<jupyter_start><jupyter_text>Import FASTQ data - Re-run plates  Original data Plates 1-6<jupyter_code>cp /sequencing/ucsd/complete_runs/190404_M05314_0165_000000000-CCHK7/*.fastq.gz /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/01_raw_fastq/original_run1_plates1-6_190404_M05314_0165_000000000-CCHK7/emp-paired-end-sequences/

qiime tools import \
  --type EMPPairedEndSequences \
  --input-path /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/01_raw_fastq/original_run1_plates1-6_190404_M05314_0165_000000000-CCHK7/emp-paired-end-sequences \
  --output-path /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/02_imported_seqs/dna_og_ITS_plates1_6_seqs.qza<jupyter_output><empty_output><jupyter_text>Plates 7-12<jupyter_code>cp /sequencing/ucsd/complete_runs/190409_M05314_0168_000000000-CCHKC/*.fastq.gz /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/01_raw_fastq/original_run2_plates7-12_190409_M05314_0168_000000000-CCHKC/emp-paired-end-sequences/

qiime tools import \
  --type EMPPairedEndSequences \
  --input-path /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/01_raw_fastq/original_run2_plates7-12_190409_M05314_0168_000000000-CCHKC/emp-paired-end-sequences \
  --output-path /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/02_imported_seqs/dna_og_ITS_plates7_12_seqs.qza<jupyter_output><empty_output><jupyter_text>Re-run on eight samples<jupyter_code>cp /sequencing/ucsd/complete_runs/190416_M05314_0171_000000000-CCGYH/*fastq.gz /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/01_raw_fastq/original_run3_eight_sample_redo_190416_M05314_0171_000000000-CCGYH/emp-paired-end-sequences/

qiime tools import \
  --type EMPPairedEndSequences \
  --input-path /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/01_raw_fastq/original_run3_eight_sample_redo_190416_M05314_0171_000000000-CCGYH/emp-paired-end-sequences \
  --output-path /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/02_imported_seqs/dna_og_ITS_plates1_6_8redos_seqs.qza<jupyter_output><empty_output><jupyter_text>Re-run for four kits High biomass<jupyter_code>cp /sequencing/ucsd_2/complete_runs/200622_M05314_0250_000000000-CVWTM/*.fastq.gz /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/01_raw_fastq/rerun_run1_high_biomass_200622_M05314_0250_000000000-CVWTM/emp-paired-end-sequences/

qiime tools import \
  --type EMPPairedEndSequences \
  --input-path /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/01_raw_fastq/rerun_run1_high_biomass_200622_M05314_0250_000000000-CVWTM/emp-paired-end-sequences \
  --output-path /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/02_imported_seqs/dna_rerun_ITS_hbm_seqs.qza<jupyter_output><empty_output><jupyter_text>Low biomass<jupyter_code>cp /sequencing/ucsd_2/complete_runs/200625_M05314_0252_000000000-J5HP8/*.fastq.gz /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/01_raw_fastq/rerun_run2_low_biomass_200625_M05314_0252_000000000-J5HP8/emp-paired-end-sequences/

qiime tools import \
  --type EMPPairedEndSequences \
  --input-path /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/01_raw_fastq/rerun_run2_low_biomass_200625_M05314_0252_000000000-J5HP8/emp-paired-end-sequences \
  --output-path /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/02_imported_seqs/dna_rerun_ITS_lbm_seqs.qza<jupyter_output><empty_output><jupyter_text>Demultiplex  Original data Plates 1-6<jupyter_code>qiime demux emp-paired \
  --i-seqs /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/02_imported_seqs/dna_og_ITS_plates1_6_seqs.qza \
  --m-barcodes-file /projects/dna_extraction_12201/round_02_six_kit_comparison/prep_info_files/12201_prep_info_its_plates1_6_excluding_8redos.txt \
  --m-barcodes-column 'barcode' \
  --p-rev-comp-mapping-barcodes \
  --o-error-correction-details /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/03_demux/dna_og_ITS_plates1_6_excluding_8redos_demux_info.qza \
  --o-per-sample-sequences /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/03_demux/dna_og_ITS_plates1_6_excluding_8redos_demux.qza

qiime demux summarize \
  --i-data /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/03_demux/dna_og_ITS_plates1_6_excluding_8redos_demux.qza \
  --o-visualization /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/03_demux/dna_og_ITS_plates1_6_excluding_8redos_demux.qzv<jupyter_output><empty_output><jupyter_text>Plates 7-12<jupyter_code>qiime demux emp-paired \
  --i-seqs /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/02_imported_seqs/dna_og_ITS_plates7_12_seqs.qza \
  --m-barcodes-file /projects/dna_extraction_12201/round_02_six_kit_comparison/prep_info_files/12201_prep_info_its_plates7_12.txt \
  --m-barcodes-column 'barcode' \
  --p-rev-comp-mapping-barcodes \
  --o-error-correction-details /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/03_demux/dna_og_ITS_plates7_12_demux_info.qza \
  --o-per-sample-sequences /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/03_demux/dna_og_ITS_plates7_12_demux.qza

qiime demux summarize \
  --i-data /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/03_demux/dna_og_ITS_plates7_12_demux.qza \
  --o-visualization /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/03_demux/dna_og_ITS_plates7_12_demux.qzv<jupyter_output><empty_output><jupyter_text>Plates 1-6, eight sample re-run<jupyter_code>qiime demux emp-paired \
  --i-seqs /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/02_imported_seqs/dna_og_ITS_plates1_6_8redos_seqs.qza \
  --m-barcodes-file /projects/dna_extraction_12201/round_02_six_kit_comparison/prep_info_files/12201_prep_info_its_plates1_6_8redos.txt \
  --m-barcodes-column 'barcode' \
  --p-rev-comp-mapping-barcodes \
  --o-error-correction-details /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/03_demux/dna_og_ITS_plates1_6_8redos_demux_info.qza \
  --o-per-sample-sequences /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/03_demux/dna_og_ITS_plates1_6_8redos_demux.qza

qiime demux summarize \
  --i-data /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/03_demux/dna_og_ITS_plates1_6_8redos_demux.qza \
  --o-visualization /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/03_demux/dna_og_ITS_plates1_6_8redos_demux.qzv<jupyter_output><empty_output><jupyter_text>Re-run for four kits High biomass<jupyter_code>qiime demux emp-paired \
  --i-seqs /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/02_imported_seqs/dna_rerun_ITS_hbm_seqs.qza \
  --m-barcodes-file /projects/dna_extraction_12201/round_02_six_kit_comparison/prep_info_files/12201_prep_info_its_rerun_hbm_11606_20210901-184822.txt \
  --m-barcodes-column 'barcode' \
  --p-rev-comp-mapping-barcodes \
  --o-error-correction-details /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/03_demux/dna_rerun_ITS_hbm_seqs_demux_info.qza \
  --o-per-sample-sequences /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/03_demux/dna_rerun_ITS_hbm_seqs_demux.qza

qiime demux summarize \
  --i-data /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/03_demux/dna_rerun_ITS_hbm_seqs_demux.qza \
  --o-visualization /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/03_demux/dna_rerun_ITS_hbm_seqs_demux.qzv<jupyter_output><empty_output><jupyter_text>Low biomass<jupyter_code>qiime demux emp-paired \
  --i-seqs /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/02_imported_seqs/dna_rerun_ITS_lbm_seqs.qza \
  --m-barcodes-file /projects/dna_extraction_12201/round_02_six_kit_comparison/prep_info_files/12201_prep_info_its_rerun_lbm_11607_20210901-184822.txt \
  --m-barcodes-column 'barcode' \
  --p-rev-comp-mapping-barcodes \
  --o-error-correction-details /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/03_demux/dna_rerun_ITS_lbm_seqs_demux_info.qza \
  --o-per-sample-sequences /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/03_demux/dna_rerun_ITS_lbm_seqs_demux.qza

qiime demux summarize \
  --i-data /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/03_demux/dna_rerun_ITS_lbm_seqs_demux.qza \
  --o-visualization /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/03_demux/dna_rerun_ITS_lbm_seqs_demux.qzv<jupyter_output><empty_output><jupyter_text>Denoise with deblur  Original data Plates 1-6<jupyter_code>#!/bin/bash
#PBS -V
#PBS -l nodes=1:ppn=16
#PBS -l walltime=12:00:00
#PBS -l mem=128gb
#PBS -M <EMAIL>
#PBS -m abe

source activate qiime2-2021.11

qiime deblur denoise-other \
  --i-demultiplexed-seqs /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/03_demux/dna_og_ITS_plates1_6_excluding_8redos_demux.qza \
  --i-reference-seqs /home/jpshaffer/mapping_db/unite_10.05.2021/sh_refs_qiime_ver8_dynamic_s_10.05.2021_dev.qza \
  --p-trim-length 150 \
  --p-jobs-to-start 16 \
  --p-sample-stats \
  --p-no-hashed-feature-ids \
  --o-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/04_denoise/dna_og_ITS_plates1_6_excluding_8redos_deblur_biom.qza \
  --o-representative-sequences /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/04_denoise/dna_og_ITS_plates1_6_excluding_8redos_deblur_seqs.qza \
  --o-stats /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/04_denoise/dna_og_ITS_plates1_6_excluding_8redos_deblur_stats.qza

qiime feature-table summarize \
  --i-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/04_denoise/dna_og_ITS_plates1_6_excluding_8redos_deblur_biom.qza \
  --o-visualization /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/04_denoise/dna_og_ITS_plates1_6_excluding_8redos_deblur_biom.qzv<jupyter_output><empty_output><jupyter_text>Plates 7-12<jupyter_code>#!/bin/bash
#PBS -V
#PBS -l nodes=1:ppn=16
#PBS -l walltime=12:00:00
#PBS -l mem=128gb
#PBS -M <EMAIL>
#PBS -m abe

source activate qiime2-2021.11

qiime deblur denoise-other \
  --i-demultiplexed-seqs /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/03_demux/dna_og_ITS_plates7_12_demux.qza \
  --i-reference-seqs /home/jpshaffer/mapping_db/unite_10.05.2021/sh_refs_qiime_ver8_dynamic_s_10.05.2021_dev.qza \
  --p-trim-length 150 \
  --p-jobs-to-start 16 \
  --p-sample-stats \
  --p-no-hashed-feature-ids \
  --o-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/04_denoise/dna_og_ITS_plates7_12_deblur_biom.qza \
  --o-representative-sequences /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/04_denoise/dna_og_ITS_plates7_12_deblur_seqs.qza \
  --o-stats /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/04_denoise/dna_og_ITS_plates7_12_deblur_stats.qza

qiime feature-table summarize \
  --i-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/04_denoise/dna_og_ITS_plates7_12_deblur_biom.qza \
  --o-visualization /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/04_denoise/dna_og_ITS_plates7_12_deblur_biom.qzv<jupyter_output><empty_output><jupyter_text>Plates 1-6, eight sample re-run<jupyter_code>#!/bin/bash
#PBS -V
#PBS -l nodes=1:ppn=16
#PBS -l walltime=12:00:00
#PBS -l mem=128gb
#PBS -M <EMAIL>
#PBS -m abe

source activate qiime2-2021.11

qiime deblur denoise-other \
  --i-demultiplexed-seqs /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/03_demux/dna_og_ITS_plates1_6_8redos_demux.qza \
  --i-reference-seqs /home/jpshaffer/mapping_db/unite_10.05.2021/sh_refs_qiime_ver8_dynamic_s_10.05.2021_dev.qza \
  --p-trim-length 150 \
  --p-jobs-to-start 16 \
  --p-sample-stats \
  --p-no-hashed-feature-ids \
  --o-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/04_denoise/dna_og_ITS_plates1_6_8redos_deblur_biom.qza \
  --o-representative-sequences /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/04_denoise/dna_og_ITS_plates1_6_8redos_deblur_seqs.qza \
  --o-stats /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/04_denoise/dna_og_ITS_plates1_6_8redos_deblur_stats.qza

qiime feature-table summarize \
  --i-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/04_denoise/dna_og_ITS_plates1_6_8redos_deblur_biom.qza \
  --o-visualization /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/04_denoise/dna_og_ITS_plates1_6_8redos_deblur_biom.qzv<jupyter_output><empty_output><jupyter_text>Re-run with four kits High biomass<jupyter_code>#!/bin/bash
#PBS -V
#PBS -l nodes=1:ppn=16
#PBS -l walltime=12:00:00
#PBS -l mem=128gb
#PBS -M <EMAIL>
#PBS -m abe

source activate qiime2-2021.11

qiime deblur denoise-other \
  --i-demultiplexed-seqs /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/03_demux/dna_rerun_ITS_hbm_seqs_demux.qza \
  --i-reference-seqs /home/jpshaffer/mapping_db/unite_10.05.2021/sh_refs_qiime_ver8_dynamic_s_10.05.2021_dev.qza \
  --p-trim-length 150 \
  --p-jobs-to-start 16 \
  --p-sample-stats \
  --p-no-hashed-feature-ids \
  --o-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/04_denoise/dna_rerun_ITS_hbm_deblur_biom.qza \
  --o-representative-sequences /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/04_denoise/dna_rerun_ITS_hbm_deblur_seqs.qza \
  --o-stats /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/04_denoise/dna_rerun_ITS_hbm_deblur_stats.qza

qiime feature-table summarize \
  --i-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/04_denoise/dna_rerun_ITS_hbm_deblur_biom.qza \
  --o-visualization /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/04_denoise/dna_rerun_ITS_hbm_deblur_biom.qzv<jupyter_output><empty_output><jupyter_text>Low biomass<jupyter_code>#!/bin/bash
#PBS -V
#PBS -l nodes=1:ppn=16
#PBS -l walltime=12:00:00
#PBS -l mem=128gb
#PBS -M <EMAIL>
#PBS -m abe

source activate qiime2-2021.11

qiime deblur denoise-other \
  --i-demultiplexed-seqs /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/03_demux/dna_rerun_ITS_lbm_seqs_demux.qza \
  --i-reference-seqs /home/jpshaffer/mapping_db/unite_10.05.2021/sh_refs_qiime_ver8_dynamic_s_10.05.2021_dev.qza \
  --p-trim-length 150 \
  --p-jobs-to-start 16 \
  --p-sample-stats \
  --p-no-hashed-feature-ids \
  --o-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/04_denoise/dna_rerun_ITS_lbm_deblur_biom.qza \
  --o-representative-sequences /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/04_denoise/dna_rerun_ITS_lbm_deblur_seqs.qza \
  --o-stats /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/04_denoise/dna_rerun_ITS_lbm_deblur_stats.qza

qiime feature-table summarize \
  --i-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/04_denoise/dna_rerun_ITS_lbm_deblur_biom.qza \
  --o-visualization /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/04_denoise/dna_rerun_ITS_lbm_deblur_biom.qzv<jupyter_output><empty_output><jupyter_text>Merge tables NOTE: 8 sample re-run from plates 1-6 did not pass deblur Round 1<jupyter_code>qiime feature-table merge \
  --i-tables /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/04_denoise/dna_og_ITS_plates1_6_excluding_8redos_deblur_biom.qza \
  --i-tables /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/04_denoise/dna_og_ITS_plates7_12_deblur_biom.qza \
  --o-merged-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/05_merged_data/dna_og_ITS_deblur_biom.qza

qiime feature-table summarize \
  --i-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/05_merged_data/dna_og_ITS_deblur_biom.qza \
  --o-visualization /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/05_merged_data/dna_og_ITS_deblur_biom.qzv

# There are 1097 samples and 5342 features<jupyter_output><empty_output><jupyter_text>Round 2<jupyter_code>qiime feature-table merge \
  --i-tables /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/04_denoise/dna_rerun_ITS_hbm_deblur_biom.qza \
  --i-tables /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/04_denoise/dna_rerun_ITS_lbm_deblur_biom.qza \
  --o-merged-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/05_merged_data/dna_rerun_ITS_deblur_biom.qza

qiime feature-table summarize \
  --i-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/05_merged_data/dna_rerun_ITS_deblur_biom.qza \
  --o-visualization /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/05_merged_data/dna_rerun_ITS_deblur_biom.qzv

# There are 737 samples and 3131 features<jupyter_output><empty_output><jupyter_text>Exclude Zymo kit from round 1<jupyter_code>qiime feature-table filter-samples \
  --i-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/05_merged_data/dna_og_ITS_deblur_biom.qza \
  --m-metadata-file /projects/dna_extraction_12201/round_02_six_kit_comparison/sample_metadata/12201_metadata.txt \
  --p-where "[extraction_kit]!='Zymo MagBead'" \
  --o-filtered-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/05_merged_data/dna_og_good_ITS_deblur_biom.qza

qiime feature-table summarize \
  --i-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/05_merged_data/dna_og_good_ITS_deblur_biom.qza \
  --o-visualization /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/05_merged_data/dna_og_good_ITS_deblur_biom.qzv

# There are 905 samples and 4834 features<jupyter_output><empty_output><jupyter_text>Merge round 1 excluding Zymo with round 2<jupyter_code>qiime feature-table merge \
  --i-tables /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/05_merged_data/dna_og_good_ITS_deblur_biom.qza \
  --i-tables /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/05_merged_data/dna_rerun_ITS_deblur_biom.qza \
  --o-merged-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/05_merged_data/dna_all_ITS_deblur_biom.qza

qiime feature-table summarize \
  --i-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/05_merged_data/dna_all_ITS_deblur_biom.qza \
  --o-visualization /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/05_merged_data/dna_all_ITS_deblur_biom.qzv

# There are 1642 samples and 6373 features<jupyter_output><empty_output><jupyter_text>Merge sequences<jupyter_code>qiime feature-table merge-seqs \
  --i-data /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/04_denoise/dna_og_ITS_plates1_6_excluding_8redos_deblur_seqs.qza \
  --i-data /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/04_denoise/dna_og_ITS_plates7_12_deblur_seqs.qza \
  --i-data /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/04_denoise/dna_rerun_ITS_hbm_deblur_seqs.qza \
  --i-data /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/04_denoise/dna_rerun_ITS_lbm_deblur_seqs.qza \
  --o-merged-data /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/05_merged_data/dna_all_ITS_deblur_seqs.qza \<jupyter_output><empty_output><jupyter_text>Profile taxonomy<jupyter_code>#!/bin/bash
#PBS -V
#PBS -l nodes=1:ppn=30
#PBS -l walltime=48:00:00
#PBS -l mem=240gb
#PBS -M <EMAIL>
#PBS -m abe

source activate qiime2-2021.11

qiime feature-classifier classify-sklearn \
  --i-classifier /home/jpshaffer/mapping_db/unite_10.05.2021/unite_qiime_nb_classifier_dynamic_s_10.05.2021_dev.qza \
  --i-reads /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/05_merged_data/dna_all_ITS_deblur_seqs.qza \
  --p-n-jobs 30 \
  --o-classification /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/06_taxonomy/dna_all_ITS_deblur_seqs_taxonomy_unite8.qza<jupyter_output><empty_output><jupyter_text>Generate barplot for merged table<jupyter_code>qiime taxa barplot \
  --i-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/05_merged_data/dna_all_ITS_deblur_biom.qza \
  --i-taxonomy /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/06_taxonomy/dna_all_ITS_deblur_seqs_taxonomy_unite8.qza \
  --m-metadata-file /projects/dna_extraction_12201/round_02_six_kit_comparison/sample_metadata/12201_metadata.txt \
  --o-visualization /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/05_merged_data/dna_all_ITS_deblur_biom_taxa_barplot_unite8.qzv<jupyter_output><empty_output><jupyter_text>NOTE: At this point Katharoseq analysis was performed and the resultant filtered table is used from this point forward. Preliminary analysis of the full dataset indicated that PowerSoil - Round 1 samples can be excluded, so they were.  Filter negative controls (blanks)  Table excluding round 1 PowerSoil, MagMAX Beta, and Homebrew (for beta-diversity analyses)<jupyter_code>qiime feature-table filter-samples \
  --i-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/07_lod/dna_all_ITS_deblur_biom_lod.qza \
  --m-metadata-file /projects/dna_extraction_12201/round_02_six_kit_comparison/sample_metadata/12201_metadata.txt \
  --p-where "[sample_type]!='control blank'" \
  --o-filtered-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/08_filtered_data/dna_all_ITS_deblur_biom_lod_noNTCs.qza

qiime feature-table summarize \
  --i-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/08_filtered_data/dna_all_ITS_deblur_biom_lod_noNTCs.qza \
  --o-visualization /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/08_filtered_data/dna_all_ITS_deblur_biom_lod_noNTCs.qzv

# There are 1016 samples and 4402 features<jupyter_output><empty_output><jupyter_text>Table including round 1 PowerSoil (for alpha-diversity analyses)<jupyter_code>qiime feature-table filter-samples \
  --i-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/07_lod/dna_bothPS_ITS_deblur_biom_lod.qza \
  --m-metadata-file /projects/dna_extraction_12201/round_02_six_kit_comparison/sample_metadata/12201_metadata.txt \
  --p-where "[sample_type]!='control blank'" \
  --o-filtered-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/08_filtered_data/dna_bothPS_ITS_deblur_biom_lod_noNTCs.qza

qiime feature-table summarize \
  --i-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/08_filtered_data/dna_bothPS_ITS_deblur_biom_lod_noNTCs.qza \
  --o-visualization /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/08_filtered_data/dna_bothPS_ITS_deblur_biom_lod_noNTCs.qzv

# There are 1185 samples and 4892 features<jupyter_output><empty_output><jupyter_text>Filter mock community samples (positive controls)  Table excluding round 1 PowerSoil, MagMAX Beta, and Homebrew (for beta-diversity analyses)<jupyter_code>qiime feature-table filter-samples \
  --i-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/08_filtered_data/dna_all_ITS_deblur_biom_lod_noNTCs.qza \
  --m-metadata-file /projects/dna_extraction_12201/round_02_six_kit_comparison/sample_metadata/12201_metadata.txt \
  --p-where "[sample_type]!='mock community'" \
  --o-filtered-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/08_filtered_data/dna_all_ITS_deblur_biom_lod_noNTCs_noMock.qza

qiime feature-table summarize \
  --i-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/08_filtered_data/dna_all_ITS_deblur_biom_lod_noNTCs_noMock.qza \
  --o-visualization /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/08_filtered_data/dna_all_ITS_deblur_biom_lod_noNTCs_noMock.qzv

# There are 841 samples and 4323 features<jupyter_output><empty_output><jupyter_text>Make table including ONLY mock community samples<jupyter_code>qiime feature-table filter-samples \
  --i-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/08_filtered_data/dna_all_ITS_deblur_biom_lod_noNTCs.qza \
  --m-metadata-file /projects/dna_extraction_12201/round_02_six_kit_comparison/sample_metadata/12201_metadata.txt \
  --p-where "[sample_type]='mock community'" \
  --o-filtered-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/08_filtered_data/dna_all_ITS_deblur_biom_lod_onlyMock.qza

qiime feature-table summarize \
  --i-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/08_filtered_data/dna_all_ITS_deblur_biom_lod_onlyMock.qza \
  --o-visualization /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/08_filtered_data/dna_all_ITS_deblur_biom_lod_onlyMock.qzv

# There are 984 samples and 5255 features<jupyter_output><empty_output><jupyter_text>Table including round 1 PowerSoil (for alpha-diversity analyses)<jupyter_code>qiime feature-table filter-samples \
  --i-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/08_filtered_data/dna_bothPS_ITS_deblur_biom_lod_noNTCs.qza \
  --m-metadata-file /projects/dna_extraction_12201/round_02_six_kit_comparison/sample_metadata/12201_metadata.txt \
  --p-where "[sample_type]!='mock community'" \
  --o-filtered-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/08_filtered_data/dna_bothPS_ITS_deblur_biom_lod_noNTCs_noMock.qza

qiime feature-table summarize \
  --i-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/08_filtered_data/dna_bothPS_ITS_deblur_biom_lod_noNTCs_noMock.qza \
  --o-visualization /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/08_filtered_data/dna_bothPS_ITS_deblur_biom_lod_noNTCs_noMock.qzv

# There are 978 samples and 4810 features<jupyter_output><empty_output><jupyter_text>Separate high- and low-biomass samples  Table excluding round 1 PowerSoil, MagMAX Beta, and Homebrew (for beta-diversity analyses) High-biomass<jupyter_code>qiime feature-table filter-samples \
  --i-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/08_filtered_data/dna_all_ITS_deblur_biom_lod_noNTCs_noMock.qza \
  --m-metadata-file /projects/dna_extraction_12201/round_02_six_kit_comparison/sample_metadata/12201_metadata.txt \
  --p-where "[biomass_plate]='high'" \
  --o-filtered-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/08_filtered_data/dna_all_ITS_deblur_biom_lod_noNTCs_noMock_hbm.qza

qiime feature-table summarize \
  --i-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/08_filtered_data/dna_all_ITS_deblur_biom_lod_noNTCs_noMock_hbm.qza \
  --o-visualization /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/08_filtered_data/dna_all_ITS_deblur_biom_lod_noNTCs_noMock_hbm.qzv

# There are 479 samples and 2229 features<jupyter_output><empty_output><jupyter_text>Low-biomass<jupyter_code>qiime feature-table filter-samples \
  --i-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/08_filtered_data/dna_all_ITS_deblur_biom_lod_noNTCs_noMock.qza \
  --m-metadata-file /projects/dna_extraction_12201/round_02_six_kit_comparison/sample_metadata/12201_metadata.txt \
  --p-where "[biomass_plate]='low'" \
  --o-filtered-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/08_filtered_data/dna_all_ITS_deblur_biom_lod_noNTCs_noMock_lbm.qza

qiime feature-table summarize \
  --i-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/08_filtered_data/dna_all_ITS_deblur_biom_lod_noNTCs_noMock_lbm.qza \
  --o-visualization /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/08_filtered_data/dna_all_ITS_deblur_biom_lod_noNTCs_noMock_lbm.qzv

# There are 362 samples and 2669 features<jupyter_output><empty_output><jupyter_text>Table including round 1 PowerSoil (for alpha-diversity analyses) High-biomass - including controls<jupyter_code>qiime feature-table filter-samples \
  --i-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/07_lod/dna_bothPS_ITS_deblur_biom_lod.qza \
  --m-metadata-file /projects/dna_extraction_12201/round_02_six_kit_comparison/sample_metadata/12201_metadata.txt \
  --p-where "[biomass_plate]='high'" \
  --o-filtered-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/08_filtered_data/dna_bothPS_ITS_deblur_biom_lod_hbm.qza

qiime feature-table summarize \
  --i-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/08_filtered_data/dna_bothPS_ITS_deblur_biom_lod_hbm.qza \
  --o-visualization /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/08_filtered_data/dna_bothPS_ITS_deblur_biom_lod_hbm.qzv

# There are 627 samples and 2416 features<jupyter_output><empty_output><jupyter_text>High biomass - excluding controls<jupyter_code>qiime feature-table filter-samples \
  --i-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/08_filtered_data/dna_bothPS_ITS_deblur_biom_lod_noNTCs_noMock.qza \
  --m-metadata-file /projects/dna_extraction_12201/round_02_six_kit_comparison/sample_metadata/12201_metadata.txt \
  --p-where "[biomass_plate]='high'" \
  --o-filtered-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/08_filtered_data/dna_bothPS_ITS_deblur_biom_lod_noNTCs_noMock_hbm.qza

qiime feature-table summarize \
  --i-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/08_filtered_data/dna_bothPS_ITS_deblur_biom_lod_noNTCs_noMock_hbm.qza \
  --o-visualization /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/08_filtered_data/dna_bothPS_ITS_deblur_biom_lod_noNTCs_noMock_hbm.qzv

# There are 551 samples and 2391 features<jupyter_output><empty_output><jupyter_text>Low-biomass - including controls<jupyter_code>qiime feature-table filter-samples \
  --i-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/07_lod/dna_bothPS_ITS_deblur_biom_lod.qza \
  --m-metadata-file /projects/dna_extraction_12201/round_02_six_kit_comparison/sample_metadata/12201_metadata.txt \
  --p-where "[biomass_plate]='low'" \
  --o-filtered-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/08_filtered_data/dna_bothPS_ITS_deblur_biom_lod_lbm.qza

qiime feature-table summarize \
  --i-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/08_filtered_data/dna_bothPS_ITS_deblur_biom_lod_lbm.qza \
  --o-visualization /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/08_filtered_data/dna_bothPS_ITS_deblur_biom_lod_lbm.qzv

# There are 613 samples and 3281 features<jupyter_output><empty_output><jupyter_text>Low biomass - excluding controls<jupyter_code>qiime feature-table filter-samples \
  --i-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/08_filtered_data/dna_bothPS_ITS_deblur_biom_lod_noNTCs_noMock.qza \
  --m-metadata-file /projects/dna_extraction_12201/round_02_six_kit_comparison/sample_metadata/12201_metadata.txt \
  --p-where "[biomass_plate]='low'" \
  --o-filtered-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/08_filtered_data/dna_bothPS_ITS_deblur_biom_lod_noNTCs_noMock_lbm.qza

qiime feature-table summarize \
  --i-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/08_filtered_data/dna_bothPS_ITS_deblur_biom_lod_noNTCs_noMock_lbm.qza \
  --o-visualization /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/08_filtered_data/dna_bothPS_ITS_deblur_biom_lod_noNTCs_noMock_lbm.qzv

# There are 427 samples and 3103 features<jupyter_output><empty_output><jupyter_text>Normalize sampling depth  Table excluding round 1 PowerSoil, MagMAX Beta, and Homebrew (for beta-diversity analyses)  Rarefy High-biomass<jupyter_code>qiime feature-table rarefy \
  --i-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/08_filtered_data/dna_all_ITS_deblur_biom_lod_noNTCs_noMock_hbm.qza \
  --p-sampling-depth 1674 \
  --o-rarefied-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/09_normalized_data/dna_all_ITS_deblur_biom_lod_noNTCs_noMock_hbm_rar1674.qza

qiime feature-table summarize \
  --i-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/09_normalized_data/dna_all_ITS_deblur_biom_lod_noNTCs_noMock_hbm_rar1674.qza \
  --o-visualization /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/09_normalized_data/dna_all_ITS_deblur_biom_lod_noNTCs_noMock_hbm_rar1674.qzv

# There are 240 samples and 1625 features<jupyter_output><empty_output><jupyter_text>Low-biomass<jupyter_code>qiime feature-table rarefy \
  --i-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/08_filtered_data/dna_all_ITS_deblur_biom_lod_noNTCs_noMock_lbm.qza \
  --p-sampling-depth 381 \
  --o-rarefied-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/09_normalized_data/dna_all_ITS_deblur_biom_lod_noNTCs_noMock_lbm_rar381.qza

qiime feature-table summarize \
  --i-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/09_normalized_data/dna_all_ITS_deblur_biom_lod_noNTCs_noMock_lbm_rar381.qza \
  --o-visualization /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/09_normalized_data/dna_all_ITS_deblur_biom_lod_noNTCs_noMock_lbm_rar381.qzv

# There are 181 samples and 1925 features<jupyter_output><empty_output><jupyter_text>Remove low-abundnace samples High-biomass<jupyter_code>qiime feature-table filter-samples \
  --i-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/08_filtered_data/dna_all_ITS_deblur_biom_lod_noNTCs_noMock_hbm.qza \
  --p-min-frequency 1674 \
  --o-filtered-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/09_normalized_data/dna_all_ITS_deblur_biom_lod_noNTCs_noMock_hbm_min1674.qza

qiime feature-table summarize \
  --i-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/09_normalized_data/dna_all_ITS_deblur_biom_lod_noNTCs_noMock_hbm_min1674.qza \
  --o-visualization /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/09_normalized_data/dna_all_ITS_deblur_biom_lod_noNTCs_noMock_hbm_min1674.qzv

# There are 240 samples and 2148 features<jupyter_output><empty_output><jupyter_text>Low-biomass<jupyter_code>qiime feature-table filter-samples \
  --i-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/08_filtered_data/dna_all_ITS_deblur_biom_lod_noNTCs_noMock_lbm.qza \
  --p-min-frequency 381 \
  --o-filtered-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/09_normalized_data/dna_all_ITS_deblur_biom_lod_noNTCs_noMock_lbm_min381.qza

qiime feature-table summarize \
  --i-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/09_normalized_data/dna_all_ITS_deblur_biom_lod_noNTCs_noMock_lbm_min381.qza \
  --o-visualization /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/09_normalized_data/dna_all_ITS_deblur_biom_lod_noNTCs_noMock_lbm_min381.qzv

# There are 181 samples and 2623 features<jupyter_output><empty_output><jupyter_text>Table including round 1 PowerSoil (for alpha-diversity analyses)  Rarefy High-biomass - including controls<jupyter_code>qiime feature-table rarefy \
  --i-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/08_filtered_data/dna_bothPS_ITS_deblur_biom_lod_hbm.qza \
  --p-sampling-depth 1171 \
  --o-rarefied-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/09_normalized_data/dna_bothPS_ITS_deblur_biom_lod_hbm_rar1171.qza

qiime feature-table summarize \
  --i-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/09_normalized_data/dna_bothPS_ITS_deblur_biom_lod_hbm_rar1171.qza \
  --o-visualization /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/09_normalized_data/dna_bothPS_ITS_deblur_biom_lod_hbm_rar1171.qzv

# There are 314 samples and 1739 features<jupyter_output><empty_output><jupyter_text>High-biomass - excluding controls<jupyter_code>qiime feature-table rarefy \
  --i-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/08_filtered_data/dna_bothPS_ITS_deblur_biom_lod_noNTCs_noMock_hbm.qza \
  --p-sampling-depth 1491 \
  --o-rarefied-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/09_normalized_data/dna_bothPS_ITS_deblur_biom_lod_noNTCs_noMock_hbm_rar1491.qza

qiime feature-table summarize \
  --i-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/09_normalized_data/dna_bothPS_ITS_deblur_biom_lod_noNTCs_noMock_hbm_rar1491.qza \
  --o-visualization /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/09_normalized_data/dna_bothPS_ITS_deblur_biom_lod_noNTCs_noMock_hbm_rar1491.qzv

# There are 276 samples and 1798 features<jupyter_output><empty_output><jupyter_text>Low-biomass - including controls<jupyter_code>qiime feature-table rarefy \
  --i-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/08_filtered_data/dna_bothPS_ITS_deblur_biom_lod_lbm.qza \
  --p-sampling-depth 456 \
  --o-rarefied-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/09_normalized_data/dna_bothPS_ITS_deblur_biom_lod_lbm_rar456.qza

qiime feature-table summarize \
  --i-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/09_normalized_data/dna_bothPS_ITS_deblur_biom_lod_lbm_rar456.qza \
  --o-visualization /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/09_normalized_data/dna_bothPS_ITS_deblur_biom_lod_lbm_rar456.qzv

# There are 307 samples and 2327 features<jupyter_output><empty_output><jupyter_text>Low-biomass - including controls<jupyter_code>qiime feature-table rarefy \
  --i-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/08_filtered_data/dna_bothPS_ITS_deblur_biom_lod_noNTCs_noMock_lbm.qza \
  --p-sampling-depth 344 \
  --o-rarefied-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/09_normalized_data/dna_bothPS_ITS_deblur_biom_lod_noNTCs_noMock_lbm_rar344.qza

qiime feature-table summarize \
  --i-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/09_normalized_data/dna_bothPS_ITS_deblur_biom_lod_noNTCs_noMock_lbm_rar344.qza \
  --o-visualization /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/09_normalized_data/dna_bothPS_ITS_deblur_biom_lod_noNTCs_noMock_lbm_rar344.qzv

# There are 214 samples and 2120 features<jupyter_output><empty_output><jupyter_text>Alpha-diversity  Table excluding round 1 PowerSoil, MagMAX Beta, and Homebrew (for comparison with sample set used for beta-diversity analyses) High-biomass<jupyter_code>qiime diversity alpha \
  --i-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/09_normalized_data/dna_all_ITS_deblur_biom_lod_noNTCs_noMock_hbm_rar1674.qza \
  --p-metric 'observed_features' \
  --o-alpha-diversity /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/10_alpha_diversity/dna_all_ITS_deblur_biom_lod_noNTCs_noMock_hbm_rar1674_alpha_richness.qza

qiime diversity alpha \
  --i-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/09_normalized_data/dna_all_ITS_deblur_biom_lod_noNTCs_noMock_hbm_rar1674.qza \
  --p-metric 'shannon' \
  --o-alpha-diversity /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/10_alpha_diversity/dna_all_ITS_deblur_biom_lod_noNTCs_noMock_hbm_rar1674_alpha_shannon.qza

qiime diversity alpha \
  --i-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/09_normalized_data/dna_all_ITS_deblur_biom_lod_noNTCs_noMock_hbm_rar1674.qza \
  --p-metric 'fisher_alpha' \
  --o-alpha-diversity /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/10_alpha_diversity/dna_all_ITS_deblur_biom_lod_noNTCs_noMock_hbm_rar1674_alpha_fishersalpha.qza<jupyter_output><empty_output><jupyter_text>Low-biomass<jupyter_code>qiime diversity alpha \
  --i-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/09_normalized_data/dna_all_ITS_deblur_biom_lod_noNTCs_noMock_lbm_rar381.qza \
  --p-metric 'observed_features' \
  --o-alpha-diversity /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/10_alpha_diversity/dna_all_ITS_deblur_biom_lod_noNTCs_noMock_lbm_rar381_alpha_richness.qza

qiime diversity alpha \
  --i-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/09_normalized_data/dna_all_ITS_deblur_biom_lod_noNTCs_noMock_lbm_rar381.qza \
  --p-metric 'shannon' \
  --o-alpha-diversity /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/10_alpha_diversity/dna_all_ITS_deblur_biom_lod_noNTCs_noMock_lbm_rar381_alpha_shannon.qza

qiime diversity alpha \
  --i-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/09_normalized_data/dna_all_ITS_deblur_biom_lod_noNTCs_noMock_lbm_rar381.qza \
  --p-metric 'fisher_alpha' \
  --o-alpha-diversity /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/10_alpha_diversity/dna_all_ITS_deblur_biom_lod_noNTCs_noMock_lbm_rar381_alpha_fishersalpha.qza<jupyter_output><empty_output><jupyter_text>Table including round 1 PowerSoil (for alpha-diversity analyses) High-biomass<jupyter_code>qiime diversity alpha \
  --i-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/09_normalized_data/dna_bothPS_ITS_deblur_biom_lod_hbm_rar1171.qza \
  --p-metric 'observed_features' \
  --o-alpha-diversity /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/10_alpha_diversity/dna_bothPS_ITS_deblur_biom_lod_hbm_rar1171_alpha_richness.qza

qiime diversity alpha \
  --i-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/09_normalized_data/dna_bothPS_ITS_deblur_biom_lod_hbm_rar1171.qza \
  --p-metric 'shannon' \
  --o-alpha-diversity /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/10_alpha_diversity/dna_bothPS_ITS_deblur_biom_lod_hbm_rar1171_alpha_shannon.qza

qiime diversity alpha \
  --i-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/09_normalized_data/dna_bothPS_ITS_deblur_biom_lod_hbm_rar1171.qza \
  --p-metric 'fisher_alpha' \
  --o-alpha-diversity /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/10_alpha_diversity/dna_bothPS_ITS_deblur_biom_lod_hbm_rar1171_alpha_fishersalpha.qza<jupyter_output><empty_output><jupyter_text>Low-biomass<jupyter_code>qiime diversity alpha \
  --i-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/09_normalized_data/dna_bothPS_ITS_deblur_biom_lod_lbm_rar456.qza \
  --p-metric 'observed_features' \
  --o-alpha-diversity /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/10_alpha_diversity/dna_bothPS_ITS_deblur_biom_lod_lbm_rar456_alpha_richness.qza

qiime diversity alpha \
  --i-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/09_normalized_data/dna_bothPS_ITS_deblur_biom_lod_lbm_rar456.qza \
  --p-metric 'shannon' \
  --o-alpha-diversity /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/10_alpha_diversity/dna_bothPS_ITS_deblur_biom_lod_lbm_rar456_alpha_shannon.qza

qiime diversity alpha \
  --i-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/09_normalized_data/dna_bothPS_ITS_deblur_biom_lod_lbm_rar456.qza \
  --p-metric 'fisher_alpha' \
  --o-alpha-diversity /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/10_alpha_diversity/dna_bothPS_ITS_deblur_biom_lod_lbm_rar456_alpha_fishersalpha.qza<jupyter_output><empty_output><jupyter_text>Beta-diversity  Generate distance matrices High-biomass<jupyter_code>qiime diversity beta \
  --i-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/09_normalized_data/dna_all_ITS_deblur_biom_lod_noNTCs_noMock_hbm_rar1674.qza \
  --p-metric 'jaccard' \
  --o-distance-matrix /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/11_beta_diversity/dna_all_ITS_deblur_biom_lod_noNTCs_noMock_hbm_rar1674_dist_jaccard.qza

qiime diversity beta \
  --i-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/09_normalized_data/dna_all_ITS_deblur_biom_lod_noNTCs_noMock_hbm_rar1674.qza \
  --p-metric 'braycurtis' \
  --o-distance-matrix /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/11_beta_diversity/dna_all_ITS_deblur_biom_lod_noNTCs_noMock_hbm_rar1674_dist_braycurtis.qza<jupyter_output><empty_output><jupyter_text>Low-biomass<jupyter_code>qiime diversity beta \
  --i-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/09_normalized_data/dna_all_ITS_deblur_biom_lod_noNTCs_noMock_lbm_rar381.qza \
  --p-metric 'jaccard' \
  --o-distance-matrix /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/11_beta_diversity/dna_all_ITS_deblur_biom_lod_noNTCs_noMock_lbm_rar381_dist_jaccard.qza

qiime diversity beta \
  --i-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/09_normalized_data/dna_all_ITS_deblur_biom_lod_noNTCs_noMock_lbm_rar381.qza \
  --p-metric 'braycurtis' \
  --o-distance-matrix /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/11_beta_diversity/dna_all_ITS_deblur_biom_lod_noNTCs_noMock_lbm_rar381_dist_braycurtis.qza<jupyter_output><empty_output><jupyter_text>Generate PCoA High-biomass<jupyter_code>qiime diversity pcoa \
  --i-distance-matrix /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/11_beta_diversity/dna_all_ITS_deblur_biom_lod_noNTCs_noMock_hbm_rar1674_dist_jaccard.qza \
  --o-pcoa /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/11_beta_diversity/dna_all_ITS_deblur_biom_lod_noNTCs_noMock_hbm_rar1674_pcoa_jaccard.qza

qiime diversity pcoa \
  --i-distance-matrix /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/11_beta_diversity/dna_all_ITS_deblur_biom_lod_noNTCs_noMock_hbm_rar1674_dist_braycurtis.qza \
  --o-pcoa /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/11_beta_diversity/dna_all_ITS_deblur_biom_lod_noNTCs_noMock_hbm_rar1674_pcoa_braycurtis.qza<jupyter_output><empty_output><jupyter_text>Low-biomass<jupyter_code>qiime diversity pcoa \
  --i-distance-matrix /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/11_beta_diversity/dna_all_ITS_deblur_biom_lod_noNTCs_noMock_lbm_rar381_dist_jaccard.qza \
  --o-pcoa /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/11_beta_diversity/dna_all_ITS_deblur_biom_lod_noNTCs_noMock_lbm_rar381_pcoa_jaccard.qza

qiime diversity pcoa \
  --i-distance-matrix /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/11_beta_diversity/dna_all_ITS_deblur_biom_lod_noNTCs_noMock_lbm_rar381_dist_braycurtis.qza \
  --o-pcoa /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/11_beta_diversity/dna_all_ITS_deblur_biom_lod_noNTCs_noMock_lbm_rar381_pcoa_braycurtis.qza<jupyter_output><empty_output><jupyter_text>Plot PCoA High-biomass<jupyter_code>qiime emperor plot \
  --i-pcoa /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/11_beta_diversity/dna_all_ITS_deblur_biom_lod_noNTCs_noMock_hbm_rar1674_pcoa_jaccard.qza \
  --m-metadata-file /projects/dna_extraction_12201/round_02_six_kit_comparison/sample_metadata/12201_metadata.txt \
  --o-visualization /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/11_beta_diversity/dna_all_ITS_deblur_biom_lod_noNTCs_noMock_hbm_rar1674_pcoa_jaccard.qzv

qiime emperor plot \
  --i-pcoa /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/11_beta_diversity/dna_all_ITS_deblur_biom_lod_noNTCs_noMock_hbm_rar1674_pcoa_braycurtis.qza \
  --m-metadata-file /projects/dna_extraction_12201/round_02_six_kit_comparison/sample_metadata/12201_metadata.txt \
  --o-visualization /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/11_beta_diversity/dna_all_ITS_deblur_biom_lod_noNTCs_noMock_hbm_rar1674_pcoa_braycurtis.qzv<jupyter_output><empty_output><jupyter_text>Low-biomass<jupyter_code>qiime emperor plot \
  --i-pcoa /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/11_beta_diversity/dna_all_ITS_deblur_biom_lod_noNTCs_noMock_lbm_rar381_pcoa_jaccard.qza \
  --m-metadata-file /projects/dna_extraction_12201/round_02_six_kit_comparison/sample_metadata/12201_metadata.txt \
  --o-visualization /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/11_beta_diversity/dna_all_ITS_deblur_biom_lod_noNTCs_noMock_lbm_rar381_pcoa_jaccard.qzv

qiime emperor plot \
  --i-pcoa /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/11_beta_diversity/dna_all_ITS_deblur_biom_lod_noNTCs_noMock_lbm_rar381_pcoa_braycurtis.qza \
  --m-metadata-file /projects/dna_extraction_12201/round_02_six_kit_comparison/sample_metadata/12201_metadata.txt \
  --o-visualization /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/11_beta_diversity/dna_all_ITS_deblur_biom_lod_noNTCs_noMock_lbm_rar381_pcoa_braycurtis.qzv<jupyter_output><empty_output><jupyter_text>Perform RPCA High-biomass<jupyter_code>qiime deicode rpca \
  --i-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/09_normalized_data/dna_all_ITS_deblur_biom_lod_noNTCs_noMock_hbm_min1674.qza \
  --p-min-feature-count 0 \
  --p-min-sample-count 0 \
  --p-min-feature-frequency 10 \
  --o-biplot /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/11_beta_diversity/dna_all_ITS_deblur_biom_lod_noNTCs_noMock_hbm_min1674_rpca_biplot.qza \
  --o-distance-matrix /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/11_beta_diversity/dna_all_ITS_deblur_biom_lod_noNTCs_noMock_hbm_min1674_rpca_dist.qza \
  --verbose

qiime emperor biplot \
  --i-biplot /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/11_beta_diversity/dna_all_ITS_deblur_biom_lod_noNTCs_noMock_hbm_min1674_rpca_biplot.qza \
  --m-sample-metadata-file /projects/dna_extraction_12201/round_02_six_kit_comparison/sample_metadata/12201_metadata.txt \
  --m-feature-metadata-file /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/06_taxonomy/dna_all_ITS_deblur_seqs_taxonomy_unite8.qza \
  --p-number-of-features 10 \
  --o-visualization /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/11_beta_diversity/dna_all_ITS_deblur_biom_lod_noNTCs_noMock_hbm_min1674_rpca_biplot.qzv<jupyter_output><empty_output><jupyter_text>Low-biomass<jupyter_code>qiime deicode rpca \
  --i-table /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/09_normalized_data/dna_all_ITS_deblur_biom_lod_noNTCs_noMock_lbm_min381.qza \
  --p-min-feature-count 0 \
  --p-min-sample-count 0 \
  --p-min-feature-frequency 10 \
  --o-biplot /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/11_beta_diversity/dna_all_ITS_deblur_biom_lod_noNTCs_noMock_lbm_min381_rpca_biplot.qza \
  --o-distance-matrix /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/11_beta_diversity/dna_all_ITS_deblur_biom_lod_noNTCs_noMock_lbm_min381_rpca_dist.qza \
  --verbose

qiime emperor biplot \
  --i-biplot /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/11_beta_diversity/dna_all_ITS_deblur_biom_lod_noNTCs_noMock_lbm_min381_rpca_biplot.qza \
  --m-sample-metadata-file /projects/dna_extraction_12201/round_02_six_kit_comparison/sample_metadata/12201_metadata.txt \
  --m-feature-metadata-file /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/06_taxonomy/dna_all_ITS_deblur_seqs_taxonomy_unite8.qza \
  --p-number-of-features 10 \
  --o-visualization /projects/dna_extraction_12201/round_02_six_kit_comparison/data/ITS/11_beta_diversity/dna_all_ITS_deblur_biom_lod_noNTCs_noMock_lbm_min381_rpca_biplot.qzv<jupyter_output><empty_output>
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