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Nesvilab / FragPipe

A cross-platform proteomics data analysis suite
http://fragpipe.nesvilab.org
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Philosopher does not print 'ion mobility' column to psm.tsv if there is no PSM but the data is from ddaPASEF #419

Closed rajeshksoni11 closed 2 years ago

rajeshksoni11 commented 3 years ago
fcyu commented 3 years ago

Thanks for your report. Can you upload your .d folders, fasta file, and fragger.params to https://www.dropbox.com/request/blovHST1fE9mOvuMM13x ?

Best,

Fengchao

On Thu, Aug 5, 2021 at 11:31 AM rajeshksoni11 @.***> wrote:

-

Describe the log_2021-08-05_11-29-12.txt https://github.com/Nesvilab/FragPipe/files/6939813/log_2021-08-05_11-29-12.txt issue or question:

Upload your log file (If a log file hasn't been generated, go to the 'Run' tab in FragPipe, click 'Export Log', zip the resulting "log_[date_time].txt" file to avoid truncation, then attach the zipped file by drag & drop here.)

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/Nesvilab/FragPipe/issues/419, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABU27W4E2LANBTNISTH2GS3T3KVDZANCNFSM5BUDBJPA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&utm_campaign=notification-email .

-- Dr. Fengchao Yu Research Investigator University of Michigan

rajeshksoni11 commented 3 years ago

Hi all, Thanks. I am uploading the folder, and another issue, java.lang.OutOfMemoryError, all the time if I search for a non-specific HLA search. I have 64GB ram and selected Ram= o(auto) and parallism= 10 Please suggest I fix the issues. best, Rajesh

From: Fengchao @.> Sent: Thursday, August 5, 2021 11:35 AM To: Nesvilab/FragPipe @.> Cc: Soni, Rajesh K. @.>; Author @.> Subject: [EXTERNAL] Re: [Nesvilab/FragPipe] Stopped (#419)

Thanks for your report. Can you upload your .d folders, fasta file, and fragger.params to https://www.dropbox.com/request/blovHST1fE9mOvuMM13x ?

Best,

Fengchao

On Thu, Aug 5, 2021 at 11:31 AM rajeshksoni11 @.***> wrote:

-

Describe the log_2021-08-05_11-29-12.txt https://github.com/Nesvilab/FragPipe/files/6939813/log_2021-08-05_11-29-12.txt issue or question:

Upload your log file (If a log file hasn't been generated, go to the 'Run' tab in FragPipe, click 'Export Log', zip the resulting "log_[date_time].txt" file to avoid truncation, then attach the zipped file by drag & drop here.)

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/Nesvilab/FragPipe/issues/419, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABU27W4E2LANBTNISTH2GS3T3KVDZANCNFSM5BUDBJPA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&utm_campaign=notification-email .

-- Dr. Fengchao Yu Research Investigator University of Michigan

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fcyu commented 3 years ago

Hi Rajesh,

Non-specific search requires lots of memory. If 64 GB is not enough for your data, you can increase the value for "split database" in MSFragger tab (the default value is 1 meaning no splitting).

Best,

Fengchao

On Thu, Aug 5, 2021 at 1:05 PM rajeshksoni11 @.***> wrote:

Hi all, Thanks. I am uploading the folder, and another issue, java.lang.OutOfMemoryError, all the time if I search for a non-specific HLA search. I have 64GB ram and selected Ram= o(auto) and parallism= 10 Please suggest I fix the issues. best, Rajesh

From: Fengchao @.> Sent: Thursday, August 5, 2021 11:35 AM To: Nesvilab/FragPipe @.> Cc: Soni, Rajesh K. @.>; Author @.> Subject: [EXTERNAL] Re: [Nesvilab/FragPipe] Stopped (#419)

Thanks for your report. Can you upload your .d folders, fasta file, and fragger.params to https://www.dropbox.com/request/blovHST1fE9mOvuMM13x ?

Best,

Fengchao

On Thu, Aug 5, 2021 at 11:31 AM rajeshksoni11 @.***> wrote:

-

Describe the log_2021-08-05_11-29-12.txt < https://github.com/Nesvilab/FragPipe/files/6939813/log_2021-08-05_11-29-12.txt

issue or question:

Upload your log file (If a log file hasn't been generated, go to the 'Run' tab in FragPipe, click 'Export Log', zip the resulting "log_[date_time].txt" file to avoid truncation, then attach the zipped file by drag & drop here.)

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/Nesvilab/FragPipe/issues/419, or unsubscribe < https://github.com/notifications/unsubscribe-auth/ABU27W4E2LANBTNISTH2GS3T3KVDZANCNFSM5BUDBJPA

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or Android < https://play.google.com/store/apps/details?id=com.github.android&utm_campaign=notification-email

.

-- Dr. Fengchao Yu Research Investigator University of Michigan

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub< https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Nesvilab_FragPipe_issues_419-23issuecomment-2D893557340&d=DwMFaQ&c=G2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U&r=3kGEWBYAR_TOTPC4fFAqpAKTOUJHGP7jqdAzaZ1xUoQ&m=Vv0AUnJce_Zi3awlNhV5ACiBnIKzikq6DMceZ79QY08&s=pnm408QC5BIiqwIlqIoJnyMpBncliQYPXkALvd16iRY&e=>, or unsubscribe< https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_ATHFHTGWGKIGIQSIB7WCRKDT3KVVHANCNFSM5BUDBJPA&d=DwMFaQ&c=G2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U&r=3kGEWBYAR_TOTPC4fFAqpAKTOUJHGP7jqdAzaZ1xUoQ&m=Vv0AUnJce_Zi3awlNhV5ACiBnIKzikq6DMceZ79QY08&s=W6-VlQ5Yucdg7dnaR-KX_xw8oMFxkAFbcavEaRZjJQQ&e=

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-- Dr. Fengchao Yu Research Investigator University of Michigan

rajeshksoni11 commented 3 years ago

Hi Fengcho, I am using the UniProt mouse database, how much value I should keep for spilt database? Best, Rajesh

Rajesh Kumar Soni , PhD Proteomics Core Manager Lasker Biomedical Research Building 3960 Broadway, 3rd Floor, Room 350D (Entrance on 166th St.) Columbia University Medical Center New York, NY 10032 Email: @.*** Tel: 212-342-4177

From: Fengchao @.> Sent: Thursday, August 5, 2021 1:09 PM To: Nesvilab/FragPipe @.> Cc: Soni, Rajesh K. @.>; Author @.> Subject: [EXTERNAL] Re: [Nesvilab/FragPipe] Stopped (#419)

Hi Rajesh,

Non-specific search requires lots of memory. If 64 GB is not enough for your data, you can increase the value for "split database" in MSFragger tab (the default value is 1 meaning no splitting).

Best,

Fengchao

On Thu, Aug 5, 2021 at 1:05 PM rajeshksoni11 @.***> wrote:

Hi all, Thanks. I am uploading the folder, and another issue, java.lang.OutOfMemoryError, all the time if I search for a non-specific HLA search. I have 64GB ram and selected Ram= o(auto) and parallism= 10 Please suggest I fix the issues. best, Rajesh

From: Fengchao @.> Sent: Thursday, August 5, 2021 11:35 AM To: Nesvilab/FragPipe @.> Cc: Soni, Rajesh K. @.>; Author @.> Subject: [EXTERNAL] Re: [Nesvilab/FragPipe] Stopped (#419)

Thanks for your report. Can you upload your .d folders, fasta file, and fragger.params to https://www.dropbox.com/request/blovHST1fE9mOvuMM13x ?

Best,

Fengchao

On Thu, Aug 5, 2021 at 11:31 AM rajeshksoni11 @.***> wrote:

-

Describe the log_2021-08-05_11-29-12.txt < https://github.com/Nesvilab/FragPipe/files/6939813/log_2021-08-05_11-29-12.txt

issue or question:

Upload your log file (If a log file hasn't been generated, go to the 'Run' tab in FragPipe, click 'Export Log', zip the resulting "log_[date_time].txt" file to avoid truncation, then attach the zipped file by drag & drop here.)

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/Nesvilab/FragPipe/issues/419, or unsubscribe < https://github.com/notifications/unsubscribe-auth/ABU27W4E2LANBTNISTH2GS3T3KVDZANCNFSM5BUDBJPA

. Triage notifications on the go with GitHub Mobile for iOS < https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675

or Android < https://play.google.com/store/apps/details?id=com.github.android&utm_campaign=notification-email

.

-- Dr. Fengchao Yu Research Investigator University of Michigan

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub< https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Nesvilab_FragPipe_issues_419-23issuecomment-2D893557340&d=DwMFaQ&c=G2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U&r=3kGEWBYAR_TOTPC4fFAqpAKTOUJHGP7jqdAzaZ1xUoQ&m=Vv0AUnJce_Zi3awlNhV5ACiBnIKzikq6DMceZ79QY08&s=pnm408QC5BIiqwIlqIoJnyMpBncliQYPXkALvd16iRY&e=>, or unsubscribe< https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_ATHFHTGWGKIGIQSIB7WCRKDT3KVVHANCNFSM5BUDBJPA&d=DwMFaQ&c=G2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U&r=3kGEWBYAR_TOTPC4fFAqpAKTOUJHGP7jqdAzaZ1xUoQ&m=Vv0AUnJce_Zi3awlNhV5ACiBnIKzikq6DMceZ79QY08&s=W6-VlQ5Yucdg7dnaR-KX_xw8oMFxkAFbcavEaRZjJQQ&e=

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-- Dr. Fengchao Yu Research Investigator University of Michigan

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fcyu commented 3 years ago

It's hard to tell because it depends on your variable modifications etc. You can try different values from small to large.

Best,

Fengchao

On Thu, Aug 5, 2021 at 1:19 PM rajeshksoni11 @.***> wrote:

Hi Fengcho, I am using the UniProt mouse database, how much value I should keep for spilt database? Best, Rajesh

Rajesh Kumar Soni , PhD Proteomics Core Manager Lasker Biomedical Research Building 3960 Broadway, 3rd Floor, Room 350D (Entrance on 166th St.) Columbia University Medical Center New York, NY 10032 Email: @.*** Tel: 212-342-4177

From: Fengchao @.> Sent: Thursday, August 5, 2021 1:09 PM To: Nesvilab/FragPipe @.> Cc: Soni, Rajesh K. @.>; Author @.> Subject: [EXTERNAL] Re: [Nesvilab/FragPipe] Stopped (#419)

Hi Rajesh,

Non-specific search requires lots of memory. If 64 GB is not enough for your data, you can increase the value for "split database" in MSFragger tab (the default value is 1 meaning no splitting).

Best,

Fengchao

On Thu, Aug 5, 2021 at 1:05 PM rajeshksoni11 @.***> wrote:

Hi all, Thanks. I am uploading the folder, and another issue, java.lang.OutOfMemoryError, all the time if I search for a non-specific HLA search. I have 64GB ram and selected Ram= o(auto) and parallism= 10 Please suggest I fix the issues. best, Rajesh

From: Fengchao @.> Sent: Thursday, August 5, 2021 11:35 AM To: Nesvilab/FragPipe @.> Cc: Soni, Rajesh K. @.>; Author @.> Subject: [EXTERNAL] Re: [Nesvilab/FragPipe] Stopped (#419)

Thanks for your report. Can you upload your .d folders, fasta file, and fragger.params to https://www.dropbox.com/request/blovHST1fE9mOvuMM13x ?

Best,

Fengchao

On Thu, Aug 5, 2021 at 11:31 AM rajeshksoni11 @.***> wrote:

-

Describe the log_2021-08-05_11-29-12.txt <

https://github.com/Nesvilab/FragPipe/files/6939813/log_2021-08-05_11-29-12.txt

issue or question:

Upload your log file (If a log file hasn't been generated, go to the 'Run' tab in FragPipe, click 'Export Log', zip the resulting "log_[date_time].txt" file to avoid truncation, then attach the zipped file by drag & drop here.)

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/Nesvilab/FragPipe/issues/419, or unsubscribe <

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or Android <

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.

-- Dr. Fengchao Yu Research Investigator University of Michigan

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fcyu commented 3 years ago

Hi Rajesh,

Thanks for your uploaded files. It took me a while to figure out the reason. It is due to a bug/feature in Philosopher, and another bug/feature in univocity-parsers which is the library used by IonQuant to parse tsv files. Regarding the univocity-parsers one, I have submitted an issue to https://github.com/uniVocity/univocity-parsers/issues/472

Regarding Philosopher, there is no ion mobility column in psm.tsv from HD_PASEF_PyR1_Ingeldig_Mdx_Trypsin_Slot2-3_1_1361. Thus, there are two different column sets in two psm.tsv files:

The first psm.tsv file image

The second psm.tsv file image

It triggers the bug/feature in univocity-parsers. Since our first run has no PSM passing FDR threshold, you can remove that run for now.

@prvst Can you change Philosopher to let it still print ion mobility column if there is no PSM but the data is from ddaPASEF? I guess the same idea should also applied to FAIMS' compensation voltage column. Not sure about TMT, though.

Thanks,

Fengchao

rajeshksoni11 commented 3 years ago

Hi Fengchao, Thanks. How to get the STY table in output? I am using Timstofpro data. Best, Rajesh

Rajesh Kumar Soni , PhD Proteomics Core Manager Lasker Biomedical Research Building 3960 Broadway, 3rd Floor, Room 350D (Entrance on 166th St.) Columbia University Medical Center New York, NY 10032 Email: @.*** Tel: 212-342-4177

From: Fengchao @.> Sent: Thursday, August 5, 2021 1:21 PM To: Nesvilab/FragPipe @.> Cc: Soni, Rajesh K. @.>; Author @.> Subject: [EXTERNAL] Re: [Nesvilab/FragPipe] Stopped (#419)

It's hard to tell because it depends on your variable modifications etc. You can try different values from small to large.

Best,

Fengchao

On Thu, Aug 5, 2021 at 1:19 PM rajeshksoni11 @.***> wrote:

Hi Fengcho, I am using the UniProt mouse database, how much value I should keep for spilt database? Best, Rajesh

Rajesh Kumar Soni , PhD Proteomics Core Manager Lasker Biomedical Research Building 3960 Broadway, 3rd Floor, Room 350D (Entrance on 166th St.) Columbia University Medical Center New York, NY 10032 Email: @.*** Tel: 212-342-4177

From: Fengchao @.> Sent: Thursday, August 5, 2021 1:09 PM To: Nesvilab/FragPipe @.> Cc: Soni, Rajesh K. @.>; Author @.> Subject: [EXTERNAL] Re: [Nesvilab/FragPipe] Stopped (#419)

Hi Rajesh,

Non-specific search requires lots of memory. If 64 GB is not enough for your data, you can increase the value for "split database" in MSFragger tab (the default value is 1 meaning no splitting).

Best,

Fengchao

On Thu, Aug 5, 2021 at 1:05 PM rajeshksoni11 @.***> wrote:

Hi all, Thanks. I am uploading the folder, and another issue, java.lang.OutOfMemoryError, all the time if I search for a non-specific HLA search. I have 64GB ram and selected Ram= o(auto) and parallism= 10 Please suggest I fix the issues. best, Rajesh

From: Fengchao @.> Sent: Thursday, August 5, 2021 11:35 AM To: Nesvilab/FragPipe @.> Cc: Soni, Rajesh K. @.>; Author @.> Subject: [EXTERNAL] Re: [Nesvilab/FragPipe] Stopped (#419)

Thanks for your report. Can you upload your .d folders, fasta file, and fragger.params to https://www.dropbox.com/request/blovHST1fE9mOvuMM13x ?

Best,

Fengchao

On Thu, Aug 5, 2021 at 11:31 AM rajeshksoni11 @.***> wrote:

-

Describe the log_2021-08-05_11-29-12.txt <

https://github.com/Nesvilab/FragPipe/files/6939813/log_2021-08-05_11-29-12.txt

issue or question:

Upload your log file (If a log file hasn't been generated, go to the 'Run' tab in FragPipe, click 'Export Log', zip the resulting "log_[date_time].txt" file to avoid truncation, then attach the zipped file by drag & drop here.)

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fcyu commented 3 years ago

Hi Rajesh,

Do you mean the phospho site table? We don’t have it for LFQ, but we are working on it. Should be available in the next version.

Best,

Fengchao

On Sun, 15 Aug 2021 at 5:34 PM, rajeshksoni11 @.***> wrote:

Hi Fengchao, Thanks. How to get the STY table in output? I am using Timstofpro data. Best, Rajesh

Rajesh Kumar Soni , PhD Proteomics Core Manager Lasker Biomedical Research Building 3960 Broadway, 3rd Floor, Room 350D https://www.google.com/maps/search/3960+Broadway,+3rd+Floor,+Room+350D?entry=gmail&source=g (Entrance on 166th St.) Columbia University Medical Center New York, NY 10032 Email: @.*** Tel: 212-342-4177

From: Fengchao @.> Sent: Thursday, August 5, 2021 1:21 PM To: Nesvilab/FragPipe @.> Cc: Soni, Rajesh K. @.>; Author @.> Subject: [EXTERNAL] Re: [Nesvilab/FragPipe] Stopped (#419)

It's hard to tell because it depends on your variable modifications etc. You can try different values from small to large.

Best,

Fengchao

On Thu, Aug 5, 2021 at 1:19 PM rajeshksoni11 @.***> wrote:

Hi Fengcho, I am using the UniProt mouse database, how much value I should keep for spilt database? Best, Rajesh

Rajesh Kumar Soni , PhD Proteomics Core Manager Lasker Biomedical Research Building 3960 Broadway, 3rd Floor, Room 350D https://www.google.com/maps/search/3960+Broadway,+3rd+Floor,+Room+350D?entry=gmail&source=g (Entrance on 166th St.) Columbia University Medical Center New York, NY 10032 Email: @.*** Tel: 212-342-4177

From: Fengchao @.> Sent: Thursday, August 5, 2021 1:09 PM To: Nesvilab/FragPipe @.> Cc: Soni, Rajesh K. @.>; Author @.> Subject: [EXTERNAL] Re: [Nesvilab/FragPipe] Stopped (#419)

Hi Rajesh,

Non-specific search requires lots of memory. If 64 GB is not enough for your data, you can increase the value for "split database" in MSFragger tab (the default value is 1 meaning no splitting).

Best,

Fengchao

On Thu, Aug 5, 2021 at 1:05 PM rajeshksoni11 @.***> wrote:

Hi all, Thanks. I am uploading the folder, and another issue, java.lang.OutOfMemoryError, all the time if I search for a non-specific HLA search. I have 64GB ram and selected Ram= o(auto) and parallism= 10 Please suggest I fix the issues. best, Rajesh

From: Fengchao @.> Sent: Thursday, August 5, 2021 11:35 AM To: Nesvilab/FragPipe @.> Cc: Soni, Rajesh K. @.>; Author @.> Subject: [EXTERNAL] Re: [Nesvilab/FragPipe] Stopped (#419)

Thanks for your report. Can you upload your .d folders, fasta file, and fragger.params to https://www.dropbox.com/request/blovHST1fE9mOvuMM13x ?

Best,

Fengchao

On Thu, Aug 5, 2021 at 11:31 AM rajeshksoni11 @.***> wrote:

-

Describe the log_2021-08-05_11-29-12.txt <

https://github.com/Nesvilab/FragPipe/files/6939813/log_2021-08-05_11-29-12.txt

issue or question:

Upload your log file (If a log file hasn't been generated, go to the 'Run' tab in FragPipe, click 'Export Log', zip the resulting "log_[date_time].txt" file to avoid truncation, then attach the zipped file by drag & drop here.)

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rajeshksoni11 commented 3 years ago

Hi Fengchao, Thank you for your quick response. Yes, i am very interested in phosho-sites table with LFQ intensities. Best, Rajesh

Rajesh Kumar Soni , PhD Proteomics Core Manager Lasker Biomedical Research Building 3960 Broadway, 3rd Floor, Room 350D (Entrance on 166th St.) Columbia University Medical Center New York, NY 10032 Email: @.*** Tel: 212-342-4177

From: Fengchao @.> Sent: Sunday, August 15, 2021 5:36 PM To: Nesvilab/FragPipe @.> Cc: Soni, Rajesh K. @.>; Author @.> Subject: [EXTERNAL] Re: [Nesvilab/FragPipe] Philosopher does not print 'ion mobility' column to psm.tsv if there is no PSM but the data is from ddaPASEF (#419)

Hi Rajesh,

Do you mean the phospho site table? We don’t have it for LFQ, but we are working on it. Should be available in the next version.

Best,

Fengchao

On Sun, 15 Aug 2021 at 5:34 PM, rajeshksoni11 @.***> wrote:

Hi Fengchao, Thanks. How to get the STY table in output? I am using Timstofpro data. Best, Rajesh

Rajesh Kumar Soni , PhD Proteomics Core Manager Lasker Biomedical Research Building 3960 Broadway, 3rd Floor, Room 350D https://www.google.com/maps/search/3960+Broadway,+3rd+Floor,+Room+350D?entry=gmail&source=g (Entrance on 166th St.) Columbia University Medical Center New York, NY 10032 Email: @.*** Tel: 212-342-4177

From: Fengchao @.> Sent: Thursday, August 5, 2021 1:21 PM To: Nesvilab/FragPipe @.> Cc: Soni, Rajesh K. @.>; Author @.> Subject: [EXTERNAL] Re: [Nesvilab/FragPipe] Stopped (#419)

It's hard to tell because it depends on your variable modifications etc. You can try different values from small to large.

Best,

Fengchao

On Thu, Aug 5, 2021 at 1:19 PM rajeshksoni11 @.***> wrote:

Hi Fengcho, I am using the UniProt mouse database, how much value I should keep for spilt database? Best, Rajesh

Rajesh Kumar Soni , PhD Proteomics Core Manager Lasker Biomedical Research Building 3960 Broadway, 3rd Floor, Room 350D https://www.google.com/maps/search/3960+Broadway,+3rd+Floor,+Room+350D?entry=gmail&source=g (Entrance on 166th St.) Columbia University Medical Center New York, NY 10032 Email: @.*** Tel: 212-342-4177

From: Fengchao @.> Sent: Thursday, August 5, 2021 1:09 PM To: Nesvilab/FragPipe @.> Cc: Soni, Rajesh K. @.>; Author @.> Subject: [EXTERNAL] Re: [Nesvilab/FragPipe] Stopped (#419)

Hi Rajesh,

Non-specific search requires lots of memory. If 64 GB is not enough for your data, you can increase the value for "split database" in MSFragger tab (the default value is 1 meaning no splitting).

Best,

Fengchao

On Thu, Aug 5, 2021 at 1:05 PM rajeshksoni11 @.***> wrote:

Hi all, Thanks. I am uploading the folder, and another issue, java.lang.OutOfMemoryError, all the time if I search for a non-specific HLA search. I have 64GB ram and selected Ram= o(auto) and parallism= 10 Please suggest I fix the issues. best, Rajesh

From: Fengchao @.> Sent: Thursday, August 5, 2021 11:35 AM To: Nesvilab/FragPipe @.> Cc: Soni, Rajesh K. @.>; Author @.> Subject: [EXTERNAL] Re: [Nesvilab/FragPipe] Stopped (#419)

Thanks for your report. Can you upload your .d folders, fasta file, and fragger.params to https://www.dropbox.com/request/blovHST1fE9mOvuMM13x ?

Best,

Fengchao

On Thu, Aug 5, 2021 at 11:31 AM rajeshksoni11 @.***> wrote:

-

Describe the log_2021-08-05_11-29-12.txt <

https://github.com/Nesvilab/FragPipe/files/6939813/log_2021-08-05_11-29-12.txt

issue or question:

Upload your log file (If a log file hasn't been generated, go to the 'Run' tab in FragPipe, click 'Export Log', zip the resulting "log_[date_time].txt" file to avoid truncation, then attach the zipped file by drag & drop here.)

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prvst commented 2 years ago

Fixed. Added to v4.1.1