Title | | » | Skyline saved file won't open probably because replicates rearranged |
Assigned To | | » | Brendan MacLean |
Type | | » | Defect |
Area | | » | Skyline |
Priority | | » | 3 |
Milestone | | » | 1.2 |
Skyline v1.1.0.2905
I suggest giving this issue high priority. It didn't cause me much harm (I'll redo ~4h of manually inspecting results). It could cause other users major loss of work/time (especially if those users didn't make incremental backups).
Problem Description:
A .sky saved file (saved by Skyline and unaltered) won't open (see attached screen shot).
Background and likely source of bug:
I imported 7 replicates (each was from 4 Thermo .RAW files, 28 files total).
I saved the file (and made a backup - it's fine).
I began to manually edit the results (reassigning peaks and removing peaks).
I decided to rearrange the sets of results ("Edit" -> "Manage Results..." -> move up/down).
I did some more manual editing, saved the file, and was unable to reopen the saved file the next day.
The error message pointed to the following lines within the .sky file:
<peptide_results>
<peptide_result replicate="MTCa" file="MTCa_f1" peak_count_ratio="1" retention_time="44.26768" />
<peptide_result replicate="MTCb" file="MTCb_f1" peak_count_ratio="1" retention_time="44.23829" />
<peptide_result replicate="MTCc" file="MTCc_f1" peak_count_ratio="1" retention_time="44.26767" />
<peptide_result replicate="MTCd" file="MTCd_f-1" peak_count_ratio="0" />
<peptide_result replicate="MTCd" file="MTCd_f2" peak_count_ratio="0" />
<peptide_result replicate="MTCe" file="MTCe_f-1" peak_count_ratio="0" />
<peptide_result replicate="MTCe" file="MTCe_f2" peak_count_ratio="0.5" retention_time="44.62411" />
<peptide_result replicate="RMTC1a" file="RMTC1a_f-1" peak_count_ratio="0" />
<peptide_result replicate="RMTC1a" file="RMTC1a_f2" peak_count_ratio="0" />
<peptide_result replicate="RMTC1b" file="RMTC1b_f-1" peak_count_ratio="0" />
<peptide_result replicate="RMTC1b" file="RMTC1b_f2" peak_count_ratio="0" />
</peptide_results>
I notice 2 possible problems. First, multiple lines are here for the same replicate (is this ever normal behavior?). Second, each <replicate> has a file ID of the form <replicate>_f# where # is 0, 1, 2, 3. My guess is that rearranging the replicates messed up the file ID's and the resulting #'s became -1, 0, 1, 2 (at least for some of the results). I suspect that you're accidentally subtracting 1 from the wrong integer variable. I see other examples of file ID #'s equal to -1 within the .sky file. I haven't attempted to reproduce the error so it's possible that it originated from something else or is somehow more complex. If you want me to try, let me know (nathan.manes@nih.gov), and also I can send you the .sky files.