Question: Bcl to fastq conversion problem in bcl2fastq-2.17
0
gravatar for BioRyder
3.8 years ago by
BioRyder160
India
BioRyder160 wrote:

Hello All,

I am facing some some problem while trying to convert bcl to fastq by using bcl2fastq-2.17 software.Partial generation of output data is the problem. R1 and R2 reads are generated for lane 4.But for Lane1,2,3, only Read2 generated and no data for other lanes.While checking the Report folder there are status report present for each lane.It will be a great help for me if any body can help me to find out the problem. Hiseq2500 is used for generating the data.

The following command I used for bcl to fastq conversion.

nohup bcl2fastq --runfolder-dir /data/coredata/genomics/hiseq/150827_SN1046_0229_BC6WPEACXX/ --output-dir /data/coredata/genomics/hiseq/150827_SN1046_0229_BC6WPEACXX/TEST/ --sample-sheet /data/coredata/genomics/hiseq/150827_SN1046_0229_BC6WPEACXX/SampleSheet.csv --use-bases-mask Y*,I8n*,Y* --barcode-mismatches 2 -l DEBUG &

Sample sheet Format is below:

[Data],,,,,,,,

Lane,Sample_ID,Sample_Name,Sample_Plate,Sample_Well,Index_ID,Index,Sample_Project,Description
1,DPWGS-00088,DPWGS-00088,,,,NoIndex,DatePalm_-_Date_Fruits,
2,DPWGS-00089,DPWGS-00089,,,,NoIndex,DatePalm_-_Date_Fruits,
3,DPWGS-00072,DPWGS-00072,,,,NoIndex,DatePalm_-_Date_Fruits,
4,DPWGS-00078,DPWGS-00078,,,,NoIndex,DatePalm_-_Date_Fruits,
5,DPWGS-00247,DPWGS-00247,,,,AGTACAAG,DatePalm_-_Date_Fruits,
5,DPWGS-00267,DPWGS-00267,,,,GACTAGTA,DatePalm_-_Date_Fruits,
6,DPWGS-00263,DPWGS-00263,,,,AGTCACTA,DatePalm_-_Date_Fruits,
6,DPWGS-00268,DPWGS-00268,,,,CAATGGAA,DatePalm_-_Date_Fruits,
7,32,32,,,,GACTAGTA,DatePalm_-_Date_Fruits,
7,DPWGS-00079,DPWGS-00079,,,,CTGAGCCA,DatePalm_-_Date_Fruits,
8,31,31,,,,NoIndex,DatePalm_-_Date_Fruits,

Status Report are below:

Flowcell Summary

Clusters (Raw) Clusters(PF) Yield (MBases)
2,243,033,353 1,710,124,620 342,025

Lane Summary

Lane PF Clusters % of the
lane
% Perfect
barcode
% One mismatch
barcode
Yield (Mbases) % PF
Clusters
% >= Q30
bases
Mean Quality
Score
1 0       46,813 74.81 75.65 33.00
2 0       40,294 64.81 72.67 32.12
3 0       46,675 91.71 87.04 35.26
4 0       13,543 26.86 53.72 27.30
5 244,751,056 100.00 97.46 1.88 48,950 84.95 79.86 33.46
6 237,309,355 100.00 72.61 25.73 47,462 91.76 87.45 35.40
7 243,656,285 100.00 92.56 6.93 48,731 90.96 86.39 35.19
8 0       49,557 83.13 80.02 33.
bcl2fastq-2.17 • 4.1k views
ADD COMMENTlink modified 3.3 years ago by Biostar ♦♦ 20 • written 3.8 years ago by BioRyder160

NoIndex changed to empty while running the script

ADD REPLYlink written 3.8 years ago by BioRyder160

Hi All,

We have identified the problem.The above mentioned problem is happened due to File format of linux Server. Bcl2fast Version is working properly in XFS file system. But If we are using gpfs file system in Linux server,bcl2fastq V2 is generating partial out put file, missing R1 or both R1 and R2. We have contacted illumina and informed the same. They are internally checking the issue of Bcl2fast with gpfs file system.

ADD REPLYlink written 3.3 years ago by BioRyder160
2
gravatar for dbrawand
3.6 years ago by
dbrawand20
dbrawand20 wrote:

I have a similar problem when writing on a NFS share. Some of the fastq files get scrambled at the end or are incomplete (gzip CRC fails on decompression)

Setting the writing threads to 1 has solved this problem in my case (option -w 1).

ADD COMMENTlink written 3.6 years ago by dbrawand20
0
gravatar for Ido Tamir
3.8 years ago by
Ido Tamir5.0k
Austria
Ido Tamir5.0k wrote:

a) techsupport@illumina.com is the best adress for this question

b) dont write noIndex, simply leave the index field empty

c) how can you have data for lane 4?

ADD COMMENTlink written 3.8 years ago by Ido Tamir5.0k
0
gravatar for BioRyder
3.8 years ago by
BioRyder160
India
BioRyder160 wrote:

hello Ido Tamir,

Thank you for your reply.Yes I have removed Noindex into empty while converting the data.Report file is based on that changes.

 

 

ADD COMMENTlink written 3.8 years ago by BioRyder160
0
gravatar for BioRyder
3.8 years ago by
BioRyder160
India
BioRyder160 wrote:

Hi All,

We have identified the problem.The above mentioned problem is happened due to File format of linux Server. Bcl2fast Version is working properly in XFS file system. But If we are using gpfs file system in Linux server,bcl2fastq V2 is generating partial out put file, missing R1 or both R1 and R2. We have contacted illumina and informed the same. They are internally checking the issue of Bcl2fast with gpfs file system. 

ADD COMMENTlink written 3.8 years ago by BioRyder160
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