Status Messages

This page provides sample status messages of a common iPiG or GeneControl run as well as their meaning. They apply to the command line and the gui version.
Sometimes, additional processing information is given in log files (*.log) in the iPiG or output directory.

iPiG

Status Messages (examples)	Descriptions
start ipig...
read ms peptides... processed 11760 of 20541 in 1 s	Imports 11760 of 20541 peptide spectrum matches (PSMs), the rest have either an uncertain format or are decoy peptides
read protein ids (1)... processed 1209 of 110056 in 22 s	Extracts several IDs from 1209 of 110056 entries in the Uniprot Mapping file. Please note, several peptides might belong to the same protein (thus the low number).
read protein ids (2)... processed 0 of 69906 in 9 s	Extracts further IDs from 0 of 69906 fasta protein entries.
read annotations... processed 2403 of 58694 in 4 s	Imports 2403 of 58694 gene annotations, selected by the extracted IDs. All isoforms are included.
read aa sequences... processed 2403 of 62378 in 7 s	Imports the corresponding amino acid translations.
map to genome (1)... processed 7920 of 11760 in 12 s	Mapping 7920 of 11760 PSMs to genome via referred genes (Annotation Mapping).
read annotations... processed 58694 of 58694 in 6 s	Imports all gene annotations.
read aa sequences... processed 58694 of 62378 in 8 s	Imports the corresponding amino acid translations.
map to genome (2)... processed 3146 of 11760 in 10 s	Mapping 3146 of 11760 PSMs to genome via all genes (Alternative Mapping).
write map peptides... processed 11066 of 11760 in 0 s	Writes the mapped PSMs to text files
write left peptides... processed 694 of 11760 in 0 s (no prots: 163, no genes: 425, no matches: 106)	Writes the unmapped PSMs to a text file. Either, there were no IDs for a PSM’s protein (no prots), the IDs didn’t linked a gene (no genes) or the amino acid sequence didn’t include the peptide (no matches).
write bed... processed 11066 of 11760 in 2 s	Writes the mapped PSMs to BED files
write gff3... processed 11066 of 11760 in 0 s	Writes the mapped PSMs to GFF3 files
done in 89 sec

GeneControl

Status Messages (examples)	Descriptions
start gene control...
read annotations... processed 77614 of 77614 in 7 s	Imports all gene annotations.
check for non-coding genes and uncommon chromosomes	Removes non-coding genes and genes on special chromosomes (e.g. “chr6_apd_hap1“)
check integrity in 64 parts with 926 genes each	Due to memory limits (heap size), the genes are divided in subparts.
part 1 of 64... read aa sequences... done read gene sequences... done	For each part, the corresponding amino acid sequences and the nucleotide sequences are imported. Nucleotide sequences get translated and compared with the amino acid sequences. Sequences are removed afterwards to free memory.
part 2 of 64... read aa sequences... done read gene sequences... done
…
done