Closed yishai99 closed 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
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 filecommand "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.xmlcommand "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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Hi Yishai,
Thanks for the positive feedback. For this specific workflow, you can keep using Percolator since it is a closed search.
Best,
Fengchao
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