{"id":583,"date":"2024-03-21T19:23:23","date_gmt":"2024-03-21T11:23:23","guid":{"rendered":"https:\/\/linguopeng.top\/?p=583"},"modified":"2024-12-12T16:12:03","modified_gmt":"2024-12-12T08:12:03","slug":"16s_lac_bif-sh","status":"publish","type":"post","link":"https:\/\/linguopeng.top\/?p=583","title":{"rendered":"16s_lac_bif.sh"},"content":{"rendered":"\n<pre class=\"wp-block-code\"><code>qiime2.slurm\n#!\/bin\/bash\n#SBATCH -p batch\n#SBATCH -N 1\n#SBATCH -n 30\n.\/qiime2.sh\n#bac: V3,17, 341F, CCTACGGGNGGCWGCAG\n#       V4, 20, 806R, GGACTACHVGGGTWTCTAAT\n#bif\uff1agreol:23,22: TCCGATTACGAYCGYGAGAAGCT\/ CSGCYTCGGTSGTCAGGAACAG\n#lac\uff1agroel:20,20: GCYGGTGCWAACCCNGTTGG\/ AANGTNCCVCGVATCTTGTT\n#!\/bin\/bash\n# HEADER - Do Not Modify!\nset -e\nshopt -s expand_aliases\nexport LC_ALL=C\n#########\nexport PATH=\"\/public\/software\/apps\/bin:\/public\/software\/apps\/bin\/singularity:\/public\/software\/apps\/go\/bin:$PATH\"\nalias qiime=\"singularity exec \/home\/stu_2\/linguopeng\/sif\/qiime2_2022.2_240110.sif qiime\"\nalias biom=\"singularity exec \/home\/stu_2\/linguopeng\/sif\/qiime2_2022.2_240110.sif biom\"\nexport lgp=\/home\/stu_2\/linguopeng\/qiime2_240314\/test\n## mkdir -p ${lgp}\/seqs\n# singularity instance start qiime2_2022.2_240110.sif qiime2\n# singularity shell instance:\/\/qiime2\nmkdir -p ${lgp}\/results\nmkdir -p ${lgp}\/results\/taxa\n## Samples_list\ncd ${lgp}\/seqs\necho \"sample-id,absolute-filepath,direction\" > Samples_list.csv\nfor i in `ls *fastq.gz | awk '{print $0}'`;\ndo\nls $i | grep 1.fastq.gz | awk -v a=`echo $i | sed s\/_R1.fastq.gz\/\/` -v b=$PWD -v c=$i '{print a\",\"b\"\/\"c\",\"\"forward\"}' >> Samples_list.csv ;\nls $i | grep 2.fastq.gz | awk -v a=`echo $i | sed s\/_R2.fastq.gz\/\/` -v b=$PWD -v c=$i '{print a\",\"b\"\/\"c\",\"\"reverse\"}' >> Samples_list.csv ;\ndone\n## import data\nqiime tools import \\\n--type 'SampleData&#91;PairedEndSequencesWithQuality]' \\\n--input-path ${lgp}\/seqs\/Samples_list.csv \\\n--output-path ${lgp}\/seqs\/demux.qza \\\n--input-format PairedEndFastqManifestPhred33\n## demux\nqiime demux summarize \\\n--i-data demux.qza \\\n--o-visualization demux.qzv\ncd ${lgp}\/results\nqiime dada2 denoise-paired \\\n--i-demultiplexed-seqs ${lgp}\/seqs\/demux.qza \\\n--p-trim-left-f 17 --p-trim-left-r 20 \\\n--p-trunc-len-f 260 --p-trunc-len-r 260 \\\n--o-table ${lgp}\/results\/table.qza \\\n--o-representative-sequences ${lgp}\/results\/rep-seqs.qza \\\n--o-denoising-stats ${lgp}\/results\/denoising-stats.qza --p-n-threads 30\nqiime feature-table summarize \\\n--i-table ${lgp}\/results\/table.qza \\\n--o-visualization ${lgp}\/results\/table.qzv \\\n--m-sample-metadata-file ${lgp}\/metadata.txt\nqiime feature-table tabulate-seqs \\\n--i-data ${lgp}\/results\/rep-seqs.qza \\\n--o-visualization ${lgp}\/results\/rep-seqs.qzv\n## exported-table\nqiime tools export \\\n--input-path ${lgp}\/results\/table.qza \\\n--output-path ${lgp}\/results\/exported-table\n## feature-table.tsv\nbiom convert -i ${lgp}\/results\/exported-table\/feature-table.biom -o ${lgp}\/results\/exported-table\/feature-table.tsv --to-tsv\n## rooted-tree.qza\nqiime phylogeny align-to-tree-mafft-fasttree \\\n--i-sequences ${lgp}\/results\/rep-seqs.qza \\\n--o-alignment ${lgp}\/results\/aligned-rep-seqs.qza \\\n--o-masked-alignment ${lgp}\/results\/masked-aligned-rep-seqs.qza \\\n--o-tree ${lgp}\/results\/unrooted-tree.qza \\\n--o-rooted-tree ${lgp}\/results\/rooted-tree.qza\n\n## alpha-rarefaction\nqiime diversity alpha-rarefaction \\\n--i-table ${lgp}\/results\/table.qza \\\n--i-phylogeny ${lgp}\/results\/rooted-tree.qza \\\n--p-max-depth 100000 \\\n--m-metadata-file ${lgp}\/metadata.txt \\\n--o-visualization ${lgp}\/results\/alpha-rarefaction.qzv\n## core-metrics-results\nqiime diversity core-metrics-phylogenetic \\\n--i-phylogeny ${lgp}\/results\/rooted-tree.qza \\\n--i-table ${lgp}\/results\/table.qza \\\n--p-sampling-depth 10000 \\\n--m-metadata-file ${lgp}\/metadata.txt \\\n--output-dir ${lgp}\/results\/core-metrics-results\n\n## chao1\u3001simpson\u3001ace\u3001euclidean\nqiime diversity alpha \\\n--i-table ${lgp}\/results\/table.qza \\\n--p-metric chao1 \\\n--o-alpha-diversity ${lgp}\/results\/core-metrics-results\/chao1_vector.qza\n\nqiime diversity alpha \\\n--i-table ${lgp}\/results\/table.qza \\\n--p-metric simpson \\\n--o-alpha-diversity ${lgp}\/results\/core-metrics-results\/simpson_vector.qza\n\nqiime diversity alpha \\\n--i-table ${lgp}\/results\/table.qza \\\n--p-metric ace \\\n--o-alpha-diversity ${lgp}\/results\/core-metrics-results\/simpson_vector.qza\n\nqiime diversity beta \\\n--i-table ${lgp}\/results\/table.qza \\\n--p-metric euclidean \\\n--o-distance-matrix ${lgp}\/results\/core-metrics-results\/euclidean_distance_matrix.qza\n## Beta_distance_significance\ndistance=\"euclidean jaccard bray_curtis unweighted_unifrac weighted_unifrac\"\nfor i in $distance;\ndo\nfor j in `awk 'NR==1{for(k=2;k&lt;=NF;k++) print $k}' ${lgp}\/metadata.txt`;\ndo\nqiime diversity beta-group-significance \\\n--i-distance-matrix ${lgp}\/results\/core-metrics-results\/${i}_distance_matrix.qza \\\n--m-metadata-file ${lgp}\/metadata.txt \\\n--m-metadata-column ${j} \\\n--o-visualization ${lgp}\/results\/core-metrics-results\/${i}_${j}_significance.qzv \\\n--p-pairwise\ndone\ndone\n# alpha_index_significance\nindex=\"observed_features evenness shannon faith_pd chao1 simpson\"\nfor k in $index;\ndo\nqiime diversity alpha-group-significance \\\n--i-alpha-diversity ${lgp}\/results\/core-metrics-results\/${k}_vector.qza \\\n--m-metadata-file ${lgp}\/metadata.txt \\\n--o-visualization ${lgp}\/results\/core-metrics-results\/${k}_significance.qzv\ndone\n## export data\nmkdir -p ${lgp}\/results\/core-metrics-results\/alpha_diversity ${lgp}\/results\/core-metrics-results\/beta_diversity\nfor i in $distance;\ndo\nqiime tools export \\\n--input-path ${lgp}\/results\/core-metrics-results\/${i}_distance_matrix.qza \\\n--output-path ${lgp}\/results\/core-metrics-results\/beta_diversity\/${i}_distance_matrix\ndone\nfor k in $index;\ndo\nqiime tools export \\\n--input-path ${lgp}\/results\/core-metrics-results\/${k}_vector.qza \\\n--output-path ${lgp}\/results\/core-metrics-results\/alpha_diversity\/${k}\ndone\n## annotation 16s\nqiime feature-classifier classify-sklearn \\\n# --i-classifier \/database\/silva-132-99-nb-341F-806R_classifier.qza \\\n--i-classifier \/home\/stu_2\/linguopeng\/database\/silva-132-99-nb-341F-806R_classifier.qza \\\n--i-reads ${lgp}\/results\/rep-seqs.qza \\\n--o-classification ${lgp}\/results\/taxa\/taxonomy.qza --p-n-jobs 30\n\nqiime metadata tabulate \\\n--m-input-file ${lgp}\/results\/taxa\/taxonomy.qza \\\n--o-visualization ${lgp}\/results\/taxa\/taxonomy.qzv\n## exported-table annotation\nqiime tools export \\\n--input-path ${lgp}\/results\/taxa\/taxonomy.qza \\\n--output-path ${lgp}\/results\/exported-table\n###############filter-samples\n# qiime feature-table filter-samples \\\n# --i-table ${lgp}\/results\/table.qza \\\n# --p-min-frequency 10000 \\\n# --o-filtered-table ${lgp}\/results\/table-10k.qza\n# qiime taxa barplot \\\n# --i-table ${lgp}\/results\/table-10k.qza \\\n# --i-taxonomy ${lgp}\/results\/taxa\/taxonomy.qza \\\n# --m-metadata-file ${lgp}\/metadata.txt \\\n# --o-visualization ${lgp}\/results\/taxa\/taxa-bar-plots.qzv\n# # filtered-table\n# qiime feature-table filter-features \\\n# --i-table ${lgp}\/results\/table-10k.qza \\\n# --p-min-frequency 50 \\\n# --p-min-samples 4 \\\n# --o-filtered-table ${lgp}\/results\/filtered-table.qza\n##############un_filter-samples\nqiime taxa barplot \\\n--i-table ${lgp}\/results\/table.qza \\\n--i-taxonomy ${lgp}\/results\/taxa\/taxonomy.qza \\\n--m-metadata-file ${lgp}\/metadata.txt \\\n--o-visualization ${lgp}\/results\/taxa\/taxa-bar-plots.qzv\nmv ${lgp}\/results\/table.qza ${lgp}\/results\/filtered-table.qza\n## rel-abundance\nmkdir -p ${lgp}\/results\/rel-abundance\nfor i in {2..6};\ndo\nqiime taxa collapse \\\n--i-table ${lgp}\/results\/filtered-table.qza \\\n--i-taxonomy ${lgp}\/results\/taxa\/taxonomy.qza \\\n--p-level $i \\\n--o-collapsed-table ${lgp}\/results\/rel-abundance\/table-l${i}.qza\nqiime feature-table relative-frequency \\\n--i-table ${lgp}\/results\/rel-abundance\/table-l${i}.qza \\\n--o-relative-frequency-table ${lgp}\/results\/rel-abundance\/rel-abun-l${i}.qza\nqiime tools export \\\n--input-path ${lgp}\/results\/rel-abundance\/rel-abun-l${i}.qza \\\n--output-path ${lgp}\/results\/rel-abun-l${i}\nbiom convert -i ${lgp}\/results\/rel-abun-l${i}\/feature-table.biom -o ${lgp}\/results\/rel-abun-l${i}\/rel-abun-l${i}.tsv --to-tsv\ndone\ncd ${lgp}\/results\/\nunzip ${lgp}\/results\/rep-seqs.qza\nmkdir -p ${lgp}\/results\/picrust2\ncp -rf ${lgp}\/results\/*\/data\/dna-sequences.fasta ${lgp}\/results\/picrust2\/\ncp -rf ${lgp}\/results\/exported-table\/feature-table.biom ${lgp}\/results\/picrust2\/\nalias picrust2_pipeline.py=\"singularity exec \/home\/stu_2\/linguopeng\/sif\/qiime2_2022.2_240110.sif picrust2_pipeline.py\"\nalias add_descriptions.py=\"singularity exec \/home\/stu_2\/linguopeng\/sif\/qiime2_2022.2_240110.sif add_descriptions.py\"\nalias pathway_pipeline.py=\"singularity exec \/home\/stu_2\/linguopeng\/sif\/qiime2_2022.2_240110.sif add_descriptions.py\"\npicrust2_pipeline.py -s ${lgp}\/results\/picrust2\/dna-sequences.fasta \\\n-i ${lgp}\/results\/picrust2\/feature-table.biom \\\n-o ${lgp}\/results\/picrust2\/picrust2_results \\\n-p 30\n## EC\u6ce8\u91ca\u7ed3\u679c\nadd_descriptions.py -i ${lgp}\/results\/picrust2\/picrust2_results\/EC_metagenome_out\/pred_metagenome_unstrat.tsv.gz -m EC \\\n-o ${lgp}\/results\/picrust2\/picrust2_results\/EC_metagenome_out\/pred_metagenome_unstrat_descrip.tsv.gz\n\n## KO\u6dfb\u52a0\u6ce8\u91ca\nadd_descriptions.py -i ${lgp}\/results\/picrust2\/picrust2_results\/KO_metagenome_out\/pred_metagenome_unstrat.tsv.gz -m KO \\\n-o ${lgp}\/results\/picrust2\/picrust2_results\/KO_metagenome_out\/pred_metagenome_unstrat_descrip.tsv.gz\n\n## pathway\u6dfb\u52a0\u6ce8\u91ca\uff0c\u57fa\u4e8eMetaCyc\u6570\u636e\u5e93\nadd_descriptions.py -i ${lgp}\/results\/picrust2\/picrust2_results\/pathways_out\/path_abun_unstrat.tsv.gz -m METACYC \\\n-o ${lgp}\/results\/picrust2\/picrust2_results\/pathways_out\/path_abun_unstrat_descrip.tsv.gz\n# \n# # #KEGG \u4ea4\u4e92\u8fd0\u884c \nsingularity shell \/home\/stu_2\/linguopeng\/sif\/qiime2_2022.2_240110.sif\npathway_pipeline.py -i ${lgp}\/results\/picrust2\/picrust2_results\/KO_metagenome_out\/pred_metagenome_unstrat.tsv.gz \\\n-o ${lgp}\/results\/picrust2\/picrust2_results\/KEGG_pathways \\--no_regroup \\\n--map  \/home\/foodbio\/miniconda3\/envs\/qiime2-2022.2\/lib\/python3.8\/site-packages\/picrust2\/default_files\/pathway_mapfiles\/KEGG_pathways_to_KO.tsv\n#KEGG\u901a\u8def\u5c42\u7ea7\u6c47\u603b\nzcat ${lgp}\/results\/picrust2\/picrust2_results\/KO_metagenome_out\/pred_metagenome_unstrat.tsv.gz \\\n> ${lgp}\/results\/picrust2\/picrust2_results\/KEGG.KO.txt\npython3 \/home\/foodbio\/summarizeAbundance.py \\\n-i ${lgp}\/results\/picrust2\/picrust2_results\/KEGG.KO.txt \\\n-m  \/home\/foodbio\/KO1-4.txt \\\n-c 2,3,4 -s ',+,+,' -n raw \\\n-o ${lgp}\/results\/picrust2\/picrust2_results\/KEGG<\/code><\/pre>\n","protected":false},"excerpt":{"rendered":"","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[1],"tags":[],"class_list":["post-583","post","type-post","status-publish","format-standard","hentry","category-uncategorized"],"_links":{"self":[{"href":"https:\/\/linguopeng.top\/index.php?rest_route=\/wp\/v2\/posts\/583","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/linguopeng.top\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/linguopeng.top\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/linguopeng.top\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/linguopeng.top\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=583"}],"version-history":[{"count":9,"href":"https:\/\/linguopeng.top\/index.php?rest_route=\/wp\/v2\/posts\/583\/revisions"}],"predecessor-version":[{"id":835,"href":"https:\/\/linguopeng.top\/index.php?rest_route=\/wp\/v2\/posts\/583\/revisions\/835"}],"wp:attachment":[{"href":"https:\/\/linguopeng.top\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=583"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/linguopeng.top\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=583"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/linguopeng.top\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=583"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}