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2 - Bed Verification failed! February 20, 2015 - 11:03 am
[Error ID: 20022015110256] Bed verification has failed: Bed 9 barcode (580000009659) differs from config bed barcode (580000006856) at /local/scratch01/clarity/bin/../lib/perl5/wtsi_clarity/epp/generic/bed_verifier.pm line 39. at /local/scratch01/clarity/bin/../lib/perl5/wtsi_clarity/epp/generic/bed_verifier.pm line 44. at /local/scratch01/clarity/bin/epp line 58.

has bed 6 configured? needs bed 9

It could be a permission issue with the file being read.

Page URL: .../clarity/work-details/26353

Error message:
2 - Bed Verification failed! February 3, 2015 - 2:40 pm
[Error ID: 03022015144030] Bed verification has failed: Can't call method "findvalue" on an undefined value
at .../wtsi_clarity/util/roles/clarity_process_io.pm line 94.
at .../wtsi_clarity/epp/generic/bed_verifier.pm line 46.
at .../bin/epp line 58.

Morninig all,

Please do not fall off your chairs but I am doing some testing. I am currently in Fluidigm STA plate creation. When I begin work it takes me to the record details screen but I then get the attached error. I am not sure if I have made a stupid error? I therefore cannot get further than this step as it aborts the process and takes me back to the ice bucket contents.

Thanks,

Lucy

There is a space before SBS96 that needs to be removed and there is a space in the Sample Concentration column in all cells/lines that needs to be removed.

wtsi_clarity::genotyping::fluidigm::assay->is_call will return 'true' for Invalid calls (results that have
been manually declared invalid with the Fluidigm software) which is not correct.

Page URL: http://web-claritytest-01.internal.sanger.ac.uk:8080/clarity/work-details/26301

Error message:
16- Print Tube Labels failed! January 30, 2015 - 11:58 amEncountered an error while executing the external program [-17ce71a6:14b3a238d2f:-77ac] Error executing command: /software/bin/perl /local/scratch01/npg_clarity/bin/print_label.pl -u {username} -p {password} -l 122-26301.

2 - Bed Verification failed! February 4, 2015 - 1:10 pm
[Error ID: 04022015130958] Bed verification has failed: Bed 9 barcode (580000009659) differs from config bed barcode (580000006856) at /local/scratch01/clarity/bin/../lib/perl5/wtsi_clarity/epp/generic/bed_verifier.pm line 41. at /local/scratch01/clarity/bin/../lib/perl5/wtsi_clarity/epp/generic/bed_verifier.pm line 46. at /local/scratch01/clarity/bin/epp line 58.

http://web-claritytest-01.internal.sanger.ac.uk:8080/clarity/work-details/26364

Instead of saying 'Unknown' for empty wells, it should say 'NTC'

Can we generate some labels for reagents ie Ethanol/water etc?

wtsi_clarity::genotyping::fluidigm::file_wrapper calls the writer method '_write_content' for the 'content' attribute. This method isn't implemented because the Moose role that provided it has been deleted from the class.

To correct this issue, we probably need to add a 'shadow_plate = 1' option to the stamping action.

Barcodes usually have a 'signature' in their bottom left corner, generated using the inputs of the process. This seems to have gone missing.

4 - Validate Tag Plate failed! March 2, 2015 - 3:00 pm
Run method is called for class wtsi_clarity::epp::isc::plate_tagger, process http://web-claritytest-01.internal.sanger.ac.uk:8080/api/v2/processes/24-28704

http://web-claritytest-01.internal.sanger.ac.uk:8080/clarity/work-details/28704

1 - Print Barcode failed! January 28, 2015 - 10:46 am[Error ID: 28012015104645] No analytes registered at reader wtsi_clarity::epp::generic::label_creator::_container (defined at .../wtsi_clarity/epp/generic/label_creator.pm line 173) line 7. at .../bin/epp line 58.

In the log we have the following entry about this error:

[Error ID: 21012015144555] XPath error : Undefined namespace prefix error : xmlXPathCompiledEval: evaluation failed at .../clarity/bin/epp line 58.
2015-01-21 14:45:55,474 ERROR pool-1-thread-4 - com.genologics.ai.ErrorMessage@70870c6e[
name=externalProgramException
message=Run method is called for class wtsi_clarity::epp::isc::calliper_analyser, process http://clarityurl:8080/api/v2/processes/24-24866
XPath error : Undefined namespace prefix
error : xmlXPathCompiledEval: evaluation failed
[Error ID: 21012015144555] XPath error : Undefined namespace prefix error : xmlXPathCompiledEval: evaluation failed at .../clarity/bin/epp line 58.

throwable=
]

The page URL: http://web-claritytest-01.internal.sanger.ac.uk:8080/clarity/work-details/26246

Error message:
2 - Bed Verification failed! January 30, 2015 - 11:40 am[Error ID: 30012015114027] Bed verification has failed: Bed 9 barcode (580000009659) differs from config bed barcode (580000006856)
at .../wtsi_clarity/epp/generic/bed_verifier.pm line 41.
at .../wtsi_clarity/epp/generic/bed_verifier.pm line 46.
at .../bin/epp line 58.

Input plate = 1 or 2
Output plate = 9 or 10

When pico analysis runs it seems to work all correctly i.e. a PDF is generated, however, the status that Clarity gives is failed with the message "Script Failed".

The results that Clarity produce are off with SequenceScape's by a factor of ~50.

This is probably because SS performs its calculations against the stock plate (which hasn't been diluted down by a factor of 10 during working dilution, and then a factor of 5 for pico dilution, hence out by a factor of 50).

Also CV is being displayed as 0.00 for every well

Means that users can not scan a plate into the ice box.

Most likely a config issue.

After generating the caliper file, this step should show the molarity values on the analytes.

From 'Post Lib PCR QC Stamp' step a '384 plate' is going to the 'Pre Capture Lib Pooling' step instead of a '96 plate'.

Raised by Lucy.

Process is failing to find a standard file with barcode 1220378476729 although seems to work fine with shorter barcode (1234 at least).

In this step there is no output plate, just tubes. So, we might add a new option to the script which allows to verify only the input bed, like '--only_input 1'.

The TECAN data mapping is correct, goes to the right wells but not very efficiently.
It should be a sorted list starting from well A:1 (1) to H:12 (96).

On QC report concentrations appears as 50x what they should.

'Undefined value on Array reference'

Signature fails for plate - possibly because there are no samples, only controls

Page URL: http://web-claritytest-01.internal.sanger.ac.uk:8080/clarity/work-details/26301

2 - Bed Verification failed! January 30, 2015 - 11:56 am[Error ID: 30012015115604] Bed verification has failed: Bed 1 can not be found in config for specified robot
at .../wtsi_clarity/epp/generic/bed_verifier.pm line 41.
at .../wtsi_clarity/epp/generic/bed_verifier.pm line 46. at .../bin/epp line 58.

We only need to verify the Input plate 1 and not the 5.

Some of our dependencies builds are failing, because their dependencies tests are failing.
We should force preinstall them, before installing our dependencies.

Page URL: .../clarity/work-details/26353

Error message:
2 - Bed Verification failed! February 3, 2015 - 11:12 am[Error ID: 03022015111208]
No callback for action bed_verification
at .../clarity/bin/epp line 34.
at .../clarity/bin/epp line 58.

Page URL: .../clarity/work-details/26360

Error message:
2 - Bed Verification failed! February 3, 2015 - 11:33 am[Error ID: 03022015113333]
No callback for action bed_verification
at .../clarity/bin/epp line 34.
at .../clarity/bin/epp line 58.

2 - Bed Verification failed! February 5, 2015 - 2:35 pm
[Error ID: 05022015143530] Bed verification has failed: Can't call method "findvalue" on an undefined value at /local/scratch01/clarity/bin/../lib/perl5/wtsi_clarity/util/roles/clarity_process_io.pm line 94. at /local/scratch01/clarity/bin/../lib/perl5/wtsi_clarity/epp/generic/bed_verifier.pm line 46. at /local/scratch01/clarity/bin/epp line 58.

http://web-claritytest-01.internal.sanger.ac.uk:8080/clarity/work-details/26353

Script hangs. Doesn't even appear as started in the EPP logs. Script works fine on other steps.

The version of XML::LibXML should be at least 2.0105, because we are using the 'to_literal_list' method from XML::LibXML::NodeList package. Earlier versions does not have this method implemented, yet.

Not sure what error message is being generated, but doesn't produce the report!

2 - Bed Verification failed! February 4, 2015 - 8:06 am
[Error ID: 04022015080634] Bed verification has failed: Bed 6 can not be found in config for specified robot at /local/scratch01/clarity/bin/../lib/perl5/wtsi_clarity/epp/generic/bed_verifier.pm line 41. at /local/scratch01/clarity/bin/../lib/perl5/wtsi_clarity/epp/generic/bed_verifier.pm line 46. at /local/scratch01/clarity/bin/epp line 58.

http://web-claritytest-01.internal.sanger.ac.uk:8080/clarity/work-details/26362

11 - Create Robot Driver File successful! February 13, 2015 - 11:57 am
at reader wtsi_clarity::epp::isc::pool_beckman_creator::internal_csv_output (defined at /local/scratch01/clarity/bin/../lib/perl5/wtsi_clarity/epp/isc/pool_beckman_creator.pm line 59) line 7.

Where does this file go so i can look at it?

At Pico Analysis, our EPP script finds the previous processes of the input artifacts from each of the 2 plates. However, if either (or both) of the plates have been through Pico DTX more than once, the script will still take the earliest version.

Needs to be take the latest version!

It prolongs the wash steps

2 - Bed Verification failed! February 13, 2015 - 12:07 pm
[Error ID: 13022015120737] Bed verification has failed: Expected source plate 2460274028854 to be paired with destination plate 2460274385803 at /local/scratch01/clarity/bin/../lib/perl5/wtsi_clarity/epp/generic/bed_verifier.pm line 41. at /local/scratch01/clarity/bin/../lib/perl5/wtsi_clarity/epp/generic/bed_verifier.pm line 46. at /local/scratch01/clarity/bin/epp line 58.

http://web-claritytest-01.internal.sanger.ac.uk:8080/clarity/work-details/26966

Displays error message 'the file has no pages'. Is fixed by Pull Request #284 but more work to be done apparently

16- Print Tube Labels failed! February 4, 2015 - 1:45 pm
Run method is called for class wtsi_clarity::epp::generic::label_creator, process http://web-claritytest-01.internal.sanger.ac.uk:8080/api/v2/processes/122-26368

http://web-claritytest-01.internal.sanger.ac.uk:8080/clarity/work-details/26368

input bed 4 580000004838

output 4, 5 mini hub 580000045695

The PDF gets generated with concentration values on just fine. However, for some reason, CV values are missing from it.