Segmentation Fault Error when using my own params file

[Nat Tay]

Hi,

I am trying to search my MS spectra against my custom database. The database I am using is a fasta file generated from rnaseq data. When I run the command: 

/home/e0470749/comet/comet.2019015.linux.exe -P/home/e0470749/comet/comet.params.new /gpfs/eplab/Nathaniel/b014p014_P_56h_M5_rep1.mgf

I get the following error:

/home/e0470749/comet/run_comet.sh: line 3: 15485 Segmentation fault      (core dumped) /home/e0470749/comet/comet.2019015.linux.exe -P/home/e0470749/comet/comet.params.new /gpfs/eplab/Nathaniel/b014p014_P_56h_M5_rep1.mgf

However, if I generate a new params file without changing any of the default settings besides the database, the program seems to run fine.

Does anyone know how to solve this issue? 

[Nat Tay]

Attaching my comet.params file

[Javan Okendo]

Tay,

Segmentation fault means you are trying to access memory which you are not allocated for in your server. Consider reducing the number of threads or just leave it at default value of 0 and the system will allocate the number of threads accordingly. I hope this helps

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[Nat Tay]

Thanks for the reply.

I've set the num of threads to 0 but get the same error. Setting it to 1 also gives the same thing.

I think the problem might be the nucleotide_reading_frame which I set to 7. If I run the params.new with just that setting changed I get the segmentation fault. 

On Monday, May 4, 2020 at 5:36:55 PM UTC+8, Javan Okendo wrote:

Tay,

Segmentation fault means you are trying to access memory which you are not allocated for in your server. Consider reducing the number of threads or just leave it at default value of 0 and the system will allocate the number of threads accordingly. I hope this helps

On Mon, May 4, 2020 at 10:41 AM Nat Tay <natt...@gmail.com> wrote:

Attaching my comet.params file

On Monday, May 4, 2020 at 4:33:04 PM UTC+8, Nat Tay wrote:

Hi,

I am trying to search my MS spectra against my custom database. The database I am using is a fasta file generated from rnaseq data. When I run the command: 

/home/e0470749/comet/comet.2019015.linux.exe -P/home/e0470749/comet/comet.params.new /gpfs/eplab/Nathaniel/b014p014_P_56h_M5_rep1.mgf

I get the following error:

/home/e0470749/comet/run_comet.sh: line 3: 15485 Segmentation fault      (core dumped) /home/e0470749/comet/comet.2019015.linux.exe -P/home/e0470749/comet/comet.params.new /gpfs/eplab/Nathaniel/b014p014_P_56h_M5_rep1.mgf

However, if I generate a new params file without changing any of the default settings besides the database, the program seems to run fine.

Does anyone know how to solve this issue? 

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[Jimmy Eng]

Nat,

I am able to replicate the problem here.  In my brief testing, Comet version 2019.01 rev. 1 completed my test search whereas versions 2019.01 rev. 2 and later are giving the segmentation fault.  So I encourage you go to download the 2019.01.1 release and use that version for this search.

I will debug this soon and include the fix in the next full release.  I don't intend to make a maintenance release for this because the use case is so rare as I don't think I've performed or tested a nucleotide database search in over a decade!  There should be no functional difference between 2019.01.1 and 2019.01.5 for your searches but if you do want a patched 2019.01.5 release, I can send you a binary once I can identify and fix the bug.

Jimmy

[Jimmy Eng]

If you want to use 2019.01.5, here's a patched linux binary that addresses this bug.

[Nat Tay]

Okay, thanks so much! Will try out the 2019.01.1 release and the new patch!