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Copy pathcarma.cfg
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125 lines (89 loc) · 4.12 KB
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#
# CARMA3 configuration file
#
# this file is read by the carma binary as well as the perl script
# that submits carma and BLAST to the SGE-grid
#
#
#
#####################################################
#general:
# in the CARMA3 paper this is parameter p
#e.g. "1.03" to increase sensitivity, default: 1.0
query_multiplier = 1.0 # double,
carma_binary = /vol/carma/CARMA3/src/carma
carma_sge_script = /vol/carma/CARMA3/src/carma3.sh
nodes_dmp = /vol/biodb/ncbi_taxonomy/nodes.dmp
merged_dmp = /vol/biodb/ncbi_taxonomy/merged.dmp
names_dmp = /vol/biodb/ncbi_taxonomy/names.dmp
# temp directory that can be accessed from all nodes in the cluster
cluster_tmp_dir = /vol/codine-tmp/
# number of jobs that are submitted on the cluster at once
maxNumberOfChunks=100 # int
NCBI_MAX=2000000 # int
#used to provide information to the end-user for WebCARMA or similar
message = MESSAGE:
# E-mail address for the SGE-cluster notification system ("none" to deactivate):
clusteremail = none
gzip_bin = /vol/gnu/bin/gzip
zcat_bin = /vol/gnu/bin/zcat
#cp_bin = /vol/gnu/bin/cp
#####################################################
# blastn and 16S
score_match = 1 # int
score_mismatch = -3 # int
score_gapopen = -1 # int
score_gapextension = -1 # int
#####################################################
#16S:
rdp_bact_aligned = /vol/metagenomics/RDP/release10_24_bact_aligned_specific.fa.gz # do not give here the original RDP file, give the file that was filtered by CARMA3 preprocessing routines
rdp_arch_aligned = /vol/metagenomics/RDP/release10_24_arch_aligned_specific.fa.gz # do not give here the original RDP file, give the file that was filtered by CARMA3 preprocessing routines
rdp_unaligned = /vol/metagenomics/RDP/release10_24_unaligned_specific.fa.gz # do not give here the original RDP file, give the file that was filtered by CARMA3 preprocessing routines
#blast_rdp_database = /vol/metagenomics/RDP/rdp_specific/rdp
blast_rdp_database = /vol/metagenomics/rdp_evaluation/rdp/rdp
blast_rdp_evalue = 10.0 # double
#####################################################
#HMMER:
hmmscan_evalue = 0.1 # double, requires the dot !
pairwise_blosum_minscore = 30.0 # double
pairwise_blosum_minoverlap = 25.0 #10.0; # double
hmmfetch_bin = /vol/biotools/bin/hmmfetch-3
hmmalign_bin = /vol/biotools/bin/hmmalign-3
hmmscan_bin = /vol/biotools/bin/hmmscan-3
pfamId2TaxId_file = /vol/carma/data/pfam24/pfamid2taxid.txt.gz
pfamA_txt_file = /vol/carma/data/pfam24/pfamA.txt.gz
gene_ontology_txt_file = /vol/carma/data/pfam24/gene_ontology.txt
pfam_A_hmm_file = /vol/biodb/pfam24/Pfam-A.hmm
# directory that contains fasta files for each Pfam family
# can be created with splitPfamFasta.pl
pfam_fasta_dir = /vol/carma/data/pfam24/Pfam-A.fasta.splitted/
blosum_file = /vol/carma/CARMA3/BLOSUM62
#####################################################
# BLASTX and BLASTN
#this are the E-values which are used for the actual BLAST-runs
blastx_evalue = 10.0 # double
blastn_evalue = 10.0 # double
blastp_evalue = 10.0 # double
#this are the E-value thresholds used for *parsing* the BLAST results. It won't make sense to choose values that are higher than those of the actual BLAST runs.
carma_blastx_evalue = 100000000.01 # double
carma_blastn_evalue = 100000000.01 # double
carma_blastp_evalue = 100000000.01 # double
carma_blastx_bitscore = 35.0 # 35.0; # double
carma_blastp_bitscore = 35.0 # 35.0; # double
carma_blastn_bitscore = 0.0 # double
carma_blastx_alignment_length = 25 #25; # int
carma_blastp_alignment_length = 25 # int
carma_blastn_alignment_length = 0 # int
LCA_top_percent = 0.10 # double
use_hard_threshold = false
blastall_script = /vol/biotools/bin/blastall-2.2.24
fastacmd_script = /vol/biotools/bin/fastacmd-2.2.24
formatdb_script = /vol/biotools/bin/formatdb-2.2.24
blast_nr_database = /vol/biodb/asn1/nr
#blast_nr_database = /vol/cluster-data/wgerlach/NR25_species/nr
#blast_nr_database = /vol/cluster-data/wgerlach/NR25_order/nr
blast_nt_database = /vol/biodb/asn1/nt
#blast_nt_database = /vol/cluster-data/wgerlach/NT25_species/nt
max_blast_description_length = 500000
# not used currently
#LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/vol/carma/CARMA3/lib/