gzip -nc > \
cat ${output_dir}/CHG_context_b38_${sample_id}.dedup.txt | python3 ${ext_chr_srt} ${LAMBDA_chr_name} | pigz -nc > \
${output_dir}/CHG_context_LAMBDA_${sample_id}.dedup.txt.gz && \
gzip ${output_dir}/CHG_context_b38_${sample_id}.dedup.txt \n\
pigz ${output_dir}/CHG_context_b38_${sample_id}.dedup.txt \n\
zcat ${output_dir}/C??_context_LAMBDA_${sample_id}.dedup.txt.gz | python3 ${meth_prop} > \
${output_dir}/Lambda_meth_prop_${sample_id}.txt"
echo -e ${CMD} > ${log_dir}/1_5_extract_MT.cmd
......
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