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Nesvilab / FragPipe

A cross-platform proteomics data analysis suite
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Error when running nonspecific-peptidome workflow FP v22 #1734

Closed yishai99 closed 3 weeks ago

yishai99 commented 3 weeks ago

Hi, I tried analyzing a set of 12 peptidomics samples (timsTOF data) and got an error. Might be related to the two databases I combined? One is Uniprot and the other is a fasta db with a different header format. Log file is attached. Thanks,

Yishai log_2024-08-17_17-33-15.txt

fcyu commented 3 weeks ago

Hi Yishai,

It seems that there were some permission issues in PeptideProphet

command "mv -f "D:\21878\msf_Tuta_Tomato\TTU_SM_21878_Tomato_Insect6_05mL_polar_8_14_2024_1591\interact-TTU_SM_21878_Tomato_Insect6_05mL_polar_8-14-2024_1591.pep.xml.tmp.a25640" "D:\21878\msf_Tuta_Tomato\TTU_SM_21878_Tomato_Insect6_05mL_polar_8_14_2024_1591\interact-TTU_SM_21878_Tomato_Insect6_05mL_polar_8-14-2024_1591.pep.xml"" failed: Operation not permitted
failed to update D:\21878\msf_Tuta_Tomato\TTU_SM_21878_Tomato_Insect6_05mL_polar_8_14_2024_1591\interact-TTU_SM_21878_Tomato_Insect6_05mL_polar_8-14-2024_1591.pep.xml from temp file D:\21878\msf_Tuta_Tomato\TTU_SM_21878_Tomato_Insect6_05mL_polar_8_14_2024_1591\interact-TTU_SM_21878_Tomato_Insect6_05mL_polar_8-14-2024_1591.pep.xml.tmp.a25640, error 2 "No such file or directory"mv: `D:\21878\msf_Tuta_Tomato\TTU_SM_21878_Tomato_Insect6_05mL_polar_8_14_2024_1591\interact-TTU_SM_21878_Tomato_Insect6_05mL_polar_8-14-2024_1591.pep.xml.tmp.a25640' and `d:\21878\msf_tuta_tomato\ttu_sm_21878_tomato_insect6_05ml_polar_8_14_2024_1591\interact-ttu_sm_21878_tomato_insect6_05ml_polar_8-14-2024_1591.pep.xml' are the same file

command "mv -f "D:\21878\msf_Tuta_Tomato\TTU_SM_21878_Tomato_Insect6_05mL_polar_8_14_2024_1591\interact-TTU_SM_21878_Tomato_Insect6_05mL_polar_8-14-2024_1591.pep.xml.tmp.a25640" "D:\21878\msf_Tuta_Tomato\TTU_SM_21878_Tomato_Insect6_05mL_polar_8_14_2024_1591\interact-TTU_SM_21878_Tomato_Insect6_05mL_polar_8-14-2024_1591.pep.xml"" failed: Operation not permitted
failed to update D:\21878\msf_Tuta_Tomato\TTU_SM_21878_Tomato_Insect6_05mL_polar_8_14_2024_1591\interact-TTU_SM_21878_Tomato_Insect6_05mL_polar_8-14-2024_1591.pep.xml from temp file D:\21878\msf_Tuta_Tomato\TTU_SM_21878_Tomato_Insect6_05mL_polar_8_14_2024_1591\interact-TTU_SM_21878_Tomato_Insect6_05mL_polar_8-14-2024_1591.pep.xml.tmp.a25640, error 2 "No such file or directory"mv: `D:\21878\msf_Tuta_Tomato\TTU_SM_21878_Tomato_Insect6_05mL_polar_8_14_2024_1591\interact-TTU_SM_21878_Tomato_Insect6_05mL_polar_8-14-2024_1591.pep.xml.tmp.a25640' and `d:\21878\msf_tuta_tomato\ttu_sm_21878_tomato_insect6_05ml_polar_8_14_2024_1591\interact-ttu_sm_21878_tomato_insect6_05ml_polar_8-14-2024_1591.pep.xml' are the same file
error: no RefreshParser data written to file D:\21878\msf_Tuta_Tomato\TTU_SM_21878_Tomato_Insect6_05mL_polar_8_14_2024_1591\interact-TTU_SM_21878_Tomato_Insect6_05mL_polar_8-14-2024_1591.pep.xml

command "mv -f "D:\21878\msf_Tuta_Tomato\TTU_SM_21878_Tomato_Insect6_05mL_polar_8_14_2024_1591\interact-TTU_SM_21878_Tomato_Insect6_05mL_polar_8-14-2024_1591.pep.xml.tmp.a25640" "D:\21878\msf_Tuta_Tomato\TTU_SM_21878_Tomato_Insect6_05mL_polar_8_14_2024_1591\interact-TTU_SM_21878_Tomato_Insect6_05mL_polar_8-14-2024_1591.pep.xml"" failed: Operation not permitted
failed to update D:\21878\msf_Tuta_Tomato\TTU_SM_21878_Tomato_Insect6_05mL_polar_8_14_2024_1591\interact-TTU_SM_21878_Tomato_Insect6_05mL_polar_8-14-2024_1591.pep.xml from temp file D:\21878\msf_Tuta_Tomato\TTU_SM_21878_Tomato_Insect6_05mL_polar_8_14_2024_1591\interact-TTU_SM_21878_Tomato_Insect6_05mL_polar_8-14-2024_1591.pep.xml.tmp.a25640, error 2 "No such file or directory"using Accurate Mass Bins

Could you switch to Percolator in the "Validation" tab, and try again? You can uncheck "MSFragger" to skip the database search since you already have the results.

Best,

Fengchao

yishai99 commented 3 weeks ago

Hi Fengchao, With Percolator it completed fine. Anything we can do about this? Thanks,

Yishai

On 17 Aug 2024, at 17:44, Fengchao @.***> wrote:

Hi Yishai,

It seems that there were some permission issues in PeptideProphet

command "mv -f "D:\21878\msf_Tuta_Tomato\TTU_SM_21878_Tomato_Insect6_05mL_polar_8_14_2024_1591\interact-TTU_SM_21878_Tomato_Insect6_05mL_polar_8-14-2024_1591.pep.xml.tmp.a25640" "D:\21878\msf_Tuta_Tomato\TTU_SM_21878_Tomato_Insect6_05mL_polar_8_14_2024_1591\interact-TTU_SM_21878_Tomato_Insect6_05mL_polar_8-14-2024_1591.pep.xml"" failed: Operation not permitted failed to update D:\21878\msf_Tuta_Tomato\TTU_SM_21878_Tomato_Insect6_05mL_polar_8_14_2024_1591\interact-TTU_SM_21878_Tomato_Insect6_05mL_polar_8-14-2024_1591.pep.xml from temp file D:\21878\msf_Tuta_Tomato\TTU_SM_21878_Tomato_Insect6_05mL_polar_8_14_2024_1591\interact-TTU_SM_21878_Tomato_Insect6_05mL_polar_8-14-2024_1591.pep.xml.tmp.a25640, error 2 "No such file or directory"mv: D:\21878\msf_Tuta_Tomato\TTU_SM_21878_Tomato_Insect6_05mL_polar_8_14_2024_1591\interact-TTU_SM_21878_Tomato_Insect6_05mL_polar_8-14-2024_1591.pep.xml.tmp.a25640' andd:\21878\msf_tuta_tomato\ttu_sm_21878_tomato_insect6_05ml_polar_8_14_2024_1591\interact-ttu_sm_21878_tomato_insect6_05ml_polar_8-14-2024_1591.pep.xml' are the same file

command "mv -f "D:\21878\msf_Tuta_Tomato\TTU_SM_21878_Tomato_Insect6_05mL_polar_8_14_2024_1591\interact-TTU_SM_21878_Tomato_Insect6_05mL_polar_8-14-2024_1591.pep.xml.tmp.a25640" "D:\21878\msf_Tuta_Tomato\TTU_SM_21878_Tomato_Insect6_05mL_polar_8_14_2024_1591\interact-TTU_SM_21878_Tomato_Insect6_05mL_polar_8-14-2024_1591.pep.xml"" failed: Operation not permitted failed to update D:\21878\msf_Tuta_Tomato\TTU_SM_21878_Tomato_Insect6_05mL_polar_8_14_2024_1591\interact-TTU_SM_21878_Tomato_Insect6_05mL_polar_8-14-2024_1591.pep.xml from temp file D:\21878\msf_Tuta_Tomato\TTU_SM_21878_Tomato_Insect6_05mL_polar_8_14_2024_1591\interact-TTU_SM_21878_Tomato_Insect6_05mL_polar_8-14-2024_1591.pep.xml.tmp.a25640, error 2 "No such file or directory"mv: D:\21878\msf_Tuta_Tomato\TTU_SM_21878_Tomato_Insect6_05mL_polar_8_14_2024_1591\interact-TTU_SM_21878_Tomato_Insect6_05mL_polar_8-14-2024_1591.pep.xml.tmp.a25640' andd:\21878\msf_tuta_tomato\ttu_sm_21878_tomato_insect6_05ml_polar_8_14_2024_1591\interact-ttu_sm_21878_tomato_insect6_05ml_polar_8-14-2024_1591.pep.xml' are the same file error: no RefreshParser data written to file D:\21878\msf_Tuta_Tomato\TTU_SM_21878_Tomato_Insect6_05mL_polar_8_14_2024_1591\interact-TTU_SM_21878_Tomato_Insect6_05mL_polar_8-14-2024_1591.pep.xml

command "mv -f "D:\21878\msf_Tuta_Tomato\TTU_SM_21878_Tomato_Insect6_05mL_polar_8_14_2024_1591\interact-TTU_SM_21878_Tomato_Insect6_05mL_polar_8-14-2024_1591.pep.xml.tmp.a25640" "D:\21878\msf_Tuta_Tomato\TTU_SM_21878_Tomato_Insect6_05mL_polar_8_14_2024_1591\interact-TTU_SM_21878_Tomato_Insect6_05mL_polar_8-14-2024_1591.pep.xml"" failed: Operation not permitted failed to update D:\21878\msf_Tuta_Tomato\TTU_SM_21878_Tomato_Insect6_05mL_polar_8_14_2024_1591\interact-TTU_SM_21878_Tomato_Insect6_05mL_polar_8-14-2024_1591.pep.xml from temp file D:\21878\msf_Tuta_Tomato\TTU_SM_21878_Tomato_Insect6_05mL_polar_8_14_2024_1591\interact-TTU_SM_21878_Tomato_Insect6_05mL_polar_8-14-2024_1591.pep.xml.tmp.a25640, error 2 "No such file or directory"using Accurate Mass Bins Could you switch to Percolator in the "Validation" tab, and try again? You can uncheck "MSFragger" to skip the database search since you already have the results.

Best,

Fengchao

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fcyu commented 3 weeks ago

Hi Yishai,

Thanks for the positive feedback. For this specific workflow, you can keep using Percolator since it is a closed search.

Best,

Fengchao