Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
GitHub / Nesvilab/philosopher issues and pull requests
#496 - troubles with generating Philosopher report .meta/pep.bin
Issue -
State: open - Opened by nissrine895 about 1 month ago
#495 - Help with understanding where files are written during the creation of combined.prot.xml
Issue -
State: open - Opened by Patrick-L-White about 1 month ago
#494 - Philosopher crashes with large pep.xml
Issue -
State: open - Opened by BernhardRetzl about 1 month ago
#493 - ERRO[11:53:33] the protein FDR filter didn't reach the desired threshold, try a higher threshold using the --prot parameter
Issue -
State: open - Opened by Luc2702 about 2 months 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
#487 - Failed Mass offset search for PAL (without PTMProphet): PeptideProphet Error Message
Issue -
State: open - Opened by chaudngo 4 months ago
#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
#481 - Philosopher 5.1.0 filter command crashed: Cannot read file. Error parsing the file
Issue -
State: closed - Opened by WeiqiangChen 7 months ago
- 7 comments
#480 - protein start and end positions not showing in combined peptides report.
Issue -
State: open - Opened by heuselm 7 months ago
- 1 comment
#479 - PTMProphet: command "chmod 664 interact-2023_01_15_ExplorisFAIMS45_55_65_Cornett_F4.mod.pep.xml" failed: Unknown error caused corrupted pep.xml and mod.pep.xml files
Issue -
State: closed - Opened by caberryhill 7 months ago
- 11 comments
#478 - PhilosopherAbacus exit code: 1 when using split database
Issue -
State: closed - Opened by yannic-chen 7 months ago
- 8 comments
#476 - fatal error: all goroutines are asleep - deadlock! in PhilosopherFilter despite threads=8
Issue -
State: closed - Opened by vicpaton 7 months ago
- 3 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
#468 - 'chmod' is not recognized as an internal or external command, operable program or batch file.
Issue -
State: closed - Opened by Maithy15 9 months ago
- 2 comments
#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
#460 - ERRO[15:34:38] Cannot read file. open .meta\db.bin: The system cannot find the file specified. Process 'PhilosopherFilter' finished, exit code: 1
Issue -
State: closed - Opened by RMeelker 10 months ago
- 5 comments
#459 - when using the iTRAQ8.workflow in FragPipe v20.0, the log shows that the analysis finished successfully, but the output matrix only includes titles without quantification results
Issue -
State: closed - Opened by qianliujia 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
#456 - Annotating the database panic: runtime error: index out of range [2] with length 1
Issue -
State: closed - Opened by jayieh 11 months ago
- 3 comments
#455 - Cannot read file. open .meta\pep.bin: The system cannot find the file specified. Cannot read file. open .meta\db.bin: The system cannot find the file specified.
Issue -
State: closed - Opened by manushiparajuli 11 months ago
- 1 comment
#454 - Error in PhilosopherFilter - exit code: 1
Issue -
State: closed - Opened by helloworld1631 11 months ago
- 8 comments
#452 - Remove the warning `Cannot read file. open .meta\meta.bin: The system cannot find the path specified.` in the `workspace --clean` command
Issue -
State: closed - Opened by fcyu 12 months ago
- 1 comment
#451 - Custom fasta database result in Philosopher: panic: runtime error: index out of range [1] with length 1
Issue -
State: closed - Opened by yannic-chen over 1 year ago
- 14 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
#448 - Feature request: Add Indistinguishable Proteins column also to psm, ion and peptide tables
Issue -
State: open - Opened by hollenstein almost 2 years ago
Labels: enhancement
#447 - Let Philosopher print errors when there are protein hits from PSMs that cannot be found in the fasta file.
Issue -
State: open - Opened by fcyu over 2 years 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
#441 - fatal error: all goroutines are asleep - deadlock! & Process 'PhilosopherFilter' finished, exit code: 2
Issue -
State: closed - Opened by MelissaVorster about 1 year ago
- 4 comments
#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
#429 - `prot.xml` was written to the temp directory but not the result directory, which resulted in the incomplete file and crashed the filter command
Issue -
State: closed - Opened by ohickl over 1 year 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
#404 - Philosopher 4.8.0, there are proteins having incorrect `protein ID`, `entry name`, `gene`, and `protein description`
Issue -
State: closed - Opened by fcyu over 1 year ago
- 2 comments
#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
#397 - labelquant duplicates TMT quantification for some channels for TMT11 in protein.tsv output
Issue -
State: closed - Opened by fstein over 1 year ago
- 5 comments
#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
#378 - philosopher-v4.5.1-RC5 seems to break tmt-integrator-3.3.3.jar and TMTIntegrator_v4.0.1.jar
Issue -
State: closed - Opened by cpanse 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