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freeseek / gtc2vcf

Tools to convert Illumina IDAT/BPM/EGT/GTC and Affymetrix CEL/CHP files to VCF
MIT License
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IDAT not found #27

Closed whecrane closed 3 years ago

whecrane commented 3 years ago

Hi freeseek, Thank you for your help yesterday and I installed the gtc2vcf successfully. But when I convert idat to gtc, the IDAT always not found at the location. I tried many times but can't solve it. I checked the bpm and egt, I am sure they are right: Chip Prefix (Guess),InfiniumPsychArray-24v1-1 I don't know why the idat not found, my idat files just like this: GSM3096512_200687150051_R01C01_Grn.idat GSM3096512_200687150051_R01C01_Red.idat

This is the log: ArrayAnalysis.NormToGenCall.CLI.App[0] [10:25:21 2352]: Crawling /media/EXTend2018/Wanghe2019/GEO/GSE113093/GSE113093_RAW for samples ... info: ArrayAnalysis.NormToGenCall.CLI.App[0] [10:25:21 3578]: Number of samples to process: 103 info: ArrayAnalysis.NormToGenCall.Services.NormToGenCallSvc[0] [10:25:21 3714]: Starting processing... Manifest file: /media/EXTend2018/Wanghe2019/GEO/GSE113093/InfiniumPsychArray-24v1-1_A1.bpm Cluster file: /media/EXTend2018/Wanghe2019/GEO/GSE113093/InfiniumPsychArray-24v1-1_A1_ClusterFile.egt Include file: Output directory: /media/EXTend2018/Wanghe2019/GEO/GSE113093 GenCall score cutoff: 0.15 GenTrain ID: 3 Gender Estimate Settings: Version: 2 MinAutosomalLoci : 100 MaxAutosomalLoci : 10000 MinXLoci : 20 MinYLoci : 20 AutosomalCallRateThreshold : 0.97 YIntensityThreshold : 0.3 XIntensityThreshold : 0.9 XHetRateThreshold : 0.1 Output Settings: Output GTC: True Output PED: False PED tab delmited: False PED use customer strand: False Number of threads: 1 Buffer size: 131072

info: ArrayAnalysis.NormToGenCall.Services.NormToGenCallSvc[0] [49m: ArrayAnalysis.NormToGenCall.Services.NormToGenCallSvc[0] [12:33:32 8929]: Failed to normalize or gencall - GSM3096512_200687150051_R01C01: IDAT not found at location: /media/EXTend2018/Wanghe2019/GEO/GSE113093/GSE113093_RAW/GSM3096512_200687150051_Red.idat at ArrayAnalysis.NormToGenCall.Services.SampleNormToGenCallSvc.LoadIdat(String idatPath, Manifest manifest) in /src/ArrayAnalysis.NormToGenCall.Services/Services/SampleNormToGenCallSvc.cs:line 63 at ArrayAnalysis.NormToGenCall.Services.SampleNormToGenCallSvc.Normalize(NormalizationBase normAlg, Manifest manifest, Byte[] transformLookups, Boolean needGreen, Boolean needRed, SampleData sample, String[] includeLociNames) in /src/ArrayAnalysis.NormToGenCall.Services/Services/SampleNormToGenCallSvc.cs:line 106 at ArrayAnalysis.NormToGenCall.Services.NormToGenCallSvc.<>c__DisplayClass7_0.b__2(SampleData sample) in /src/ArrayAnalysis.NormToGenCall.Services/Services/NormToGenCallSvc.cs:line 113 ...There are many idat files fault like this.

Best wishes, Crane

freeseek commented 3 years ago

If you read the error message:

 [12:33:32 8929]: Failed to normalize or gencall - GSM3096512_200687150051_R01C01: IDAT not found at location: /media/EXTend2018/Wanghe2019/GEO/GSE113093/GSE113093_RAW/GSM3096512_200687150051_Red.idat

It shows that iaap-cli is looking for file GSM3096512_200687150051_Red.idat rather than file GSM3096512_200687150051_R01C01_Red.idat. How did it get to look for that? Well, someone at Illumina made the beautiful assumption that IDAT files are named xxx_xxx_Grn.idat and xxx_xxx_Red.idat and someone from NCBI GEO made the beautiful assumption that it is okay to rename IDAT files.

You put the two things together and that's what you get, unfortunately. I mostly blame Illumina here though.