It is possible to generate FASTQ files, even if a MiSeq run does not
complete. To do so, determine the last cycle with a complete set of
*.bcl files, modify run files, and requeue analysis. This bulletin
describes how to generate FASTQ files from an incomplete run using
Before you start:
- If you plan to do secondary analysis on the MiSeq, make sure
that a sequencing run is not in progress and that MiSeq Reporter is
ready for analysis.
- If you opted for BaseSpace, it is not
possible to generate FASTQ files from a partial run and save the
analysis in BaseSpace. The analysis must be performed locally.
- If the run stopped before completing the index reads (ie, in
Read 1), it is not possible to demultiplex your samples.
- Make sure that the RTAComplete.txt file is
not present in the run folder.
Steps to take:
- Go to
and check which cycle was the last to generate all *.bcl files. If
v3 reagents were used, there are 38 *.bcl files per cycle. If v2
reagents were used, there are 28 *.bcl files per cycle.
*If .bcl files are not present, it might be possible to
recover them by manually launching RTA. To do so, contact
Illumina Technical Support
Calculate how many cycles have been successfully
completed and extracted.
Run stopped at cycle 207 in a 2 x 150 + 6 bp index run. If
the last cycle with complete *.bcl files was cycle 206, it is a
good rule of thumb not to push against the last cycle with
complete *.bcl files. Select the previous complete cycle from
which to do the analysis. In this case, it is
cycle 205. The run breakdown is (R1) 150 + (R2 Index) 6 +
(R3) 49 = 205 cycles.
- Backup the original RunInfo.xml and
SampleSheet.csv files by renaming them to something like
RunInfo.xml.BAK and SampleSheet.csv.BAK. Using
Notepad, edit these documents and save the edited documents as
RunInfo.xml and SampleSheet.csv in the root run folder
in MiSeqAnalysis. If the reverse read of a paired-end run – Read 3
in the following example – has not been performed, delete the
corresponding line in RunInfo.xml and
<Read Number="2" IsIndexedRead="Y"
- Copy an RTAComplete.txt file from a successful run
folder and paste it into your run folder.
- You can
expect to see the run queued in MiSeq Reporter and a
QueuedForAnalysis.txt file created in the run folder in
MiSeqAnalysis. To make sure that the run has been requeued in MiSeq
Reporter, point a web browser window to http://localhost:8042 and
look for your run in the list opened with the Analyses