{"id":571,"date":"2024-03-21T10:05:38","date_gmt":"2024-03-21T02:05:38","guid":{"rendered":"https:\/\/linguopeng.top\/?p=571"},"modified":"2025-04-10T10:20:58","modified_gmt":"2025-04-10T02:20:58","slug":"meta-sh","status":"publish","type":"post","link":"https:\/\/linguopeng.top\/?p=571","title":{"rendered":"meta.sh"},"content":{"rendered":"\n<pre class=\"wp-block-code\"><code>meta.slurm\n#!\/bin\/bash\n#SBATCH -p batch\n#SBATCH -n 30\n# sh meta.sh\n.\/meta.sh\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 fastqc=\"singularity exec \/public\/bio\/database\/sif\/MetaGenome.sif fastqc\"\nalias fastp=\"singularity exec \/public\/bio\/database\/sif\/MetaGenome.sif fastp\"\nalias bowtie2-build=\"singularity exec \/public\/bio\/database\/sif\/MetaGenome.sif bowtie2-build\"\nalias bowtie2=\"singularity exec \/public\/bio\/database\/sif\/MetaGenome.sif bowtie2\"\nalias samtools=\"singularity exec \/public\/bio\/database\/sif\/MetaGenome.sif samtools\"\nalias kraken2=\"singularity exec \/public\/bio\/database\/sif\/MetaGenome.sif kraken2\"\nalias bracken=\"singularity exec \/public\/bio\/database\/sif\/MetaGenome.sif bracken\"\nalias kraken-biom=\"singularity exec \/public\/bio\/database\/sif\/MetaGenome.sif kraken-biom\"\nalias biom=\"singularity exec \/public\/bio\/database\/sif\/MetaGenome.sif biom\"\nalias megahit=\"singularity exec \/public\/bio\/database\/sif\/MetaGenome.sif megahit\"\nalias quast.py=\"singularity  exec \/public\/bio\/database\/sif\/MetaGenome.sif quast.py \"\nalias prokka=\"singularity  exec \/public\/bio\/database\/sif\/MetaGenome.sif prokka \"\nalias seqtk=\"singularity  exec \/public\/bio\/database\/sif\/MetaGenome.sif seqtk \"\nalias cd-hit-est=\"singularity  exec \/public\/bio\/database\/sif\/MetaGenome.sif cd-hit-est \"\nalias perl=\"singularity  exec \/public\/bio\/database\/sif\/MetaGenome.sif perl \"\nalias salmon=\"singularity  exec \/public\/bio\/database\/sif\/MetaGenome.sif salmon\"\nalias emapper.py=\"singularity  exec \/public\/bio\/database\/sif\/emapper.sif emapper.py\"\nalias emapperx.R=\"singularity  exec \/public\/bio\/database\/sif\/emapper.sif emapperx.R\"\nalias diamond=\"singularity exec \/public\/bio\/database\/sif\/MetaGenome.sif diamond\"\nalias salmon=\"singularity exec \/public\/bio\/database\/sif\/MetaGenome.sif salmon\"\nalias Rscript=\"singularity  exec \/public\/bio\/database\/sif\/MetaGenome.sif Rscript\"\n#level=S\n# # HEADER END\n# cd \/home\/stu_2\/PRL\/\n# mkdir -p P1.data_filter\/01.quality\n# cd P1.data_filter\/01.quality\n# mkdir .\/qc\n# #########fastqc#######\n# for i in `ls \/home\/stu_2\/PRL\/cleanreads | grep _clean_r1.gz`\n# do\n# fastqc  --outdir .\/qc  --threads 16  \/home\/stu_2\/PRL\/cleanreads\/${i%_clean_r1.gz*}_clean_r1.gz  \/home\/stu_2\/PRL\/cleanreads\/${i%_clean_r1.gz*}_clean_r2.gz \n# done\n# #########fastp#######\n# mkdir .\/clean_data\n# for i in `ls \/home\/stu_2\/PRL\/cleanreads | grep _clean_r1.gz`\n# do\n# fastp  --thread  16 -i \/home\/stu_2\/PRL\/cleanreads\/${i%_clean_r1.gz*}_clean_r1.gz -I  \/home\/stu_2\/PRL\/cleanreads\/${i%_clean_r1.gz*}_clean_r2.gz  -o clean_data\/${i%_clean_r1.gz*}_1.fq.gz -O clean_data\/${i%_clean_r1.gz*}_2.fq.gz -j  clean_data\/${i%_clean_r1.gz*}.fastp.json -h  clean_data\/${i%_clean_r1.gz*}.fastp.html\n# done\n# #########bowtie2#######\n# # bowtie2-build  genome.fa genome.db\n# # bowtie2-build  c57.fa c57.db \n# # bowtie2-build  hg38.fa hg38.db\n# cd ..\n# mkdir -p 02.contaminant &amp;&amp; cd 02.contaminant\n# #########sam#######\n# mkdir -p sam\n# for i in `ls \/home\/stu_2\/PRL\/cleanreads | grep _clean_r1.gz`\n# do\n# bowtie2 --threads 24 -x \/home\/stu_2\/linguopeng\/database\/genome\/hg38.db  -1 ..\/01.quality\/clean_data\/${i%_clean_r1.gz*}_1.fq.gz -2 ..\/01.quality\/clean_data\/${i%_clean_r1.gz*}_2.fq.gz -S .\/sam\/${i%_clean_r1.gz*}.sam 2>.\/sam\/${i%_clean_r1.gz*}.map.log \n# done\n# #########bam#######\n# mkdir -p bam\n# for i in `ls \/home\/stu_2\/PRL\/cleanreads | grep _clean_r1.gz`\n# do\n# samtools  view -@ 24 -f 12 .\/sam\/${i%_clean_r1.gz*}.sam >.\/bam\/${i%_clean_r1.gz*}.unmap.bam \n# done\n# rm -rf sam\n# #########fastq#######\n# mkdir clean_unmap\n# for i in `ls \/home\/stu_2\/PRL\/cleanreads | grep _clean_r1.gz`\n# do\n# samtools fastq -1 .\/clean_unmap\/${i%_clean_r1.gz*}_1.clean.fq.gz -2 .\/clean_unmap\/${i%_clean_r1.gz*}_2.clean.fq.gz -s .\/clean_unmap\/${i%_clean_r1.gz*}_singleton.clean.fq.gz .\/bam\/${i%_clean_r1.gz*}.unmap.bam \n# done\n# #######kraken2#######\n# cd \/home\/stu_2\/PRL\/P1.data_filter\/02.contaminant\n# cd ..\/..\/\n# mkdir -p P2.Taxonomic_profiling\/1.taxon &amp;&amp; cd P2.Taxonomic_profiling\/1.taxon\n# mkdir kraken\n# for i in `ls \/home\/stu_2\/PRL\/cleanreads | grep _clean_r1.gz`\n# do\n# kraken2 --threads 24 --paired --db \/home\/stu_2\/linguopeng\/database\/k2 --report kraken\/${i%_clean_r1.gz*}.kreport --output kraken\/${i%_clean_r1.gz*}.kraken \/home\/stu_2\/PRL\/P1.data_filter\/02.contaminant\/clean_unmap\/${i%_clean_r1.gz*}_1.clean.fq.gz \/home\/stu_2\/PRL\/P1.data_filter\/02.contaminant\/clean_unmap\/${i%_clean_r1.gz*}_2.clean.fq.gz \n# done\n# ##########bracken#######\n# cd \/home\/stu_2\/PRL\/P2.Taxonomic_profiling\/1.taxon\n# # mkdir out_$level\n# # for i in `ls \/home\/stu_2\/PRL\/cleanreads | grep _clean_r1.gz`\n# # do\n# # bracken -d \/home\/stu_2\/linguopeng\/database\/k2 -i  kraken\/${i%_clean_r1.gz*}.kreport -o out_$level\/${i%_clean_r1.gz*}.bracken.$level -w out_$level\/${i%_clean_r1.gz*}.kreport  -l  $level -t 24\n# # done\n# kraken-biom  kraken\/*.kreport --max S  -o  .\/out_$level\/$level.biom  \n# biom  convert -i  .\/out_$level\/$level.biom -o  .\/out_$level\/$level.count.tsv.tmp  --to-tsv --header-key taxonomy\n# sed 's\/; g__\\(&#91;^;]\\+\\); s__\/; g__\\1; s__\\1 \/'   .\/out_$level\/$level.count.tsv.tmp >  .\/out_$level\/$level.taxID.count.tsv\n# sed  '\/^#\/! s\/^&#91;0-9]\\+\\t\\(.*&#91;A-Za-z]\\+__\\(&#91;^;]\\+\\)\\)$\/\\2\\t\\1\/'  .\/out_$level\/$level.taxID.count.tsv  >  .\/out_$level\/$level.taxName.count.tsv\n# sed -e '1d' -e '2s\/^#\/\/' .\/out_$level\/$level.taxName.count.tsv | awk -F \"\\t\" -v OFS=\"\\t\" '{NF--; print}' | sed 's\/\\t$\/\/' > .\/out_$level\/$level.count.tsv\n# Rscript  \/home\/stu_2\/linguopeng\/script\/draw_taxonBarplot.R    out_$level\/$level.count.tsv  10   out_$level\/$level.count.out\n# mkdir -p \/home\/stu_2\/PRL\/P3.Assembly_annotation\/01.megahit &amp;&amp; cd \/home\/stu_2\/PRL\/P3.Assembly_annotation\/01.megahit\n# for i in `ls \/home\/stu_2\/PRL\/P1.data_filter\/02.contaminant\/clean_unmap | grep _1.clean.fq.gz`\n# do\n# megahit \\\n   # -1 \/home\/stu_2\/PRL\/P1.data_filter\/02.contaminant\/clean_unmap\/${i%_1.clean.fq.gz*}_1.clean.fq.gz \\\n   # -2 \/home\/stu_2\/PRL\/P1.data_filter\/02.contaminant\/clean_unmap\/${i%_1.clean.fq.gz*}_2.clean.fq.gz \\\n   # --min-contig-len 500 \\\n   # --tmp-dir  .\/ \\\n   # --memory  0.8 \\\n   # --num-cpu-threads 24 \\\n   # --out-dir ${i%_clean_r1.gz*}_megahit \\\n   # --out-prefix  ${i%_clean_r1.gz*}\t\n# done\n# mkdir \/home\/stu_2\/PRL\/P3.Assembly_annotation\/02.quast  &amp;&amp; cd \/home\/stu_2\/PRL\/P3.Assembly_annotation\/02.quast\n# for i in `ls \/home\/stu_2\/PRL\/P1.data_filter\/02.contaminant\/clean_unmap | grep _1.clean.fq.gz`\n# do\n# ln -s \/home\/stu_2\/PRL\/P3.Assembly_annotation\/01.megahit\/${i%_1.clean.fq.gz*}_1.clean.fq.gz_megahit\/${i%_1.clean.fq.gz*}_1.clean.fq.gz.contigs.fa  .\/${i%_1.clean.fq.gz*}.megahit.fa\n# quast.py .\/${i%_1.clean.fq.gz*}.megahit.fa\n# done\n# mkdir -p \/home\/stu_2\/PRL\/P3.Assembly_annotation\/03.prokka  \n# cd \/home\/stu_2\/PRL\/P3.Assembly_annotation\/03.prokka \n# for i in `ls \/home\/stu_2\/PRL\/P1.data_filter\/02.contaminant\/clean_unmap | grep _1.clean.fq.gz`\n# do\n# ln -s \/home\/stu_2\/PRL\/P3.Assembly_annotation\/01.megahit\/${i%_1.clean.fq.gz*}_1.clean.fq.gz_megahit\/${i%_1.clean.fq.gz*}_1.clean.fq.gz.contigs.fa .\/${i%_1.clean.fq.gz*}.contigs.fa \n# prokka --outdir ${i%_1.clean.fq.gz*}_prokka --prefix ${i%_1.clean.fq.gz*} --addgenes --addmrna --locustag ${i%_1.clean.fq.gz*} --kingdom Bacteria --metagenome --cpus 24 .\/${i%_1.clean.fq.gz*}.contigs.fa \n# done\n# mkdir -p \/home\/stu_2\/PRL\/P3.Assembly_annotation\/04.cdhit \n# cd \/home\/stu_2\/PRL\/P3.Assembly_annotation\/04.cdhit \n# cat  ..\/03.prokka\/*_prokka\/*.ffn > all.trans.fa\n# cat  ..\/03.prokka\/*_prokka\/*.faa > all.pep.fa\n# sed -n \"s\/^>\\(\\S\\+\\).*$\/\\1\/p\"  all.pep.fa > all.cds.id\n# seqtk subseq  all.trans.fa all.cds.id > all.cds.fa\n# cd-hit-est -i all.cds.fa  -o  all.cds.cdhit -c 0.95 -aS 0.9  -M 204800 -T 30 \n# cp  all.cds.cdhit  unigene_cds.fasta\n# awk '$1 ~\/^>\/{print $1}'  all.cds.cdhit | sed 's\/^>\/\/' > unigene.id\n# seqtk  subseq  all.pep.fa unigene.id > unigene_pep.fasta\n# awk '{if($1~\/^>\/){printf $1 $2} else if($NF ~ \/*$\/){print \"\\t\"$3}}' all.cds.cdhit.clstr |sed 's\/>\/\/g; s\/...$\/\/'|awk '{print $2\"\\t\"$1}'  > map_id.txt\n# perl \/home\/stu_2\/linguopeng\/script\/map_data_ids  map_id.txt  unigene_cds.fasta \n# perl \/home\/stu_2\/linguopeng\/script\/map_data_ids  map_id.txt  unigene_pep.fasta\n# cd  \/home\/stu_2\/PRL\/P3.Assembly_annotation &amp;&amp; mkdir 05.abundance &amp;&amp; cd  05.abundance\n# ln  -s   ..\/04.cdhit\/unigene_cds.fasta\n# cd  \/home\/stu_2\/PRL\/P3.Assembly_annotation\/05.abundance\n# salmon index -t  unigene_cds.fasta  -i  unigene_index -p 30\n#for i in `ls \/home\/stu_2\/PRL\/P1.data_filter\/02.contaminant\/clean_unmap | grep _1.clean.fq.gz`\n#do\n#salmon  quant --validateMappings  --meta -p 30   -i  unigene_index  -l IU   -1 \/home\/stu_2\/PRL\/P1.data_filter\/02.contaminant\/clean_unmap\/${i%_1.clean.fq.gz*}_1.clean.fq.gz -2  \/home\/stu_2\/PRL\/P1.data_filter\/02.contaminant\/clean_unmap\/${i%_1.clean.fq.gz*}_2.clean.fq.gz  -o quants\/${i%_1.clean.fq.gz*}.quant\n#done\n# mkdir \/home\/stu_2\/PRL\/P3.Assembly_annotation\/06.eggnog\n# cd \/home\/stu_2\/PRL\/P3.Assembly_annotation\/06.eggnog\n# emapper.py -i unigene_pep.fasta -o my --itype proteins -m diamond --cpu 30 --override 1>emapper.log 2>&amp;1 \n# emapperx.R my.emapper.annotations unigene_pep.fasta\n# mkdir \/home\/stu_2\/PRL\/P3.Assembly_annotation\/07.uniprot\n# cd \/home\/stu_2\/PRL\/P3.Assembly_annotation\/07.uniprot\n# ln -s ..\/04.cdhit\/unigene_pep.fasta\n# diamond blastp  \\\n #   --db \/home\/stu_2\/linguopeng\/database\/uniprot\/uniref90 \\\n  #  --query  unigene_pep.fasta \\\n   # --out unigene_pep.uniref90.m6 \\\n   # --threads 30 \\\n   # --outfmt 6 \\\n   # --max-target-seqs 1 \\\n   # --evalue 1e-5\n## \u57fa\u4e8eidmapping \u63d0\u53d6GO\u6ce8\u91ca\u4fe1\u606f\n# cd \/home\/stu_2\/PRL\/P3.Assembly_annotation\/07.uniprot\n# perl \/home\/stu_2\/linguopeng\/script\/uniref90_idmapping.pl \\\n  #  unigene_pep.uniref90.m6 \\\n #   \/home\/stu_2\/linguopeng\/database\/uniprot\/idmapping_selected.tab \\\n #   > unigene_pep.uniref90.GOanno\n# Rscript  \/home\/stu_2\/linguopeng\/script\/GOmapperx.R  unigene_pep.uniref90.GOanno \n# cd \/home\/stu_2\/PRL\/P3.Assembly_annotation\/05.abundance\n# quants=` ls quants\/ | awk '{print \"quants\/\"$1 }' | tr '\\n'  ' ' `\n# names=` ls quants\/ | sed 's\/.quant$\/\/'| tr '\\n'   ' '  `\n# salmon quantmerge --quants $quants --names  $names  --column tpm -o unigenens.tpm\n# salmon quantmerge --quants $quants --names  $names  --column numreads -o unigenens.count\n# sed '1s\/^Name\\t\/\/' unigenens.count > unigenens.count.matrix\n# perl  \/home\/stu_2\/linguopeng\/script\/run_DE_analysis.pl \\\n# --matrix unigenens.count.matrix  \\\n# --method DESeq2 \\\n# --samples_file  sample.txt \\\n# --contrasts contrasts_FH_SC.txt \\\n# --output DE_out_FH_vs_SC\n# perl  \/home\/stu_2\/linguopeng\/script\/run_DE_analysis.pl \\\n# --matrix unigenens.count.matrix  \\\n# --method DESeq2 \\\n# --samples_file  sample.txt \\\n# --contrasts contrasts_SH_SC.txt \\\n# --output DE_out_SH_vs_SC\n# perl  \/home\/stu_2\/linguopeng\/script\/run_DE_analysis.pl \\\n# --matrix unigenens.count.matrix  \\\n# --method DESeq2 \\\n# --samples_file  sample.txt \\\n# --contrasts contrasts_SH_FH.txt \\\n# --output DE_out_SH_vs_FH\n# perl  \/home\/stu_2\/linguopeng\/script\/run_DE_analysis.pl     --matrix unigenens.count.matrix      --method DESeq2     --samples_file  sample.txt     --contrasts contrasts_SH_SC.txt     --output DE_out_SH_SC\n# #ln -s  \/home\/stu_2\/PRL\/P3.Assembly_annotation\/06.eggnog\/R_Library\/ .\n# #ln -s ..\/06.eggnog\/my.emapper.annotations\n# Rscript \\\n# ..\/..\/..\/linguopeng\/script\/enrich_analysis.R \\\n# .\/DE_out\/unigenens.count.matrix.FH_vs_SC.DESeq2.DE_results \\\n# .\/unigene.annotations \\\n# .\/DE_out\/unigenens.count.matrix.FH_vs_SC.DESeq2.DE_results.enrich\n# \n# cd \/home\/stu_2\/PRL\/P3.Assembly_annotation\/08.vfdb\n# diamond blastp  \\\n# --db \/home\/stu_2\/PRL\/P3.Assembly_annotation\/08.vfdb\/VFDB_setB \\\n# --query  unigene_pep.fasta \\\n# --out unigene_pep.vfdb.m6 \\\n# --threads 20 \\\n# --outfmt 6 \\\n# --max-target-seqs 1 \\\n# --evalue 1e-5\nlevel=P\ncd \/home\/stu_2\/PRL\/P2.Taxonomic_profiling\/01.taxon\n# mkdir out_$level\n# for i in `ls \/home\/stu_2\/PRL\/cleanreads | grep _clean_r1.gz`\n# do\n# bracken -d \/home\/stu_2\/linguopeng\/database\/k2 -i  kraken\/${i%_clean_r1.gz*}.kreport -o out_$level\/${i%_clean_r1.gz*}.bracken.$level -w out_$level\/${i%_clean_r1.gz*}.kreport  -l  $level -t 24\n# done\nkraken-biom  kraken\/*.kreport --max P -o  .\/out_$level\/$level.biom \nbiom  convert -i  .\/out_$level\/$level.biom -o  .\/out_$level\/$level.count.tsv.tmp  --to-tsv --header-key taxonomy\nsed 's\/; g__\\(&#91;^;]\\+\\); s__\/; g__\\1; s__\\1 \/'   .\/out_$level\/$level.count.tsv.tmp >  .\/out_$level\/$level.taxID.count.tsv\nsed  '\/^#\/! s\/^&#91;0-9]\\+\\t\\(.*&#91;A-Za-z]\\+__\\(&#91;^;]\\+\\)\\)$\/\\2\\t\\1\/'  .\/out_$level\/$level.taxID.count.tsv  >  .\/out_$level\/$level.taxName.count.tsv\nsed -e '1d' -e '2s\/^#\/\/' .\/out_$level\/$level.taxName.count.tsv | awk -F \"\\t\" -v OFS=\"\\t\" '{NF--; print}' | sed 's\/\\t$\/\/' > .\/out_$level\/$level.count.tsv\nRscript  \/home\/stu_2\/linguopeng\/script\/draw_taxonBarplot.R    out_$level\/$level.count.tsv  10   out_$level\/$level.count.out\n#test\n#ls *.fna |awk -F \"_\" '{print$1,$2,$3,$4}' >sample.txt\ncat sample.txt | while read  group sample   fq1 fq2 \ndo \n\techo singularity exec ..\/..\/software\/MetaGenome.sif kraken2  --threads 4 --quick --paired --db ..\/..\/Database\/K2\/  --report $sample.kreport --output $sample.kraken  $fq1 $fq2 \ndone > step1.run_kraken2.sh \n#test\n#test\ngene=abp1\n # HEADER END\n  #########bowtie2#######\n  # download special genecluster fa in NCBI\n  #bowtie2-build  abp1.fa abp1.db\n   #########sam#######\n   mkdir -p  \/home\/stu_2\/PRL\/iald\/abp1\/sam\n   for i in `ls \/home\/stu_2\/PRL\/P1.data_filter\/02.contaminant\/clean_unmap\/ | grep _1.clean.fq.gz`\n   do\n\t   bowtie2 --threads 30 -x \/home\/stu_2\/PRL\/iald\/abp1\/${gene}.db  -1 \/home\/stu_2\/PRL\/P1.data_filter\/02.contaminant\/clean_unmap\/${i%_1.clean.fq.gz}_1.clean.fq.gz -2 \/home\/stu_2\/PRL\/P1.data_filter\/02.contaminant\/clean_unmap\/${i%_1.clean.fq.gz}_2.clean.fq.gz -S \/home\/stu_2\/PRL\/iald\/abp1\/sam\/${i%_1.clean.fq.gz}.${gene}.sam 2> \/home\/stu_2\/PRL\/iald\/abp1\/sam\/${i%_1.clean.fq.gz}.${gene}.map.log \n   done \n    #########bam#######\n    mkdir -p \/home\/stu_2\/PRL\/iald\/abp1\/bam\n    for i in `ls \/home\/stu_2\/PRL\/P1.data_filter\/02.contaminant\/clean_unmap\/ | grep _1.clean.fq.gz`\n    do\n\t    samtools  view -@ 24 -BF 12 \/home\/stu_2\/PRL\/iald\/abp1\/sam\/${i%_1.clean.fq.gz}.${gene}.sam >\/home\/stu_2\/PRL\/iald\/abp1\/bam\/${i%_1.clean.fq.gz}.${gene}.map.bam \n    done\n    rm -r \/home\/stu_2\/PRL\/iald\/abp1\/sam\n    #########count#########\n    ls \/home\/stu_2\/PRL\/iald\/abp1\/bam > \/home\/stu_2\/PRL\/iald\/abp1\/bam\/name.txt\n    for i in `ls \/home\/stu_2\/PRL\/P1.data_filter\/02.contaminant\/clean_unmap\/ | grep _1.clean.fq.gz`\n    do\n\t    cat \/home\/stu_2\/PRL\/iald\/abp1\/bam\/${i%_1.clean.fq.gz}.${gene}.map.bam | wc -l >> \/home\/stu_2\/PRL\/iald\/abp1\/bam\/${gene}.count_map.txt\n    done\n\n    for i in `ls \/home\/stu_2\/PRL\/P1.data_filter\/02.contaminant\/clean_unmap\/ | grep _1.clean.fq.gz`\n    do\n\t    cat \/home\/stu_2\/PRL\/iald\/abp1\/bam\/${i%_1.clean.fq.gz}.${gene}.map.bam | wc -l >> \/home\/stu_2\/PRL\/iald\/abp1\/bam\/${gene}.count_all.txt\n    done\n    cat \/home\/stu_2\/PRL\/iald\/abp1\/bam\/${gene}.count_map.txt \/home\/stu_2\/PRL\/iald\/abp1\/bam\/${gene}.count_all.txt > \/home\/stu_2\/PRL\/iald\/abp1\/bam\/${gene}.all.txt\n#test\nfind . -name \"*contigs.fa\" -print0 | xargs -0 -I {} cp {} .\/\nfind \/home\/stu_2\/PRL\/P3.Assembly_annotation\/ -name \"*contigs.fa\" -print0 | xargs -0 -I {} ln {} .\/\n\nln -s \/home\/stu_2\/PRL\/P3.Assembly_annotation\/01.megahit\/${i%_1.clean.fq.gz*}_1.clean.fq.gz_megahit\/${i%_1.clean.fq.gz*}_1.clean.fq.gz.contigs.fa .\/${i%_1.clean.fq.gz*}.contigs.fa\n#test<\/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-571","post","type-post","status-publish","format-standard","hentry","category-uncategorized"],"_links":{"self":[{"href":"https:\/\/linguopeng.top\/index.php?rest_route=\/wp\/v2\/posts\/571","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=571"}],"version-history":[{"count":10,"href":"https:\/\/linguopeng.top\/index.php?rest_route=\/wp\/v2\/posts\/571\/revisions"}],"predecessor-version":[{"id":842,"href":"https:\/\/linguopeng.top\/index.php?rest_route=\/wp\/v2\/posts\/571\/revisions\/842"}],"wp:attachment":[{"href":"https:\/\/linguopeng.top\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=571"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/linguopeng.top\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=571"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/linguopeng.top\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=571"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}