Add MOCAT scipts and config files

MOCAT_analysis/Combined/biogas_plant/MOCAT.cfg

+#####################################
+#          MOCAT Config File        #
+#####################################
+
+
+##################################
+#         GLOBAL SETTINGS        #
+##################################
+MOCAT_dir                : /work/projects/ecosystem_biology/local_tools/MOCAT/
+MOCAT_data_type          : solexaqa [fastx,solexaqa]
+MOCAT_paired_end         : yes [yes,no]
+MOCAT_SGE_parallell_env  : smp [smp,mpi,-or other setting on your system-]
+MOCAT_mapping_mode       : allbest [allbest,random,unique]
+MOCAT_qsub_system        : none [SGE,PBS,none]
+MOCAT_zip_program        : pigz [gzip,pigz]
+MOCAT_default_reads      : reads.processed ['reads.processed','DATABASE']
+MOCAT_zip_level          : 1 [1-9]
+MOCAT_SGE_qsub_add_param : [-l mem_free=6G -l h_vmem=6G] 
+MOCAT_PBS_qsub_add_param : [-l select=mem=6gb] 
+MOCAT_LSF_qsub_add_param : [-l select=mem=6gb]
+MOCAT_LSF_queue          : []
+MOCAT_LSF_memory_limit   : []
+MOCAT_umask              : 0022 [0022]
+MOCAT_pre_execute        : [umask 0002]
+MOCAT_prompt_before_run  : no [yes,no]
+
+
+##################################
+#      READ TRIM AND FILTER      #
+##################################
+readtrimfilter_length_cutoff               : 40
+readtrimfilter_qual_cutoff                 : 20
+readtrimfilter_use_sanger_scale            : auto [yes,no,auto]
+readtrimfilter_trim_5_prime                : yes [yes,no]
+readtrimfilter_use_precalc_5prime_trimming : no  [yes,no]
+
+
+##################################
+#            SCREEN              #    
+##################################
+screen_length_cutoff    : 30
+screen_percent_cutoff   : 90
+screen_soap_seed_length : 30
+screen_soap_max_mm      : 10
+screen_soap_cmd         : -M 4 [-M 4]
+screen_save_format      : sam [soap,sam]
+
+
+##################################
+#             FILTER             #
+##################################
+filter_psort_buffer         : 2G
+filter_length_cutoff        : 45
+filter_percent_cutoff       : 95
+filter_paired_end_filtering : yes [yes,no]
+filter_remove_mapping_files : no  [yes.no]
+filter_make_unique_sorted   : no [yes.no]
+filter_samtools_memory      : 50000000000 [50000000000] (Memory allocation in bytes, this setting is only used if 'filter_make_unique_sorted' is set to 'yes')
+
+
+##################################
+#       SCREEN FASTA FILE        #    
+##################################
+screen_fasta_file_blast_e_value          : 0.00001 
+screen_fasta_file_blast_read_min_length  : 10
+screen_fasta_file_additional_usearch_cmd : []
+screen_fasta_file_usearch_version        : 6 [5,6]
+screen_fasta_file_usearch_version_5_exe  : usearch
+screen_fasta_file_usearch_version_6_exe  : usearch
+
+##################################
+#           PROFILING            #
+##################################
+profiling_paired_end_filtering           : yes [yes,no]
+
+##################################
+#            ASSEMBLY            #
+##################################
+assembly_soap_version                : 1.06 [1.05,1.06]
+assembly_calculate_insert_size_using : mapping [assembly,mapping]
+assembly_db_for_calc_insertsize      : 1506MG (used if specified 'mapping' above)
+assembly_scaftig_min_length          : 500
+
+
+##################################
+#        ASSEMBLY REVISION       #
+##################################
+assembly_revision_scaftig_min_length : 500
+
+
+##################################
+#         GENE PREDICTION        #
+##################################
+gene_prediction_software     : Prodigal [MetaGeneMark,Prodigal]
+gene_prediction_input        : scaftig [scaftig,contig,scafSeq] (if revised assembly, can only be 'scaftig')
+gene_prediction_prodigal_cmd : -f gff [-f xxx, -none-] (-p, -o, -a, -d, -i already set at runtime in MOCAT)
+
+
+##################################
+#      EXPERIMENTAL SETTINGS     #
+##################################
+realtime_status_use   : no [yes,no] (setting this to 'yes' shows current status of jobs, if realtime_status_print is set to 'yes', and also stores required resources in log folder)
+realtime_status_print : yes [yes,no]
+realtime_status_show  : no [yes,no]
+realtime_status_timer : 5
+realtime_status_log   : no
+realtime_status_fix_1 : -here you can add hostname that are not clusters-
+realtime_status_fix_2 : -here you can add hostname that are not clusters-
+
+# END OF FILE #

MOCAT_analysis/Combined/biogas_plant/runALL.sh

+#!/bin/bash
+#oarsub -lcpu=1,walltime=72:00:00  -p "memcpu='258538'" -n mocatLux ./run.sh
+
+samples=samples
+log=$samples.log
+
+source $HOME/.profile
+source $HOME/.bashrc
+
+export PERL5LIB=$PERL5LIB:/work/projects/ecosystem_biology/local_tools/MOCAT/src
+PATH=$PATH:/work/projects/ecosystem_biology/local_tools/MOCAT/src
+export PATH
+#MOCAT.pl -sf $samples -rtf -cpus 8 >$log 2>>$log 
+
+#MOCAT.pl -sf $samples -s hg19 -cpus 8 >>$log 2>>$log
+#MOCAT.pl -sf $samples -a -r hg19 -cpus 8 >>$log 2>>$log
+#MOCAT.pl -sf $samples -ar -cpus 8 -r hg19 >>$log 2>>$log
+#MOCAT.pl -sf $samples -gp assembly.revised -cpus 8 -r hg19 >>$log 2>>$log
+#MOCAT.pl -sf $samples -ss -cpus 8  >>$log 2>>$log
+
+MOCAT.pl -sf $samples -a -cpus 8 >>$log 2>>$log
+MOCAT.pl -sf $samples -ar -cpus 8  >>$log 2>>$log
+MOCAT.pl -sf $samples -gp assembly.revised -cpus 8  >>$log 2>>$log
+MOCAT.pl -sf $samples -ss -cpus 8  >>$log 2>>$log
+

MOCAT_analysis/Combined/human_fecal/MOCAT.cfg

+#####################################
+#          MOCAT Config File        #
+#####################################
+
+
+##################################
+#         GLOBAL SETTINGS        #
+##################################
+MOCAT_dir                : /work/projects/ecosystem_biology/local_tools/MOCAT/
+MOCAT_data_type          : solexaqa [fastx,solexaqa]
+MOCAT_paired_end         : yes [yes,no]
+MOCAT_SGE_parallell_env  : smp [smp,mpi,-or other setting on your system-]
+MOCAT_mapping_mode       : allbest [allbest,random,unique]
+MOCAT_qsub_system        : none [SGE,PBS,none]
+MOCAT_zip_program        : pigz [gzip,pigz]
+MOCAT_default_reads      : reads.processed ['reads.processed','DATABASE']
+MOCAT_zip_level          : 1 [1-9]
+MOCAT_SGE_qsub_add_param : [-l mem_free=6G -l h_vmem=6G] 
+MOCAT_PBS_qsub_add_param : [-l select=mem=6gb] 
+MOCAT_LSF_qsub_add_param : [-l select=mem=6gb]
+MOCAT_LSF_queue          : []
+MOCAT_LSF_memory_limit   : []
+MOCAT_umask              : 0022 [0022]
+MOCAT_pre_execute        : [umask 0002]
+MOCAT_prompt_before_run  : no [yes,no]
+
+
+##################################
+#      READ TRIM AND FILTER      #
+##################################
+readtrimfilter_length_cutoff               : 40
+readtrimfilter_qual_cutoff                 : 20
+readtrimfilter_use_sanger_scale            : auto [yes,no,auto]
+readtrimfilter_trim_5_prime                : yes [yes,no]
+readtrimfilter_use_precalc_5prime_trimming : no  [yes,no]
+
+
+##################################
+#            SCREEN              #    
+##################################
+screen_length_cutoff    : 30
+screen_percent_cutoff   : 90
+screen_soap_seed_length : 30
+screen_soap_max_mm      : 10
+screen_soap_cmd         : -M 4 [-M 4]
+screen_save_format      : sam [soap,sam]
+
+
+##################################
+#             FILTER             #
+##################################
+filter_psort_buffer         : 2G
+filter_length_cutoff        : 45
+filter_percent_cutoff       : 95
+filter_paired_end_filtering : yes [yes,no]
+filter_remove_mapping_files : no  [yes.no]
+filter_make_unique_sorted   : no [yes.no]
+filter_samtools_memory      : 50000000000 [50000000000] (Memory allocation in bytes, this setting is only used if 'filter_make_unique_sorted' is set to 'yes')
+
+
+##################################
+#       SCREEN FASTA FILE        #    
+##################################
+screen_fasta_file_blast_e_value          : 0.00001 
+screen_fasta_file_blast_read_min_length  : 10
+screen_fasta_file_additional_usearch_cmd : []
+screen_fasta_file_usearch_version        : 6 [5,6]
+screen_fasta_file_usearch_version_5_exe  : usearch
+screen_fasta_file_usearch_version_6_exe  : usearch
+
+##################################
+#           PROFILING            #
+##################################
+profiling_paired_end_filtering           : yes [yes,no]
+
+##################################
+#            ASSEMBLY            #
+##################################
+assembly_soap_version                : 1.06 [1.05,1.06]
+assembly_calculate_insert_size_using : mapping [assembly,mapping]
+assembly_db_for_calc_insertsize      : 1506MG (used if specified 'mapping' above)
+assembly_scaftig_min_length          : 500
+
+
+##################################
+#        ASSEMBLY REVISION       #
+##################################
+assembly_revision_scaftig_min_length : 500
+
+
+##################################
+#         GENE PREDICTION        #
+##################################
+gene_prediction_software     : Prodigal [MetaGeneMark,Prodigal]
+gene_prediction_input        : scaftig [scaftig,contig,scafSeq] (if revised assembly, can only be 'scaftig')
+gene_prediction_prodigal_cmd : -f gff [-f xxx, -none-] (-p, -o, -a, -d, -i already set at runtime in MOCAT)
+
+
+##################################
+#      EXPERIMENTAL SETTINGS     #
+##################################
+realtime_status_use   : no [yes,no] (setting this to 'yes' shows current status of jobs, if realtime_status_print is set to 'yes', and also stores required resources in log folder)
+realtime_status_print : yes [yes,no]
+realtime_status_show  : no [yes,no]
+realtime_status_timer : 5
+realtime_status_log   : no
+realtime_status_fix_1 : -here you can add hostname that are not clusters-
+realtime_status_fix_2 : -here you can add hostname that are not clusters-
+
+# END OF FILE #

MOCAT_analysis/Combined/human_fecal/runALL.sh

+#!/bin/bash
+#oarsub -lcpu=1,walltime=72:00:00  -p "memcpu='258538'" -n mocatLux ./run.sh
+
+samples=samples
+log=$samples.log
+
+source $HOME/.profile
+source $HOME/.bashrc
+
+export PERL5LIB=$PERL5LIB:/work/projects/ecosystem_biology/local_tools/MOCAT/src
+PATH=$PATH:/work/projects/ecosystem_biology/local_tools/MOCAT/src
+export PATH
+MOCAT.pl -sf $samples -rtf -cpus 8 >$log 2>>$log 
+MOCAT.pl -sf $samples -s hg19 -cpus 8 >>$log 2>>$log
+MOCAT.pl -sf $samples -a -r hg19 -cpus 8 >>$log 2>>$log
+MOCAT.pl -sf $samples -ar -cpus 8 -r hg19 >>$log 2>>$log
+MOCAT.pl -sf $samples -gp assembly.revised -cpus 8 -r hg19 >>$log 2>>$log
+MOCAT.pl -sf $samples -ss -cpus 8  >>$log 2>>$log

MOCAT_analysis/Combined/simulated_data/MOCAT.cfg

+#####################################
+#          MOCAT Config File        #
+#####################################
+
+
+##################################
+#         GLOBAL SETTINGS        #
+##################################
+MOCAT_dir                : /work/projects/ecosystem_biology/local_tools/MOCAT/
+MOCAT_data_type          : solexaqa [fastx,solexaqa]
+MOCAT_paired_end         : yes [yes,no]
+MOCAT_SGE_parallell_env  : smp [smp,mpi,-or other setting on your system-]
+MOCAT_mapping_mode       : allbest [allbest,random,unique]
+MOCAT_qsub_system        : none [SGE,PBS,none]
+MOCAT_zip_program        : pigz [gzip,pigz]
+MOCAT_default_reads      : reads.processed ['reads.processed','DATABASE']
+MOCAT_zip_level          : 1 [1-9]
+MOCAT_SGE_qsub_add_param : [-l mem_free=6G -l h_vmem=6G] 
+MOCAT_PBS_qsub_add_param : [-l select=mem=6gb] 
+MOCAT_LSF_qsub_add_param : [-l select=mem=6gb]
+MOCAT_LSF_queue          : []
+MOCAT_LSF_memory_limit   : []
+MOCAT_umask              : 0022 [0022]
+MOCAT_pre_execute        : [umask 0002]
+MOCAT_prompt_before_run  : no [yes,no]
+
+
+##################################
+#      READ TRIM AND FILTER      #
+##################################
+readtrimfilter_length_cutoff               : 40
+readtrimfilter_qual_cutoff                 : 20
+readtrimfilter_use_sanger_scale            : auto [yes,no,auto]
+readtrimfilter_trim_5_prime                : yes [yes,no]
+readtrimfilter_use_precalc_5prime_trimming : no  [yes,no]
+
+
+##################################
+#            SCREEN              #    
+##################################
+screen_length_cutoff    : 30
+screen_percent_cutoff   : 90
+screen_soap_seed_length : 30
+screen_soap_max_mm      : 10
+screen_soap_cmd         : -M 4 [-M 4]
+screen_save_format      : sam [soap,sam]
+
+
+##################################
+#             FILTER             #
+##################################
+filter_psort_buffer         : 2G
+filter_length_cutoff        : 45
+filter_percent_cutoff       : 95
+filter_paired_end_filtering : yes [yes,no]
+filter_remove_mapping_files : no  [yes.no]
+filter_make_unique_sorted   : no [yes.no]
+filter_samtools_memory      : 50000000000 [50000000000] (Memory allocation in bytes, this setting is only used if 'filter_make_unique_sorted' is set to 'yes')
+
+
+##################################
+#       SCREEN FASTA FILE        #    
+##################################
+screen_fasta_file_blast_e_value          : 0.00001 
+screen_fasta_file_blast_read_min_length  : 10
+screen_fasta_file_additional_usearch_cmd : []
+screen_fasta_file_usearch_version        : 6 [5,6]
+screen_fasta_file_usearch_version_5_exe  : usearch
+screen_fasta_file_usearch_version_6_exe  : usearch
+
+##################################
+#           PROFILING            #
+##################################
+profiling_paired_end_filtering           : yes [yes,no]
+
+##################################
+#            ASSEMBLY            #
+##################################
+assembly_soap_version                : 1.06 [1.05,1.06]
+assembly_calculate_insert_size_using : mapping [assembly,mapping]
+assembly_db_for_calc_insertsize      : 1506MG (used if specified 'mapping' above)
+assembly_scaftig_min_length          : 500
+
+
+##################################
+#        ASSEMBLY REVISION       #
+##################################
+assembly_revision_scaftig_min_length : 500
+
+
+##################################
+#         GENE PREDICTION        #
+##################################
+gene_prediction_software     : Prodigal [MetaGeneMark,Prodigal]
+gene_prediction_input        : scaftig [scaftig,contig,scafSeq] (if revised assembly, can only be 'scaftig')
+gene_prediction_prodigal_cmd : -f gff [-f xxx, -none-] (-p, -o, -a, -d, -i already set at runtime in MOCAT)
+
+
+##################################
+#      EXPERIMENTAL SETTINGS     #
+##################################
+realtime_status_use   : no [yes,no] (setting this to 'yes' shows current status of jobs, if realtime_status_print is set to 'yes', and also stores required resources in log folder)
+realtime_status_print : yes [yes,no]
+realtime_status_show  : no [yes,no]
+realtime_status_timer : 5
+realtime_status_log   : no
+realtime_status_fix_1 : -here you can add hostname that are not clusters-
+realtime_status_fix_2 : -here you can add hostname that are not clusters-
+
+# END OF FILE #

MOCAT_analysis/Combined/simulated_data/runALL.sh

+#!/bin/bash
+#oarsub -lcpu=1,walltime=72:00:00  -p "memcpu='258538'" -n mocatLux ./run.sh
+
+samples=samples
+log=$samples.log
+
+source $HOME/.profile
+source $HOME/.bashrc
+
+export PERL5LIB=$PERL5LIB:/work/projects/ecosystem_biology/local_tools/MOCAT/src
+PATH=$PATH:/work/projects/ecosystem_biology/local_tools/MOCAT/src
+export PATH
+MOCAT.pl -sf $samples -rtf -cpus 8 >$log 2>>$log 
+MOCAT.pl -sf $samples -a -cpus 8 >>$log 2>>$log
+MOCAT.pl -sf $samples -ar -cpus 8  >>$log 2>>$log
+MOCAT.pl -sf $samples -gp assembly.revised -cpus 8  >>$log 2>>$log
+MOCAT.pl -sf $samples -ss -cpus 8  >>$log 2>>$log

MOCAT_analysis/Combined/wastewater_sludge/MOCAT.cfg

+#####################################
+#          MOCAT Config File        #
+#####################################
+
+
+##################################
+#         GLOBAL SETTINGS        #
+##################################
+MOCAT_dir                : /work/projects/ecosystem_biology/local_tools/MOCAT/
+MOCAT_data_type          : solexaqa [fastx,solexaqa]
+MOCAT_paired_end         : yes [yes,no]
+MOCAT_SGE_parallell_env  : smp [smp,mpi,-or other setting on your system-]
+MOCAT_mapping_mode       : allbest [allbest,random,unique]
+MOCAT_qsub_system        : none [SGE,PBS,none]
+MOCAT_zip_program        : pigz [gzip,pigz]
+MOCAT_default_reads      : reads.processed ['reads.processed','DATABASE']
+MOCAT_zip_level          : 1 [1-9]
+MOCAT_SGE_qsub_add_param : [-l mem_free=6G -l h_vmem=6G] 
+MOCAT_PBS_qsub_add_param : [-l select=mem=6gb] 
+MOCAT_LSF_qsub_add_param : [-l select=mem=6gb]
+MOCAT_LSF_queue          : []
+MOCAT_LSF_memory_limit   : []
+MOCAT_umask              : 0022 [0022]
+MOCAT_pre_execute        : [umask 0002]
+MOCAT_prompt_before_run  : no [yes,no]
+
+
+##################################
+#      READ TRIM AND FILTER      #
+##################################
+readtrimfilter_length_cutoff               : 40
+readtrimfilter_qual_cutoff                 : 20
+readtrimfilter_use_sanger_scale            : auto [yes,no,auto]
+readtrimfilter_trim_5_prime                : yes [yes,no]
+readtrimfilter_use_precalc_5prime_trimming : no  [yes,no]
+
+
+##################################
+#            SCREEN              #    
+##################################
+screen_length_cutoff    : 30
+screen_percent_cutoff   : 90
+screen_soap_seed_length : 30
+screen_soap_max_mm      : 10
+screen_soap_cmd         : -M 4 [-M 4]
+screen_save_format      : sam [soap,sam]
+
+
+##################################
+#             FILTER             #
+##################################
+filter_psort_buffer         : 2G
+filter_length_cutoff        : 45
+filter_percent_cutoff       : 95
+filter_paired_end_filtering : yes [yes,no]
+filter_remove_mapping_files : no  [yes.no]
+filter_make_unique_sorted   : no [yes.no]
+filter_samtools_memory      : 50000000000 [50000000000] (Memory allocation in bytes, this setting is only used if 'filter_make_unique_sorted' is set to 'yes')
+
+
+##################################
+#       SCREEN FASTA FILE        #    
+##################################
+screen_fasta_file_blast_e_value          : 0.00001 
+screen_fasta_file_blast_read_min_length  : 10
+screen_fasta_file_additional_usearch_cmd : []
+screen_fasta_file_usearch_version        : 6 [5,6]
+screen_fasta_file_usearch_version_5_exe  : usearch
+screen_fasta_file_usearch_version_6_exe  : usearch
+
+##################################
+#           PROFILING            #
+##################################
+profiling_paired_end_filtering           : yes [yes,no]
+
+##################################
+#            ASSEMBLY            #
+##################################
+assembly_soap_version                : 1.06 [1.05,1.06]
+assembly_calculate_insert_size_using : mapping [assembly,mapping]
+assembly_db_for_calc_insertsize      : 1506MG (used if specified 'mapping' above)
+assembly_scaftig_min_length          : 500
+
+
+##################################
+#        ASSEMBLY REVISION       #
+##################################
+assembly_revision_scaftig_min_length : 500
+
+
+##################################
+#         GENE PREDICTION        #
+##################################
+gene_prediction_software     : Prodigal [MetaGeneMark,Prodigal]
+gene_prediction_input        : scaftig [scaftig,contig,scafSeq] (if revised assembly, can only be 'scaftig')
+gene_prediction_prodigal_cmd : -f gff [-f xxx, -none-] (-p, -o, -a, -d, -i already set at runtime in MOCAT)
+
+
+##################################
+#      EXPERIMENTAL SETTINGS     #
+##################################
+realtime_status_use   : no [yes,no] (setting this to 'yes' shows current status of jobs, if realtime_status_print is set to 'yes', and also stores required resources in log folder)
+realtime_status_print : yes [yes,no]
+realtime_status_show  : no [yes,no]
+realtime_status_timer : 5
+realtime_status_log   : no
+realtime_status_fix_1 : -here you can add hostname that are not clusters-
+realtime_status_fix_2 : -here you can add hostname that are not clusters-
+
+# END OF FILE #

MOCAT_analysis/Combined/wastewater_sludge/runALL.sh

+#!/bin/bash
+#oarsub -lcpu=1,walltime=72:00:00  -p "memcpu='258538'" -n mocatLux ./run.sh
+
+samples=samples
+log=$samples.log
+
+source $HOME/.profile
+source $HOME/.bashrc
+
+export PERL5LIB=$PERL5LIB:/work/projects/ecosystem_biology/local_tools/MOCAT/src
+PATH=$PATH:/work/projects/ecosystem_biology/local_tools/MOCAT/src
+export PATH
+#MOCAT.pl -sf $samples -rtf -cpus 8 >$log 2>>$log 
+
+#MOCAT.pl -sf $samples -s hg19 -cpus 8 >>$log 2>>$log
+#MOCAT.pl -sf $samples -a -r hg19 -cpus 8 >>$log 2>>$log
+#MOCAT.pl -sf $samples -ar -cpus 8 -r hg19 >>$log 2>>$log
+#MOCAT.pl -sf $samples -gp assembly.revised -cpus 8 -r hg19 >>$log 2>>$log
+#MOCAT.pl -sf $samples -ss -cpus 8  >>$log 2>>$log
+
+MOCAT.pl -sf $samples -a -cpus 8 >>$log 2>>$log
+MOCAT.pl -sf $samples -ar -cpus 8  >>$log 2>>$log
+MOCAT.pl -sf $samples -gp assembly.revised -cpus 8 >>$log 2>>$log
+MOCAT.pl -sf $samples -ss -cpus 8  >>$log 2>>$log
+

MOCAT_analysis/MG/biogas_plant/MOCAT.cfg

+#####################################
+#          MOCAT Config File        #
+#####################################
+
+
+##################################
+#         GLOBAL SETTINGS        #
+##################################
+MOCAT_dir                : /work/projects/ecosystem_biology/local_tools/MOCAT/
+MOCAT_data_type          : solexaqa [fastx,solexaqa]
+MOCAT_paired_end         : yes [yes,no]
+MOCAT_SGE_parallell_env  : smp [smp,mpi,-or other setting on your system-]
+MOCAT_mapping_mode       : allbest [allbest,random,unique]
+MOCAT_qsub_system        : none [SGE,PBS,none]
+MOCAT_zip_program        : pigz [gzip,pigz]
+MOCAT_default_reads      : reads.processed ['reads.processed','DATABASE']
+MOCAT_zip_level          : 1 [1-9]
+MOCAT_SGE_qsub_add_param : [-l mem_free=6G -l h_vmem=6G] 
+MOCAT_PBS_qsub_add_param : [-l select=mem=6gb] 
+MOCAT_LSF_qsub_add_param : [-l select=mem=6gb]
+MOCAT_LSF_queue          : []
+MOCAT_LSF_memory_limit   : []
+MOCAT_umask              : 0022 [0022]
+MOCAT_pre_execute        : [umask 0002]
+MOCAT_prompt_before_run  : no [yes,no]
+
+
+##################################
+#      READ TRIM AND FILTER      #
+##################################
+readtrimfilter_length_cutoff               : 40
+readtrimfilter_qual_cutoff                 : 20
+readtrimfilter_use_sanger_scale            : auto [yes,no,auto]
+readtrimfilter_trim_5_prime                : yes [yes,no]
+readtrimfilter_use_precalc_5prime_trimming : no  [yes,no]
+
+
+##################################
+#            SCREEN              #    
+##################################
+screen_length_cutoff    : 30
+screen_percent_cutoff   : 90
+screen_soap_seed_length : 30
+screen_soap_max_mm      : 10
+screen_soap_cmd         : -M 4 [-M 4]
+screen_save_format      : sam [soap,sam]
+
+
+##################################
+#             FILTER             #
+##################################
+filter_psort_buffer         : 2G
+filter_length_cutoff        : 45
+filter_percent_cutoff       : 95
+filter_paired_end_filtering : yes [yes,no]
+filter_remove_mapping_files : no  [yes.no]
+filter_make_unique_sorted   : no [yes.no]
+filter_samtools_memory      : 50000000000 [50000000000] (Memory allocation in bytes, this setting is only used if 'filter_make_unique_sorted' is set to 'yes')
+
+
+##################################
+#       SCREEN FASTA FILE        #    
+##################################
+screen_fasta_file_blast_e_value          : 0.00001 
+screen_fasta_file_blast_read_min_length  : 10
+screen_fasta_file_additional_usearch_cmd : []
+screen_fasta_file_usearch_version        : 6 [5,6]
+screen_fasta_file_usearch_version_5_exe  : usearch
+screen_fasta_file_usearch_version_6_exe  : usearch
+
+##################################
+#           PROFILING            #
+##################################
+profiling_paired_end_filtering           : yes [yes,no]
+
+##################################
+#            ASSEMBLY            #
+##################################
+assembly_soap_version                : 1.06 [1.05,1.06]
+assembly_calculate_insert_size_using : mapping [assembly,mapping]
+assembly_db_for_calc_insertsize      : 1506MG (used if specified 'mapping' above)
+assembly_scaftig_min_length          : 500
+
+
+##################################
+#        ASSEMBLY REVISION       #
+##################################
+assembly_revision_scaftig_min_length : 500
+