Commit 35847d7c authored by Shaman Narayanasamy's avatar Shaman Narayanasamy
Browse files

Add file with all IMP commands

parent b804a6b1
#### The commands below are for the new analysis for the paper restructuring.
## Simulated mock (SM)
nohup python3.4 IMP -m /mnt/md1200/snarayanasamy/IMP_data/simulated_data/MG/73_species_MG_R1_new.fq -m /mnt/md1200/snarayanasamy/IMP_data/simulated_data/MG/73_species_MG_R2_new.fq -t /mnt/md1200/snarayanasamy/IMP_data/simulated_data/MT/73_species_MT_R1_new.fq -t /mnt/md1200/snarayanasamy/IMP_data/simulated_data/MT/73_species_MT_R2_new.fq -o /mnt/md1200/snarayanasamy/IMP_analysis/simulated_data_output_20160412-idba -c conf/bigbug_config.imp.json -a idba >> simulated_data_20160412-idba.log &
nohup python3.4 IMP -m /mnt/md1200/snarayanasamy/IMP_data/simulated_data/MG/73_species_MG_R1_new.fq -m /mnt/md1200/snarayanasamy/IMP_data/simulated_data/MG/73_species_MG_R2_new.fq -t /mnt/md1200/snarayanasamy/IMP_data/simulated_data/MT/73_species_MT_R1_new.fq -t /mnt/md1200/snarayanasamy/IMP_data/simulated_data/MT/73_species_MT_R2_new.fq -o /mnt/md1200/snarayanasamy/IMP_analysis/simulated_data_output_20160416-megahit -c conf/bigbug_config.imp.json -a megahit >> simulated_data_20160416-megahit.log &
## Anerobic biogas (BG) digester data
python3.4 IMP -m /mnt/md1200/snarayanasamy/archived_raw_data/PRJEB8813/MG/PRJEB8813_MG.R1.fq.gz -m /mnt/md1200/snarayanasamy/archived_raw_data/PRJEB8813/MG/PRJEB8813_MG.R2.fq.gz -t /mnt/md1200/snarayanasamy/archived_raw_data/PRJEB8813/MT/ERR843255_1.fastq.gz -t /mnt/md1200/snarayanasamy/archived_raw_data/PRJEB8813/MT/ERR843255_2.fastq.gz -o /home/snarayanasamy/Work/IMP_analysis/PRJEB8813_20160226-idba -c /home/snarayanasamy/Work/tools/IMP/conf/PRJEB8813_bigbug_IMP_config.imp.json
python3.4 IMP -m /mnt/md1200/snarayanasamy/archived_raw_data/PRJEB8813/MG/PRJEB8813_MG.R1.fq.gz -m /mnt/md1200/snarayanasamy/archived_raw_data/PRJEB8813/MG/PRJEB8813_MG.R2.fq.gz -t /mnt/md1200/snarayanasamy/archived_raw_data/PRJEB8813/MT/ERR843255_1.fastq.gz -t /mnt/md1200/snarayanasamy/archived_raw_data/PRJEB8813/MT/ERR843255_2.fastq.gz -o /home/snarayanasamy/Work/IMP_analysis/PRJEB8813_20160226-megahit -c /home/snarayanasamy/Work/tools/IMP/conf/PRJEB8813_bigbug_IMP_config.imp.json -a megahit
## Human microbiome (HF1-5)
# HF1
python3.4 IMP -m /mnt/md1200/snarayanasamy/IMP_data/Huttenhower/X310763260/X310763260_MG_R1.fq -m /mnt/md1200/snarayanasamy/IMP_data/Huttenhower/X310763260/X310763260_MG_R2.fq -t /mnt/md1200/snarayanasamy/IMP_data/Huttenhower/X310763260/X310763260_MT_R1.fq -t /mnt/md1200/snarayanasamy/IMP_data/Huttenhower/X310763260/X310763260_MT_R2.fq -o /home/snarayanasamy/Work/IMP_analysis/X310763260_20151005-idba -c conf/bigbug_config.imp.json
python3.4 IMP -m /mnt/md1200/snarayanasamy/IMP_data/Huttenhower/X310763260/X310763260_MG_R1.fq -m /mnt/md1200/snarayanasamy/IMP_data/Huttenhower/X310763260/X310763260_MG_R2.fq -t /mnt/md1200/snarayanasamy/IMP_data/Huttenhower/X310763260/X310763260_MT_R1.fq -t /mnt/md1200/snarayanasamy/IMP_data/Huttenhower/X310763260/X310763260_MT_R2.fq -o /home/snarayanasamy/Work/IMP_analysis/X310763260_20151006-megahit -c conf/bigbug_config.imp.json -a megahit
# HF2
nohup python3.4 IMP -m /mnt/md1200/snarayanasamy/IMP_data/Huttenhower/X311245214/X311245214_MG_R1.fq -m /mnt/md1200/snarayanasamy/IMP_data/Huttenhower/X311245214/X311245214_MG_R2.fq -t /mnt/md1200/snarayanasamy/IMP_data/Huttenhower/X311245214/X311245214_MT_R1.fq -t /mnt/md1200/snarayanasamy/IMP_data/Huttenhower/X311245214/X311245214_MT_R2.fq -o /home/snarayanasamy/Work/IMP_analysis/X311245214_20160229-idba -c conf/bigbug_config.imp.json >> X31124521_IMP.log
nohup python3.4 IMP -m /mnt/md1200/snarayanasamy/IMP_data/Huttenhower/X311245214/X311245214_MG_R1.fq -m /mnt/md1200/snarayanasamy/IMP_data/Huttenhower/X311245214/X311245214_MG_R2.fq -t /mnt/md1200/snarayanasamy/IMP_data/Huttenhower/X311245214/X311245214_MT_R1.fq -t /mnt/md1200/snarayanasamy/IMP_data/Huttenhower/X311245214/X311245214_MT_R2.fq -o /home/snarayanasamy/Work/IMP_analysis/X311245214_20160229-megahit -c conf/bigbug_config.imp.json -a megahit >> X31124521_IMP-megahit.log
# HF3
nohup python3.4 IMP -m /mnt/md1200/snarayanasamy/IMP_data/Huttenhower/X316192082/MG/X316192082_MG_R1.fq -m /mnt/md1200/snarayanasamy/IMP_data/Huttenhower/X316192082/MG/X316192082_MG_R2.fq -t /mnt/md1200/snarayanasamy/IMP_data/Huttenhower/X316192082/MT/X316192082_MT_R1.fq -t /mnt/md1200/snarayanasamy/IMP_data/Huttenhower/X316192082/MT/X316192082_MT_R2.fq -o /mnt/md1200/snarayanasamy/IMP_analysis/X316192082_20160302-idba -c conf/bigbug_config.imp.json >> X316192082_IMP.log &
nohup python3.4 IMP -m /mnt/md1200/snarayanasamy/IMP_data/Huttenhower/X316192082/MG/X316192082_MG_R1.fq -m /mnt/md1200/snarayanasamy/IMP_data/Huttenhower/X316192082/MG/X316192082_MG_R2.fq -t /mnt/md1200/snarayanasamy/IMP_data/Huttenhower/X316192082/MT/X316192082_MT_R1.fq -t /mnt/md1200/snarayanasamy/IMP_data/Huttenhower/X316192082/MT/X316192082_MT_R2.fq -o /home/snarayanasamy/Work/IMP_analysis/X316192082_20160302-megahit -c conf/bigbug_config.imp.json -a megahit >> X316192082_IMP-megahit.log &
# HF4
nohup python3.4 IMP -m /mnt/md1200/snarayanasamy/IMP_data/Huttenhower/X316701492/MG/X316701492_MG_R1.fq -m /mnt/md1200/snarayanasamy/IMP_data/Huttenhower/X316701492/MG/X316701492_MG_R2.fq -t /mnt/md1200/snarayanasamy/IMP_data/Huttenhower/X316701492/MT/X316701492_MT_R1.fq -t /mnt/md1200/snarayanasamy/IMP_data/Huttenhower/X316701492/MT/X316701492_MT_R2.fq -o /home/snarayanasamy/Work/IMP_analysis/X316701492_20160307-idba -c conf/bigbug_config.imp.json >> X316701492_IMP.log &
nohup python3.4 IMP -m /mnt/md1200/snarayanasamy/IMP_data/Huttenhower/X316701492/MG/X316701492_MG_R1.fq -m /mnt/md1200/snarayanasamy/IMP_data/Huttenhower/X316701492/MG/X316701492_MG_R2.fq -t /mnt/md1200/snarayanasamy/IMP_data/Huttenhower/X316701492/MT/X316701492_MT_R1.fq -t /mnt/md1200/snarayanasamy/IMP_data/Huttenhower/X316701492/MT/X316701492_MT_R2.fq -o /home/snarayanasamy/Work/IMP_analysis/X316701492_20160307-megahit -c conf/bigbug_config.imp.json -a megahit >> X316701492_IMP-megahit.log &
# HF5
nohup python3.4 IMP -m /mnt/md1200/snarayanasamy/IMP_data/Huttenhower/X317690558/MG/X317690558_MG_R1.fq -m /mnt/md1200/snarayanasamy/IMP_data/Huttenhower/X317690558/MG/X317690558_MG_R2.fq -t /mnt/md1200/snarayanasamy/IMP_data/Huttenhower/X317690558/MT/X317690558_MT_R1.fq -t /mnt/md1200/snarayanasamy/IMP_data/Huttenhower/X317690558/MT/X317690558_MT_R2.fq -o /mnt/md1200/snarayanasamy/IMP_analysis/X317690558_20160308-idba -c conf/bigbug_config.imp.json >> X317690558_IMP.log &
nohup python3.4 IMP -m /mnt/md1200/snarayanasamy/IMP_data/Huttenhower/X317690558/MG/X317690558_MG_R1.fq -m /mnt/md1200/snarayanasamy/IMP_data/Huttenhower/X317690558/MG/X317690558_MG_R2.fq -t /mnt/md1200/snarayanasamy/IMP_data/Huttenhower/X317690558/MT/X317690558_MT_R1.fq -t /mnt/md1200/snarayanasamy/IMP_data/Huttenhower/X317690558/MT/X317690558_MT_R2.fq -o /home/snarayanasamy/Work/IMP_analysis/X317690558_20160308-megahit -c conf/bigbug_config.imp.json -a megahit >> X317690558_IMP-megahit.log &
## Wastewater (WW) sludge samples
## WW1
python3.4 IMP -m /mnt/md1200/snarayanasamy/IMP_data/A02/Lux_Lipids_Community-250111_DNA_TACTTCGG_L007_R1_001.fastq -m /mnt/md1200/snarayanasamy/IMP_data/A02/Lux_Lipids_Community-250111_DNA_TACTTCGG_L007_R2_001.fastq -t /mnt/md1200/snarayanasamy/IMP_data/A02/Lux-Lipids-Community-RNAlater-50ng_CGATGT_L006_R1_001.fastq -t /mnt/md1200/snarayanasamy/IMP_data/A02/Lux-Lipids-Community-RNAlater-50ng_CGATGT_L006_R2_001.fastq -o /home/snarayanasamy/Work/IMP_analysis/A02_20151006-idba -c conf/bigbug_config.imp.json
python3.4 IMP -m /mnt/md1200/snarayanasamy/IMP_data/A02/Lux_Lipids_Community-250111_DNA_TACTTCGG_L007_R1_001.fastq -m /mnt/md1200/snarayanasamy/IMP_data/A02/Lux_Lipids_Community-250111_DNA_TACTTCGG_L007_R2_001.fastq -t /mnt/md1200/snarayanasamy/IMP_data/A02/Lux-Lipids-Community-RNAlater-50ng_CGATGT_L006_R1_001.fastq -t /mnt/md1200/snarayanasamy/IMP_data/A02/Lux-Lipids-Community-RNAlater-50ng_CGATGT_L006_R2_001.fastq -o /home/snarayanasamy/Work/IMP_analysis/A02_20151007-megahit -c conf/bigbug_config.imp.json -a megahit
# WW2
nohup python3.4 /home/snarayanasamy/Work/tools/IMP/IMP -m /mnt/md1200/snarayanasamy/archived_raw_data/LAO/Metagenomic/time_series/D32/LAO_Metagenome-D32_TACCGAGC_L004_R1_001.fastq.bz2 -m /mnt/md1200/snarayanasamy/archived_raw_data/LAO/Metagenomic/time_series/D32/LAO_Metagenome-D32_TACCGAGC_L004_R2_001.fastq.bz2 -t /mnt/md1200/snarayanasamy/archived_raw_data/LAO/Metatranscriptomic/time_series/D32/LAO_Metatranscriptome-D32_TAGCTT_L003_R1_001.fastq.bz2 -t /mnt/md1200/snarayanasamy/archived_raw_data/LAO/Metatranscriptomic/time_series/D32/LAO_Metatranscriptome-D32_TAGCTT_L003_R2_001.fastq.bz2 -o /mnt/md1200/snarayanasamy/IMP_analysis/D32_20160302-idba -c /home/snarayanasamy/Work/tools/IMP/conf/LAO_bigbug_IMP_MS_config.imp.json >> D32_IMP.log &
nohup python3.4 /home/snarayanasamy/Work/tools/IMP/IMP -m /mnt/md1200/snarayanasamy/archived_raw_data/LAO/Metagenomic/time_series/D32/LAO_Metagenome-D32_TACCGAGC_L004_R1_001.fastq.bz2 -m /mnt/md1200/snarayanasamy/archived_raw_data/LAO/Metagenomic/time_series/D32/LAO_Metagenome-D32_TACCGAGC_L004_R2_001.fastq.bz2 -t /mnt/md1200/snarayanasamy/archived_raw_data/LAO/Metatranscriptomic/time_series/D32/LAO_Metatranscriptome-D32_TAGCTT_L003_R1_001.fastq.bz2 -t /mnt/md1200/snarayanasamy/archived_raw_data/LAO/Metatranscriptomic/time_series/D32/LAO_Metatranscriptome-D32_TAGCTT_L003_R2_001.fastq.bz2 -o /mnt/md1200/snarayanasamy/IMP_analysis/D32_20151227-megahit-megahit -a megahit -c /home/snarayanasamy/Work/tools/IMP/conf/LAO_bigbug_IMP_MS_config.imp.json >> D32_IMP.log &
# WW3
nohup python3.4 IMP -m /mnt/md1200/snarayanasamy/IMP_data/D36/LAO_Metagenome_D36_TTACTCGC_L007_R1_001.fastq.bz2 -m /mnt/md1200/snarayanasamy/IMP_data/D36/LAO_Metagenome_D36_TTACTCGC_L007_R2_001.fastq.bz2 -t /mnt/md1200/snarayanasamy/IMP_data/D36/LAO_Metatranscriptome_D36_CGATGT_L006_R1_001.fastq.bz2 -t /mnt/md1200/snarayanasamy/IMP_data/D36/LAO_Metatranscriptome_D36_CGATGT_L006_R2_001.fastq.bz2 -o /home/snarayanasamy/Work/IMP_analysis/D36_20140307-idba -c /home/snarayanasamy/Work/tools/IMP/conf/LAO_bigbug_config.imp.json >> D36_IMP.log &
nohup python3.4 IMP -m /mnt/md1200/snarayanasamy/IMP_data/D36/LAO_Metagenome_D36_TTACTCGC_L007_R1_001.fastq.bz2 -m /mnt/md1200/snarayanasamy/IMP_data/D36/LAO_Metagenome_D36_TTACTCGC_L007_R2_001.fastq.bz2 -t /mnt/md1200/snarayanasamy/IMP_data/D36/LAO_Metatranscriptome_D36_CGATGT_L006_R1_001.fastq.bz2 -t /mnt/md1200/snarayanasamy/IMP_data/D36/LAO_Metatranscriptome_D36_CGATGT_L006_R2_001.fastq.bz2 -o /home/snarayanasamy/Work/IMP_analysis/D36_20160101-megahit -a megahit -c /home/snarayanasamy/Work/tools/IMP/conf/LAO_bigbug_config.imp.json >> D36_IMP.log &
# WW4
nohup python3.4 /home/snarayanasamy/Work/tools/IMP/IMP -m /mnt/md1200/snarayanasamy/archived_raw_data/LAO/Metagenomic/time_series/D49/LAO_Metagenome_D49_TAGACGGA_L008_R1_001.fastq.bz2 -m /mnt/md1200/snarayanasamy/archived_raw_data/LAO/Metagenomic/time_series/D49/LAO_Metagenome_D49_TAGACGGA_L008_R2_001.fastq.bz2 -t /mnt/md1200/snarayanasamy/archived_raw_data/LAO/Metatranscriptomic/time_series/D49/LAO_Metatranscriptome_D49_ATCACG_L008_R1_001.fastq.bz2 -t /mnt/md1200/snarayanasamy/archived_raw_data/LAO/Metatranscriptomic/time_series/D49/LAO_Metatranscriptome_D49_ATCACG_L008_R2_001.fastq.bz2 -o /home/snarayanasamy/Work/IMP_analysis/D49_20160302-idba -c /home/snarayanasamy/Work/tools/IMP/conf/LAO_bigbug_config.imp.json >> D49_IMP.log &
nohup python3.4 /home/snarayanasamy/Work/tools/IMP/IMP -m /mnt/md1200/snarayanasamy/archived_raw_data/LAO/Metagenomic/time_series/D49/LAO_Metagenome_D49_TAGACGGA_L008_R1_001.fastq.bz2 -m /mnt/md1200/snarayanasamy/archived_raw_data/LAO/Metagenomic/time_series/D49/LAO_Metagenome_D49_TAGACGGA_L008_R2_001.fastq.bz2 -t /mnt/md1200/snarayanasamy/archived_raw_data/LAO/Metatranscriptomic/time_series/D49/LAO_Metatranscriptome_D49_ATCACG_L008_R1_001.fastq.bz2 -t /mnt/md1200/snarayanasamy/archived_raw_data/LAO/Metatranscriptomic/time_series/D49/LAO_Metatranscriptome_D49_ATCACG_L008_R2_001.fastq.bz2 -o /home/snarayanasamy/Work/IMP_analysis/D49_20160115-megahit -a megahit -c /home/snarayanasamy/Work/tools/IMP/conf/LAO_bigbug_config.imp.json >> D49_IMP.log &
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