FAQ

A sequencing run was completed, but it doesn't appear in openBIS browser

This can be due to a multitude of reasons.

• The first place to look into is the backup log files on the MiSeq computer where the run was sequenced. Launch Cygwin and look for error messages in the log file backupt2timavo.log in the home directory. Some error messages are simply due to the fact that for some files it was impossible to set the creation date correctly.
• If files were correctly copied into datamover, connect from MiSeq computer with ssh ozagor@datamover. This should work passwordless as public keys have been set up. No directory should still be present in ~/data/outgoing/; when file .MARKER_is_finished_directory_name is created they are moved to the openBIS dropbox. Some information can be found by looking into files /tmp/datamover_daemon.err and /tmp/datamover_daemon.log.
• If nothing strange is found in the log files, go to openBIS with the browser and look into Utilities --> Dropbox monitor.

I need to register a run and its samples again

Sometimes there are errors in the sample sheet that result in wrong demultiplexing. In these cases, one has to delete all samples from openBIS in the browser and register again.

Select all relevant samples in the experiment MISEQ_SAMPLES (click on the first, then Shift + click on the last) and delete them. If the project is RESISTANCE, delete also the samples in experiment RESISTANCE_TESTS. Finally, delete the run from MISEQ_RUNS. Then go to Trash and empty it selecting "Delete permanently".
WATCH OUT: be extra careful in deleting everything from the relevant MiSeq run. Sample names are unique and trying to register a sample with a name already present will result in an error.

Then go to the MiSeq computer where the run was sequenced and identify the root folder of the run. This is /cygdrive/d/Illumina/MiSeqOutput/YYMMDD-MiSeq_run_name (in Cygwin, while in Windows Explorer it is D:\Illumina\...). Delete the hidden file .UPLOADED_RUN from this folder. Double-click on the desktop icon "backup2timavo" again, wait a few minutes and check in openBIS browser again.

Samples are present, but they are not correctly mapped (no parent/child relationship)

Log into nevoso and check the log file pybis_script.log in the home directory. This script is usually run every hour, so the modification time of the log file should never been older than an hour before (give ls -lrht and check the time of the computer with the command date, it is UTC). If it's much older, the script has stopped running, check the crontab file with crontab -l. If there are errors reported in the log file, act accordingly.

How can I download a fastq file stored in openBIS?

Go to MISEQ_SAMPLE --> Data Sets --> click on the code --> click on the folder with the sample identifier --> click on the fastq.gz file

How can I download multiple data files?

The answer might be found in the openBIS documentation under downloading of data using CIFEX.

What do I do if I get an error message?

It depends on the error message.