


gp-read-xtandem.py -e 0.05 -o combined_second_step_60_baria_30_ctrl_nonbaria_env_read.xml ../60_baria_env/metapappso_condor/test_run/*_second_step_60_baria_env.xml ../30_ctrl_nonbaria_env/metapappso_condor/test_run/*_second_step_30_ctrl_nonbaria_env.xml


#build mega results of the second step 60 + 30 :


olangella@proteus1:/gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_env$ gp-read-xtandem.py -e 0.05 -o combined_second_step_60_baria_30_ctrl_nonbaria_env_read.xml ../60_baria_env/metapappso_condor/test_run/*_second_step_60_baria_env.xml ../30_ctrl_nonbaria_env/metapappso_condor/test_run/*_second_step_30_ctrl_nonbaria_env.xml
Read files : ../60_baria_env/metapappso_condor/test_run/011_20MC0351_1_Env_second_step_60_baria_env.xml
Read files : ../60_baria_env/metapappso_condor/test_run/019_20MC0081_1_Env_second_step_60_baria_env.xml
Read files : ../60_baria_env/metapappso_condor/test_run/025_20MC0081_6_Env_second_step_60_baria_env.xml
Read files : ../60_baria_env/metapappso_condor/test_run/031_20MC0351_6_Env_second_step_60_baria_env.xml
Read files : ../60_baria_env/metapappso_condor/test_run/047_20MC0324_1_Env_second_step_60_baria_env.xml
Read files : ../60_baria_env/metapappso_condor/test_run/053_20MC0071_1_Env_second_step_60_baria_env.xml
Read files : ../60_baria_env/metapappso_condor/test_run/067_20MC0324_6_Env_second_step_60_baria_env.xml
Read files : ../60_baria_env/metapappso_condor/test_run/079_20MC0071_6_Env_second_step_60_baria_env.xml
Read files : ../60_baria_env/metapappso_condor/test_run/095_20MC0329_6_Env_second_step_60_baria_env.xml
Read files : ../60_baria_env/metapappso_condor/test_run/101_20MC0019_1_Env_second_step_60_baria_env.xml
Read files : ../60_baria_env/metapappso_condor/test_run/123_20MC0019_6_Env_second_step_60_baria_env.xml
Read files : ../60_baria_env/metapappso_condor/test_run/133_20MC0329_1_Env_second_step_60_baria_env.xml
Read files : ../60_baria_env/metapappso_condor/test_run/145_20MC0050_1_Env_second_step_60_baria_env.xml
Read files : ../60_baria_env/metapappso_condor/test_run/147_20MC0037_6_Env_second_step_60_baria_env.xml
Read files : ../60_baria_env/metapappso_condor/test_run/153_20MC0207_1_Env_second_step_60_baria_env.xml
Read files : ../60_baria_env/metapappso_condor/test_run/161_20MC0037_1_Env_second_step_60_baria_env.xml
Read files : ../60_baria_env/metapappso_condor/test_run/163_20MC0050_6_Env_second_step_60_baria_env.xml
Read files : ../60_baria_env/metapappso_condor/test_run/167_20MC0207_6_Env_second_step_60_baria_env.xml
Read files : ../60_baria_env/metapappso_condor/test_run/183_20MC0115_6_Env_second_step_60_baria_env.xml
Read files : ../60_baria_env/metapappso_condor/test_run/191_20MC0007_1_Env_second_step_60_baria_env.xml
Read files : ../60_baria_env/metapappso_condor/test_run/221_20MC0115_1_Env_second_step_60_baria_env.xml
Read files : ../60_baria_env/metapappso_condor/test_run/225_20MC0007_6_Env_second_step_60_baria_env.xml
Read files : ../60_baria_env/metapappso_condor/test_run/247_20MC0040_6_Env_second_step_60_baria_env.xml
Read files : ../60_baria_env/metapappso_condor/test_run/251_20MC0109_1_Env_second_step_60_baria_env.xml
Read files : ../60_baria_env/metapappso_condor/test_run/257_20MC0109_6_Env_second_step_60_baria_env.xml
Read files : ../60_baria_env/metapappso_condor/test_run/267_20MC0040_1_Env_second_step_60_baria_env.xml
Read files : ../60_baria_env/metapappso_condor/test_run/279_20MC0002_1_Env_second_step_60_baria_env.xml
Read files : ../60_baria_env/metapappso_condor/test_run/283_20MC0347_1_Env_second_step_60_baria_env.xml
Read files : ../60_baria_env/metapappso_condor/test_run/291_20MC0200_1_Env_second_step_60_baria_env.xml
Read files : ../60_baria_env/metapappso_condor/test_run/295_20MC0200_6_Env_second_step_60_baria_env.xml
Read files : ../60_baria_env/metapappso_condor/test_run/297_20MC0002_6_Env_second_step_60_baria_env.xml
Read files : ../60_baria_env/metapappso_condor/test_run/299_20MC0347_6_Env_second_step_60_baria_env.xml
Read files : ../60_baria_env/metapappso_condor/test_run/315_20MC0034_1_Env_second_step_60_baria_env.xml
Read files : ../60_baria_env/metapappso_condor/test_run/329_20MC0297_1_Env_second_step_60_baria_env.xml
Read files : ../60_baria_env/metapappso_condor/test_run/331_20MC0034_6_Env_second_step_60_baria_env.xml
Read files : ../60_baria_env/metapappso_condor/test_run/343_20MC0297_6_Env_second_step_60_baria_env.xml
Read files : ../60_baria_env/metapappso_condor/test_run/381_20MC0017_1_Env_second_step_60_baria_env.xml
Read files : ../60_baria_env/metapappso_condor/test_run/383_20MC0017_6_Env_second_step_60_baria_env.xml
Read files : ../60_baria_env/metapappso_condor/test_run/389_20MC0235_6_Env_second_step_60_baria_env.xml
Read files : ../60_baria_env/metapappso_condor/test_run/399_20MC0235_1_Env_second_step_60_baria_env.xml
Read files : ../60_baria_env/metapappso_condor/test_run/419_20MC0147_1_Env_second_step_60_baria_env.xml
Read files : ../60_baria_env/metapappso_condor/test_run/435_20MC0039_6_Env_second_step_60_baria_env.xml
Read files : ../60_baria_env/metapappso_condor/test_run/437_20MC0039_1_Env_second_step_60_baria_env.xml
Read files : ../60_baria_env/metapappso_condor/test_run/439_20MC0147_6_Env_second_step_60_baria_env.xml
Read files : ../60_baria_env/metapappso_condor/test_run/467_20MC0306_1_Env_second_step_60_baria_env.xml
Read files : ../60_baria_env/metapappso_condor/test_run/469_20MC0038_6_Env_second_step_60_baria_env.xml
Read files : ../60_baria_env/metapappso_condor/test_run/471_20MC0306_6_Env_second_step_60_baria_env.xml
Read files : ../60_baria_env/metapappso_condor/test_run/475_20MC0038_1_Env_second_step_60_baria_env.xml
Read files : ../60_baria_env/metapappso_condor/test_run/511_20MC0117_1_Env_second_step_60_baria_env.xml
Read files : ../60_baria_env/metapappso_condor/test_run/515_20MC0199_1_Env_second_step_60_baria_env.xml
Read files : ../60_baria_env/metapappso_condor/test_run/527_20MC0117_6_Env_second_step_60_baria_env.xml
Read files : ../60_baria_env/metapappso_condor/test_run/531_20MC0199_6_Env_second_step_60_baria_env.xml
Read files : ../60_baria_env/metapappso_condor/test_run/555_20MC0344_1_Env_second_step_60_baria_env.xml
Read files : ../60_baria_env/metapappso_condor/test_run/557_20MC0344_6_Env_second_step_60_baria_env.xml
Read files : ../60_baria_env/metapappso_condor/test_run/575_20MC0379_1_Env_second_step_60_baria_env.xml
Read files : ../60_baria_env/metapappso_condor/test_run/581_20MC0379_6_Env_second_step_60_baria_env.xml
Read files : ../60_baria_env/metapappso_condor/test_run/605_20MC0113_6_Env_second_step_60_baria_env.xml
Read files : ../60_baria_env/metapappso_condor/test_run/609_20MC0113_1_Env_second_step_60_baria_env.xml
Read files : ../60_baria_env/metapappso_condor/test_run/619_20MC0091_1_Env_second_step_60_baria_env.xml
Read files : ../60_baria_env/metapappso_condor/test_run/631_20MC0091_6_Env_second_step_60_baria_env.xml
Read files : ../30_ctrl_nonbaria_env/metapappso_condor/test_run/021_14MC0900_0_Env_second_step_30_ctrl_nonbaria_env.xml
Read files : ../30_ctrl_nonbaria_env/metapappso_condor/test_run/033_14MC0981_0_Env_second_step_30_ctrl_nonbaria_env.xml
Read files : ../30_ctrl_nonbaria_env/metapappso_condor/test_run/057_14MC0953_0_Env_second_step_30_ctrl_nonbaria_env.xml
Read files : ../30_ctrl_nonbaria_env/metapappso_condor/test_run/059_14MC0984_0_Env_second_step_30_ctrl_nonbaria_env.xml
Read files : ../30_ctrl_nonbaria_env/metapappso_condor/test_run/107_14MC0989_0_Env_second_step_30_ctrl_nonbaria_env.xml
Read files : ../30_ctrl_nonbaria_env/metapappso_condor/test_run/149_14MC0983_0_Env_second_step_30_ctrl_nonbaria_env.xml
Read files : ../30_ctrl_nonbaria_env/metapappso_condor/test_run/151_14MC0941_0_Env_second_step_30_ctrl_nonbaria_env.xml
Read files : ../30_ctrl_nonbaria_env/metapappso_condor/test_run/155_14MC0912_0_Env_second_step_30_ctrl_nonbaria_env.xml
Read files : ../30_ctrl_nonbaria_env/metapappso_condor/test_run/211_14MC0915_0_Env_second_step_30_ctrl_nonbaria_env.xml
Read files : ../30_ctrl_nonbaria_env/metapappso_condor/test_run/219_14MC0964_0_Env_second_step_30_ctrl_nonbaria_env.xml
Read files : ../30_ctrl_nonbaria_env/metapappso_condor/test_run/249_14MC0956_0_Env_second_step_30_ctrl_nonbaria_env.xml
Read files : ../30_ctrl_nonbaria_env/metapappso_condor/test_run/261_14MC0927_0_Env_second_step_30_ctrl_nonbaria_env.xml
Read files : ../30_ctrl_nonbaria_env/metapappso_condor/test_run/303_14MC0942_0_Env_second_step_30_ctrl_nonbaria_env.xml
Read files : ../30_ctrl_nonbaria_env/metapappso_condor/test_run/345_14MC0985_0_Env_second_step_30_ctrl_nonbaria_env.xml
Read files : ../30_ctrl_nonbaria_env/metapappso_condor/test_run/347_14MC0918_0_Env_second_step_30_ctrl_nonbaria_env.xml
Read files : ../30_ctrl_nonbaria_env/metapappso_condor/test_run/353_14MC0925_0_Env_second_step_30_ctrl_nonbaria_env.xml
Read files : ../30_ctrl_nonbaria_env/metapappso_condor/test_run/357_14MC0943_0_Env_second_step_30_ctrl_nonbaria_env.xml
Read files : ../30_ctrl_nonbaria_env/metapappso_condor/test_run/377_14MC0931_0_Env_second_step_30_ctrl_nonbaria_env.xml
Read files : ../30_ctrl_nonbaria_env/metapappso_condor/test_run/393_14MC0946_0_Env_second_step_30_ctrl_nonbaria_env.xml
Read files : ../30_ctrl_nonbaria_env/metapappso_condor/test_run/405_14MC0944_0_Env_second_step_30_ctrl_nonbaria_env.xml
Read files : ../30_ctrl_nonbaria_env/metapappso_condor/test_run/421_14MC0932_0_Env_second_step_30_ctrl_nonbaria_env.xml
Read files : ../30_ctrl_nonbaria_env/metapappso_condor/test_run/445_14MC0948_0_Env_second_step_30_ctrl_nonbaria_env.xml
Read files : ../30_ctrl_nonbaria_env/metapappso_condor/test_run/477_14MC0968_0_Env_second_step_30_ctrl_nonbaria_env.xml
Read files : ../30_ctrl_nonbaria_env/metapappso_condor/test_run/493_14MC0986_0_Env_second_step_30_ctrl_nonbaria_env.xml
Read files : ../30_ctrl_nonbaria_env/metapappso_condor/test_run/533_14MC0975_0_Env_second_step_30_ctrl_nonbaria_env.xml
Read files : ../30_ctrl_nonbaria_env/metapappso_condor/test_run/535_14MC0954_0_Env_second_step_30_ctrl_nonbaria_env.xml
Read files : ../30_ctrl_nonbaria_env/metapappso_condor/test_run/545_14MC0990_0_Env_second_step_30_ctrl_nonbaria_env.xml
Read files : ../30_ctrl_nonbaria_env/metapappso_condor/test_run/573_14MC0930_0_Env_second_step_30_ctrl_nonbaria_env.xml
Read files : ../30_ctrl_nonbaria_env/metapappso_condor/test_run/597_14MC0977_0_Env_second_step_30_ctrl_nonbaria_env.xml
Read files : ../30_ctrl_nonbaria_env/metapappso_condor/test_run/633_14MC0978_0_Env_second_step_30_ctrl_nonbaria_env.xml


olangella@proteus1:/gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_env$ tail combined_second_step_60_baria_30_ctrl_nonbaria_env_read.xml
</psm>
</scan>
<scan num="115318" z="2" mhObs="1824.975024">
<psm seq="DLTYQVVLGEYNLAVK" mhTheo="1824.9746" evalue="0.00015" prot="sp|P09093|CEL3A_HUMAN Chymotrypsin-like elastase family member 3A OS=Homo sapiens OX=9606 GN=CELA3A PE=1 SV=3">
</psm>
<psm seq="DLTYQVVLGEYNLAVK" mhTheo="1824.9746" evalue="0.00015" prot="tr|Q96QL8|Q96QL8_HUMAN Elastase 3A, pancreatic OS=Homo sapiens OX=9606 GN=ELA3A PE=2 SV=1">
</psm>
</scan>
</sample>
</peptide_result>


metapappso_create_fasta_enhanced.py -x combined_second_step_60_baria_30_ctrl_nonbaria_env_read.xml -f /gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/softs/database/meta_total.fasta -o combined_proteome_60_baria_30_ctrl_nonbaria_env.fasta


olangella@proteus1:/gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_env$ metapappso_create_fasta_enhanced.py -x combined_second_step_60_baria_30_ctrl_nonbaria_env_read.xml -f /gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/softs/database/meta_total.fasta -o combined_proteome_60_baria_30_ctrl_nonbaria_env.fasta
('Searching in ', '/gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/softs/database/meta_total.fasta')
('File ', 'combined_proteome_60_baria_30_ctrl_nonbaria_env.fasta', ' written')








olangella@proteus1:/gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_env$ mkdir metapappso_condor
olangella@proteus1:/gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_env$ mkdir metapappso_condor/params
olangella@proteus1:/gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_env$ mkdir metapappso_condor/test_run


cat > step3.sh <<EOF
####################################
############ THIRD STEP ############
####################################


###################### Directories  60_baria_env ###########################
# directories which will be created to stores the results
params_d="/gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_env/metapappso_condor/params"
output_d="/gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_env/metapappso_condor/test_run"
job_name="60_baria_30_ctrl_nonbaria_env"

# evalue threshold to use
evalue="0.05"
# models to use (MUST be in the models directory)
models_d="/gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/softs/presets"
model_first_f="Lumos_04112019_PROTEOCARDIS_FIRST_STEP_AB.xml"
model_second_f="Lumos_04112019_PROTEOCARDIS_SECOND_STEP_AB.xml"
model_third_f="Lumos_04112019_PROTEOCARDIS_THIRD_STEP_AB.xml"



echo -e "Universe   = vanilla\nnotification   = Error\nRank       = Mips\nrequest_memory= 80000\nrequest_cpus = 15\nExecutable = /usr/bin/tandem\nLog        = /gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_env/metapappso_condor/params/htcondor_step_3_60_baria_30_ctrl_nonbaria_env.log\nOutput        = /gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_env/metapappso_condor/params/htcondor_step_3_60_baria_30_ctrl_nonbaria_env.\$(Process).out\nError        = /gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_env/metapappso_condor/params/htcondor_step_3_60_baria_30_ctrl_nonbaria_env.\$(Process).error\n" > /gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_env/metapappso_condor/params/htcondor_step_3_60_baria_30_ctrl_nonbaria_env.submit



# create database for third step
echo -e "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<bioml label=\"x! taxon-to-file matching list\">\n<taxon label=\"usedefined\">\n<file format=\"peptide\" URL=\"/gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/softs/database/uniprot-human-20211006.fasta\"></file>\n<file format=\"peptide\" URL=\"/gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/softs/database/contaminants_standards.fasta\"></file>\n<file format=\"peptide\" URL=\"/gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_env/combined_proteome_60_baria_30_ctrl_nonbaria_env.fasta\"></file>\n</taxon>\n</bioml>" > /gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_env/metapappso_condor/params/xtandem_database_third_step_60_baria_30_ctrl_nonbaria_env.database


spectra_d="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env_baria"

for sample in $(cat /gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_env/list_samples.txt)
do
        if [ -f ${output_d}/${sample}_third_step_${job_name}.xml ]
        then
                echo "$(date) The third step of sample $sample has already been identified. Pass to next sample." >> ${params_d}/$stdout
        else
        	# create parameter files specific to the samples
		echo -e "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<bioml label=\"${sample}_${job_name}_third_step.xml\">\n<note type=\"heading\">Paths</note>\n<note type=\"input\" label=\"list path, default parameters\">${models_d}/${model_third_f}</note>\n<note type=\"input\" label=\"list path, taxonomy information\">${params_d}/xtandem_database_third_step_${job_name}.database</note>\n<note type=\"input\" label=\"spectrum, path\">${spectra_d}/${sample}.mzXML</note>\n<note type=\"heading\">Protein general</note>\n<note type=\"input\" label=\"protein, taxon\">usedefined</note>\n<note type=\"heading\">Output</note>\n<note type=\"input\" label=\"output, path\">${output_d}/${sample}_third_step_${job_name}.xml</note>\n</bioml>" > ${params_d}/xtandem_param_${sample}_third_step_${job_name}.param
                # launching third step
                echo -e "Arguments        = ${params_d}/xtandem_param_${sample}_third_step_${job_name}.param\nQueue\n" >> ${params_d}/htcondor_step_3_${job_name}.submit
	fi
done


spectra_d="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env/"
for sample in $(cat /gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/30_ctrl_nonbaria_env/list_samples.txt)
do
        if [ -f ${output_d}/${sample}_third_step_${job_name}.xml ]
        then
                echo "$(date) The third step of sample $sample has already been identified. Pass to next sample." >> ${params_d}/$stdout
        else
        	# create parameter files specific to the samples
		echo -e "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<bioml label=\"${sample}_${job_name}_third_step.xml\">\n<note type=\"heading\">Paths</note>\n<note type=\"input\" label=\"list path, default parameters\">${models_d}/${model_third_f}</note>\n<note type=\"input\" label=\"list path, taxonomy information\">${params_d}/xtandem_database_third_step_${job_name}.database</note>\n<note type=\"input\" label=\"spectrum, path\">${spectra_d}/${sample}.mzXML</note>\n<note type=\"heading\">Protein general</note>\n<note type=\"input\" label=\"protein, taxon\">usedefined</note>\n<note type=\"heading\">Output</note>\n<note type=\"input\" label=\"output, path\">${output_d}/${sample}_third_step_${job_name}.xml</note>\n</bioml>" > ${params_d}/xtandem_param_${sample}_third_step_${job_name}.param
                # launching third step
                echo -e "Arguments        = ${params_d}/xtandem_param_${sample}_third_step_${job_name}.param\nQueue\n" >> ${params_d}/htcondor_step_3_${job_name}.submit
	fi
done
EOF

olangella@proteus1:/gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_env$ condor_submit metapappso_condor/params/htcondor_step_3_60_baria_30_ctrl_nonbaria_env.submit 
Submitting job(s)..........................................................................................
90 job(s) submitted to cluster 2004.


#reading


olangella@proteus1:/gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_env$ gp-read-xtandem.py -e 0.05 -o /gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_env/metapappso_condor/test_run/combined_third_step_60_baria_30_ctrl_nonbaria_env_read.xml /gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_env/metapappso_condor/test_run/*_third_step_60_baria_30_ctrl_nonbaria_env.xml
Read files : /gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_env/metapappso_condor/test_run/011_20MC0351_1_Env_third_step_60_baria_30_ctrl_nonbaria_env.xml
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Read files : /gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_env/metapappso_condor/test_run/605_20MC0113_6_Env_third_step_60_baria_30_ctrl_nonbaria_env.xml
Read files : /gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_env/metapappso_condor/test_run/609_20MC0113_1_Env_third_step_60_baria_30_ctrl_nonbaria_env.xml
Read files : /gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_env/metapappso_condor/test_run/619_20MC0091_1_Env_third_step_60_baria_30_ctrl_nonbaria_env.xml
Read files : /gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_env/metapappso_condor/test_run/631_20MC0091_6_Env_third_step_60_baria_30_ctrl_nonbaria_env.xml
Read files : /gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_env/metapappso_condor/test_run/633_14MC0978_0_Env_third_step_60_baria_30_ctrl_nonbaria_env.xml


#grouping

ia_30_ctrl_nonbaria_env/metapappso_condor/test_run/combined_third_step_60_baria_30_ctrl_nonbaria_env_read.xml -o /gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_env/metapappso_condor/test_run/grouping_60_baria_30_ctrl_nonbaria_env.xml --decoy-regexp "(^conta\|.*|.*\|reversed$)"
New output : /gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_env/metapappso_condor/test_run/grouping_60_baria_30_ctrl_nonbaria_env.xml
New input : /gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_env/metapappso_condor/test_run/combined_third_step_60_baria_30_ctrl_nonbaria_env_read.xml
New pepbyprot : 2
New peprepro : 1
Begin reading data
removing non informative on a single group (16858 on 16887)
removing non informative on a single group (16859 on 16887)
removing non informative on a single group (16860 on 16887)
removing non informative on a single group (16861 on 16887)
removing non informative on a single group (16862 on 16887)
removing non informative on a single group (16863 on 16887)
removing non informative on a single group (16864 on 16887)
removing non informative on a single group (16865 on 16887)
removing non informative on a single group (16866 on 16887)
removing non informative on a single group (16867 on 16887)
removing non informative on a single group (16868 on 16887)
removing non informative on a single group (16869 on 16887)
removing non informative on a single group (16870 on 16887)
removing non informative on a single group (16871 on 16887)
removing non informative on a single group (16872 on 16887)
removing non informative on a single group (16873 on 16887)
removing non informative on a single group (16874 on 16887)
removing non informative on a single group (16875 on 16887)
removing non informative on a single group (16876 on 16887)
removing non informative on a single group (16877 on 16887)
removing non informative on a single group (16878 on 16887)
removing non informative on a single group (16879 on 16887)
removing non informative on a single group (16880 on 16887)
removing non informative on a single group (16881 on 16887)
removing non informative on a single group (16882 on 16887)
removing non informative on a single group (16883 on 16887)
removing non informative on a single group (16884 on 16887)
removing non informative on a single group (16885 on 16887)
removing non informative on a single group (16886 on 16887)
removing non informative on a single group (16887 on 16887)
removing non informative subgroups finished, remaining 19684 groups
numbering 19684 groups
grouping finished
End group creation : 
Begin Export
Finish Export

olangella@proteus1:/gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_env$ gp-output-peptide-counting.py -i /gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_env/metapappso_condor/test_run/grouping_60_baria_30_ctrl_nonbaria_env.xml -o /gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_env/metapappso_condor/test_run/peptide_counting_60_baria_30_ctrl_nonbaria_env.txt
olangella@proteus1:/gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_env$ gp-output-peptide-list.py -i /gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_env/metapappso_condor/test_run/grouping_60_baria_30_ctrl_nonbaria_env.xml -o /gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_env/metapappso_condor/test_run/peptide_list_60_baria_30_ctrl_nonbaria_env.txt
olangella@proteus1:/gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_env$ gp-output-protein-counting.py -i /gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_env/metapappso_condor/test_run/grouping_60_baria_30_ctrl_nonbaria_env.xml -o /gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_env/metapappso_condor/test_run/protein_counting_60_baria_30_ctrl_nonbaria_env.txt
olangella@proteus1:/gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_env$ gp-output-protein-list.py -i /gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_env/metapappso_condor/test_run/grouping_60_baria_30_ctrl_nonbaria_env.xml -o /gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_env/metapappso_condor/test_run/protein_list_60_baria_30_ctrl_nonbaria_env.txt
olangella@proteus1:/gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_env$  gp-fdr-peptide -i /gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_env/metapappso_condor/test_run/grouping_60_baria_30_ctrl_nonbaria_env.xml > /gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_env/metapappso_condor/test_run/FDR_60_baria_30_ctrl_nonbaria_env.txt

olangella@proteus1:/gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_env$ cat /gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_env/metapappso_condor/test_run/FDR_60_baria_30_ctrl_nonbaria_env.txt
target psms	2.3254e+06
decoy psms	10333
FDR	0.00444354	(0.444354%)


olangella@proteus1:/gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_env$ gp-output-masschroqml.py -i metapappso_condor/test_run/grouping_60_baria_30_ctrl_nonbaria_env.xml -o mcq_60_baria_30_ctrl_nonbaria_env.masschroqml


****************** config MassChroQ *****************************

<?xml version="1.0" encoding="utf-8" ?>
<masschroq>
  <rawdata>
    <data_file id="samp1" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env_baria/011_20MC0351_1_Env.mzXML" type="profile" />
    <data_file id="samp2" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env_baria/019_20MC0081_1_Env.mzXML" type="profile" />
    <data_file id="samp3" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env/021_14MC0900_0_Env.mzXML" type="profile" />
    <data_file id="samp4" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env_baria/025_20MC0081_6_Env.mzXML" type="profile" />
    <data_file id="samp5" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env_baria/031_20MC0351_6_Env.mzXML" type="profile" />
    <data_file id="samp6" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env/033_14MC0981_0_Env.mzXML" type="profile" />
    <data_file id="samp7" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env_baria/047_20MC0324_1_Env.mzXML" type="profile" />
    <data_file id="samp8" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env_baria/053_20MC0071_1_Env.mzXML" type="profile" />
    <data_file id="samp9" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env/057_14MC0953_0_Env.mzXML" type="profile" />
    <data_file id="samp10" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env/059_14MC0984_0_Env.mzXML" type="profile" />
    <data_file id="samp11" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env_baria/067_20MC0324_6_Env.mzXML" type="profile" />
    <data_file id="samp12" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env_baria/079_20MC0071_6_Env.mzXML" type="profile" />
    <data_file id="samp13" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env_baria/095_20MC0329_6_Env.mzXML" type="profile" />
    <data_file id="samp14" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env_baria/101_20MC0019_1_Env.mzXML" type="profile" />
    <data_file id="samp15" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env/107_14MC0989_0_Env.mzXML" type="profile" />
    <data_file id="samp16" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env_baria/123_20MC0019_6_Env.mzXML" type="profile" />
    <data_file id="samp17" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env_baria/133_20MC0329_1_Env.mzXML" type="profile" />
    <data_file id="samp18" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env_baria/145_20MC0050_1_Env.mzXML" type="profile" />
    <data_file id="samp19" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env_baria/147_20MC0037_6_Env.mzXML" type="profile" />
    <data_file id="samp20" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env/149_14MC0983_0_Env.mzXML" type="profile" />
    <data_file id="samp21" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env/151_14MC0941_0_Env.mzXML" type="profile" />
    <data_file id="samp22" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env_baria/153_20MC0207_1_Env.mzXML" type="profile" />
    <data_file id="samp23" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env/155_14MC0912_0_Env.mzXML" type="profile" />
    <data_file id="samp24" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env_baria/161_20MC0037_1_Env.mzXML" type="profile" />
    <data_file id="samp25" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env_baria/163_20MC0050_6_Env.mzXML" type="profile" />
    <data_file id="samp26" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env_baria/167_20MC0207_6_Env.mzXML" type="profile" />
    <data_file id="samp27" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env_baria/183_20MC0115_6_Env.mzXML" type="profile" />
    <data_file id="samp28" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env_baria/191_20MC0007_1_Env.mzXML" type="profile" />
    <data_file id="samp29" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env/211_14MC0915_0_Env.mzXML" type="profile" />
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    <data_file id="samp32" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env_baria/225_20MC0007_6_Env.mzXML" type="profile" />
    <data_file id="samp33" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env_baria/247_20MC0040_6_Env.mzXML" type="profile" />
    <data_file id="samp34" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env/249_14MC0956_0_Env.mzXML" type="profile" />
    <data_file id="samp35" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env_baria/251_20MC0109_1_Env.mzXML" type="profile" />
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    <data_file id="samp37" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env/261_14MC0927_0_Env.mzXML" type="profile" />
    <data_file id="samp38" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env_baria/267_20MC0040_1_Env.mzXML" type="profile" />
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    <data_file id="samp40" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env_baria/283_20MC0347_1_Env.mzXML" type="profile" />
    <data_file id="samp41" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env_baria/291_20MC0200_1_Env.mzXML" type="profile" />
    <data_file id="samp42" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env_baria/295_20MC0200_6_Env.mzXML" type="profile" />
    <data_file id="samp43" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env_baria/297_20MC0002_6_Env.mzXML" type="profile" />
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    <data_file id="samp46" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env_baria/315_20MC0034_1_Env.mzXML" type="profile" />
    <data_file id="samp47" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env_baria/329_20MC0297_1_Env.mzXML" type="profile" />
    <data_file id="samp48" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env_baria/331_20MC0034_6_Env.mzXML" type="profile" />
    <data_file id="samp49" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env_baria/343_20MC0297_6_Env.mzXML" type="profile" />
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    <data_file id="samp52" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env/353_14MC0925_0_Env.mzXML" type="profile" />
    <data_file id="samp53" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env/357_14MC0943_0_Env.mzXML" type="profile" />
    <data_file id="samp54" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env/377_14MC0931_0_Env.mzXML" type="profile" />
    <data_file id="samp55" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env_baria/381_20MC0017_1_Env.mzXML" type="profile" />
    <data_file id="samp56" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env_baria/383_20MC0017_6_Env.mzXML" type="profile" />
    <data_file id="samp57" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env_baria/389_20MC0235_6_Env.mzXML" type="profile" />
    <data_file id="samp58" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env/393_14MC0946_0_Env.mzXML" type="profile" />
    <data_file id="samp59" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env_baria/399_20MC0235_1_Env.mzXML" type="profile" />
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    <data_file id="samp61" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env_baria/419_20MC0147_1_Env.mzXML" type="profile" />
    <data_file id="samp62" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env/421_14MC0932_0_Env.mzXML" type="profile" />
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    <data_file id="samp64" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env_baria/437_20MC0039_1_Env.mzXML" type="profile" />
    <data_file id="samp65" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env_baria/439_20MC0147_6_Env.mzXML" type="profile" />
    <data_file id="samp66" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env/445_14MC0948_0_Env.mzXML" type="profile" />
    <data_file id="samp67" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env_baria/467_20MC0306_1_Env.mzXML" type="profile" />
    <data_file id="samp68" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env_baria/469_20MC0038_6_Env.mzXML" type="profile" />
    <data_file id="samp69" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env_baria/471_20MC0306_6_Env.mzXML" type="profile" />
    <data_file id="samp70" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env_baria/475_20MC0038_1_Env.mzXML" type="profile" />
    <data_file id="samp71" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env/477_14MC0968_0_Env.mzXML" type="profile" />
    <data_file id="samp72" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env/493_14MC0986_0_Env.mzXML" type="profile" />
    <data_file id="samp73" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env_baria/511_20MC0117_1_Env.mzXML" type="profile" />
    <data_file id="samp74" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env_baria/515_20MC0199_1_Env.mzXML" type="profile" />
    <data_file id="samp75" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env_baria/527_20MC0117_6_Env.mzXML" type="profile" />
    <data_file id="samp76" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env_baria/531_20MC0199_6_Env.mzXML" type="profile" />
    <data_file id="samp77" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env/533_14MC0975_0_Env.mzXML" type="profile" />
    <data_file id="samp78" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env/535_14MC0954_0_Env.mzXML" type="profile" />
    <data_file id="samp79" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env/545_14MC0990_0_Env.mzXML" type="profile" />
    <data_file id="samp80" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env_baria/555_20MC0344_1_Env.mzXML" type="profile" />
    <data_file id="samp81" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env_baria/557_20MC0344_6_Env.mzXML" type="profile" />
    <data_file id="samp82" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env/573_14MC0930_0_Env.mzXML" type="profile" />
    <data_file id="samp83" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env_baria/575_20MC0379_1_Env.mzXML" type="profile" />
    <data_file id="samp84" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env_baria/581_20MC0379_6_Env.mzXML" type="profile" />
    <data_file id="samp85" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env/597_14MC0977_0_Env.mzXML" type="profile" />
    <data_file id="samp86" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env_baria/605_20MC0113_6_Env.mzXML" type="profile" />
    <data_file id="samp87" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env_baria/609_20MC0113_1_Env.mzXML" type="profile" />
    <data_file id="samp88" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env_baria/619_20MC0091_1_Env.mzXML" type="profile" />
    <data_file id="samp89" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env_baria/631_20MC0091_6_Env.mzXML" type="profile" />
    <data_file id="samp90" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env/633_14MC0978_0_Env.mzXML" type="profile" />
  </rawdata>
  <groups>
    <group id="G01" data_ids="samp1 samp2 samp3 samp4 samp5 samp6 samp7 samp8 samp9 samp10 samp11 samp12 samp13 samp14 samp15 samp16 samp17 samp18 samp19 samp20 samp21 samp22 samp23 samp24 samp25 samp26 samp27 samp28 samp29 samp30 samp31 samp32 samp33 samp34 samp35 samp36 samp37 samp38 samp39 samp40 samp41 samp42 samp43 samp44 samp45 samp46 samp47 samp48 samp49 samp50 samp51 samp52 samp53 samp54 samp55 samp56 samp57 samp58 samp59 samp60 samp61 samp62 samp63 samp64 samp65 samp66 samp67 samp68 samp69 samp70 samp71 samp72 samp73 samp74 samp75 samp76 samp77 samp78 samp79 samp80 samp81 samp82 samp83 samp84 samp85 samp86 samp87 samp88 samp89 samp90" />
  </groups>

  
  
  -----


   <alignments>
    <alignment_methods>
      <alignment_method id="ms2_1">
        <ms2>
          <ms2_tendency_halfwindow>10</ms2_tendency_halfwindow>
          <ms2_smoothing_halfwindow>15</ms2_smoothing_halfwindow>
          <ms1_smoothing_halfwindow>0</ms1_smoothing_halfwindow>
        </ms2>
      </alignment_method>
    </alignment_methods>
    <align group_id="G01" method_id="ms2_1" reference_data_id="samp19" />
  </alignments>
  <quantification_methods>
    <quantification_method id="quant_1">
      <xic_extraction xic_type="max">
        <ppm_range min="10" max="10" />
      </xic_extraction>
      <xic_filters>
        <anti_spike half="5" />
      </xic_filters>
      <peak_detection>
        <detection_zivy>
          <mean_filter_half_edge>2</mean_filter_half_edge>
          <minmax_half_edge>4</minmax_half_edge>
          <maxmin_half_edge>3</maxmin_half_edge>
          <detection_threshold_on_max>50000</detection_threshold_on_max>
          <detection_threshold_on_min>30000</detection_threshold_on_min>
        </detection_zivy>
      </peak_detection>
    </quantification_method>
  </quantification_methods>
  <quantification>
    <quantification_results>
      <quantification_result output_file="XIC_result" format="tsv" />
      <!-- <quantification_result output_file="results" format="masschroqml" /> -->
    </quantification_results>
    <quantify id="q1" withingroup="G01" quantification_method_id ="quant_1">
      <peptides_in_peptide_list mode="post_matching" ni_min_abundance="0.8" />
    </quantify>
  </quantification>

  
  
  
  olangella@proteus1:/gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_env$ masschroq-condor.pl -h
Usage: masschroq-condor.pl [OPTION] [FILE]
Perform Mass Chromatogram Quantification as indicated in XML input FILE via masschroq on a condor system.
Options:
  -m, --mem			required memory in gigabytes
  -c, --cpus			required number of cpus
  -h, --help			display this help and exit
  -p, --parse-peptides		perform peptide text file parsing only, no quantification. If the identified peptides are given to masschroq via peptide text files (defined in FILE), he parses them, creates a new file called parsed-peptides_FILE which contains the FILE content (minus the lines relative to thr peptide text files to parse) plus the parsed peptides information. By default masschroq continues analysis and quantification on this new file. Use this option if you want masschroq only to parse the petide files but not to continue quantification on them. This allows you to check the parsed peptides and to add trace information on specific peptides before quantification.
  --ondisk		dump unmatched peak collections to the temporary directory to save memory.
For additional information, see the MassChroQ Homepage :
http://pappso.inra.fr/bioinfo/masschroq/


olangella@proteus1:/gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_env$ masschroq-condor.pl -m 80 -c 15 --ondisk mcq_60_baria_30_ctrl_nonbaria_env.masschroqml 
mcq_60_baria_30_ctrl_nonbaria_env.masschroqmlmasschroq condor submission file submit_condor_masschroq.txt created
condor job temporary directory /gorgone/pappso/tmp/temp_masschroq_condor_job7Tw_ created
Starting masschroq in condor
Submitting job(s).
1 job(s) submitted to cluster 2045.



olangella@proteus1:/gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_env$ condor_rm 2045
All jobs in cluster 2045 have been marked for removal
 
 olangella@proteus1:/gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_env$ masschroq-condor.pl -m 200 -c 15 --ondisk mcq_60_baria_30_ctrl_nonbaria_env.masschroqml 
mcq_60_baria_30_ctrl_nonbaria_env.masschroqmlmasschroq condor submission file submit_condor_masschroq.txt created
condor job temporary directory /gorgone/pappso/tmp/temp_masschroq_condor_jobVSA_ created
Starting masschroq in condor
Submitting job(s).
1 job(s) submitted to cluster 2046.

olangella@proteus1:/gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_env$ vi mcq_60_baria_30_ctrl_nonbaria_env.masschroqml 
olangella@proteus1:/gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_env$ masschroq-condor.pl -m 200 -c 15 --ondisk mcq_60_baria_30_ctrl_nonbaria_env.masschroqml 
mcq_60_baria_30_ctrl_nonbaria_env.masschroqmlmasschroq condor submission file submit_condor_masschroq.txt created
condor job temporary directory /gorgone/pappso/tmp/temp_masschroq_condor_jobNwy0 created
Starting masschroq in condor
Submitting job(s).
1 job(s) submitted to cluster 2047.


olangella@proteus1:/gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_env$ cat /gorgone/pappso/tmp/temp_masschroq_condor_jobNwy0/masschroq.error 
Oops! an error occurred in MassChroQ. Dont Panic :
error reading masschroqML input file '/gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_env/mcq_60_baria_30_ctrl_nonbaria_env.masschroqml' :
Parse error at line 49, column 192:
cannot find input file : /gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_Env/Samples_ALL_Env303_14MC0942_0_Env.mzXML 

olangella@proteus1:/gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_env$ vi mcq_60_baria_30_ctrl_nonbaria_env.masschroqml 
olangella@proteus1:/gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_env$ masschroq-condor.pl -m 200 -c 15 --ondisk mcq_60_baria_30_ctrl_nonbaria_env.masschroqml 
mcq_60_baria_30_ctrl_nonbaria_env.masschroqmlmasschroq condor submission file submit_condor_masschroq.txt created
condor job temporary directory /gorgone/pappso/tmp/temp_masschroq_condor_jobPIh5 created
Starting masschroq in condor
Submitting job(s).
1 job(s) submitted to cluster 2049.


the sample containing the more common peptides with all others is : 147_20MC0037_6_Env => samp19
rerun it with this sample as reference for alignment


olangella@proteus1:/gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_env$ mv XIC_result.d XIC_result.d_october
olangella@proteus1:/gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_env$ masschroq-condor.pl -m 200 -c 15 --ondisk mcq_60_baria_30_ctrl_nonbaria_env.masschroqml
mcq_60_baria_30_ctrl_nonbaria_env.masschroqmlmasschroq condor submission file submit_condor_masschroq.txt created
condor job temporary directory /gorgone/pappso/tmp/temp_masschroq_condor_jobNB4z created
Starting masschroq in condor
Submitting job(s).
1 job(s) submitted to cluster 2057.
