Warnings in .vidjil files⚓︎
These warnings are found in .vidjil files and alert the user on some unusual result.
They will be displayed in the Vidjil web application. Some warnings are related to individual clones or reads,
whereas some others are related to the dataset or the programs used. They can be produced by vidjil-algo
or by any RepSeq program or script willing to inform the user.
The following list is a work-in-progress, with links to gitlab issues in Vidjil. Warnings which were implemented ([x]) have a fixed code that should not be changed for backward compatibility.
Generic errors⚓︎
- W0x Outdated program
- Outdated germlines
- Strange parameters: xxxx xxxx
- W0z Unknown error
- W09 Program interrupted, output data may be not complete
Output of a pre-process ~"server-pre-process"⚓︎
- W10 Few assembled reads #2243
- W1z Other pre-processing warning/error
Output of an analysis, global warnings⚓︎
- W20 Very few V(D)J recombinations found (0.7%)
- W21 Doubtful e-value multiplier
- W2x Sequences with known adapters #1669
- W2x CDR3 detection without gapped germlines #2187 (ou bien par clone ?)
Output of an analysis, warnings on some clonotypes⚓︎
MRD analysis⚓︎
- W31 This clone is identified as a spike and has a very low or very high normalization factor compared to other spikes for the given locus
- W32 This clone is identified as a spike that should have been found in the sample but was not
Read quality⚓︎
- W40 Low quality #1544
Clonotype quality (KmerSegmenter in vidjil-algo)⚓︎
- W50 Short or shifted window in vidjil-algo
- W51 Low coverage (0.112)
- Bad e-value (0.xxx) #1437/#1566/#1889
- W53 Similar to another clonotype
- Possible strand ambiguity
Strange recombination (FineSegmenter in vidjil-algo), V and J genes⚓︎
- Potential co-linear genome match (pos xxxxxx) #1664 #1629
- W61 Non-recombined D7-27/J1 sequence #2232
- W62 Region(s) length below expected range
- W63 Region(s) length above expected range
- W64 Region(s) nucleotide count not a multiple of 3
- Potential di-mer #2820
- Very large deletion (xxx bp) #2909
- Unexpected recombination
- High probability clonotype ?
- W68 V(D)J designation failed, possibly complex or not recombined sequence #4818
- W69 Several V/J candidate genes with equal probability #3575
Strange recombination (FineSegmenter in vidjil-algo), D gene, N regions*⚓︎
- W7x Mutations near breakpoint #1412
- Palindromic sequence ?
- D with bad e-value ?