Error when running nonspecific-peptidome workflow FP v22

[yishai99]

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]

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]

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' 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 — Reply to this email directly, view it on GitHub <#1734 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AE5PDYYVTPB3QTP4CRMPUGTZR5OVHAVCNFSM6AAAAABMVPHGDKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEOJUHA3TSMZZG4>. You are receiving this because you authored the thread.

[fcyu]

Hi Yishai,

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

Best,

Fengchao