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lwaldron/testvincecmdfiles

Created October 14, 2020 15:02
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testvincecmdfiles
system("gsutil cp gs://biocbbs_2020a/cmd3out/uploads/GuptaA_2019.metaphlan_bugs_list.stool.rda .")
load("GuptaA_2019.metaphlan_bugs_list.stool.rda")
head(rownames(GuptaA_2019.metaphlan_bugs_list.stool)) #first 3 look wrong
grep("CIBIO", rownames(GuptaA_2019.metaphlan_bugs_list.stool)) #there are 60 with CIBIO in the rowname
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Here's what the head command looks like:

> head(rownames(GuptaA_2019.metaphlan_bugs_list.stool))
[1] "#/shares/CIBIO-Storage/CM/scratch/users/paolo.manghi/anaconda3/envs/mpa/bin/metaphlan --nproc 4 --input_type fastq --bowtie2db /shares/CIBIO-Storage/CM/news/users/francesco.beghini/hg/chocophlan/export_201901/metaphlan2/mpa_v30_CHOCOPhlAn_201901 --index mpa_v30_CHOCOPhlAn_201901 --force --bowtie2_exe /shares/CIBIO-Storage/CM/news/users/francesco.beghini/bowtie2-2.3.4.3-linux-x86_64/bowtie2 --bowtie2out /shares/CIBIO-Storage/CM/scratch/data/meta/GuptaA_2019/metaphlan-3.0_v30_CHOCOPhlAn_201901/GupDM_JP/GupDM_JP.bowtie2.bz2 --samout /shares/CIBIO-Storage/CM/scratch/data/meta/GuptaA_2019/metaphlan-3.0_v30_CHOCOPhlAn_201901/GupDM_JP/GupDM_JP.sam.bz2 -o /shares/CIBIO-Storage/CM/scratch/data/meta/GuptaA_2019/metaphlan-3.0_v30_CHOCOPhlAn_201901/GupDM_JP/GupDM_JP_profile.tsv"
[2] "#SampleID"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
[3] "#clade_name"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
[4] "k__Bacteria"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
[5] "k__Archaea"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
[6] "k__Bacteria|p__Bacteroidetes"

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