Issue 2402: MiSeq data transfer to LabKey database

Assigned To:rwiseman
Type:Website Issue
Area:Genetics Services
Opened:2013-07-29 by rwiseman
Changed:2013-09-04 by Salendra Singh
Resolved:2013-09-04 by Salendra Singh
2013-07-29 rwiseman
Title»MiSeq data transfer to LabKey database
Assigned To»gstarrett
Notify»Salendra Singh
Type»Website Issue
Area»Genetics Services
MiSeq run 113 hasn't transferred into LabKey automatically so we have to go through the process of getting the FASTQ files off the MiSeq and gzipping them manually before running the genotyping script on the server back in the PCR room (this also appears to be offline). This will be a good exercise for you to go through with Patrick & Patrick after group meeting this morning. Then you can work with our friends a LabKey to sort out what needs to be done to get the raw data transferred from the instrument over to our server. This has been a problem for Dawn and Becca's last 4 runs (#105,108,111 & 112) even though it was working for our MHC runs until yesterday.

2013-09-04 Salendra Singh
Assigned Togstarrett»Salendra Singh
The Data Transfer and Processing is working fine for both Automatic and Manual Transfers. During the Troubleshooting process, I found out various issues with the transfers that are as follows.
     1.    The firewall settings were not letting the Bonobo-Biolinux server to make a connection with the Illumina MiSeq Machine.
     2.    After the data transfer was complete from Illumina MiSeq to Bonobo the script was not processing the data to be transferred to LabKey server at WNPRC.
Both the issues were taken care of by manually setting up for the import and data process.

For manual transfer of data from MiSeq to LabKey Follow experiment: 13628

The present status of the various studies which couldn’t got transferred to LabKey is:
    •    RUN 113: Successfully uploaded on LabKey
    •    RUN 112: Successfully uploaded on LabKey
    •    Run 111: Run ended up in recursive data process. Leading to script not allowing to further processing of data. (Files on Bononbo-Biolinux)
    •    Run 108: Files on Bonobo Couldn’t got processed
    •    Run 105: File that is generated by Illumina MiSeq machine on completion of run was not generated because of unknown reasons. Leading in failure of the transfer.

At present all the scripts and processes are working fine with some problems like low speed at LabKey Server.

2013-09-04 Salendra Singh
resolve as Fixed
Assigned ToSalendra Singh»rwiseman