


gp-read-xtandem.py -e 0.05 -o combined_second_step_60_baria_30_ctrl_nonbaria_cyt_read.xml ../60_baria_cyt/metapappso_condor/test_run/*_second_step_60_baria_cyt.xml ../30_ctrl_nonbaria_cyt/metapappso_condor/test_run/*_second_step_30_ctrl_nonbaria_cyt.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_cyt$ gp-read-xtandem.py -e 0.05 -o combined_second_step_60_baria_30_ctrl_nonbaria_cyt_read.xml ../60_baria_cyt/metapappso_condor/test_run/*_second_step_60_baria_cyt.xml ../30_ctrl_nonbaria_cyt/metapappso_condor/test_run/*_second_step_30_ctrl_nonbaria_cyt.xml
Read files : ../60_baria_cyt/metapappso_condor/test_run/006_20MC0207_6_Cyt_second_step_60_baria_cyt.xml
Read files : ../60_baria_cyt/metapappso_condor/test_run/014_20MC0207_1_Cyt_second_step_60_baria_cyt.xml
Read files : ../60_baria_cyt/metapappso_condor/test_run/022_20MC0037_6_Cyt_second_step_60_baria_cyt.xml
Read files : ../60_baria_cyt/metapappso_condor/test_run/026_20MC0050_1_Cyt_second_step_60_baria_cyt.xml
Read files : ../60_baria_cyt/metapappso_condor/test_run/030_20MC0050_6_Cyt_second_step_60_baria_cyt.xml
Read files : ../60_baria_cyt/metapappso_condor/test_run/038_20MC0037_1_Cyt_second_step_60_baria_cyt.xml
Read files : ../60_baria_cyt/metapappso_condor/test_run/047_20MC0351_1_Cyt_second_step_60_baria_cyt.xml
Read files : ../60_baria_cyt/metapappso_condor/test_run/067_20MC0081_6_Cyt_second_step_60_baria_cyt.xml
Read files : ../60_baria_cyt/metapappso_condor/test_run/077_20MC0081_1_Cyt_second_step_60_baria_cyt.xml
Read files : ../60_baria_cyt/metapappso_condor/test_run/081_20MC0351_6_Cyt_second_step_60_baria_cyt.xml
Read files : ../60_baria_cyt/metapappso_condor/test_run/113_20MC0329_1_Cyt_second_step_60_baria_cyt.xml
Read files : ../60_baria_cyt/metapappso_condor/test_run/121_20MC0019_6_Cyt_second_step_60_baria_cyt.xml
Read files : ../60_baria_cyt/metapappso_condor/test_run/143_20MC0071_1_Cyt_second_step_60_baria_cyt.xml
Read files : ../60_baria_cyt/metapappso_condor/test_run/147_20MC0324_6_Cyt_second_step_60_baria_cyt.xml
Read files : ../60_baria_cyt/metapappso_condor/test_run/151_20MC0071_6_Cyt_second_step_60_baria_cyt.xml
Read files : ../60_baria_cyt/metapappso_condor/test_run/169_20MC0324_1_Cyt_second_step_60_baria_cyt.xml
Read files : ../60_baria_cyt/metapappso_condor/test_run/181_20MC0200_1_Cyt_second_step_60_baria_cyt.xml
Read files : ../60_baria_cyt/metapappso_condor/test_run/183_20MC0002_1_Cyt_second_step_60_baria_cyt.xml
Read files : ../60_baria_cyt/metapappso_condor/test_run/185_20MC0002_6_Cyt_second_step_60_baria_cyt.xml
Read files : ../60_baria_cyt/metapappso_condor/test_run/191_20MC0347_1_Cyt_second_step_60_baria_cyt.xml
Read files : ../60_baria_cyt/metapappso_condor/test_run/199_20MC0347_6_Cyt_second_step_60_baria_cyt.xml
Read files : ../60_baria_cyt/metapappso_condor/test_run/207_20MC0200_6_Cyt_second_step_60_baria_cyt.xml
Read files : ../60_baria_cyt/metapappso_condor/test_run/231_20MC0297_6_Cyt_second_step_60_baria_cyt.xml
Read files : ../60_baria_cyt/metapappso_condor/test_run/239_20MC0297_1_Cyt_second_step_60_baria_cyt.xml
Read files : ../60_baria_cyt/metapappso_condor/test_run/241_20MC0034_1_Cyt_second_step_60_baria_cyt.xml
Read files : ../60_baria_cyt/metapappso_condor/test_run/251_20MC0034_6_Cyt_second_step_60_baria_cyt.xml
Read files : ../60_baria_cyt/metapappso_condor/test_run/271_20MC0040_6_Cyt_second_step_60_baria_cyt.xml
Read files : ../60_baria_cyt/metapappso_condor/test_run/291_20MC0040_1_Cyt_second_step_60_baria_cyt.xml
Read files : ../60_baria_cyt/metapappso_condor/test_run/293_20MC0109_1_Cyt_second_step_60_baria_cyt.xml
Read files : ../60_baria_cyt/metapappso_condor/test_run/295_20MC0109_6_Cyt_second_step_60_baria_cyt.xml
Read files : ../60_baria_cyt/metapappso_condor/test_run/305_20MC0007_6_Cyt_second_step_60_baria_cyt.xml
Read files : ../60_baria_cyt/metapappso_condor/test_run/309_20MC0007_1_Cyt_second_step_60_baria_cyt.xml
Read files : ../60_baria_cyt/metapappso_condor/test_run/313_20MC0115_1_Cyt_second_step_60_baria_cyt.xml
Read files : ../60_baria_cyt/metapappso_condor/test_run/333_20MC0115_6_Cyt_second_step_60_baria_cyt.xml
Read files : ../60_baria_cyt/metapappso_condor/test_run/367_20MC0147_1_Cyt_second_step_60_baria_cyt.xml
Read files : ../60_baria_cyt/metapappso_condor/test_run/369_20MC0039_6_Cyt_second_step_60_baria_cyt.xml
Read files : ../60_baria_cyt/metapappso_condor/test_run/381_20MC0147_6_Cyt_second_step_60_baria_cyt.xml
Read files : ../60_baria_cyt/metapappso_condor/test_run/387_20MC0039_1_Cyt_second_step_60_baria_cyt.xml
Read files : ../60_baria_cyt/metapappso_condor/test_run/417_20MC0306_6_Cyt_second_step_60_baria_cyt.xml
Read files : ../60_baria_cyt/metapappso_condor/test_run/423_20MC0038_6_Cyt_second_step_60_baria_cyt.xml
Read files : ../60_baria_cyt/metapappso_condor/test_run/425_20MC0038_1_Cyt_second_step_60_baria_cyt.xml
Read files : ../60_baria_cyt/metapappso_condor/test_run/427_20MC0306_1_Cyt_second_step_60_baria_cyt.xml
Read files : ../60_baria_cyt/metapappso_condor/test_run/473_20MC0017_1_Cyt_second_step_60_baria_cyt.xml
Read files : ../60_baria_cyt/metapappso_condor/test_run/481_20MC0235_6_Cyt_second_step_60_baria_cyt.xml
Read files : ../60_baria_cyt/metapappso_condor/test_run/483_20MC0017_6_Cyt_second_step_60_baria_cyt.xml
Read files : ../60_baria_cyt/metapappso_condor/test_run/487_20MC0235_1_Cyt_second_step_60_baria_cyt.xml
Read files : ../60_baria_cyt/metapappso_condor/test_run/509_20MC0199_6_Cyt_second_step_60_baria_cyt.xml
Read files : ../60_baria_cyt/metapappso_condor/test_run/511_20MC0117_1_Cyt_second_step_60_baria_cyt.xml
Read files : ../60_baria_cyt/metapappso_condor/test_run/527_20MC0117_6_Cyt_second_step_60_baria_cyt.xml
Read files : ../60_baria_cyt/metapappso_condor/test_run/535_20MC0199_1_Cyt_second_step_60_baria_cyt.xml
Read files : ../60_baria_cyt/metapappso_condor/test_run/547_20MC0379_1_Cyt_second_step_60_baria_cyt.xml
Read files : ../60_baria_cyt/metapappso_condor/test_run/549_20MC0379_6_Cyt_second_step_60_baria_cyt.xml
Read files : ../60_baria_cyt/metapappso_condor/test_run/555_20MC0344_6_Cyt_second_step_60_baria_cyt.xml
Read files : ../60_baria_cyt/metapappso_condor/test_run/575_20MC0344_1_Cyt_second_step_60_baria_cyt.xml
Read files : ../60_baria_cyt/metapappso_condor/test_run/593_20MC0113_6_Cyt_second_step_60_baria_cyt.xml
Read files : ../60_baria_cyt/metapappso_condor/test_run/599_20MC0091_1_Cyt_second_step_60_baria_cyt.xml
Read files : ../60_baria_cyt/metapappso_condor/test_run/623_20MC0091_6_Cyt_second_step_60_baria_cyt.xml
Read files : ../60_baria_cyt/metapappso_condor/test_run/625_20MC0113_1_Cyt_second_step_60_baria_cyt.xml
Read files : ../60_baria_cyt/metapappso_condor/test_run/87_20MC0329_6_Cyt_second_step_60_baria_cyt.xml
Read files : ../60_baria_cyt/metapappso_condor/test_run/99_20MC0019_1_Cyt_second_step_60_baria_cyt.xml
Read files : ../30_ctrl_nonbaria_cyt/metapappso_condor/test_run/012_14MC0983_0_Cyt_second_step_30_ctrl_nonbaria_cyt.xml
Read files : ../30_ctrl_nonbaria_cyt/metapappso_condor/test_run/018_14MC0941_0_Cyt_second_step_30_ctrl_nonbaria_cyt.xml
Read files : ../30_ctrl_nonbaria_cyt/metapappso_condor/test_run/032_14MC0912_0_Cyt_second_step_30_ctrl_nonbaria_cyt.xml
Read files : ../30_ctrl_nonbaria_cyt/metapappso_condor/test_run/049_14MC0981_0_Cyt_second_step_30_ctrl_nonbaria_cyt.xml
Read files : ../30_ctrl_nonbaria_cyt/metapappso_condor/test_run/059_14MC0900_0_Cyt_second_step_30_ctrl_nonbaria_cyt.xml
Read files : ../30_ctrl_nonbaria_cyt/metapappso_condor/test_run/123_14MC0989_0_Cyt_second_step_30_ctrl_nonbaria_cyt.xml
Read files : ../30_ctrl_nonbaria_cyt/metapappso_condor/test_run/141_14MC0953_0_Cyt_second_step_30_ctrl_nonbaria_cyt.xml
Read files : ../30_ctrl_nonbaria_cyt/metapappso_condor/test_run/153_14MC0984_0_Cyt_second_step_30_ctrl_nonbaria_cyt.xml
Read files : ../30_ctrl_nonbaria_cyt/metapappso_condor/test_run/211_14MC0942_0_Cyt_second_step_30_ctrl_nonbaria_cyt.xml
Read files : ../30_ctrl_nonbaria_cyt/metapappso_condor/test_run/225_14MC0943_0_Cyt_second_step_30_ctrl_nonbaria_cyt.xml
Read files : ../30_ctrl_nonbaria_cyt/metapappso_condor/test_run/227_14MC0925_0_Cyt_second_step_30_ctrl_nonbaria_cyt.xml
Read files : ../30_ctrl_nonbaria_cyt/metapappso_condor/test_run/229_14MC0985_0_Cyt_second_step_30_ctrl_nonbaria_cyt.xml
Read files : ../30_ctrl_nonbaria_cyt/metapappso_condor/test_run/237_14MC0918_0_Cyt_second_step_30_ctrl_nonbaria_cyt.xml
Read files : ../30_ctrl_nonbaria_cyt/metapappso_condor/test_run/279_14MC0927_0_Cyt_second_step_30_ctrl_nonbaria_cyt.xml
Read files : ../30_ctrl_nonbaria_cyt/metapappso_condor/test_run/283_14MC0956_0_Cyt_second_step_30_ctrl_nonbaria_cyt.xml
Read files : ../30_ctrl_nonbaria_cyt/metapappso_condor/test_run/323_14MC0964_0_Cyt_second_step_30_ctrl_nonbaria_cyt.xml
Read files : ../30_ctrl_nonbaria_cyt/metapappso_condor/test_run/345_14MC0915_0_Cyt_second_step_30_ctrl_nonbaria_cyt.xml
Read files : ../30_ctrl_nonbaria_cyt/metapappso_condor/test_run/375_14MC0948_0_Cyt_second_step_30_ctrl_nonbaria_cyt.xml
Read files : ../30_ctrl_nonbaria_cyt/metapappso_condor/test_run/377_14MC0932_0_Cyt_second_step_30_ctrl_nonbaria_cyt.xml
Read files : ../30_ctrl_nonbaria_cyt/metapappso_condor/test_run/433_14MC0968_0_Cyt_second_step_30_ctrl_nonbaria_cyt.xml
Read files : ../30_ctrl_nonbaria_cyt/metapappso_condor/test_run/449_14MC0944_0_Cyt_second_step_30_ctrl_nonbaria_cyt.xml
Read files : ../30_ctrl_nonbaria_cyt/metapappso_condor/test_run/453_14MC0931_0_Cyt_second_step_30_ctrl_nonbaria_cyt.xml
Read files : ../30_ctrl_nonbaria_cyt/metapappso_condor/test_run/489_14MC0946_0_Cyt_second_step_30_ctrl_nonbaria_cyt.xml
Read files : ../30_ctrl_nonbaria_cyt/metapappso_condor/test_run/499_14MC0986_0_Cyt_second_step_30_ctrl_nonbaria_cyt.xml
Read files : ../30_ctrl_nonbaria_cyt/metapappso_condor/test_run/521_14MC0975_0_Cyt_second_step_30_ctrl_nonbaria_cyt.xml
Read files : ../30_ctrl_nonbaria_cyt/metapappso_condor/test_run/525_14MC0990_0_Cyt_second_step_30_ctrl_nonbaria_cyt.xml
Read files : ../30_ctrl_nonbaria_cyt/metapappso_condor/test_run/531_14MC0954_0_Cyt_second_step_30_ctrl_nonbaria_cyt.xml
Read files : ../30_ctrl_nonbaria_cyt/metapappso_condor/test_run/557_14MC0977_0_Cyt_second_step_30_ctrl_nonbaria_cyt.xml
Read files : ../30_ctrl_nonbaria_cyt/metapappso_condor/test_run/581_14MC0930_0_Cyt_second_step_30_ctrl_nonbaria_cyt.xml
Read files : ../30_ctrl_nonbaria_cyt/metapappso_condor/test_run/603_14MC0978_0_Cyt_second_step_30_ctrl_nonbaria_cyt.xml




olangella@proteus1:/gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_cyt$ tail combined_second_step_60_baria_30_ctrl_nonbaria_cyt_read.xml 
</psm>
<psm seq="HYAHVDCPGHADYVK" mhTheo="1768.7864" evalue="1e-15" prot="MH0421_GL0094690  [gene]  locus=C1700564_1:3:356:-[Lack 3'-end]">
<mod aa="C" pos="7" mod="57.02146" />
</psm>
<psm seq="HYAHVDCPGHADYVK" mhTheo="1768.7864" evalue="1e-15" prot="SRS017127_2724_NODE_14_length_121632_cov_127.249_96 # 99662 # 100849 # -1 # ID=14_96;partial=00;start_type=ATG;rbs_motif=AATAA;rbs_spacer=10bp;gc_cont=0.390">
<mod aa="C" pos="7" mod="57.02146" />
</psm>
</scan>
</sample>
</peptide_result>

olangella@proteus1:/gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_cyt$ metapappso_create_fasta_enhanced.py -x combined_second_step_60_baria_30_ctrl_nonbaria_cyt_read.xml  -f /gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/softs/database/meta_total.fasta -o combined_proteome_60_baria_30_ctrl_nonbaria_cyt.fasta
('Searching in ', '/gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/softs/database/meta_total.fasta')
('File ', 'combined_proteome_60_baria_30_ctrl_nonbaria_cyt.fasta', ' written')

olangella@proteus1:/gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_cyt$ mkdir metapappso_condor
olangella@proteus1:/gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_cyt$ mkdir metapappso_condor/params
olangella@proteus1:/gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_cyt$ mkdir metapappso_condor/test_run




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


###################### Directories  60_baria_cyt ###########################
# directories which will be created to stores the results
params_d="/gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_cyt/metapappso_condor/params"
output_d="/gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_cyt/metapappso_condor/test_run"
job_name="60_baria_30_ctrl_nonbaria_cyt"

# 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_cyt/metapappso_condor/params/htcondor_step_3_60_baria_30_ctrl_nonbaria_cyt.log\nOutput        = /gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_cyt/metapappso_condor/params/htcondor_step_3_60_baria_30_ctrl_nonbaria_cyt.\$(Process).out\nError        = /gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_cyt/metapappso_condor/params/htcondor_step_3_60_baria_30_ctrl_nonbaria_cyt.\$(Process).error\n" > /gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_cyt/metapappso_condor/params/htcondor_step_3_60_baria_30_ctrl_nonbaria_cyt.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_cyt/combined_proteome_60_baria_30_ctrl_nonbaria_cyt.fasta\"></file>\n</taxon>\n</bioml>" > /gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_cyt/metapappso_condor/params/xtandem_database_third_step_60_baria_30_ctrl_nonbaria_cyt.database


spectra_d="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_baria"
for sample in $(cat /gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_cyt/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"
for sample in $(cat /gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/30_ctrl_nonbaria_cyt/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_cyt$ bash step3.sh 

olangella@proteus1:/gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_cyt$ condor_submit metapappso_condor/params/htcondor_step_3_60_baria_30_ctrl_nonbaria_cyt.submit 
Submitting job(s)..........................................................................................
90 job(s) submitted to cluster 2009.



olangella@proteus1:/gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_cyt$ gp-read-xtandem.py -e 0.05 -o /gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_cyt/metapappso_condor/test_run/combined_third_step_60_baria_30_ctrl_nonbaria_cyt_read.xml /gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_cyt/metapappso_condor/test_run/*_third_step_60_baria_30_ctrl_nonbaria_cyt.xml
Read files : /gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_cyt/metapappso_condor/test_run/006_20MC0207_6_Cyt_third_step_60_baria_30_ctrl_nonbaria_cyt.xml



gp-grouping -i /gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_cyt/metapappso_condor/test_run/combined_third_step_60_baria_30_ctrl_nonbaria_cyt_read.xml -o /gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_cyt/metapappso_condor/test_run/grouping_60_baria_30_ctrl_nonbaria_cyt.xml --decoy-regexp "(^conta\|.*|.*\|reversed$)"


removing non informative on a single group (13948 on 13954)
removing non informative on a single group (13949 on 13954)
removing non informative on a single group (13950 on 13954)
removing non informative on a single group (13951 on 13954)
removing non informative on a single group (13952 on 13954)
removing non informative on a single group (13953 on 13954)
removing non informative on a single group (13954 on 13954)
removing non informative subgroups finished, remaining 16484 groups
numbering 16484 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_cyt$ 
olangella@proteus1:/gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_cyt$ 
olangella@proteus1:/gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_cyt$ gp-output-peptide-counting.py -i /gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_cyt/metapappso_condor/test_run/grouping_60_baria_30_ctrl_nonbaria_cyt.xml -o /gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_cyt/metapappso_condor/test_run/peptide_counting_60_baria_30_ctrl_nonbaria_cyt.txt
olangella@proteus1:/gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_cyt$ gp-output-peptide-list.py -i /gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_cyt/metapappso_condor/test_run/grouping_60_baria_30_ctrl_nonbaria_cyt.xml -o /gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_cyt/metapappso_condor/test_run/peptide_list_60_baria_30_ctrl_nonbaria_cyt.txt
olangella@proteus1:/gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_cyt$ gp-output-protein-counting.py -i /gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_cyt/metapappso_condor/test_run/grouping_60_baria_30_ctrl_nonbaria_cyt.xml -o /gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_cyt/metapappso_condor/test_run/protein_counting_60_baria_30_ctrl_nonbaria_cyt.txt
olangella@proteus1:/gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_cyt$ gp-output-protein-list.py -i /gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_cyt/metapappso_condor/test_run/grouping_60_baria_30_ctrl_nonbaria_cyt.xml -o /gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_cyt/metapappso_condor/test_run/protein_list_60_baria_30_ctrl_nonbaria_cyt.txt
olangella@proteus1:/gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_cyt$ gp-fdr-peptide -i /gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_cyt/metapappso_condor/test_run/combined_third_step_60_baria_30_ctrl_nonbaria_cyt_read.xml > /gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_cyt/metapappso_condor/test_run/FDR_60_baria_30_ctrl_nonbaria_cyt.txt

olangella@proteus1:/gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_cyt$ cat /gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_cyt/metapappso_condor/test_run/FDR_60_baria_30_ctrl_nonbaria_cyt.txt
target psms	3.55099e+06
decoy psms	9502
FDR	0.00267588	(0.267588%)


olangella@proteus1:/gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_cyt$ gp-output-masschroqml.py -i metapappso_condor/test_run/grouping_60_baria_30_ctrl_nonbaria_cyt.xml -o mcq_60_baria_30_ctrl_nonbaria_cyt.masschroqml




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


  <rawdata>
    <data_file id="samp1" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_baria/006_20MC0207_6_Cyt.mzXML" type="profile" />
    <data_file id="samp2" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL/012_14MC0983_0_Cyt.mzXML" type="profile" />
    <data_file id="samp3" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_baria/014_20MC0207_1_Cyt.mzXML" type="profile" />
    <data_file id="samp4" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL/018_14MC0941_0_Cyt.mzXML" type="profile" />
    <data_file id="samp5" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_baria/022_20MC0037_6_Cyt.mzXML" type="profile" />
    <data_file id="samp6" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_baria/026_20MC0050_1_Cyt.mzXML" type="profile" />
    <data_file id="samp7" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_baria/030_20MC0050_6_Cyt.mzXML" type="profile" />
    <data_file id="samp8" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL/032_14MC0912_0_Cyt.mzXML" type="profile" />
    <data_file id="samp9" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_baria/038_20MC0037_1_Cyt.mzXML" type="profile" />
    <data_file id="samp10" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_baria/047_20MC0351_1_Cyt.mzXML" type="profile" />
    <data_file id="samp11" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL/049_14MC0981_0_Cyt.mzXML" type="profile" />
    <data_file id="samp12" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL/059_14MC0900_0_Cyt.mzXML" type="profile" />
    <data_file id="samp13" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_baria/067_20MC0081_6_Cyt.mzXML" type="profile" />
    <data_file id="samp14" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_baria/077_20MC0081_1_Cyt.mzXML" type="profile" />
    <data_file id="samp15" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_baria/081_20MC0351_6_Cyt.mzXML" type="profile" />
    <data_file id="samp16" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_baria/113_20MC0329_1_Cyt.mzXML" type="profile" />
    <data_file id="samp17" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_baria/121_20MC0019_6_Cyt.mzXML" type="profile" />
    <data_file id="samp18" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL/123_14MC0989_0_Cyt.mzXML" type="profile" />
    <data_file id="samp19" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL/141_14MC0953_0_Cyt.mzXML" type="profile" />
    <data_file id="samp20" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_baria/143_20MC0071_1_Cyt.mzXML" type="profile" />
    <data_file id="samp21" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_baria/147_20MC0324_6_Cyt.mzXML" type="profile" />
    <data_file id="samp22" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_baria/151_20MC0071_6_Cyt.mzXML" type="profile" />
    <data_file id="samp23" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL/153_14MC0984_0_Cyt.mzXML" type="profile" />
    <data_file id="samp24" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_baria/169_20MC0324_1_Cyt.mzXML" type="profile" />
    <data_file id="samp25" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_baria/181_20MC0200_1_Cyt.mzXML" type="profile" />
    <data_file id="samp26" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_baria/183_20MC0002_1_Cyt.mzXML" type="profile" />
    <data_file id="samp27" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_baria/185_20MC0002_6_Cyt.mzXML" type="profile" />
    <data_file id="samp28" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_baria/191_20MC0347_1_Cyt.mzXML" type="profile" />
    <data_file id="samp29" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_baria/199_20MC0347_6_Cyt.mzXML" type="profile" />
    <data_file id="samp30" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_baria/207_20MC0200_6_Cyt.mzXML" type="profile" />
    <data_file id="samp31" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL/211_14MC0942_0_Cyt.mzXML" type="profile" />
    <data_file id="samp32" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL/225_14MC0943_0_Cyt.mzXML" type="profile" />
    <data_file id="samp33" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL/227_14MC0925_0_Cyt.mzXML" type="profile" />
    <data_file id="samp34" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL/229_14MC0985_0_Cyt.mzXML" type="profile" />
    <data_file id="samp35" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_baria/231_20MC0297_6_Cyt.mzXML" type="profile" />
    <data_file id="samp36" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL/237_14MC0918_0_Cyt.mzXML" type="profile" />
    <data_file id="samp37" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_baria/239_20MC0297_1_Cyt.mzXML" type="profile" />
    <data_file id="samp38" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_baria/241_20MC0034_1_Cyt.mzXML" type="profile" />
    <data_file id="samp39" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_baria/251_20MC0034_6_Cyt.mzXML" type="profile" />
    <data_file id="samp40" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_baria/271_20MC0040_6_Cyt.mzXML" type="profile" />
    <data_file id="samp41" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL/279_14MC0927_0_Cyt.mzXML" type="profile" />
    <data_file id="samp42" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL/283_14MC0956_0_Cyt.mzXML" type="profile" />
    <data_file id="samp43" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_baria/291_20MC0040_1_Cyt.mzXML" type="profile" />
    <data_file id="samp44" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_baria/293_20MC0109_1_Cyt.mzXML" type="profile" />
    <data_file id="samp45" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_baria/295_20MC0109_6_Cyt.mzXML" type="profile" />
    <data_file id="samp46" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_baria/305_20MC0007_6_Cyt.mzXML" type="profile" />
    <data_file id="samp47" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_baria/309_20MC0007_1_Cyt.mzXML" type="profile" />
    <data_file id="samp48" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_baria/313_20MC0115_1_Cyt.mzXML" type="profile" />
    <data_file id="samp49" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL/323_14MC0964_0_Cyt.mzXML" type="profile" />
    <data_file id="samp50" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_baria/333_20MC0115_6_Cyt.mzXML" type="profile" />
    <data_file id="samp51" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL/345_14MC0915_0_Cyt.mzXML" type="profile" />
    <data_file id="samp52" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_baria/367_20MC0147_1_Cyt.mzXML" type="profile" />
    <data_file id="samp53" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_baria/369_20MC0039_6_Cyt.mzXML" type="profile" />
    <data_file id="samp54" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL/375_14MC0948_0_Cyt.mzXML" type="profile" />
    <data_file id="samp55" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL/377_14MC0932_0_Cyt.mzXML" type="profile" />
    <data_file id="samp56" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_baria/381_20MC0147_6_Cyt.mzXML" type="profile" />
    <data_file id="samp57" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_baria/387_20MC0039_1_Cyt.mzXML" type="profile" />
    <data_file id="samp58" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_baria/417_20MC0306_6_Cyt.mzXML" type="profile" />
    <data_file id="samp59" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_baria/423_20MC0038_6_Cyt.mzXML" type="profile" />
    <data_file id="samp60" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_baria/425_20MC0038_1_Cyt.mzXML" type="profile" />
    <data_file id="samp61" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_baria/427_20MC0306_1_Cyt.mzXML" type="profile" />
    <data_file id="samp62" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL/433_14MC0968_0_Cyt.mzXML" type="profile" />
    <data_file id="samp63" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL/449_14MC0944_0_Cyt.mzXML" type="profile" />
    <data_file id="samp64" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL/453_14MC0931_0_Cyt.mzXML" type="profile" />
    <data_file id="samp65" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_baria/473_20MC0017_1_Cyt.mzXML" type="profile" />
    <data_file id="samp66" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_baria/481_20MC0235_6_Cyt.mzXML" type="profile" />
    <data_file id="samp67" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_baria/483_20MC0017_6_Cyt.mzXML" type="profile" />
    <data_file id="samp68" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_baria/487_20MC0235_1_Cyt.mzXML" type="profile" />
    <data_file id="samp69" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL/489_14MC0946_0_Cyt.mzXML" type="profile" />
    <data_file id="samp70" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL/499_14MC0986_0_Cyt.mzXML" type="profile" />
    <data_file id="samp71" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_baria/509_20MC0199_6_Cyt.mzXML" type="profile" />
    <data_file id="samp72" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_baria/511_20MC0117_1_Cyt.mzXML" type="profile" />
    <data_file id="samp73" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL/521_14MC0975_0_Cyt.mzXML" type="profile" />
    <data_file id="samp74" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL/525_14MC0990_0_Cyt.mzXML" type="profile" />
    <data_file id="samp75" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_baria/527_20MC0117_6_Cyt.mzXML" type="profile" />
    <data_file id="samp76" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL/531_14MC0954_0_Cyt.mzXML" type="profile" />
    <data_file id="samp77" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_baria/535_20MC0199_1_Cyt.mzXML" type="profile" />
    <data_file id="samp78" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_baria/547_20MC0379_1_Cyt.mzXML" type="profile" />
    <data_file id="samp79" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_baria/549_20MC0379_6_Cyt.mzXML" type="profile" />
    <data_file id="samp80" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_baria/555_20MC0344_6_Cyt.mzXML" type="profile" />
    <data_file id="samp81" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL/557_14MC0977_0_Cyt.mzXML" type="profile" />
    <data_file id="samp82" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_baria/575_20MC0344_1_Cyt.mzXML" type="profile" />
    <data_file id="samp83" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL/581_14MC0930_0_Cyt.mzXML" type="profile" />
    <data_file id="samp84" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_baria/593_20MC0113_6_Cyt.mzXML" type="profile" />
    <data_file id="samp85" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_baria/599_20MC0091_1_Cyt.mzXML" type="profile" />
    <data_file id="samp86" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL/603_14MC0978_0_Cyt.mzXML" type="profile" />
    <data_file id="samp87" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_baria/623_20MC0091_6_Cyt.mzXML" type="profile" />
    <data_file id="samp88" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_baria/625_20MC0113_1_Cyt.mzXML" type="profile" />
    <data_file id="samp89" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_baria/87_20MC0329_6_Cyt.mzXML" type="profile" />
    <data_file id="samp90" format="mzxml" path="/gorgone/pappso/moulon/users/Ariane/Proteocardis/link_mzXML_by_dataset/Samples_ALL_baria/99_20MC0019_1_Cyt.mzXML" type="profile" />
  </rawdata>





  -----


   <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="samp46" />
  </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>

  
  
  
  
  
  
  
  
  


the sample containing the more common peptides with all others is : 305_20MC0007_6_Cyt => samp46
rerun it with this sample as reference for alignment







olangella@proteus1:/gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_cyt$ vi mcq_60_baria_30_ctrl_nonbaria_cyt.masschroqml 
olangella@proteus1:/gorgone/pappso/moulon/users/Olivier/proteocardis/new_identification/60_baria_30_ctrl_nonbaria_cyt$ masschroq-condor.pl -m 200 -c 15 --ondisk mcq_60_baria_30_ctrl_nonbaria_cyt.masschroqml 
mcq_60_baria_30_ctrl_nonbaria_cyt.masschroqmlmasschroq condor submission file submit_condor_masschroq.txt created
condor job temporary directory /gorgone/pappso/tmp/temp_masschroq_condor_jobRpqJ created
Starting masschroq in condor
Submitting job(s).
1 job(s) submitted to cluster 2064.




