Error when creating index

[Tang888]

Hi I am trying to create index. 

The command: 

crux tide-index --overwrite T --missed-cleavages 2 --mods-spec K+229.162932 --mods-spec 3M+15.994915 --mods-spec 3STY+79.966331 --nterm-peptide-mods-spec X+229.16293 uniprotkb_proteome_UP000005640_AND_revi_2024_03_26.fasta human_swissprot_TMT11_oxM_pSTY

I got the following error:

WARNING: The output directory 'crux-output' already exists.
Existing files will be overwritten.
WARNING: The file 'crux-output/tide-index.log.txt' already exists and will be overwritten.
INFO: CPU: compute1-exec-283.ris.wustl.edu
INFO: Crux version: 4.1-e4b2f4d-2021-10-13
INFO: Sun Mar 31 21:22:11 UTC 2024
INFO: Beginning tide-index.
INFO: Running tide-index...
INFO: Writing results to output directory 'human_swissprot_TMT11_oxM_pSTY'.
INFO: Reading uniprotkb_proteome_UP000005640_AND_revi_2024_03_26.fasta and computing unmodified peptides...
INFO: Ignoring 17 peptide sequences containing unrecognized characters.
INFO: Generated 5750947 targets, including duplicates.
INFO: Failed to generate decoys for 460 low complexity peptides.
INFO: Generated 2673683 decoys.
INFO: Generating 1 decoy per target
INFO: Reading proteins
INFO: Wrote 100000 peptides
INFO: Wrote 200000 peptides
INFO: Wrote 300000 peptides
INFO: Wrote 400000 peptides
INFO: Wrote 500000 peptides
INFO: Wrote 600000 peptides
INFO: Wrote 700000 peptides
INFO: Wrote 800000 peptides
INFO: Wrote 900000 peptides
INFO: Wrote 1000000 peptides
INFO: Wrote 1100000 peptides
INFO: Wrote 1200000 peptides
INFO: Wrote 1300000 peptides
INFO: Wrote 1400000 peptides
INFO: Wrote 1500000 peptides
INFO: Wrote 1600000 peptides
INFO: Wrote 1700000 peptides
INFO: Wrote 1800000 peptides
INFO: Wrote 1900000 peptides
INFO: Wrote 2000000 peptides
INFO: Wrote 2100000 peptides
INFO: Wrote 2200000 peptides
INFO: Wrote 2300000 peptides
INFO: Wrote 2400000 peptides
INFO: Wrote 2500000 peptides
INFO: Wrote 2600000 peptides
INFO: Wrote 2700000 peptides
INFO: Wrote 2800000 peptides
INFO: Wrote 2900000 peptides
INFO: Wrote 3000000 peptides
INFO: Wrote 3100000 peptides
INFO: Wrote 3200000 peptides
INFO: Wrote 3300000 peptides
INFO: Wrote 3400000 peptides
INFO: Wrote 3500000 peptides
INFO: Wrote 3600000 peptides
INFO: Wrote 3700000 peptides
INFO: Wrote 3800000 peptides
INFO: Wrote 3900000 peptides
INFO: Wrote 4000000 peptides
INFO: Wrote 4100000 peptides
INFO: Wrote 4200000 peptides
INFO: Wrote 4300000 peptides
INFO: Wrote 4400000 peptides
INFO: Wrote 4500000 peptides
INFO: Wrote 4600000 peptides
INFO: Wrote 4700000 peptides
INFO: Wrote 4800000 peptides
INFO: Wrote 4900000 peptides
INFO: Wrote 5000000 peptides
INFO: Wrote 5100000 peptides
INFO: Wrote 5200000 peptides
INFO: Wrote 5300000 peptides
INFO: Skipped 3076804 duplicate targets and 5877 duplicate decoys.
INFO: Wrote 2674143 targets and 2667806 decoys.
INFO: Computing modified peptides...
INFO: Created 135325237 peptides.
INFO: Precomputing theoretical spectra...
[libprotobuf FATAL /data/TeamCity/buildAgent/work/ce28e5f252fac2d1/src/app/tide/peptide_peaks.cc:94] CHECK failed: writer.Write(&pb_peptide):
FATAL: An exception occurred: CHECK failed: writer.Write(&pb_peptide): 

Could anyone please help? Thank you!

[William Stafford Noble]

I believe you are running out of disk space. Your index contains about 200 million peptides, which is a lot!  If you have more space available on a different volume, then you can specify its location using the --temp-dir option.

Bill

On Sun, Mar 31, 2024 at 6:09 PM Tang888 <qich...@gmail.com> wrote:

Hi I am trying to create index.   The command:   crux tide-index --overwrite T --missed-cleavages 2 --mods-spec K+229. 162932 --mods-spec 3M+15. 994915 --mods-spec 3STY+79. 966331 --nterm-peptide-mods-spec X+229. 16293 uniprotkb_proteome_UP000005640_AND_revi_2024_03_26. fasta

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[William Stafford Noble]

By the way, I noticed that you tried to specify three different types of mods like this:

--mods-spec K+229.162932 --mods-spec 3M+15.994915 --mods-spec 3STY+79.966331

This will actually only give you the phosphorylation modification.  If you want all three, the correct syntax is

--mods-spec K+229.162932,3M+15.994915,3STY+79.966331

Bill