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Freequant: corrupted pepXML file. iTraq4 experiment
Hi, we're encountering an error while searching an iTraq4 dataset from CPTAC. Looks like one of the pepXML is corrupted judging on the file sizes. How should we work around the problem in order to complete the analysis?
Thanks! Wen
Directory of G:\contrib\A_36_GC_early_onset_PDC000214\results_isoform\N5381T5760
10/17/2022 09:38 PM 129,792,842 FN01_N5381T5760_180min_10ug_C1_053015.pepXML 10/17/2022 09:38 PM 130,252,487 FN02_N5381T5760_180min_10ug_C2_053015.pepXML 10/17/2022 09:39 PM 130,096,557 FN03_N5381T5760_180min_10ug_C1_053015.pepXML 10/17/2022 09:39 PM 131,206,680 FN04_N5381T5760_180min_10ug_C2_053015.pepXML 10/17/2022 09:40 PM 133,732,627 FN05_N5381T5760_180min_10ug_C1_053015.pepXML 10/17/2022 09:41 PM 89,938,341 FN06_N5381T5760_180min_10ug_C2_053015.pepXML 10/17/2022 09:41 PM 136,035,527 FN07_N5381T5760_180min_10ug_C1_053015.pepXML
- 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.)
the pepXML is the output from MSFragger right? If the file is corrupted, why dont you run Fragger again?
FN06_N5381T5760_180min_10ug_C2_053015.zip
Hi, I took a closer look at the offending pepXML file attached. Looks like it has the proper ending tag. The file is quite a bit smaller than the other ones in the folder. Not sure if re-run the search would help.
... </search_hit> </search_result> </spectrum_query> </msms_run_summary> </msms_pipeline_analysis>
Thanks! Wen
Process 'FreeQuant' finished, exit code: 0
FreeQuant [Work dir: G:\contrib\A_36_GC_early_onset_PDC000214\results_isoform\N5381T5760]
E:\Tools\FragPipe\FragPipe-jpe-18\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe freequant --ptw 0.4 --tol 10 --dir G:\contrib\A_36_GC_early_onset_PDC000214\mzML\N5381T5760
INFO[04:29:36] Executing Label-free quantification v4.4.0
INFO[04:30:06] Indexing PSM information
INFO[04:30:11] Reading spectra and tracing peaks
INFO[04:30:11] Processing FN01_N5381T5760_180min_10ug_C1_053015
INFO[04:30:47] Processing FN02_N5381T5760_180min_10ug_C2_053015
INFO[04:31:25] Processing FN03_N5381T5760_180min_10ug_C1_053015
INFO[04:32:01] Processing FN04_N5381T5760_180min_10ug_C2_053015
INFO[04:32:39] Processing FN05_N5381T5760_180min_10ug_C1_053015
INFO[04:33:18] Processing FN06_N5381T5760_180min_10ug_C2_053015
panic: Cannot decode packed binary. XML syntax error on line 3802344: unexpected EOF
goroutine 1 [running]: philosopher/lib/msg.callLogrus({0xc0c1c69e50, 0x4d}, {0xa912c0, 0x1?}) /workspace/philosopher/lib/msg/msg.go:319 +0x354 philosopher/lib/msg.DecodeMsgPck({0xbe0040?, 0xc034ff8240?}, {0xa912c0, 0x5}) /workspace/philosopher/lib/msg/msg.go:120 +0x6e philosopher/lib/psi.(*IndexedMzML).Parse(0xc1235b3ed0, {0xc104648000, 0x63}) /workspace/philosopher/lib/psi/psi.go:115 +0x17b philosopher/lib/mzn.(*MsData).Read(0xc1235b45d0, {0xc104648000, 0x63}) /workspace/philosopher/lib/mzn/mzn.go:194 +0x66 philosopher/lib/qua.peakIntensity({0x0, {{0x0, 0x0}, {0x0, 0x0}, {0x0, 0x0}, {0x0, 0x0}, {0x0, ...}, ...}, ...}, ...) /workspace/philosopher/lib/qua/lfq.go:92 +0xd5d philosopher/lib/qua.RunLabelFreeQuantification({{0x0, 0x0}, {0x0, 0x0}, {0xa90d40, 0x4}, {0xc00013a0c0, 0x38}, {0x0, 0x0}, ...}) /workspace/philosopher/lib/qua/qua.go:46 +0xed philosopher/cmd.glob..func6(0x20342e0?, {0xa90ca0?, 0x6?, 0x6?}) /workspace/philosopher/cmd/freequant.go:50 +0x29a github.com/spf13/cobra.(*Command).execute(0x20342e0, {0xc000166060, 0x6, 0x6}) /home/prvst/go/pkg/mod/github.com/spf13/[email protected]/command.go:844 +0x663 github.com/spf13/cobra.(*Command).ExecuteC(0x2032b40) /home/prvst/go/pkg/mod/github.com/spf13/[email protected]/command.go:945 +0x37c github.com/spf13/cobra.(*Command).Execute(...) /home/prvst/go/pkg/mod/github.com/spf13/[email protected]/command.go:885 philosopher/cmd.Execute() /workspace/philosopher/cmd/root.go:35 +0x25 main.main() /workspace/philosopher/main.go:25 +0x90 Process 'FreeQuant' finished, exit code: 2 Process returned non-zero exit code, stopping ERRO[04:33:37] Cannot decode packed binary. XML syntax error on line 3802344: unexpected EOF
Cancelling 207 remaining tasks
Thanks for your suggestion!
I repeated the mzML conversion with the latest "msconvert" from "ProteoWizard3.0.22293.189308e". Before launching the search on the complete dataset, I was able to successfully search one arbitrary iTraq4 plex (N13T236). However, the plex "N5381T5760" that gave me the error before still yielded the same error as shown in the log file.
Do you think that something is silently wrong about the "FN06_N5381T5760_180min_10ug_C2_053015" run? If so, is there a way to bypass it, so we can complete the overall search? Missing one run from a 24-fractions experiment is probably OK.
Thanks! Wen
log_2022-10-26_12-35-23_failed_plex.txt fully
Hi, here is the pepXML file I was referring to. Let me know if you need the whole plex.
Wen
FN06_N5381T5760_180min_10ug_C2_053015.zip
Hi, can you see if you can access the Box folder via the link? The upload will take some time, but the folder should be there.
https://az.box.com/s/1ar441189nakjlvdoe5kcn7vgboigzsl
Wen
Hi, the Box folder containing the raw, mzML and MsFragger output is now ready. I've also placed the sample manifest in the folder for your reference.
https://az.box.com/s/1ar441189nakjlvdoe5kcn7vgboigzsl
Thanks! Wen
Actually, that's unnecessary. I took the faulty mzML and converted myself from raw again, and got the same problem; the file does not seem to convert all the way to the end. The most likely reason is that you might have a bad raw file. My suggestion is that you try copying from the source again, if possible. In case not, just put it aside.
Thanks for looking into the issue! I was able to complete the search once I removed the offending pepXML and innteract* files in this folder.
Wen