Output Hash File¶
The output hash file is a CSV file, containing one row per output MinKNOW file. It is intended to confirm the integrity of the written output data.
Paths¶
The following path patterns are used to place the data on disk:
| File | Path Pattern |
|---|---|
| Output Hash File | output_hash_{flow_cell_id}_{daq_start_time}_{short_protocol_run_id}.csv |
See the Patterns documentation for more information on file patterns.
Columns¶
runid¶
[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}| Examples |
|---|
e4994c62-93f9-439a-bc8f-d20c95a137a5 |
A random-generated uuid for the sequencing protocol (eg:
e4994c62-93f9-439a-bc8f-d20c95a137a5) This consists only of lower-case ASCII letters
(a-z), digits (0-9) and dashes (-). This maps to the protocol_run_id in the pod5 file.
protocol_group_id¶
[a-zA-Z0-9_\.-]+| Examples |
|---|
My_Group |
my-group-1 |
Set by the user in the GUI as "Experiment ID".
flow_cell_id¶
[A-Z0-9-]+| Examples |
|---|
FXX12345 |
PXX12345 |
AAA123 |
The human-readable identifier for the flow cell (eg: FAK54854).
sample_id¶
[a-zA-Z0-9_\.-]+| Examples |
|---|
My_Sample |
my-sample-1 |
Set by the user in the GUI as "Sample ID".
file_hash¶
|[0-9a-f]{64}| Examples |
|---|
e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855 |
The sha256 hash of the file. Can be empty for files which we do not calculate a hash for, e.g. pod5 files
file_path¶
[a-zA-Z0-9_@\./\\-]+| Examples |
|---|
bam_pass/foo.bam |
sequencing_summary_FLG-TEST01_d6b3339f.txt |
The protocol relative path to the output file.
barcode¶
|unclassified|mixed|barcode([0-9]+)| Examples |
|---|
|
unclassified |
barcode01 |
The barcode for the data in the file
barcode_alias¶
|[a-zA-Z0-9_@\.]+| Examples |
|---|
|
my_sample |
sample01 |
The user-supplied alias for the barcode. Empty if barcoding is not running. The same as barcode
if the user did not supply an alias.
basecall_status¶
|pass|fail|skip|not_run|pass_or_fail|all|target| Examples |
|---|
|
pass |
fail |
skip |
not_run |
pass_or_fail |
all |
target |
When files are separated by basecall status of their reads, this field will indicate the file's status. pass/fail/skip correspond to files which contain a single basecall_status. not_run corresponds to files which contain reads that did not have the basecaller enabled pass_or_fail corresponds to files which contain reads that were either passed or failed by the basecaller all is for files which don't discriminate against basecall status target is for files which were specifically selected for in the basecall configuration -- this status is not currently used