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GMH_pipe.cfg
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GMH_pipe.cfg
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[PIPELINE]
useSlurm = 1
usePeregrineJobQueues = 0
doBBduk = 1
doKnead = 1
doQC = 1
doMeta3 = 1
doMeta4 = 1
doKraken2 = 0
doStrainPhlan3 = 1
doStrainPhlan4 = 1
doHumann3 = 1
doHumann3.6 = 1
doVFDB_SB = 1
doCARD_SB = 1
doAssemblyMetaSpades = 0
doAssemblyMegaHit = 0
doSVFinder = 0
useNodeTMP = 1
jobOut = JOB_OUT
doProfiling = 0
doPanPhlan = 1
doBinningMWrap = 1
doBinRefiningMWrap = 1
doBinAnnotationCheckM = 1
doBinAnnotationGTDBK = 1
doBinQuantification = 1
doBinAnnotationBAKTA = 0
[INIT]
modules = Anaconda3/2022.05
paths =
condaEnv = /scratch/hb-tifn/condas/conda_biobakery4/
memory = 48G
cpus = 2
threads = 2
time = 8:00:00
[BBDUK]
modules = Anaconda3/2022.05
paths =
condaEnv = /scratch/hb-tifn/condas/conda_BBduk
memory = 16G
cpus = 4
threads = 4
time = 1:59:00
adapters = /scratch/hb-tifn/tools/GMH_pipeline/adapters/adapters.fa
bbdukparams = ktrim=r k=23 mink=11 hdist=1 tpe tbo
[QC]
modules = Anaconda3/2022.05
paths =
condaEnv = /scratch/hb-tifn/condas/conda_biobakery4/
memory = 4G
cpus = 4
threads = 4
time = 0:19:00
fastqc = fastqc
[KNEAD]
modules = Anaconda3/2022.05
paths =
kneadversion = biobakery3
condaEnv = /scratch/hb-tifn/condas/conda_biobakery3/
memory = 24G
cpus = 4
threads = 4
time = 5:59:00
kneaddata = kneaddata
db = /scratch/hb-tifn/DBs/human_genomes/hg37dec_v0.1
mergeResults = 0
doTrimIfUsingBBduk = 1
trimmomatic = /scratch/hb-tifn/condas/conda_biobakery4/share/trimmomatic-0.39-2/
trimmomaticOptions = --fastqc fastqc --sequencer-source none --trimmomatic-options "LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:50"
options = --bypass-trf --reorder
keepHumanReads = 1
cleanTmp = 1
knead3parser = /scratch/hb-tifn/tools/GMH_pipeline/utils/knead3parser.py
[METAPHLAN3]
modules = Anaconda3/2022.05
condaEnv = /scratch/hb-tifn/condas/conda_biobakery3/
paths =
memory = 20G
cpus = 4
threads = 4
bowtie2_exe = bowtie2
bowtie2_build = bowtie2-build
time = 4:00:00
metaphlan = metaphlan
metaphlanDB = /scratch/hb-tifn/condas/conda_biobakery3/lib/python3.9/site-packages/metaphlan/metaphlan_databases/
metaphlanOptions = --force --index mpa_vJan21_CHOCOPhlAnSGB_202103 -t rel_ab_w_read_stats --unknown_estimation
[METAPHLAN4]
modules = Anaconda3/2022.05
condaEnv = /scratch/hb-tifn/condas/conda_biobakery4/
paths =
memory = 20G
cpus = 4
threads = 4
bowtie2_exe = bowtie2
bowtie2_build = bowtie2-build
time = 6:00:00
metaphlan = metaphlan
metaphlanDB = /scratch/hb-tifn/condas/conda_biobakery4/lib/python3.9/site-packages/metaphlan/metaphlan_databases/
metaphlanOptions = --force --unclassified_estimation
[STRAINPHLAN3]
modules = Anaconda3/2022.05
condaEnv = /scratch/hb-tifn/condas/conda_biobakery3/
paths =
memory = 16G
cpus = 8
threads = 16
samples2markers = sample2markers.py
bowtie2_exe = bowtie2
bowtie2_build = bowtie2-build
time = 3:59:00
[STRAINPHLAN4]
modules = Anaconda3/2022.05
condaEnv = /scratch/hb-tifn/condas/conda_biobakery4/
paths =
memory = 4G
cpus = 1
threads = 1
samples2markers = sample2markers.py
bowtie2_exe = bowtie2
bowtie2_build = bowtie2-build
time = 0:29:00
[HUMANN3]
modules = Anaconda3/2022.05
condaEnv = /scratch/hb-tifn/condas/conda_biobakery3/
paths =
memory = 32gb
cpus = 8
threads = 16
time = 15:59:00
humann = humann
cleanup = 1
[HUMANN3.6]
modules = Anaconda3/2022.05
condaEnv = /scratch/hb-tifn/condas/conda_biobakery4/
paths =
memory = 48gb
cpus = 8
threads = 8
time = 15:59:00
humann = humann
cleanup = 1
[VFDB_SB]
modules = Anaconda3/2022.05
condaEnv = /scratch/hb-tifn/condas/conda_assemblers
paths =
memory = 8gb
cpus = 8
threads = 16
time = 3:59:00
parser = /scratch/hb-tifn/tools/GMH_pipeline/utils/parseVFDBshortBRED.py
shortbred = shortbred_quantify.py
fasta = /scratch/hb-tifn/DBs/shortbred_markers/markers_VFDB/VFDB_core_annotated_sb.fa
markers = /scratch/hb-tifn/DBs/shortbred_markers/markers_VFDB/markers_core_VFDB.fa
annotation = /scratch/hb-tifn/DBs/shortbred_markers/markers_VFDB/VFDB_annotation.csv
usearch = /scratch/hb-tifn/tools/GMH_pipeline/utils/usearch10.0.240_i86linux32
[CARD_SB]
modules = Anaconda3/2022.05
condaEnv = /scratch/hb-tifn/condas/conda_assemblers
paths =
memory = 8gb
cpus = 8
threads = 16
time = 3:59:00
shortbred = shortbred_quantify.py
fasta = /scratch/hb-tifn/DBs/shortbred_markers/markers_CARD_2018_11/CARD_2018_11_merged_prot.fa
markers = /scratch/hb-tifn/DBs/shortbred_markers/markers_CARD_2018_11/markers_CARD_2018_11.fa
usearch = /scratch/hb-tifn/tools/GMH_pipeline/utils/usearch10.0.240_i86linux32
[ASSEMBLY_METASPADES]
modules = Anaconda3/2022.05
condaEnv = /scratch/hb-tifn/condas/conda_assemblers
paths =
memory = 40gb
cpus = 8
threads = 8
time = 9:59:00
assemblerPath = metaspades.py
extraparams =
[ASSEMBLY_MEGAHIT]
modules = Anaconda3/2022.05
condaEnv = /scratch/hb-tifn/condas/conda_assemblers
paths =
memory = 40gb
cpus = 8
threads = 8
time = 9:59:00
assemblerPath = megahit
extraparams =
[BINNING_METAWRAP]
modules = Anaconda3/2022.05
condaEnv = /scratch/hb-tifn/condas/conda_metawrap
paths =
memory = 16gb
cpus = 8
threads = 8
time = 6:30:00
assembler = MEGAHIT
minContigLength = 1000
[BIN_REFINING_METAWRAP]
modules = Anaconda3/2022.05
condaEnv = /scratch/hb-tifn/condas/conda_metawrap
paths =
memory = 48gb
cpus = 8
threads = 8
time = 6:30:00
COMPLETENESS_MIN=50
CONTAMINATION_MAX=10
[BIN_ANNOTATION_CHECKM]
modules = Anaconda3/2022.05
condaEnv = /scratch/hb-tifn/condas/conda_metawrap/
paths =
memory = 50gb
cpus = 8
threads = 8
time = 1:59:00
input = bins_metawrap_refined
[BIN_ANNOTATION_GTDBK]
modules = Anaconda3/2022.05
condaEnv = /scratch/hb-tifn/condas/conda_GTDB_TK/
paths =
memory = 64gb
cpus = 8
threads = 8
time = 2:59:00
input = bins_metawrap_refined
GTDBK_DB = /scratch/hb-tifn/DBs/DB_GTDB/release207_v2
[BIN_ANNOTATION_BAKTA]
modules = Anaconda3/2022.05
condaEnv = /scratch/hb-tifn/condas/conda_BAKTA
paths =
memory = 64gb
cpus = 8
threads = 8
time = 1:59:00
input = bins_metawrap_refined
GTDBK_DB = /scratch/hb-tifn/DBs/BAKTA_DB_v17/db
[BIN_QUANTIFICATION]
modules = Anaconda3/2022.05
condaEnv = /scratch/hb-tifn/condas/conda_metawrap/
paths =
memory = 8gb
cpus = 4
threads = 4
time = 0:30:00
input = bins_metawrap_refined
[BIN_PANGENOMICS_ROARY]
[KRAKEN2]
modules = Anaconda3/2022.05
condaEnv = /scratch/hb-tifn/condas/conda_kraken2/
paths =
memory = 48gb
cpus = 1
threads = 1
time = 3:59:00
krakenDB = /scratch/hb-tifn/DBs/kraken2_db_uhgg_v2.0.1/
krakenPath = kraken2
krakenExtraParams = --confidence 0.50
krakenReportFixer = /scratch/hb-tifn/tools/GMH_pipeline/utils/Kraken/fixKraken2report.py
brackenPath = bracken
brackenReadThreshold = 10
brackenLevel = S
brackenReadLt = 150
brackenExtraParams =
krakenToMP3 = /scratch/hb-tifn/tools/GMH_pipeline/utils/Kraken/krakenReportToMP3.py
[MERGE_RESULTS]
condaModule = Anaconda3/2022.05
condaBiobakery = /scratch/hb-tifn/condas/conda_biobakery4
kneaddataMerger = /scratch/hb-tifn/tools/GMH_pipeline/utils/mergeKneadReadReports.py
vfdbSbMerger = /scratch/hb-tifn/tools/GMH_pipeline/utils/mergeVFDB.py
cardSbMerger = /scratch/hb-tifn/tools/GMH_pipeline/utils/mergeCARD.py
[SVFINDER]
modules = Anaconda3/2022.05
condaEnv = /scratch/hb-tifn/condas/conda_SVfinder/
paths = /scratch/hb-tifn/tools/GEM
memory = 64gb
cpus = 1
threads = 1
time = 0-23:59:00
fastq_pair = fastq_pair
ICRA = /scratch/hb-tifn/tools/SGVFinder/src/ICRA_cmd.py
[SVFINDER2]
modules = Anaconda3/2022.05
condaEnv = /scratch/hb-tifn/condas/conda_SVfinder/
paths = /scratch/hb-tifn/tools/GEM
memory = 30gb
cpus = 1
threads = 1
time = 00:29:00
fastq_pair = fastq_pair
SGVF = /scratch/hb-tifn/tools/SGVFinder/src/SGVF_PerFile_cmd.py
SGVF_READL = 150
SGVF_COV = 0.01
SGVF_RATEPARAM = 10
CLEANUP = 0
[PANPHLAN]
modules = Anaconda3/2022.05
condaEnv = /scratch/hb-tifn/condas/conda_biobakery3/
paths =
memory = 16gb
cpus = 8
threads = 8
panphlan_map = panphlan_map.py
panphlan_DBs = /scratch/hb-tifn/DBs/panphlan3/panphlan_DBs
time = 1:59:00
domulticlades = 1
clades = Faecalibacterium_prausnitzii,Roseburia_hominis