huiyinc
commented
4 years ago Hi Can you please share me your psm.tsv file? Thank you.
Huiyin
clin888 notifications@github.com 於 2020年5月22日 週五 下午4:53寫道：
I got empty output files except column header. please help. Thanks
---input command clin@gizmoj8:~/bin$ java -jar TMTIntegrator_v1.1.10.jar ../params/tmt-i_param_v1.1.10.yml ../psm/*_psm.tsv
--yaml file tmtintegrator: path: /new_test_052120/bin/TMTIntegrator_v1.1.10.jar # path to TMT-Integrator jar memory: 30 # memory allocation, in Gb protein_database: /new_test_052120/2020-05-21-decoys-contam-UP000005640_Human_120119.fasta # protein fasta file output: output_040620 # the location of output files channel_num: 11 # number of channels in the multiplex (e.g. 10, 11) ref_tag: Bridge_Sample_pool # unique tag for identifying the reference channel (Bridge sample added to each multiplex) groupby: -1 # level of data summarization(0: PSM aggregation to the gene level; 1: protein; 2: peptide sequence; 3: multiple PTM sites; 4: single PTM site; -1: generate reports at all levels) psm_norm: false # perform additional retention time-based normalization at the PSM level outlier_removal: true # perform outlier removal prot_norm: -1 # normalization (0: None; 1: MD (median centering); 2: GN (median centering + variance scaling); -1: generate reports with all normalization options) min_pep_prob: 0.9 # minimum PSM probability threshold (in addition to FDR-based filtering by Philosopher) min_purity: 0.5 # ion purity score threshold min_percent: 0.05 # remove low intensity PSMs (e.g. value of 0.05 indicates removal of PSMs with the summed TMT reporter ions intensity in the lowest 5% of all PSMs) unique_pep: false # allow PSMs with unique peptides only (if true) or unique plus razor peptides (if false), as classified by Philosopher and defined in PSM.tsv files unique_gene: 0 # additional, gene-level uniqueness filter (0: allow all PSMs; 1: remove PSMs mapping to more than one GENE with evidence of expression in the dataset; 2:remove all PSMs mapping to more than one GENE in the fasta file) best_psm: true # keep the best PSM only (highest summed TMT intensity) among all redundant PSMs within the same LC-MS run prot_exclude: none # exclude proteins with specified tags at the beginning of the accession number (e.g. none: no exclusion; sp|,tr| : exclude protein with sp| or tr|) allow_overlabel: true # allow PSMs with TMT on S (when overlabeling on S was allowed in the database search) allow_unlabeled: false # allow PSMs without TMT tag or acetylation on the peptide n-terminus mod_tag: none # PTM info for generation of PTM-specific reports (none: for Global data; S[167],T[181],Y[243]: for Phospho; K[170]: for K-Acetyl) min_site_prob: -1 # site localization confidence threshold (-1: for Global; 0: as determined by the search engine; above 0 (e.g. 0.75): PTMProphet probability, to be used with phosphorylation only) ms1_int: true # use MS1 precursor ion intensity (if true) or MS2 reference intensity (if false) as part of the reference sample abundance estimation top3_pep: true # use top 3 most intense peptide ions as part of the reference sample abundance estimation print_RefInt: false # print individual reference sample abundance estimates for each multiplex in the final reports (in addition to the combined reference sample abundance estimate) add_Ref: -1 # add an artificial reference channel if there is no reference channel or export raw abundance (-1: don't add the reference; 0: use summation as the reference; 1: use average as the reference; 2: use median as the reference; 3: export raw abundance) max_pep_prob_thres: 0 # the threshold for maximum peptide probability min_ntt: 0 # minimum allowed number of enzymatic termini --process UpdateColumns--- 1.77472 min. Start to process GroupBy=0_protNorm=0 LoadPsms--- 0.13982 min. Take log and normalize--- 0.65032 min. PSM normalization--- 0.00000 min. outlierRemoval--- 0.77623 min. Collapse--- 0.15132 min. protNorm--- 0.00000 min. Report--- 0.00242 min. Start to process GroupBy=0_protNorm=1 LoadPsms--- 0.12253 min. Take log and normalize--- 0.60372 min. PSM normalization--- 0.00000 min. outlierRemoval--- 0.80607 min. Collapse--- 0.15032 min. protNorm--- 0.00212 min. Report--- 0.00173 min. Start to process GroupBy=0_protNorm=2 LoadPsms--- 0.11977 min. Take log and normalize--- 0.64130 min. PSM normalization--- 0.00000 min. outlierRemoval--- 0.74962 min. Collapse--- 0.15168 min. protNorm--- 0.00387 min. Report--- 0.00185 min. Start to process GroupBy=1_protNorm=0 LoadPsms--- 0.12507 min. Take log and normalize--- 0.63535 min. PSM normalization--- 0.00000 min. outlierRemoval--- 0.77122 min. Collapse--- 0.13087 min. protNorm--- 0.00000 min. Report--- 0.00212 min. Start to process GroupBy=1_protNorm=1 LoadPsms--- 0.12343 min. Take log and normalize--- 0.62368 min. PSM normalization--- 0.00000 min. outlierRemoval--- 0.75733 min. Collapse--- 0.12618 min. protNorm--- 0.00155 min. Report--- 0.00175 min. Start to process GroupBy=1_protNorm=2 LoadPsms--- 0.12723 min. Take log and normalize--- 0.61918 min. PSM normalization--- 0.00000 min. outlierRemoval--- 0.77793 min. Collapse--- 0.12832 min. protNorm--- 0.00302 min. Report--- 0.00190 min. Start to process GroupBy=2_protNorm=0 LoadPsms--- 0.12068 min. Take log and normalize--- 0.64787 min. PSM normalization--- 0.00000 min. outlierRemoval--- 0.40338 min. Collapse--- 0.12495 min. protNorm--- 0.00000 min. Report--- 0.01012 min. Start to process GroupBy=2_protNorm=1 LoadPsms--- 0.12813 min. Take log and normalize--- 0.66542 min. PSM normalization--- 0.00000 min. outlierRemoval--- 0.41818 min. Collapse--- 0.12407 min. protNorm--- 0.02733 min. Report--- 0.01023 min. Start to process GroupBy=2_protNorm=2 LoadPsms--- 0.12267 min. Take log and normalize--- 0.64667 min. PSM normalization--- 0.00000 min. outlierRemoval--- 0.41577 min. Collapse--- 0.12855 min. protNorm--- 0.05318 min. Report--- 0.00832 min.
Finish!!!
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-- Hui-Yin Chang, 張彙音 Research Fellow Department of Pathology University of Michigan
clin888
I got empty output files except column header. please help. Thanks
---input command clin@gizmoj8:~/bin$ java -jar TMTIntegrator_v1.1.10.jar ../params/tmt-i_param_v1.1.10.yml ../psm/*_psm.tsv
--yaml file tmtintegrator: path: /new_test_052120/bin/TMTIntegrator_v1.1.10.jar # path to TMT-Integrator jar memory: 30 # memory allocation, in Gb protein_database: /new_test_052120/2020-05-21-decoys-contam-UP000005640_Human_120119.fasta # protein fasta file output: output_040620 # the location of output files channel_num: 11 # number of channels in the multiplex (e.g. 10, 11) ref_tag: Bridge_Sample_pool # unique tag for identifying the reference channel (Bridge sample added to each multiplex) groupby: -1 # level of data summarization(0: PSM aggregation to the gene level; 1: protein; 2: peptide sequence; 3: multiple PTM sites; 4: single PTM site; -1: generate reports at all levels) psm_norm: false # perform additional retention time-based normalization at the PSM level outlier_removal: true # perform outlier removal prot_norm: -1 # normalization (0: None; 1: MD (median centering); 2: GN (median centering + variance scaling); -1: generate reports with all normalization options) min_pep_prob: 0.9 # minimum PSM probability threshold (in addition to FDR-based filtering by Philosopher) min_purity: 0.5 # ion purity score threshold min_percent: 0.05 # remove low intensity PSMs (e.g. value of 0.05 indicates removal of PSMs with the summed TMT reporter ions intensity in the lowest 5% of all PSMs) unique_pep: false # allow PSMs with unique peptides only (if true) or unique plus razor peptides (if false), as classified by Philosopher and defined in PSM.tsv files unique_gene: 0 # additional, gene-level uniqueness filter (0: allow all PSMs; 1: remove PSMs mapping to more than one GENE with evidence of expression in the dataset; 2:remove all PSMs mapping to more than one GENE in the fasta file) best_psm: true # keep the best PSM only (highest summed TMT intensity) among all redundant PSMs within the same LC-MS run prot_exclude: none # exclude proteins with specified tags at the beginning of the accession number (e.g. none: no exclusion; sp|,tr| : exclude protein with sp| or tr|) allow_overlabel: true # allow PSMs with TMT on S (when overlabeling on S was allowed in the database search) allow_unlabeled: false # allow PSMs without TMT tag or acetylation on the peptide n-terminus mod_tag: none # PTM info for generation of PTM-specific reports (none: for Global data; S[167],T[181],Y[243]: for Phospho; K[170]: for K-Acetyl) min_site_prob: -1 # site localization confidence threshold (-1: for Global; 0: as determined by the search engine; above 0 (e.g. 0.75): PTMProphet probability, to be used with phosphorylation only) ms1_int: true # use MS1 precursor ion intensity (if true) or MS2 reference intensity (if false) as part of the reference sample abundance estimation top3_pep: true # use top 3 most intense peptide ions as part of the reference sample abundance estimation print_RefInt: false # print individual reference sample abundance estimates for each multiplex in the final reports (in addition to the combined reference sample abundance estimate) add_Ref: -1 # add an artificial reference channel if there is no reference channel or export raw abundance (-1: don't add the reference; 0: use summation as the reference; 1: use average as the reference; 2: use median as the reference; 3: export raw abundance) max_pep_prob_thres: 0 # the threshold for maximum peptide probability min_ntt: 0 # minimum allowed number of enzymatic termini
--process UpdateColumns--- 1.77472 min. Start to process GroupBy=0_protNorm=0 LoadPsms--- 0.13982 min. Take log and normalize--- 0.65032 min. PSM normalization--- 0.00000 min. outlierRemoval--- 0.77623 min. Collapse--- 0.15132 min. protNorm--- 0.00000 min. Report--- 0.00242 min.
Start to process GroupBy=0_protNorm=1 LoadPsms--- 0.12253 min. Take log and normalize--- 0.60372 min. PSM normalization--- 0.00000 min. outlierRemoval--- 0.80607 min. Collapse--- 0.15032 min. protNorm--- 0.00212 min. Report--- 0.00173 min.
Start to process GroupBy=0_protNorm=2 LoadPsms--- 0.11977 min. Take log and normalize--- 0.64130 min. PSM normalization--- 0.00000 min. outlierRemoval--- 0.74962 min. Collapse--- 0.15168 min. protNorm--- 0.00387 min. Report--- 0.00185 min.
Start to process GroupBy=1_protNorm=0 LoadPsms--- 0.12507 min. Take log and normalize--- 0.63535 min. PSM normalization--- 0.00000 min. outlierRemoval--- 0.77122 min. Collapse--- 0.13087 min. protNorm--- 0.00000 min. Report--- 0.00212 min.
Start to process GroupBy=1_protNorm=1 LoadPsms--- 0.12343 min. Take log and normalize--- 0.62368 min. PSM normalization--- 0.00000 min. outlierRemoval--- 0.75733 min. Collapse--- 0.12618 min. protNorm--- 0.00155 min. Report--- 0.00175 min.
Start to process GroupBy=1_protNorm=2 LoadPsms--- 0.12723 min. Take log and normalize--- 0.61918 min. PSM normalization--- 0.00000 min. outlierRemoval--- 0.77793 min. Collapse--- 0.12832 min. protNorm--- 0.00302 min. Report--- 0.00190 min.
Start to process GroupBy=2_protNorm=0 LoadPsms--- 0.12068 min. Take log and normalize--- 0.64787 min. PSM normalization--- 0.00000 min. outlierRemoval--- 0.40338 min. Collapse--- 0.12495 min. protNorm--- 0.00000 min. Report--- 0.01012 min.
Start to process GroupBy=2_protNorm=1 LoadPsms--- 0.12813 min. Take log and normalize--- 0.66542 min. PSM normalization--- 0.00000 min. outlierRemoval--- 0.41818 min. Collapse--- 0.12407 min. protNorm--- 0.02733 min. Report--- 0.01023 min.
Start to process GroupBy=2_protNorm=2 LoadPsms--- 0.12267 min. Take log and normalize--- 0.64667 min. PSM normalization--- 0.00000 min. outlierRemoval--- 0.41577 min. Collapse--- 0.12855 min. protNorm--- 0.05318 min. Report--- 0.00832 min.
Finish!!!