Problem Files Generated during Processing¶

The problem. files are generated during the intake and processing of records prior to the generation of the check files. Presence of these files generally indicate that a component of processing failed, and the batch needs fixed and resubmitted.

Checking file formatting and contents:¶

problem.no.FinalReport.file: Checking input files; no FinalReport zip file found for SampleSheet zip for 'labcode fname'

problem.org: Validating organization; Invalid lab or possible new lab found

problem.chip.type: Validating chip type; invalid chip found or mismatching chip type for chip designated by number of SNPs inside Final Report file

problem.invalid.date: Checking input file date; incoming file has a future date (invalid)

problem.[ss_file/fr_file]: Directory creation problem; Can not create directory in /edclob/[lab]/FinalReport/[file_date]; Duplicate file-date directory for lab

Sample Sheet Processing¶

problem.requester: Missing requester or invalid requester in file

problem.BadSampleID: Bad/invalid sample ID in file

problem.DupBarcode: Duplicate sentrix barcode/position in file

problem.InvalidNominator: Invalid nominator specified in file

problem.InvalidBarcode: Bad/invalid sentrix barcode/position in file

problem.InvalidTissue: Invalid tissue source in file

Final Report Processing¶

problem.NoValidGenotypes: Empty genotypes.txt file for the lab and file_date

problem.InvalidAllele: Invalid allele value in file; Not 0/1/2/5

problem.MissingSampleID: Missing sample ID in file

problem.DupSampID: Duplicate sample ID in file, which generated a duplicate barcode and position

problem.InvalidSNPnum: Invalid number of SNPs in file

problem.NonMatchingSampleID: Non-matching sample IDs in file

EDCLOB Processing¶

problem.DuplicateData: Multiple occurrences of ‘Opening CLOBDB2’; attempt to grep line with ‘Opening CLOBDB2’ was not successful; Could also be that duplicate barcode/position values were found

problem.deadlock: EDCLOB job abended due to a deadlock situation

problem.Insertion: Job was abended due to an inserted nomination from the web query

problem.mult.genotypes: Animal in file has multiple genotypes with only one of the records having a sire/dam conflict

problem.non_zero_RC: EDCLOB ended with a non-zero return code