Closed GoogleCodeExporter closed 9 years ago
I cant find a sequence (<domain seq=".*" ... > which contains a ">" or is empty.
Havent looked at source code though... error message might be misleading
though....
Original comment by i.really...@googlemail.com
on 18 Mar 2014 at 11:03
I'm pretty sure this bug is related to this one
http://code.google.com/p/searchgui/issues/detail?id=23. It would seem that a
FASTA header is mistaken for a protein sequence.
I've improved the error message so that it will now state:
Error parsing the sequence of "your_accession". Protein sequence:
"your_sequence".
But will also try to improve our FASTA file parsing so that this should not
happen in future version. A new version of PeptideShaker will be available
shortly.
Original comment by harald.b...@gmail.com
on 18 Mar 2014 at 9:49
this issue is independent of
http://code.google.com/p/searchgui/issues/detail?id=23
I fixed the DB before running SearchGUI.
Peptideshaker will also go through a couple of steps before crashing:
Wed Mar 19 15:15:40 CET 2014 Importing sequences from
all_concatenated_target_decoy.fasta. Wed Mar 19 15:17:18 CET
2014 FASTA file import completed. Wed Mar 19 15:17:18 CET
2014 Establishing local database connection. Wed Mar 19 15:17:24
CET 2014 Reading identification files. Wed Mar 19 15:17:24 CET
2014 Parsing Toni_20130527_AE_Exp87_sample11_01.t.xml. Wed Mar
19 15:17:53 CET 2014 Importing
Toni_20130527_AE_Exp87_sample11_01.mgf Wed Mar 19 15:17:53 CET
2014 Toni_20130527_AE_Exp87_sample11_01.mgf imported. Wed Mar 19
15:17:53 CET 2014 Importing PSMs from
Toni_20130527_AE_Exp87_sample11_01.t.xml Wed Mar 19 15:26:01 CET
2014 File import completed. 34968 first hits imported (284
secondary) from 36556 spectra. Wed Mar 19 15:26:01 CET
2014 [32563 first hits passed the initial filtering] Wed Mar 19
15:26:01 CET 2014 Computing assumptions probabilities. Wed Mar
19 15:26:01 CET 2014 Saving assumptions probabilities. Wed Mar
19 15:26:01 CET 2014 Selecting best peptide per spectrum. Wed
Mar 19 15:26:23 CET 2014 Computing PSM probabilities. Wed Mar 19
15:26:23 CET 2014 Scoring PTMs in PSMs (D-score and A-score) Wed
Mar 19 15:27:28 CET 2014 Thresholding PTM localizations. Wed Mar
19 15:27:28 CET 2014 Resolving peptide inference issues. Wed Mar
19 15:27:46 CET 2014 Saving probabilities, building peptides and
proteins. Wed Mar 19 15:28:49 CET 2014 Simplifying protein
groups. Wed Mar 19 15:29:04 CET 2014 481 unlikely mappings
found. (82% non-enzymatic accessions, 17% lower evidence accessions, 1% not
characterized accessions) Wed Mar 19 15:29:04 CET
2014 Generating peptide map. Wed Mar 19 15:29:20 CET
2014 Computing peptide probabilities. Wed Mar 19 15:29:20 CET
2014 Saving peptide probabilities. Wed Mar 19 15:29:20 CET
2014 Generating protein map. Wed Mar 19 15:29:21 CET
2014 Resolving protein inference issues, inferring peptide and
protein PI status. Wed Mar 19 15:31:24 CET 2014 Importing Data
Canceled! Wed Mar 19 15:31:24 CET 2014 An error occured while
loading the identification files: Wed Mar 19 15:31:24 CET
2014 No amino acid found for letter >.
Original comment by i.really...@googlemail.com
on 19 Mar 2014 at 2:56
Well, maybe the issues are not directly linked but the main problem seems to be
the same. One of the proteins in your FASTA file does not have a protein
sequence, hence the next line, starting with '>...' is assumed to be the
protein sequence and PeptideShaker then fails trying to convert '>" into an
amino acid.
But as stated above this should be fixed in the new upcoming versions of
SearchGUI and PeptideShaker. In the meantime I'd recommend double checking your
FASTA files for protein headers without sequence, and delete the related
database index files (the .fasta.cui files stored next to the FASTA files).
This should solve the problem. Let me know if this is not the case.
I will let you know when the new versions are available. Hopefully later this
week or early next week.
Original comment by harald.b...@gmail.com
on 19 Mar 2014 at 4:30
Original issue reported on code.google.com by
i.really...@googlemail.com
on 18 Mar 2014 at 10:57