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problem with analysis in linux #87

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ofleitas opened this issue Jan 17, 2025 · 1 comment
Open

problem with analysis in linux #87

ofleitas opened this issue Jan 17, 2025 · 1 comment

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@ofleitas
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ofleitas commented Jan 17, 2025 •
edited by wenbostar
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Hello

I am trying to run pepquery in linux but it did not work for me. I ran successfully the same analysis in windows .

This is my free memory

(base) ofm@ofm-Nitro-AN515-58:~$ free --giga
               total        used        free      shared  buff/cache   available
Mem:              12           2           9           0           0           9
Swap:              4           1           2


The output when I try to run in linux is this:

(base) ofm@ofm-Nitro-AN515-58:~$ java -Xmx16G -jar /home/ofm/Documents/Programs/pepquery-2.0.2/pepquery-2.0.2.jar -b a -db swissprot:human -hc -o pepquery/ -s 1 -i MFLCFQMLKLLLSTPWAPSSAELKNLLLCFLLFLLNQYLFGNNFKLTDNI -t protein 
2025-01-17 08:30:55 [INFO ] main.java.util.CParameterSet[load_default_parameter_sets:146] - Load 12 parameter sets.
2025-01-17 08:30:55 [INFO ] main.java.util.MSDataSet[load_default_datasets:147] - Load 48 MS/MS datasets.
2025-01-17 08:30:55 [INFO ] main.java.pg.PeptideSearchMT[main:180] - The number of MS/MS datasets selected: 5, CPTAC_Prospective_Breast_BI_Acetylome_PDC000239,CPTAC_UCEC_Discovery_Study_Acetylome_PDC000226,CPTAC_LUAD_Discovery_Study_Acetylome_PDC000224,CPTAC_GBM_Discovery_Study_Acetylome_PDC000245,CPTAC_LSCC_Discovery_Study_Acetylome_PDC000233
2025-01-17 08:30:55 [INFO ] main.java.pg.PeptideSearchMT[search_multiple_datasets:732] - Searching MS/MS dataset: CPTAC_Prospective_Breast_BI_Acetylome_PDC000239. 4 left, 0 finished.
2025-01-17 08:30:55 [INFO ] main.java.download.FileDownload[download_single_file:523] - Download file ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/reference_proteomes/Eukaryota/UP000005640/UP000005640_9606.fasta.gz to pepquery//database/UP000005640_9606.fasta.gz
2025-01-17 08:30:58 [INFO ] main.java.download.FileDownload[download_single_file:531] - Download file ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/reference_proteomes/Eukaryota/UP000005640/UP000005640_9606.fasta.gz to pepquery//database/UP000005640_9606.fasta.gz done
2025-01-17 08:30:59 [INFO ] main.java.pg.CParameter[updateCParameter:846] - Task type: novel protein identification
2025-01-17 08:30:59 [INFO ] uk.ac.ebi.pride.utilities.pridemod.io.unimod.xml.unmarshaller.UnimodUnmarshallerFactory[initializeUnmarshaller:41] - Unmarshaller Initialized
2025-01-17 08:30:59 [INFO ] main.java.OpenModificationSearch.ModificationDB[importPTMsFromUnimod:355] - All modifications in unimod:1375
2025-01-17 08:30:59 [INFO ] main.java.pg.PeptideSearchMT[search:243] - Start analysis
#############################################
PepQuery parameter:
2025-01-17 08:30:59 [INFO ] main.java.pg.DatabaseInput[getEnzymeByIndex:263] - Use enzyme:Trypsin
PepQuery version: 2.0.2
PepQuery command line: -b a -db swissprot:human -hc -o pepquery/ -s 1 -i MFLCFQMLKLLLSTPWAPSSAELKNLLLCFLLFLLNQYLFGNNFKLTDNI -t protein
Fixed modification: 1,11,12 = Carbamidomethylation of C,TMT 10-plex of K,TMT 10-plex of peptide N-term
Variable modification: 2,6 = Oxidation of M,Acetylation of K
Max allowed variable modification: 3
Add AA substitution: false
Enzyme: 1 = Trypsin
Max Missed cleavages: 2
Precursor mass tolerance: 20.0
Range of allowed isotope peak errors: 0
Precursor ion mass tolerance unit: ppm
Fragment ion mass tolerance: 0.05
Fragment ion mass tolerance unit: Da
Scoring algorithm: 1 = Hyperscore
Min score: 12.0
Min peaks: 10
Min peptide length: 7
Max peptide length: 45
Min peptide mass: 500.0
Max peptide mass: 10000.0
Random peptide number: 10000
Fast mode: false
CPU: 16
#############################################
2025-01-17 08:30:59 [INFO ] main.java.pg.PeptideSearchMT[search:250] - Spectrum ID type:1, use 1-based number as index for a spectrum.
2025-01-17 08:30:59 [INFO ] main.java.pg.PeptideSearchMT[search:253] - Step 1: target peptide sequence preparation and initial filtering ...
2025-01-17 08:30:59 [INFO ] main.java.pg.InputProcessor[run:157] - The input is a protein sequence.
2025-01-17 08:30:59 [INFO ] main.java.pg.DatabaseInput[getEnzymeByIndex:263] - Use enzyme:Trypsin
2025-01-17 08:30:59 [INFO ] main.java.pg.InputProcessor[digest:272] - The number of protein sequences:1
2025-01-17 08:30:59 [INFO ] main.java.pg.InputProcessor[run:171] - Peptides:8
2025-01-17 08:30:59 [INFO ] main.java.pg.InputProcessor[searchRefDB:413] - Don't find indexed database:pepquery//database/UP000005640_9606.fasta.sqldb
2025-01-17 08:30:59 [INFO ] main.java.pg.InputProcessor[searchRefDB:414] - Use database:pepquery//database/UP000005640_9606.fasta
2025-01-17 08:30:59 [INFO ] main.java.pg.PepMapping[init:62] - Load db file: pepquery//database/UP000005640_9606.fasta
2025-01-17 08:30:59 [INFO ] main.java.pg.PepMapping[init:78] - Start indexing fasta file
2025-01-17 08:31:00 [INFO ] main.java.pg.PepMapping[init:88] - Indexing took 0.352294418 seconds and consumes 31.183676 MB
2025-01-17 08:31:00 [INFO ] main.java.pg.InputProcessor[run:178] - MFLCFQMLK is not exist in the reference protein database.
2025-01-17 08:31:00 [INFO ] main.java.pg.InputProcessor[run:178] - LLLSTPWAPSSAELK is not exist in the reference protein database.
2025-01-17 08:31:00 [INFO ] main.java.pg.InputProcessor[run:178] - MFLCFQMLKLLLSTPWAPSSAELK is not exist in the reference protein database.
2025-01-17 08:31:00 [INFO ] main.java.pg.InputProcessor[run:178] - NLLLCFLLFLLNQYLFGNNFK is not exist in the reference protein database.
2025-01-17 08:31:00 [INFO ] main.java.pg.InputProcessor[run:178] - MFLCFQMLKLLLSTPWAPSSAELKNLLLCFLLFLLNQYLFGNNFK is not exist in the reference protein database.
2025-01-17 08:31:00 [INFO ] main.java.pg.InputProcessor[run:178] - LLLSTPWAPSSAELKNLLLCFLLFLLNQYLFGNNFK is not exist in the reference protein database.
2025-01-17 08:31:00 [INFO ] main.java.pg.InputProcessor[run:178] - NLLLCFLLFLLNQYLFGNNFKLTDNI is not exist in the reference protein database.
2025-01-17 08:31:00 [INFO ] main.java.pg.InputProcessor[run:178] - LLLSTPWAPSSAELKNLLLCFLLFLLNQYLFGNNFKLTDNI is not exist in the reference protein database.
2025-01-17 08:31:00 [INFO ] main.java.pg.PeptideSearchMT[search:395] - Total target peptides:8, unique peptides:8, shared peptides:0
2025-01-17 08:31:00 [INFO ] main.java.pg.PeptideSearchMT[search:407] - Valid target peptides: 8
2025-01-17 08:31:00 [INFO ] main.java.pg.PeptideSearchMT[generatePeptideInputs:1330] - Generate peptide objects ...
2025-01-17 08:31:00 [INFO ] main.java.pg.PeptideSearchMT[generatePeptideInputs:1341] - CPU: 8
2025-01-17 08:31:00 [INFO ] main.java.pg.PeptideSearchMT[generatePeptideInputs:1359] - Generate peptide objects done.
2025-01-17 08:31:00 [INFO ] main.java.pg.PeptideSearchMT[search:413] - Step 1: target peptide sequence preparation and initial filtering done: time elapsed = 0.11 min
2025-01-17 08:31:00 [INFO ] main.java.pg.PeptideSearchMT[search:418] - Step 2: candidate spectra retrieval and PSM scoring ...
2025-01-17 08:31:01 [INFO ] main.java.msio.MsdataMatch[get_all_indexed_ms_file:87] - Used CPUs: 16
2025-01-17 08:31:01 [INFO ] main.java.msio.MsdataMatch[get_all_indexed_ms_file:88] - Download 90 index MS/MS files ...
2025-01-17 08:31:03 [WARN ] main.java.msio.IndexFileDownloadWorker[download:35] - s3://zhanglab-pepquery/msms_library/Prospective_Breast_BI_Acetylome_PDC000239/63446.mgf doesn't exist
2025-01-17 08:31:03 [WARN ] main.java.msio.IndexFileDownloadWorker[download:35] - s3://zhanglab-pepquery/msms_library/Prospective_Breast_BI_Acetylome_PDC000239/57512.mgf doesn't exist
2025-01-17 08:31:03 [WARN ] main.java.msio.IndexFileDownloadWorker[download:35] - s3://zhanglab-pepquery/msms_library/Prospective_Breast_BI_Acetylome_PDC000239/63284.mgf doesn't exist
2025-01-17 08:31:03 [WARN ] main.java.msio.IndexFileDownloadWorker[download:35] - s3://zhanglab-pepquery/msms_library/Prospective_Breast_BI_Acetylome_PDC000239/63445.mgf doesn't exist
2025-01-17 08:31:04 [WARN ] main.java.msio.IndexFileDownloadWorker[download:35] - s3://zhanglab-pepquery/msms_library/Prospective_Breast_BI_Acetylome_PDC000239/61252.mgf doesn't exist
2025-01-17 08:31:04 [WARN ] main.java.msio.IndexFileDownloadWorker[download:35] - s3://zhanglab-pepquery/msms_library/Prospective_Breast_BI_Acetylome_PDC000239/61413.mgf doesn't exist
2025-01-17 08:31:04 [WARN ] main.java.msio.IndexFileDownloadWorker[download:35] - s3://zhanglab-pepquery/msms_library/Prospective_Breast_BI_Acetylome_PDC000239/59383.mgf doesn't exist
2025-01-17 08:31:05 [WARN ] main.java.msio.IndexFileDownloadWorker[download:35] - s3://zhanglab-pepquery/msms_library/Prospective_Breast_BI_Acetylome_PDC000239/61412.mgf doesn't exist
2025-01-17 08:31:05 [WARN ] main.java.msio.IndexFileDownloadWorker[download:35] - s3://zhanglab-pepquery/msms_library/Prospective_Breast_BI_Acetylome_PDC000239/61253.mgf doesn't exist
2025-01-17 08:31:05 [WARN ] main.java.msio.IndexFileDownloadWorker[download:35] - s3://zhanglab-pepquery/msms_library/Prospective_Breast_BI_Acetylome_PDC000239/63124.mgf doesn't exist
2025-01-17 08:31:05 [WARN ] main.java.msio.IndexFileDownloadWorker[download:35] - s3://zhanglab-pepquery/msms_library/Prospective_Breast_BI_Acetylome_PDC000239/61572.mgf doesn't exist
2025-01-17 08:31:05 [WARN ] main.java.msio.IndexFileDownloadWorker[download:35] - s3://zhanglab-pepquery/msms_library/Prospective_Breast_BI_Acetylome_PDC000239/61573.mgf doesn't exist
2025-01-17 08:31:05 [WARN ] main.java.msio.IndexFileDownloadWorker[download:35] - s3://zhanglab-pepquery/msms_library/Prospective_Breast_BI_Acetylome_PDC000239/59381.mgf doesn't exist
2025-01-17 08:31:05 [WARN ] main.java.msio.IndexFileDownloadWorker[download:35] - s3://zhanglab-pepquery/msms_library/Prospective_Breast_BI_Acetylome_PDC000239/59542.mgf doesn't exist
2025-01-17 08:31:05 [WARN ] main.java.msio.IndexFileDownloadWorker[download:35] - s3://zhanglab-pepquery/msms_library/Prospective_Breast_BI_Acetylome_PDC000239/59541.mgf doesn't exist
2025-01-17 08:31:05 [WARN ] main.java.msio.IndexFileDownloadWorker[download:35] - s3://zhanglab-pepquery/msms_library/Prospective_Breast_BI_Acetylome_PDC000239/54410.mgf doesn't exist
2025-01-17 08:31:06 [WARN ] main.java.msio.IndexFileDownloadWorker[download:35] - s3://zhanglab-pepquery/msms_library/Prospective_Breast_BI_Acetylome_PDC000239/59382.mgf doesn't exist
2025-01-17 08:31:06 [WARN ] main.java.msio.IndexFileDownloadWorker[download:35] - s3://zhanglab-pepquery/msms_library/Prospective_Breast_BI_Acetylome_PDC000239/61414.mgf doesn't exist
2025-01-17 08:31:06 [WARN ] main.java.msio.IndexFileDownloadWorker[download:35] - s3://zhanglab-pepquery/msms_library/Prospective_Breast_BI_Acetylome_PDC000239/61415.mgf doesn't exist
2025-01-17 08:31:06 [WARN ] main.java.msio.IndexFileDownloadWorker[download:35] - s3://zhanglab-pepquery/msms_library/Prospective_Breast_BI_Acetylome_PDC000239/54411.mgf doesn't exist
2025-01-17 08:31:06 [WARN ] main.java.msio.IndexFileDownloadWorker[download:35] - s3://zhanglab-pepquery/msms_library/Prospective_Breast_BI_Acetylome_PDC000239/61575.mgf doesn't exist
2025-01-17 08:31:06 [WARN ] main.java.msio.IndexFileDownloadWorker[download:35] - s3://zhanglab-pepquery/msms_library/Prospective_Breast_BI_Acetylome_PDC000239/63286.mgf doesn't exist
2025-01-17 08:31:07 [WARN ] main.java.msio.IndexFileDownloadWorker[download:35] - s3://zhanglab-pepquery/msms_library/Prospective_Breast_BI_Acetylome_PDC000239/57511.mgf doesn't exist
2025-01-17 08:31:08 [INFO ] main.java.pg.SpectraInput[readSpectraFromMSMSlibrary:371] - Used CPUs: 8
2025-01-17 08:31:08 [WARN ] main.java.msio.MsLibrarySearchWorker[loadSpectra:201] - File doesn't exist:pepquery//CPTAC_Prospective_Breast_BI_Acetylome_PDC000239/index/61572.mgf
2025-01-17 08:31:08 [WARN ] main.java.msio.MsLibrarySearchWorker[loadSpectra:201] - File doesn't exist:pepquery//CPTAC_Prospective_Breast_BI_Acetylome_PDC000239/index/61573.mgf
2025-01-17 08:31:08 [WARN ] main.java.msio.MsLibrarySearchWorker[loadSpectra:201] - File doesn't exist:pepquery//CPTAC_Prospective_Breast_BI_Acetylome_PDC000239/index/61575.mgf
2025-01-17 08:31:08 [WARN ] main.java.msio.MsLibrarySearchWorker[loadSpectra:201] - File doesn't exist:pepquery//CPTAC_Prospective_Breast_BI_Acetylome_PDC000239/index/54410.mgf
2025-01-17 08:31:08 [WARN ] main.java.msio.MsLibrarySearchWorker[loadSpectra:201] - File doesn't exist:pepquery//CPTAC_Prospective_Breast_BI_Acetylome_PDC000239/index/54411.mgf
2025-01-17 08:31:08 [WARN ] main.java.msio.MsLibrarySearchWorker[loadSpectra:201] - File doesn't exist:pepquery//CPTAC_Prospective_Breast_BI_Acetylome_PDC000239/index/61252.mgf
2025-01-17 08:31:08 [WARN ] main.java.msio.MsLibrarySearchWorker[loadSpectra:201] - File doesn't exist:pepquery//CPTAC_Prospective_Breast_BI_Acetylome_PDC000239/index/61253.mgf
2025-01-17 08:31:08 [WARN ] main.java.msio.MsLibrarySearchWorker[loadSpectra:201] - File doesn't exist:pepquery//CPTAC_Prospective_Breast_BI_Acetylome_PDC000239/index/61412.mgf
2025-01-17 08:31:08 [WARN ] main.java.msio.MsLibrarySearchWorker[loadSpectra:201] - File doesn't exist:pepquery//CPTAC_Prospective_Breast_BI_Acetylome_PDC000239/index/61413.mgf
2025-01-17 08:31:08 [WARN ] main.java.msio.MsLibrarySearchWorker[loadSpectra:201] - File doesn't exist:pepquery//CPTAC_Prospective_Breast_BI_Acetylome_PDC000239/index/61414.mgf
2025-01-17 08:31:08 [WARN ] main.java.msio.MsLibrarySearchWorker[loadSpectra:201] - File doesn't exist:pepquery//CPTAC_Prospective_Breast_BI_Acetylome_PDC000239/index/61415.mgf
2025-01-17 08:31:08 [WARN ] main.java.msio.MsLibrarySearchWorker[loadSpectra:201] - File doesn't exist:pepquery//CPTAC_Prospective_Breast_BI_Acetylome_PDC000239/index/63445.mgf
2025-01-17 08:31:08 [WARN ] main.java.msio.MsLibrarySearchWorker[loadSpectra:201] - File doesn't exist:pepquery//CPTAC_Prospective_Breast_BI_Acetylome_PDC000239/index/63446.mgf
2025-01-17 08:31:08 [WARN ] main.java.msio.MsLibrarySearchWorker[loadSpectra:201] - File doesn't exist:pepquery//CPTAC_Prospective_Breast_BI_Acetylome_PDC000239/index/63124.mgf
2025-01-17 08:31:08 [WARN ] main.java.msio.MsLibrarySearchWorker[loadSpectra:201] - File doesn't exist:pepquery//CPTAC_Prospective_Breast_BI_Acetylome_PDC000239/index/57511.mgf
2025-01-17 08:31:08 [WARN ] main.java.msio.MsLibrarySearchWorker[loadSpectra:201] - File doesn't exist:pepquery//CPTAC_Prospective_Breast_BI_Acetylome_PDC000239/index/57512.mgf
2025-01-17 08:31:08 [WARN ] main.java.msio.MsLibrarySearchWorker[loadSpectra:201] - File doesn't exist:pepquery//CPTAC_Prospective_Breast_BI_Acetylome_PDC000239/index/59381.mgf
2025-01-17 08:31:08 [WARN ] main.java.msio.MsLibrarySearchWorker[loadSpectra:201] - File doesn't exist:pepquery//CPTAC_Prospective_Breast_BI_Acetylome_PDC000239/index/59382.mgf
2025-01-17 08:31:08 [WARN ] main.java.msio.MsLibrarySearchWorker[loadSpectra:201] - File doesn't exist:pepquery//CPTAC_Prospective_Breast_BI_Acetylome_PDC000239/index/59383.mgf
2025-01-17 08:31:08 [WARN ] main.java.msio.MsLibrarySearchWorker[loadSpectra:201] - File doesn't exist:pepquery//CPTAC_Prospective_Breast_BI_Acetylome_PDC000239/index/59541.mgf
2025-01-17 08:31:08 [WARN ] main.java.msio.MsLibrarySearchWorker[loadSpectra:201] - File doesn't exist:pepquery//CPTAC_Prospective_Breast_BI_Acetylome_PDC000239/index/59542.mgf
2025-01-17 08:31:08 [WARN ] main.java.msio.MsLibrarySearchWorker[loadSpectra:201] - File doesn't exist:pepquery//CPTAC_Prospective_Breast_BI_Acetylome_PDC000239/index/63284.mgf
2025-01-17 08:31:08 [WARN ] main.java.msio.MsLibrarySearchWorker[loadSpectra:201] - File doesn't exist:pepquery//CPTAC_Prospective_Breast_BI_Acetylome_PDC000239/index/63286.mgf
2025-01-17 08:31:11 [INFO ] main.java.pg.SpectraInput[readSpectraFromMSMSlibrary:393] - Matched spectra: 122
2025-01-17 08:31:11 [INFO ] main.java.pg.SpectraInput[readSpectraFromMSMSlibrary:406] - Delete downloaded MS/MS index files.
2025-01-17 08:31:11 [INFO ] main.java.pg.PeptideSearchMT[search:456] - Time elapsed: 0.28 min
2025-01-17 08:31:11 [INFO ] main.java.pg.PeptideSearchMT[search:476] - Step 2: candidate spectra retrieval and PSM scoring done: time elapsed = 0.28 min
2025-01-17 08:31:11 [INFO ] main.java.pg.PeptideSearchMT[search:480] - Step 3-4: competitive filtering based on reference sequences and statistical evaluation ...
2025-01-17 08:31:11 [INFO ] main.java.pg.PeptideSearchMT[search:515] - Don't find indexed database:pepquery//database/UP000005640_9606.fasta.sqldb
2025-01-17 08:31:11 [INFO ] main.java.pg.PeptideSearchMT[search:522] - Use database:pepquery//database/UP000005640_9606.fasta
2025-01-17 08:31:11 [INFO ] main.java.pg.DatabaseInput[getEnzymeByIndex:263] - Use enzyme:Trypsin
2025-01-17 08:31:13 [INFO ] main.java.pg.DatabaseInput[protein_digest:474] - Protein sequences:20650, total unique peptide sequences:2339195
2025-01-17 08:31:13 [INFO ] main.java.pg.DatabaseInput[protein_digest:475] - Time used for protein digestion:2 s.
2025-01-17 08:31:28 [INFO ] main.java.pg.DatabaseInput[generate_reference_peptide_index:522] - Generating peptide forms is done!
Killed
(base) ofm@ofm-Nitro-AN515-58:~$
@wenbostar
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It seems this is a memory issue. Could you try it on a linux computer with larger memory?

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