Issue loading some spectra.

[Bdegraaf1234]

I am finding quite a lot of errors like these:

out of range errors:

terminate called after throwing an instance of 'std::out_of_range'
  what():  vector::_M_range_check: __n (which is 10000) >= this->size() (which is 10000)
Aborted (core dumped)

terminate called after throwing an instance of 'std::out_of_range'
free(): invalid size
Aborted (core dumped)

in addition; I have found that I am not able to set the number of iterations using the -i flag

.../msCRUSH/bin$ ./mscrush_on_general_charge -f test.mgf -c .../default_settings -i 2000
--Output HyperParams Begins--
<bool> peak intensity log normalized: Yes
<bool> remove precursor peak: Yes
<float> precursor mass tolerance(Da): 0.05
<float> max peak mz: 2000
<float> min peak mz: 200
<float> min cosine sim for clustering: 0.65
<float> mz scale after nomrlization: 1000
<float> fragment precision: 0.8
<float> shared peak mz eps: 0.2
<int> clustering iteration: 100
<int> hash functions per hash table: 15
<int> hash function dimension: 2251
<int> topK strongest peaks per bin: 5
<int> threads to use: 20
<int> window(bin) size: 100
<string> consensus spectra file prefix: consensus
<string> clustering result file prefix: .../default_settings
--Output HyperParams Ends--

This is on Windows subsystem Linux, where I have been able to run the clustering algorithm and consnsus file generation for other files. Do you have any idea what the problem is?

[leiwang-me]

Hello,

Thanks for your interest in our msCRUSH.

Can you please share the command you used and respective dataset, for each of the two errors you had?

Thanks, Lei

On Thu, Sep 12, 2019 at 7:15 AM Bdegraaf1234 notifications@github.com wrote:

I am finding quite a lot of errors like these:

out of range errors:

terminate called after throwing an instance of 'std::out_of_range' what(): vector::_M_range_check: __n (which is 10000) >= this->size() (which is 10000) Aborted (core dumped)

terminate called after throwing an instance of 'std::out_of_range' free(): invalid size Aborted (core dumped)

in addition; I have found that I am not able to set the number of iterations using the -i flag

.../msCRUSH/bin$ ./mscrush_on_general_charge -f test.mgf -c .../default_settings -i 2000 --Output HyperParams Begins--

peak intensity log normalized: Yes remove precursor peak: Yes precursor mass tolerance(Da): 0.05 max peak mz: 2000 min peak mz: 200 min cosine sim for clustering: 0.65 mz scale after nomrlization: 1000 fragment precision: 0.8 shared peak mz eps: 0.2 clustering iteration: 100 hash functions per hash table: 15 hash function dimension: 2251 topK strongest peaks per bin: 5 threads to use: 20 window(bin) size: 100 consensus spectra file prefix: consensus clustering result file prefix: .../default_settings --Output HyperParams Ends-- This is on Windows subsystem Linux, where I have been able to run the clustering algorithm and consnsus file generation for other files. Do you have any idea what the problem is? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub , or mute the thread .

[Bdegraaf1234]

Hi! thanks for your quick response, I would have to see about sharing the datasets, but the command was really default:

.../msCRUSH/bin$ ./mscrush_on_general_charge -f test.mgf -c .../default_settings

and

.../msCRUSH/bin$ ./mscrush_on_general_charge -f .../Test/20180505_OR16_Ag6_tamar002_SA_mabs_a_hcd.mgf

[Bdegraaf1234]

also these same commands work for other files, it really appears to be an issue in the file so I understand your need to see it, I will report back as soon as I have permission or a similar problem with a public file

[leiwang-me]

Thanks, that helps. From your description, it seems related to some specific file. Could you also verify that you followed the instructions in the msCRUSH page?

Thanks, Lei

On Thu, Sep 12, 2019 at 9:11 AM Bdegraaf1234 notifications@github.com wrote:

also these same commands work for other files, it really appears to be an issue in the file so I understand your need to see it, I will report back as soon as I have permission or a similar problem with a public file

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/COL-IU/msCRUSH/issues/3?email_source=notifications&email_token=ACSSK7C5DFXNVZX275KCZ2LQJJE2TA5CNFSM4IWDA4OKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD6SAYJQ#issuecomment-530844710, or mute the thread https://github.com/notifications/unsubscribe-auth/ACSSK7A3U5ZVMCYRQ34PPXTQJJE2TANCNFSM4IWDA4OA .

[Bdegraaf1234]

I reproduced the error with another file. however, it is ~1 gigabyte, so i transfer it by wetransfer: file

this is the file that produced this error

terminate called after throwing an instance of 'std::out_of_range'
  what():  vector::_M_range_check: __n (which is 10000) >= this->size() (which is 10000)
Aborted (core dumped)