PSM p-value error

[Shiri Tsour]

Hello, 

I am searching MS data using Tide (via SearchGui) with this command: 

tide search command: 

/scratch/tsour.s/S1_tide/SearchGUI-4.1.7/resources/Tide/linux/crux tide-search --compute-sp F /scratch/tsour.s/S1_tide/SearchGUI-4.1.7/resources/temp/peak_lists/01CPTAC_CCRCC_W_JHU_20171007_LUMOS_f01.ms2 /scratch/tsour.s/S1_tide/SearchGUI-4.1.7/resources/temp/search_engines/tide/fasta-index --overwrite T --top-match 10 --precursor-window 20.0 --precursor-window-type ppm --fileroot 01CPTAC_CCRCC_W_JHU_20171007_LUMOS_f01 --exact-p-value T --output-dir /scratch/tsour.s/S1_tide/SearchGUI-4.1.7/resources/temp/search_engines/tide/crux-output --spectrum-min-mz 0.0 --min-peaks 20 --spectrum-charge all --max-precursor-charge 7 --remove-precursor-peak F --remove-precursor-tolerance 1.5 --print-search-progress 1000 --use-flanking-peaks F --use-neutral-loss-peaks F --mz-bin-width 1.0005079 --mz-bin-offset 0.0 --num-threads 24 --concat F --txt-output T --sqt-output F --pepxml-output F --mzid-output F --pin-output F --verbosity 30  

I have encountered the following error: 

Sat Jan 15 14:13:52 EST 2022 Processing 01CPTAC_CCRCC_W_JHU_20171007_LUMOS_f01.ms2 with Tide.
INFO: Writing results to output directory '/scratch/tsour.s/S1_tide/SearchGUI-4.1.7/resources/temp/search_engines/tide/crux-output'.
INFO: CPU: c0168
INFO: Crux version: 4.1-e4b2f4d-2021-10-13
INFO: Sat Jan 15 14:13:52 EST 2022
INFO: Beginning tide-search.
INFO: Running tide-search...
INFO: Number of Threads: 24
INFO: Reading index /scratch/tsour.s/S1_tide/SearchGUI-4.1.7/resources/temp/search_engines/tide/fasta-index
INFO: Read 334711 target proteins
INFO: Converting /scratch/tsour.s/S1_tide/SearchGUI-4.1.7/resources/temp/peak_lists/01CPTAC_CCRCC_W_JHU_20171007_LUMOS_f01.ms2 to spectrumrecords format
INFO: Elapsed time starting conversion: 17.9 s
INFO: Converting ms_level 2 ...
INFO: Reading spectrum file /scratch/tsour.s/S1_tide/SearchGUI-4.1.7/resources/temp/search_engines/tide/crux-output/01CPTAC_CCRCC_W_JHU_20171007_LUMOS_f01.01CPTAC_CCRCC_W_JHU_20171007_LUMOS_f01.ms2.spectrumrecords.tmp.
INFO: Read 36408 spectra.
INFO: Starting search.

FATAL: PSM p-value should not be equal to 0.0
FATAL: PSM p-value should not be equal to 0.0
*** Error in `/scratch/tsour.s/S1_tide/SearchGUI-4.1.7/resources/Tide/linux/crux': free(): corrupted unsorted chunks: 0x00000000e54b37f0 ***

Sat Jan 15 14:14:39 EST 2022 Tide Searching finished for 01CPTAC_CCRCC_W_JHU_20171007_LUMOS_f01.ms2 (46.5 seconds).

Sat Jan 15 14:14:39 EST 2022 Zipping output files.
10% 20% 30% 40% 50% 60% 70% 80% 90%
Sat Jan 15 14:14:39 EST 2022 Search Completed (6 minutes 10.0 seconds).

Search Completed.

Output files are generated, but there are only a few dozen PSMs. 

I was successful with an older version of Crux (also via SearchGUI command line), but was not able to calculate p-values, which I need. 

The searchGUI developers updated Tide/Crux for me, but then recommended I reach out here because they do not understand the error. 

I am hoping for some help resolving this!

Thank you, 
Shiri

[William S Noble]

Sorry for the delay; this email went to my spam folder for some reason.

This is a pretty unusual error. The operating system seems to have given you this one:

*** Error in `/scratch/tsour.s/S1_tide/SearchGUI-4.1.7/resources/Tide/linux/crux': free(): corrupted unsorted chunks: 0x00000000e54b37f0 ***

I suspect that this is the result of our threading bug. Can you try your command with num-threads=1?

Bill

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[Shiri Tsour]

Hi Bill, 

Thanks for your response. I was able to get it working properly with num-threads=1. I ran Tide directly, without SearchGUI, which may have helped too.

Shiri