Ecosyste.ms: Issues

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GitHub / Nesvilab/philosopher issues and pull requests

#494 - Philosopher crashes with large pep.xml

Issue - State: open - Opened by BernhardRetzl about 1 month ago

#492 - 'PhilosopherFilter' finished, exit code: 1

Issue - State: closed - Opened by Patrick-W1345 2 months ago - 11 comments

#491 - FragPipe 20.0 is not compatible with Philosopher 5.1.0

Issue - State: closed - Opened by ndtivendale 2 months ago - 2 comments

#486 - Missing protein coverage column

Issue - State: open - Opened by lyons89 4 months ago

#485 - Philosopher: Cannot read file. Error parsing the file.

Issue - State: open - Opened by WenSheng-Ye 4 months ago - 4 comments

#482 - FragPipe 19.1 is not compatible with Philosopher 5.1.0

Issue - State: closed - Opened by WenSheng-Ye 6 months ago - 1 comment

#478 - PhilosopherAbacus exit code: 1 when using split database

Issue - State: closed - Opened by yannic-chen 7 months ago - 8 comments

#475 - peptide prophet xml parsing error

Issue - State: closed - Opened by mremachine1 7 months ago - 5 comments

#474 - Format error in combined_protein.tsv when MS1 quant is disabled

Issue - State: open - Opened by hollenstein 8 months ago - 1 comment

#472 - Cannot read file/Error parsing the file

Issue - State: closed - Opened by WenSheng-Ye 8 months ago - 6 comments

#470 - Fix a crash when there are no non-zero TMT intensities and removelow …

Pull Request - State: closed - Opened by fcyu 8 months ago - 1 comment

#469 - Error opening a temp file

Issue - State: closed - Opened by Maithy15 9 months ago - 1 comment

#467 - Spaces in the path of the tool broke FragPipe

Issue - State: closed - Opened by mbimegan 9 months ago - 8 comments

#466 - Bump golang.org/x/net from 0.8.0 to 0.17.0

Pull Request - State: closed - Opened by dependabot[bot] 9 months ago - 1 comment
Labels: dependencies

#465 - an error with Proteinprophet

Issue - State: closed - Opened by xyzcc2007 9 months ago - 2 comments

#464 - FDR ISSUE

Issue - State: open - Opened by kwynne71 10 months ago - 2 comments

#463 - Fatal error: all goroutines are asleep - deadlock! during the filter command

Issue - State: closed - Opened by mart5176 10 months ago - 3 comments

#462 - add IBT-16 isobaric tag

Pull Request - State: closed - Opened by dpolasky 10 months ago

#461 - Error running FAIMS data

Issue - State: closed - Opened by mikmoux 10 months ago - 1 comment

#458 - Parsing of custom databases

Issue - State: closed - Opened by magnusarntzen 10 months ago - 2 comments

#457 - 32 plex support for labelquant

Pull Request - State: closed - Opened by dpolasky 10 months ago

#454 - Error in PhilosopherFilter - exit code: 1

Issue - State: closed - Opened by helloworld1631 11 months ago - 8 comments

#450 - Missing Intensity values in msstats.csv TMT channel columns

Issue - State: closed - Opened by Monod79 12 months ago - 14 comments

#449 - Philsopher filter error: cannot find .meta\pep.bin

Issue - State: closed - Opened by ndtivendale almost 1 year ago - 1 comment

#446 - Philosopher v5.0 gives errors

Issue - State: closed - Opened by jasminesmn about 1 year ago - 4 comments

#444 - ProteinProphet batchconvert not recognized

Issue - State: closed - Opened by BrendonSeale about 1 year ago - 8 comments

#442 - fix #441

Pull Request - State: closed - Opened by guoci about 1 year ago

#440 - Wrong matching of protein_id

Issue - State: closed - Opened by She1111 about 1 year ago - 12 comments

#439 - FrapPipe v20.0 Processing interrupted, stopping MSFragger

Issue - State: closed - Opened by SamueldelaCamaraFuentes about 1 year ago - 1 comment

#438 - Philosopher error: Cannot read file

Issue - State: closed - Opened by SamueldelaCamaraFuentes about 1 year ago - 3 comments

#437 - Problem installing philosopher for Fragpipe 20.0

Issue - State: closed - Opened by tobimaile about 1 year ago - 8 comments

#436 - Error in the PhilosopherFilter step

Issue - State: closed - Opened by helloworld1631 about 1 year ago - 4 comments

#435 - Non-English characters in the folder name break ProteinProphet

Issue - State: closed - Opened by hongweizhao1 about 1 year ago - 2 comments

#434 - Non-English characters in the folder name break ProteinProphet

Issue - State: closed - Opened by hongweizhao1 about 1 year ago - 3 comments

#433 - Philosopher - non-zero exit code

Issue - State: closed - Opened by brunoalex7 about 1 year ago - 5 comments

#432 - fix bug introduced in 0f80898 for xtag masses

Pull Request - State: closed - Opened by dpolasky about 1 year ago - 1 comment

#430 - Adjust `I` and `L` in the psm.tsv, peptide.tsv, and ion.tsv after razor assignment

Issue - State: open - Opened by fcyu over 2 years ago - 11 comments

#428 - allow skipping of protxml parsing

Pull Request - State: closed - Opened by guoci over 1 year ago

#426 - fix threading bug

Pull Request - State: closed - Opened by guoci over 1 year ago

#425 - contaminant peptide in my result

Issue - State: closed - Opened by qianqli over 1 year ago - 3 comments
Labels: help wanted

#424 - Optimize db annotate

Pull Request - State: closed - Opened by guoci over 1 year ago

#422 - optimize IO for speed and size

Pull Request - State: closed - Opened by guoci over 1 year ago

#421 - E2e70

Pull Request - State: closed - Opened by prvst over 1 year ago

#420 - updating changelog

Pull Request - State: closed - Opened by prvst over 1 year ago

#419 - Bump golang.org/x/net from 0.4.0 to 0.7.0

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago
Labels: dependencies

#418 - Optimize round 2 `filter`

Pull Request - State: closed - Opened by guoci over 1 year ago - 1 comment
Labels: enhancement, on hold

#417 - Bump golang.org/x/image from 0.2.0 to 0.5.0

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago
Labels: dependencies

#416 - parallelize report

Pull Request - State: closed - Opened by guoci over 1 year ago - 1 comment
Labels: enhancement

#415 - Allow external tuning of Go runtime

Pull Request - State: closed - Opened by guoci over 1 year ago - 3 comments
Labels: enhancement

#412 - Error: Cannot decode packed binary. strconv.ParseInt: parsing "63781": value out of range

Issue - State: closed - Opened by ArthurViode over 1 year ago - 8 comments
Labels: help wanted

#411 - panic: runtime error: index out of range [1] with length 1

Issue - State: closed - Opened by Hereje-CL over 1 year ago - 10 comments

#410 - Philosopher 4.8.1: there are decoy proteins in the `protein` column of `psm.tsv`

Issue - State: closed - Opened by fcyu over 1 year ago - 1 comment

#409 - I/L corrected peptides are not present in the reports.

Issue - State: closed - Opened by fcyu over 1 year ago - 2 comments

#408 - Philosopher does not write the position info to peptide.tsv and ion.tsv in a workflow without Quant

Issue - State: closed - Opened by glycohezhu over 1 year ago - 4 comments
Labels: enhancement

#407 - Philosopher does not allow certain characters in Gene names

Issue - State: closed - Opened by fstein over 1 year ago - 2 comments
Labels: enhancement

#406 - Dev

Pull Request - State: closed - Opened by prvst over 1 year ago

#405 - Philosopher 4.8.1-rc1: some PSMs' protein starts and ends are not correct

Issue - State: closed - Opened by fcyu over 1 year ago - 1 comment

#403 - Dev

Pull Request - State: closed - Opened by prvst over 1 year ago

#402 - philosopher report nothing

Issue - State: closed - Opened by fcgportal over 1 year ago - 1 comment

#400 - Dev

Pull Request - State: closed - Opened by prvst over 1 year ago

#399 - fix https://github.com/Nesvilab/FragPipe/issues/878

Pull Request - State: closed - Opened by guoci over 1 year ago

#398 - Cannot decode packed binary. strconv.ParseUint: parsing "66601": value out of range

Issue - State: closed - Opened by ArthurViode over 1 year ago - 5 comments
Labels: enhancement

#396 - MSFragger open search for TMT data

Issue - State: closed - Opened by Yonghao-Holden over 1 year ago - 2 comments

#394 - Dev

Pull Request - State: closed - Opened by prvst over 1 year ago

#392 - Can't download Philosopher

Issue - State: closed - Opened by ZhangXiangye over 1 year ago - 1 comment
Labels: help wanted

#390 - Importing TMTIntegrator parameter file

Issue - State: closed - Opened by Yonghao-Holden over 1 year ago - 4 comments
Labels: help wanted

#389 - Invalid or corrupt jarfile

Issue - State: closed - Opened by Yonghao-Holden over 1 year ago - 2 comments
Labels: help wanted

#388 - panic: runtime error: index out of range [2] with length 0

Issue - State: closed - Opened by tobiasko over 1 year ago - 1 comment

#387 - Cannot decode packed binary

Issue - State: closed - Opened by ndtivendale over 1 year ago - 14 comments
Labels: help wanted

#386 - philosopher pipeline error at the step "Running TMT-Integrator"

Issue - State: closed - Opened by JasonYJWei over 1 year ago - 19 comments
Labels: help wanted

#385 - Parameter setting

Issue - State: closed - Opened by JasonYJWei over 1 year ago - 6 comments
Labels: help wanted

#384 - Fix division by zero in Purity calculation

Pull Request - State: closed - Opened by chhh over 1 year ago - 1 comment

#381 - problem DDA based generating library on MSFragger

Issue - State: closed - Opened by Caesaryears almost 2 years ago - 2 comments

#377 - Remove --raw flag since Philosopher does not support Thermo raw format

Issue - State: closed - Opened by fcyu almost 2 years ago - 3 comments

#375 - `philosopher-v4.5.1-RC5 database --id UP000299084,UP000504605,UP000030684` does not work anymore

Issue - State: closed - Opened by cpanse almost 2 years ago - 2 comments
Labels: bug

#374 - ${PHILOSOPHER} database --custom and --add option do not work

Issue - State: closed - Opened by cpanse almost 2 years ago - 1 comment

#373 - Dev

Pull Request - State: closed - Opened by prvst almost 2 years ago

#372 - "panic: Cannot execute program. there was an error with PeptideProphet"

Issue - State: closed - Opened by jossmi almost 2 years ago - 2 comments
Labels: help wanted