Commit f0a6601e authored by Shaman Narayanasamy's avatar Shaman Narayanasamy
Browse files

Add MOCAT scipts and config files

parent 29ee315d
#####################################
# 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 #
#!/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 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 #
#!/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 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 #
#!/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 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 #
#!/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 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