Question: Bcl to fastq Conversion Problem
0
BioRyder • 160 wrote:
Hello,
Below are the summary of Bcl to fastq conversion by using bcl2fastq v2.16.0.10 .In Output folder only lane 4 and 5 are having R1 and R2 reads (18 GB ) and remaining all lanes (1,2,3,6,7,8) are having R1 and R2 reads with zero size. If We are looking into lane summary ,last four columns are showing there were data generated for all lanes. Can any one tell me why the data are missing and reports showing data generated... ?
| Clusters (Raw) | Clusters(PF) | Yield (MBases) |
|---|---|---|
| 3,861,446,400 | 2,333,759,444 | 704,795 |
Flowcell Summary
Lane Summary
| Lane | Raw data | Filtered data | |||||||
|---|---|---|---|---|---|---|---|---|---|
| # | Clusters | % of the lane |
% Perfect barcode |
% One mismatch barcode |
Clusters | Yield (Mbases) | % PF Clusters |
% >= Q30 bases |
Mean Quality Score |
| 1 | 482,680,800 | 100.00 | 0.00 | 0.00 | 315,981,885 | 95,427 | 65.46 | 87.52 | 37.35 |
| 2 | 482,680,800 | 100.00 | 0.00 | 0.00 | 294,018,812 | 88,794 | 60.91 | 87.41 | 37.31 |
| 3 | 482,680,800 | 100.00 | 0.00 | 0.00 | 306,362,193 | 92,521 | 63.47 | 86.42 | 37.07 |
| 4 | 482,680,800 | 100.00 | 0.00 | 0.00 | 312,679,038 | 94,429 | 64.78 | 87.17 | 37.22 |
| 5 | 482,680,800 | 100.00 | 0.00 | 0.00 | 269,671,083 | 81,441 | 55.87 | 84.35 | 36.42 |
| 6 | 482,680,800 | 100.00 | 0.00 | 0.00 | 302,801,644 | 91,446 | 62.73 | 84.90 | 36.60 |
| 7 | 482,680,800 | 100.00 | 0.00 | 0.00 | 218,432,818 | 65,967 | 45.25 | 77.27 | 34.33 |
| 8 | 482,680,800 | 100.00 | 0.00 | 0.00 | 313,811,971 | 94,771 | 65.01 | 86.58 | 37.12 |
Is everything ending up in the Undetermined_*.fastq.gz files? That would explain the results. This would indicate that your sample sheet is incorrect.
Hello Devon Ryan,
There is no Undetermined_*.fastq.gz files in out put directory , Because I have not mentioned any index in Sampleshee.csv to convert bcl to fastq.
Below is the Index file .
[Header],,,,,,,,
IEMFileVersion,4,,,,,,,
Date,1/12/15,,,,,,,
Workflow,GenerateFASTQ,,,,,,,
Application,HISeq FASTQ Only,,,,,,,
Assay,,,,,,,,
Description,,,,,,,,
Chemistry,Default,,,,,,,
,,,,,,,,
[Reads],,,,,,,,
151,,,,,,,,
151,,,,,,,,
,,,,,,,,
[Settings],,,,,,,,
ReverseComplement,0,,,,,,,
Adapter,AGATCGGAAGAGCACACGTCTGAACTCCAGTCA,,,,,,,
AdapterRead2,AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT,,,,,,,
,,,,,,,,
[Data],,,,,,,,
Lane,Sample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,Sample_Project,Description
1,PhiX_Sample_Stock,PhiX_Sample_Stock,,,,,PhiX,
2,Spix_44G,Spix_44G,,,,,Spix_Macaw,
3,Spix_45G,Spix_45G,,,,,Spix_Macaw,
4,PhiX_Sample_Stock,PhiX_Sample_Stock,,,,,PhiX,
5,Spix_73G,Spix_73G,,,,,Spix_Macaw,
6,Spix_74G,Spix_74G,,,,,Spix_Macaw,
7,Spix_95G,Spix_95G,,,,,Spix_Macaw,
8,Spix_109G,Spix_109G,,,,,Spix_Macaw,
Presumably it's hitting an error, check the log file.
We haven't switched to v2, but v1 would exhibit this behavior if there were missing .bcl or .stats files. You can add the relevant flags (in v1, I believe it's '--ignore-missing-stats --ignore-missing-bcl') and try again.