Dear David, 1) Just to make it clear, my problem is, iprophet works on some subsets of my 300 files, but does not work all subsets. My each subset has same no of files. For those have segmentation errors, there are no outputs being generated. 2) My peptideprophet and iprophet setting is as follows, xinteract -Ninteract-$f.pep.xml -OARPd -dDECOY -PPM $f.tandem.pep.xml InterProphetParser THREADS=32 DECOY=DECOY MINPROB=0.9 `\ls interact-*is280*.pep.xml` is280.interact.ipro.pep.xml 3) iprophet error and peptideprophet output tail are also attached for your information. Hope it helps. Rachel
On Wednesday, July 22, 2015 at 3:00:11 PM UTC+8, Rachel wrote: > > I tried to merge ~300 pepxml files using xinteract, it failed for the > command line is too long. Can anyone tell what is maximum no of pepxml we > can merge using xinteract? > > Thanks so much! > > Rachel > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
processing interact-qpg_qe_150529_01_is280_ief1.pep.xml... <parameter name="RT" value="2875.76"/> <parameter name="RT_score" value="1.32"/> </search_score_summary> </peptideprophet_result> </analysis_result> </search_hit> </search_result> </spectrum_query> </msms_run_summary> </msms_pipeline_analysis> processing interact-qpg_qe_150529_02_is280_ief2.pep.xml... <parameter name="RT" value="2651.87"/> <parameter name="RT_score" value="1.68"/> </search_score_summary> </peptideprophet_result> </analysis_result> </search_hit> </search_result> </spectrum_query> </msms_run_summary> </msms_pipeline_analysis> processing interact-qpg_qe_150529_03_is280_ief3.pep.xml... <parameter name="RT" value="4803.39"/> <parameter name="RT_score" value="-2.00"/> </search_score_summary> </peptideprophet_result> </analysis_result> </search_hit> </search_result> </spectrum_query> </msms_run_summary> </msms_pipeline_analysis> processing interact-qpg_qe_150529_04_is280_ief4.pep.xml... <parameter name="RT" value="2755.52"/> <parameter name="RT_score" value="1.16"/> </search_score_summary> </peptideprophet_result> </analysis_result> </search_hit> </search_result> </spectrum_query> </msms_run_summary> </msms_pipeline_analysis> processing interact-qpg_qe_150529_05_is280_ief5.pep.xml... <parameter name="RT" value="2875.76"/> <parameter name="RT_score" value="2.24"/> </search_score_summary> </peptideprophet_result> </analysis_result> </search_hit> </search_result> </spectrum_query> </msms_run_summary> </msms_pipeline_analysis> processing interact-qpg_qe_150529_06_is280_ief6.pep.xml... <parameter name="RT" value="2875.76"/> <parameter name="RT_score" value="2.42"/> </search_score_summary> </peptideprophet_result> </analysis_result> </search_hit> </search_result> </spectrum_query> </msms_run_summary> </msms_pipeline_analysis> processing interact-qpg_qe_150529_07_is280_ief7.pep.xml... <parameter name="RT" value="3464.72"/> <parameter name="RT_score" value="1.31"/> </search_score_summary> </peptideprophet_result> </analysis_result> </search_hit> </search_result> </spectrum_query> </msms_run_summary> </msms_pipeline_analysis> processing interact-qpg_qe_150529_08_is280_ief8.pep.xml... <parameter name="RT" value="3991.18"/> <parameter name="RT_score" value="0.14"/> </search_score_summary> </peptideprophet_result> </analysis_result> </search_hit> </search_result> </spectrum_query> </msms_run_summary> </msms_pipeline_analysis> processing interact-qpg_qe_150529_09_is280_ief9.pep.xml... <parameter name="RT" value="1941.19"/> <parameter name="RT_score" value="4.28"/> </search_score_summary> </peptideprophet_result> </analysis_result> </search_hit> </search_result> </spectrum_query> </msms_run_summary> </msms_pipeline_analysis> processing interact-qpg_qe_150529_10_is280_ief10.pep.xml... <parameter name="RT" value="3449.44"/> <parameter name="RT_score" value="1.09"/> </search_score_summary> </peptideprophet_result> </analysis_result> </search_hit> </search_result> </spectrum_query> </msms_run_summary> </msms_pipeline_analysis> processing interact-qpg_qe_150529_11_is280_ief11.pep.xml... <parameter name="RT" value="4154.37"/> <parameter name="RT_score" value="-0.37"/> </search_score_summary> </peptideprophet_result> </analysis_result> </search_hit> </search_result> </spectrum_query> </msms_run_summary> </msms_pipeline_analysis> processing interact-qpg_qe_150529_12_is280_ief12.pep.xml... <parameter name="RT" value="3637.97"/> <parameter name="RT_score" value="0.83"/> </search_score_summary> </peptideprophet_result> </analysis_result> </search_hit> </search_result> </spectrum_query> </msms_run_summary> </msms_pipeline_analysis> processing interact-qpg_qe_150529_13_is280_ief13.pep.xml... <parameter name="RT" value="3444.99"/> <parameter name="RT_score" value="1.27"/> </search_score_summary> </peptideprophet_result> </analysis_result> </search_hit> </search_result> </spectrum_query> </msms_run_summary> </msms_pipeline_analysis> processing interact-qpg_qe_150529_14_is280_ief14.pep.xml... <parameter name="RT" value="2673.32"/> <parameter name="RT_score" value="2.60"/> </search_score_summary> </peptideprophet_result> </analysis_result> </search_hit> </search_result> </spectrum_query> </msms_run_summary> </msms_pipeline_analysis> processing interact-qpg_qe_150529_15_is280_ief15.pep.xml... <parameter name="RT" value="5672.61"/> <parameter name="RT_score" value="-2.00"/> </search_score_summary> </peptideprophet_result> </analysis_result> </search_hit> </search_result> </spectrum_query> </msms_run_summary> </msms_pipeline_analysis> processing interact-qpg_qe_150529_16_is280_ief16.pep.xml... <parameter name="RT" value="3477.00"/> <parameter name="RT_score" value="1.00"/> </search_score_summary> </peptideprophet_result> </analysis_result> </search_hit> </search_result> </spectrum_query> </msms_run_summary> </msms_pipeline_analysis> processing interact-qpg_qe_150529_17_is280_ief17.pep.xml... <parameter name="RT" value="3444.99"/> <parameter name="RT_score" value="1.27"/> </search_score_summary> </peptideprophet_result> </analysis_result> </search_hit> </search_result> </spectrum_query> </msms_run_summary> </msms_pipeline_analysis> processing interact-qpg_qe_150529_18_is280_ief18.pep.xml... <parameter name="RT" value="4324.41"/> <parameter name="RT_score" value="-0.70"/> </search_score_summary> </peptideprophet_result> </analysis_result> </search_hit> </search_result> </spectrum_query> </msms_run_summary> </msms_pipeline_analysis> processing interact-qpg_qe_150529_19_is280_ief19.pep.xml... <parameter name="RT" value="4803.39"/> <parameter name="RT_score" value="-1.63"/> </search_score_summary> </peptideprophet_result> </analysis_result> </search_hit> </search_result> </spectrum_query> </msms_run_summary> </msms_pipeline_analysis> processing interact-qpg_qe_150529_20_is280_ief20.pep.xml... <parameter name="RT" value="4466.88"/> <parameter name="RT_score" value="-1.24"/> </search_score_summary> </peptideprophet_result> </analysis_result> </search_hit> </search_result> </spectrum_query> </msms_run_summary> </msms_pipeline_analysis> processing interact-qpg_qe_150529_21_is280_ief21.pep.xml... <parameter name="RT" value="3444.99"/> <parameter name="RT_score" value="1.52"/> </search_score_summary> </peptideprophet_result> </analysis_result> </search_hit> </search_result> </spectrum_query> </msms_run_summary> </msms_pipeline_analysis> processing interact-qpg_qe_150529_22_is280_ief22.pep.xml... <parameter name="RT" value="2135.93"/> <parameter name="RT_score" value="3.16"/> </search_score_summary> </peptideprophet_result> </analysis_result> </search_hit> </search_result> </spectrum_query> </msms_run_summary> </msms_pipeline_analysis> processing interact-qpg_qe_150529_23_is280_ief23.pep.xml... <parameter name="RT" value="2457.96"/> <parameter name="RT_score" value="2.23"/> </search_score_summary> </peptideprophet_result> </analysis_result> </search_hit> </search_result> </spectrum_query> </msms_run_summary> </msms_pipeline_analysis> processing interact-qpg_qe_150529_24_is280_ief24.pep.xml... <parameter name="RT" value="1956.88"/> <parameter name="RT_score" value="3.37"/> </search_score_summary> </peptideprophet_result> </analysis_result> </search_hit> </search_result> </spectrum_query> </msms_run_summary> </msms_pipeline_analysis>
