PromethION Beta (PCT0052) Final report
03 Nov 22, 20:40 — 06 Nov 22, 20:42 · X0222 · MU1301 · 2-E3-H3
Protocol run ID: 012537b7-c929-4cde-8a3b-b19cdfde4fd7
DATA OUTPUT
Estimated bases
4.72 Gb
Data produced
230.1 GB
Reads generated
5.89 M
Estimated N50
1.04 kb
BASECALLING
Reads called
100%
Bases called (min Q score: 7)
4.06 Gb
245.52 Mb
RUN DURATION
Elapsed time
72 hours of 72 hours
Run status
Finished
Flow cell type
FLO-PRO002
Flow cell type alias
FLO-PRO002
Flow cell ID
PAM69124
Kit type
SQK-RNA002
Specified run length
72hrs
Active channel selection
On
Pore scan freq.
1.5hrs
Reserved pores
On
Read splitting
Off
Basecalling
High-accuracy model
Modified basecalling
Off
FAST5 output
vbz_compress
FAST5 reads per file
4000
FASTQ output
gzip_compress
FASTQ reads per file
4000
BAM output
Off
Bulk file output
Off
Data location
/data/./X0222/MU1301/20221103_2040_2-E3-H3_PAM69124_012537b7
MinKNOW
22.08.6
Bream
7.2.8
Configuration
5.2.5
Guppy
6.2.7
MinKNOW Core
5.2.2
The read length graph shows the total number of bases vs the read length. The longest 1% of strands are classified as outliers, and excluded to allow focus on the main body of data.
Legend
Basecalled
Estimated
Estimated N50
1.04 kb
% Basecalled
100%
The longest 1% of strands are classified as outliers, and aggregated into groups to show their relative amounts.
| Read length (kb) | Aggregated reads (Mb) |
|---|---|
| 2.625 - 4.625 | 39.32 |
| 4.625 - 6.625 | 1.21 |
| 6.625 - 7.9375 | 0.08 |
The cumulative output shows the total amount of bases or reads sequenced over time by your device.
Bases
Legend
Estimated
Predicted total number of bases, prior to basecalling
Passed
Bases equal to or above the quality score threshold.
Failed
Bases below the quality score threshold.
Reads
Legend
Total
Total number of reads, including passed, failed and skipped.
Passed
Reads equal to or above the quality score threshold.
Failed
Reads below the quality score threshold.
Skipped
Reads that will not be basecalled. Post run basecalling is possible.
The quality score is calculated as basecalling is performed on your device. Reads that fall below the minimum value of 7 will be classified as failed reads. You can alter the accepted minimum quality score in MinKNOW.
Legend
Mode
The most frequent quality score of reads in the run.
Spread
The spread of quality scores, found by calculating full width half maximum.
Min. quality score
Minimum quality score to be accepted as a passed read.
Quality score low
This can be due to the translocation speed being out of the accepted range, which can correlate to low quality scores. If you see that the translocation speed is out of the accepted range in the below graph, please see the Flow Cell refuelling page linked here for further troubleshooting.
The Pore activity graph shows the performance of your sample as it is being sequenced during a run.
Legend
Sequencing
Pore currently sequencing
Adapter
Pore currently sequencing adapter
Pore available
Pore available for sequencing
Unavailable
Pore unavailable for sequencing
Active feedback
Channel ejecting analyte
No pore
No pore detected in channel
Out of range-high
Current is positive but unavailable for sequencing
Multiple
Multiple pores detected. Unavailable for sequencing.
Saturated
The channel has switched off as current levels exceed hardware limitations
Out of range-low
Current is negative but unavailable for sequencing
Zero
Pore currently unavailable for sequencing
Channel disabled
Channel is disabled and awaiting another pore scan
Unclassified
Pore status unknown
General
Some commonly seen issues are excess pores classified as Recovering, Open Pore, or Free Adapter. To find out what advice is applicable for your run, visit the user guide.
A Pore scan is performed at configurable time intervals to determine the current status of pores within channels on a Flow Cell. For this run a Pore scan is performed every 1.5hrs.
Legend
Single Pore
Pore in channel available for sequencing
Reserved Pore
Pore in reserve, will return to available when required
Saturated
Possible contamination in the sample
Zero
No current is passing through this pore, possibly due to bubbles on the membrane
Unavailable
Pore inhibited from sequencing
Inactive
Pore no longer suitable for further sequencing
High proportion Unavailable
Possible contaminants in library blocking the pore. Consider using the Flow Cell Wash Kit, and reloading a library.
High proportion Inactive
If localised to one area of the Flow Cell, this could indicate that an air bubble has been introduced during the flushing/loading steps. If inactivity is spread across the Flow Cell this could be caused by improper loading of the library, please refer to the user guide for further support.
The translocation speed is the rate at which DNA/RNA travels through pores as it is being sequenced.
Legend
Median
75% quartile
25% quartile
Accepted range
Low speed
Check that the Flow Cell is within the target temperature range.
Note
Low-quality and short reads are not included in this graph.
The temperature of the Flow Cell over the run time.
Legend
Measured
Target
Out of range
Check that the Flow Cell is correctly seated and firmly pushed down into the device. Ensure ambient temperature is always within the specified range for your device in the user guide.
Air flow should be good but not excessive. Excessive amounts of cool air blowing on the device could prevent it from reaching target temperature.
SYSTEM MESSAGES
System messages are a record of the events that occurred in the time covered by this report.
Byte
B
Kilobyte
KB
Megabyte
MB
Gigabyte
GB
Terabyte
TB
Base
b
Kilobase
kb
Megabase
Mb
Gigabase
Gb
Terabase
Tb
Minutes
mins
Hours
hrs