# MinION Mk1B (MN32863) Final report

22 Feb 23, 08:19 — 22 Feb 23, 08:38 · Test17 · Test17 · MN32863
Protocol run ID: 85c46a1a-4791-4521-bcda-a807b6ea90ff
Run summary

## DATA OUTPUT

Estimated bases
1.91 Mb
Data produced
53.29 MB
Reads generated
4.28 k
Estimated N50
425

## BASECALLING

Reads called
100%
Bases called (min Q score: 1)
1.54 Mb
0

## RUN DURATION

#### Elapsed time

15 minutes of 15 minutes

#### Run status

#### Finished

View unit abbreviations used in this report
Run configuration

##
RUN SETUP

Flow cell type
FLO-MIN106
Flow cell type alias
FLO-MIN106
Flow cell ID
FAV65050
Kit type
SQK-RBK110-96

##
RUN SETTINGS

Specified run length
0.25 hrs
Active channel selection
On
Pore scan freq.
0.25 hrs
Reserved pores
On
Minimum read length
200 bp
Read splitting
Off
Basecalling
Fast model, 450 bps
Modified basecalling
Off
Trim barcodes
On
Mid-read barcode filtering
On

##
DATA OUTPUT SETTINGS

FAST5 output
vbz_compress
FAST5 reads per file
20
FASTQ output
gzip_compress
FASTQ reads per file
20
BAM output
Off
Bulk file output
Off
Data location
/home/idun/test_watcher/data/PathoSense_Diagnostics/Test17/Test17/20230222_0919_MN32863_FAV65050_85c46a1a

##
SOFTWARE VERSIONS

MinKNOW
22.12.7
Bream
7.4.8
Configuration
5.4.7
Guppy
6.4.6
MinKNOW Core
5.4.3
Sequence output

##
READ LENGTHS · OUTLIERS REMOVED

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
425
% Basecalled
100%

##
OUTLIERS

The longest 1% of strands are classified as outliers, and aggregated into groups to show their relative amounts.

Read length (kb) | Aggregated reads (kb)
--- | ---
28.75 - 29 | 15.38

##
BARCODED READS

The total number of bases for each barcode is calculated and displayed below.

Total bases (Gb) | Barcodes
--- | ---
0–1 | barcode01 (Reads: 0) barcode02 (Reads: 0) barcode03 (Reads: 0) barcode04 (Reads: 0) barcode05 (Reads: 0) barcode06 (Reads: 0) barcode07 (Reads: 0) barcode08 (Reads: 0) barcode09 (Reads: 0) barcode10 (Reads: 0) barcode11 (Reads: 0) barcode12 (Reads: 0) barcode13 (Reads: 0) barcode14 (Reads: 0) barcode15 (Reads: 0) barcode16 (Reads: 0) barcode17 (Reads: 0) barcode18 (Reads: 0) barcode19 (Reads: 0) barcode20 (Reads: 0) barcode21 (Reads: 0) barcode22 (Reads: 0) barcode23 (Reads: 0) barcode24 (Reads: 0) barcode25 (Reads: 0) barcode26 (Reads: 0) barcode27 (Reads: 0) barcode28 (Reads: 0) barcode29 (Reads: 0) barcode30 (Reads: 0) barcode31 (Reads: 0) barcode32 (Reads: 0) barcode33 (Reads: 0) barcode34 (Reads: 0) barcode35 (Reads: 0) barcode36 (Reads: 0) barcode37 (Reads: 0) barcode38 (Reads: 0) barcode39 (Reads: 0) barcode40 (Reads: 0) barcode41 (Reads: 0) barcode42 (Reads: 0) barcode43 (Reads: 0) barcode44 (Reads: 0) barcode45 (Reads: 0) barcode46 (Reads: 0) barcode47 (Reads: 0) barcode48 (Reads: 0) barcode49 (Reads: 0) barcode50 (Reads: 0) barcode51 (Reads: 0) barcode52 (Reads: 0) barcode53 (Reads: 0) barcode54 (Reads: 0) barcode55 (Reads: 0) barcode56 (Reads: 0) barcode57 (Reads: 58) barcode58 (Reads: 50) barcode59 (Reads: 216) barcode60 (Reads: 137) barcode61 (Reads: 91) barcode62 (Reads: 134) barcode63 (Reads: 103) barcode64 (Reads: 98) barcode65 (Reads: 95) barcode66 (Reads: 161) barcode67 (Reads: 271) barcode68 (Reads: 204) barcode69 (Reads: 191) barcode70 (Reads: 132) barcode71 (Reads: 0) barcode72 (Reads: 0) barcode73 (Reads: 0) barcode74 (Reads: 0) barcode75 (Reads: 0) barcode76 (Reads: 0) barcode77 (Reads: 0) barcode78 (Reads: 0) barcode79 (Reads: 0) barcode80 (Reads: 0) barcode81 (Reads: 0) barcode82 (Reads: 0) barcode83 (Reads: 0) barcode84 (Reads: 0) barcode85 (Reads: 0) barcode86 (Reads: 0) barcode87 (Reads: 0) barcode88 (Reads: 0) barcode89 (Reads: 0) barcode90 (Reads: 0) barcode91 (Reads: 0) barcode92 (Reads: 0) barcode93 (Reads: 0) barcode94 (Reads: 0) barcode95 (Reads: 0) barcode96 (Reads: 0)

##
CUMULATIVE OUTPUT

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.

##
QUALITY SCORE

The quality score is calculated as basecalling is performed on your device. Reads that fall below the minimum value of 1 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.

####
Troubleshooting

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.

Run health

##
PORE ACTIVITY

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
Out of range-low
Current is negative but unavailable for sequencing
Multiple
Multiple pores detected. Unavailable for sequencing.
Saturated
The channel has switched off as current levels exceed hardware limitations
Zero
Pore currently unavailable for sequencing
Channel disabled
Channel is disabled and awaiting another pore scan
Unclassified
Pore status unknown

####
Troubleshooting

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.

##
PORE SCAN

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 0.2 hrs.

#### Legend

Pore available
Pore in channel available for sequencing
Reserved pore
Pore in reserve, will return to available when required
Unavailable
Pore inhibited from sequencing
Saturated
Possible contamination in the sample
Zero
No current is passing through this pore, possibly due to bubbles on the membrane
Inactive
Pore no longer suitable for further sequencing

####
Troubleshooting

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.

##
TRANSLOCATION SPEED

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

####
Troubleshooting

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.

##
TEMPERATURE

The temperature of the Flow Cell over the run time.

#### Legend

Measured
Target

####
Troubleshooting

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.

Run log

## SYSTEM MESSAGES

System messages are a record of the events that occurred in the time covered by this report.

Errors
None
Warnings
Disk usage alert · 22 Feb 23, 08:24
Disk usage alert – you only have 379 GB of space free, which is insufficient for the run. Please free up some space, otherwise your run will stop in approximately 111d 8h 41m.
Events
Disk space · 22 Feb 23, 08:19
Disk / has 379 GB space remaining
Waiting for temperature · 22 Feb 23, 08:19
Waiting up to 300 seconds for temperature to stabilise at 34.0°C
Starting · 22 Feb 23, 08:22
Starting sequencing procedure
Pore scan starting · 22 Feb 23, 08:22
Performing Pore Scan
Pore scan result · 22 Feb 23, 08:25
Pore scan for flow cell FAV65050 has found a total of 87 pores. 75 pores available for immediate sequencing
Message · 22 Feb 23, 08:37
The sequencing run has finished, but basecalling may continue
UNIT ABBREVIATIONS
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Base
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Kilobase
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Megabase
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Gigabase
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Minutes
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Hours
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