Commit 475b03c8 authored by Shaman Narayanasamy's avatar Shaman Narayanasamy
Browse files

Add CAMI commands

parent 29ee315d
#!/bin/bash -l
## CAMI is a benchmark simulated data set. This runs IMP when only MG data is povided
COMMAND=$1
## Low complexity
LOG=CAMI_low-idba.log
CMD="
time python3.4 /home/snarayanasamy/Work/tools/IMP_new/IMP/IMP \
-m /mnt/md1200/snarayanasamy/IMP_data/CAMI/Low_Complexity_Test_Dataset/LCTD.1.fq \
-m /mnt/md1200/snarayanasamy/IMP_data/CAMI/Low_Complexity_Test_Dataset/LCTD.2.fq \
-o /mnt/md1200/snarayanasamy/IMP_analysis/CAMI_low-idba \
-c conf/bigbug.conf.imp.json --current -a idba \
-d /home/snarayanasamy/Work/tools/IMP_new/IMP/db \
$COMMAND"
echo $CMD > $LOG
$CMD >> 2&>> $LOG
LOG=CAMI_low-megahit.log
CMD="
time python3.4 /home/snarayanasamy/Work/tools/IMP_new/IMP/IMP \
-m /mnt/md1200/snarayanasamy/IMP_data/CAMI/Low_Complexity_Test_Dataset/LCTD.1.fq \
-m /mnt/md1200/snarayanasamy/IMP_data/CAMI/Low_Complexity_Test_Dataset/LCTD.2.fq \
-o /mnt/md1200/snarayanasamy/IMP_analysis/CAMI_low-megahit \
-c conf/bigbug.conf.imp.json --current -a megahit \
-d /home/snarayanasamy/Work/tools/IMP_new/IMP/db \
$COMMAND"
echo $CMD > $LOG
$CMD >> 2&>> $LOG
#
### Medium complexity
LOG=CAMI_medium-idba.log
CMD="
time python3.4 /home/snarayanasamy/Work/tools/IMP_new/IMP/IMP \
-m /mnt/md1200/snarayanasamy/IMP_data/CAMI/Medium_Complexity_Test_Dataset/MCTD.1.fq \
-m /mnt/md1200/snarayanasamy/IMP_data/CAMI/Medium_Complexity_Test_Dataset/MCTD.2.fq \
-o /mnt/md1200/snarayanasamy/IMP_analysis/CAMI_medium-idba \
-c conf/bigbug.conf.imp.json --current -a idba \
-d /home/snarayanasamy/Work/tools/IMP_new/IMP/db \
$COMMAND"
echo $CMD > $LOG
$CMD >> 2&>> $LOG
LOG=CAMI_medium-megahit.log
CMD="
time python3.4 /home/snarayanasamy/Work/tools/IMP_new/IMP/IMP \
-m /mnt/md1200/snarayanasamy/IMP_data/CAMI/Medium_Complexity_Test_Dataset/MCTD.1.fq \
-m /mnt/md1200/snarayanasamy/IMP_data/CAMI/Medium_Complexity_Test_Dataset/MCTD.2.fq \
-o /mnt/md1200/snarayanasamy/IMP_analysis/CAMI_medium-megahit \
-c conf/bigbug.conf.imp.json --current -a megahit \
-d /home/snarayanasamy/Work/tools/IMP_new/IMP/db \
$COMMAND"
echo $CMD > $LOG
$CMD >> 2&>> $LOG
### High complexity
LOG=CAMI_high-idba.log
CMD="
time python3.4 /home/snarayanasamy/Work/tools/IMP_new/IMP/IMP \
-m /mnt/md1200/snarayanasamy/IMP_data/CAMI/High_Complexity_Dataset/HCTD.1.fq \
-m /mnt/md1200/snarayanasamy/IMP_data/CAMI/High_Complexity_Dataset/HCTD.2.fq \
-o /mnt/md1200/snarayanasamy/IMP_analysis/CAMI_high-idba \
-c conf/bigbug.conf.imp.json --current -a idba \
-d /home/snarayanasamy/Work/tools/IMP_new/IMP/db \
$COMMAND"
echo $CMD > $LOG
$CMD >> 2&>> $LOG
LOG=CAMI_high-megahit.log
CMD="
time python3.4 /home/snarayanasamy/Work/tools/IMP_new/IMP/IMP \
-m /mnt/md1200/snarayanasamy/IMP_data/CAMI/High_Complexity_Dataset/HCTD.1.fq \
-m /mnt/md1200/snarayanasamy/IMP_data/CAMI/High_Complexity_Dataset/HCTD.2.fq \
-o /mnt/md1200/snarayanasamy/IMP_analysis/CAMI_high-megahit \
-c conf/bigbug.conf.imp.json --current -a megahit \
-d /home/snarayanasamy/Work/tools/IMP_new/IMP/db \
$COMMAND"
echo $CMD > $LOG
$CMD >> 2&>> $LOG
{
"threads": 8,
"mem_per_core_gb": 32,
"mem_total_gb": 256
}
{
"threads": 8,
"mem_per_core_gb": 32,
"mem_total_gb": 256
"preprocessing_filtering": "false"
}
{
"threads": 16,
"memory_total_gb": 500,
"memory_per_core_gb": 32,
"tmp_dir": "tmp",
"imp_src": "src",
"raws": {
"Metagenomics": "",
"Metatranscriptomics": ""
},
"sample": "test",
"outputdir": "/output",
"db_path": "/databases",
"preprocessing_filtering": true,
"trimmomatic": {
"pkg_url": "https://webdav-r3lab.uni.lu/public/R3lab/IMP/Trimmomatic-Src-0.32.zip",
"adapter": "TruSeq3",
"leading": 20,
"minlen": 40,
"palindrome_clip_threshold": 30,
"simple_clip_threshold": 10,
"trailing": 20,
"seed_mismatch": 2,
"window_size": 1,
"window_quality": 3,
"strictness": 0.5,
"target_length": 40,
"jarfile": "/home/imp/lib/trimmomatic-0.32.jar"
},
"idba_ud": {
"mink": 25,
"maxk": 99,
"step": 4,
"perid": 0.98
},
"vizbin": {
"dimension": 50,
"kmer": 5,
"size": 4,
"theta": 0.5,
"perp": 30,
"cutoff": 1000,
"jarfile": "/home/imp/lib/VizBin-dist.jar"
},
"human_filtering": {
"filter": "hg38",
"url": "http://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz"
},
"sortmerna": {
"pkg_url": "https://webdav-r3lab.uni.lu/public/R3lab/IMP/sortmerna.2.0.tgz",
"scripts_path": "/home/imp/lib",
"files": [
"rfam-5.8s-database-id98",
"silva-arc-16s-id95",
"silva-bac-16s-id90",
"silva-euk-18s-id95",
"rfam-5s-database-id98",
"silva-arc-23s-id98",
"silva-bac-23s-id98",
"silva-euk-28s-id98"
]
},
"prokka": {
"pkg_url": "https://webdav-r3lab.uni.lu/public/R3lab/IMP/prokka-1.11.tar.gz",
"databases": [
"cm/Bacteria.i1i",
"genus/Staphylococcus.phr",
"hmm/CLUSTERS.hmm.h3f",
"kingdom/Archaea/sprot.phr"
]
},
"kegg": {
"db_ec2pthy": "http://rest.kegg.jp/link/ec/pathway",
"db_hierarchy": "http://rest.kegg.jp/list/pathway"
},
"preload": {
"test": "",
"test2": ""
}
}
{
"threads": 8,
"memory_total_gb": 256,
"memory_per_core_gb": 32,
"preprocessing_filtering": false,
"trimmomatic": {
"adapter": "TruSeq2"
}
}
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment