read_diann resulting in much fewer fragments than example

[sooheon]

Using my own DIA-NN output and the same FASTA used to generate speclib for DIA-NN input, the output of read-diann results in fewer rows than the input, by half (140k rows => 70k rows). This results in dismal phosphosite/pept ID depth downstream, on the order of a few hundred.

No error during read_diann execution... what could be causing this?

Expected is for the fragment "explosion" to give 12x more rows.

[sooheon]

-v output:

Activate siteloc (use -h for help) ...
Loading FASTA files:
1) Processing [...fasta]
Inserted 104602 proteins into peptide tree.

Processing input file [...tsv].
Skipping input line nr 41936. Sequence look-up error nr 1 :AFSTEK
Skipping input line nr 41937. Sequence look-up error nr 2 :AFSTEK
Skipping input line nr 41938. Sequence look-up error nr 3 :AFSTEK
Skipping input line nr 41939. Sequence look-up error nr 4 :AFSTEK
Skipping input line nr 41940. Sequence look-up error nr 5 :AFSTEK
Skipping input line nr 41941. Sequence look-up error nr 6 :AFSTEK
Skipping input line nr 41942. Sequence look-up error nr 7 :AFSTEK
Skipping input line nr 41943. Sequence look-up error nr 8 :AFSTEK
Skipping input line nr 41944. Sequence look-up error nr 9 :AFSTEK
Skipping input line nr 41945. Sequence look-up error nr 10 :AFSTEK
Skipping input line nr 41946. Sequence look-up error nr 11 :AFSTEK
Skipping input line nr 41947. Sequence look-up error nr 12 :AFSTEK
Skipping input line nr 41948. Sequence look-up error nr 13 :AFSTEK
Skipping input line nr 41949. Sequence look-up error nr 14 :AFSTEK
Skipping input line nr 41950. Sequence look-up error nr 15 :AFSTEK
Skipping input line nr 41951. Sequence look-up error nr 16 :AFSTEK
Skipping input line nr 41952. Sequence look-up error nr 17 :AFSTEK
Skipping input line nr 41953. Sequence look-up error nr 18 :AFSTEK
Skipping input line nr 41954. Sequence look-up error nr 19 :AFSTEK
Skipping input line nr 41955. Sequence look-up error nr 20 :AFSTEK
Skipping input line nr 41956. Sequence look-up error nr 21 :AFSTEK
Skipping input line nr 41957. Sequence look-up error nr 22 :AFSTEK
Skipping input line nr 41958. Sequence look-up error nr 23 :AFSTEK
Skipping input line nr 41959. Sequence look-up error nr 24 :AFSTEK

[sooheon]

-v output with example data file (Phospho_EGF_diAID.tsv) finishes with these two lines, so it seems like the conversion is prematurely stopping without any log:

Skipped 217 lines with peptide backbone sequences not found in FASTA files.
Wrote output to file phospho_egf_report.tsv.

[tvpham]

If I remember correctly, these are contaminant proteins from a MaxQuant search.

[sooheon]

Yeah skipping contaminants is fine, but for the example data the program concludes with a message "wrote output to..." and in my case it does not.