addons.update-checker WARN onUpdateCheckComplete failed to parse update manifest: [Exception... "Update manifest is missing a required addons property

Dear Qiime 2 users,
I am running the feature classifer for my rRNA reads sorted from metatranscriptome datasets.

qiime feature-classifier classify-consensus-vsearch --i-query pear-end-demux-filtered-derepseqs.qza --i-reference-reads 97_otus.qza --i-reference-taxonomy 97_ref-taxonomy.qza --o-classification vsearch_otu --p-threads 20

But I came across the following warning. I have no idea why it happens and how it will influenced my final output results.

1572700178737 addons.repository WARN Search failed when repopulating cache
1572700179458 addons.update-checker WARN onUpdateCheckComplete failed to parse update manifest: [Exception… “Update manifest is missing a required addons property.” nsresult: “0x80004005 (NS_ERROR_FAILURE)” location: “JS frame :: resource://gre/modules/addons/AddonUpdateChecker.jsm :: getRequiredProperty :: line 473” data: no] Stack trace: getRequiredProperty()@resource://gre/modules/addons/AddonUpdateChecker.jsm:473 < parseJSONManifest()@resource://gre/modules/addons/AddonUpdateChecker.jsm:483 < UpdateParser.prototype.onLoad/parser()@resource://gre/modules/addons/AddonUpdateChecker.jsm:655 < UpdateParser.prototype.onLoad()@resource://gre/modules/addons/AddonUpdateChecker.jsm:675 < UpdateParser/<()@resource://gre/modules/addons/AddonUpdateChecker.jsm:593
1572700179477 addons.update-checker WARN onUpdateCheckComplete failed to parse update manifest: [Exception… “Update manifest is missing a required addons property.” nsresult: “0x80004005 (NS_ERROR_FAILURE)” location: “JS frame :: resource://gre/modules/addons/AddonUpdateChecker.jsm :: getRequiredProperty :: line 473” data: no] Stack trace: getRequiredProperty()@resource://gre/modules/addons/AddonUpdateChecker.jsm:473 < parseJSONManifest()@resource://gre/modules/addons/AddonUpdateChecker.jsm:483 < UpdateParser.prototype.onLoad/parser()@resource://gre/modules/addons/AddonUpdateChecker.jsm:655 < UpdateParser.prototype.onLoad()@resource://gre/modules/addons/AddonUpdateChecker.jsm:675 < UpdateParser/<()@resource://gre/modules/addons/AddonUpdateChecker.jsm:593
1572700179492 addons.update-checker WARN onUpdateCheckComplete failed to parse update manifest: [Exception… “Update manifest is missing a required addons property.” nsresult: “0x80004005 (NS_ERROR_FAILURE)” location: “JS frame :: resource://gre/modules/addons/AddonUpdateChecker.jsm :: getRequiredProperty :: line 473” data: no] Stack trace: getRequiredProperty()@resource://gre/modules/addons/AddonUpdateChecker.jsm:473 < parseJSONManifest()@resource://gre/modules/addons/AddonUpdateChecker.jsm:483 < UpdateParser.prototype.onLoad/parser()@resource://gre/modules/addons/AddonUpdateChecker.jsm:655 < UpdateParser.prototype.onLoad()@resource://gre/modules/addons/AddonUpdateChecker.jsm:675 < UpdateParser/<()@resource://gre/modules/addons/AddonUpdateChecker.jsm:593
1572700179523 addons.update-checker WARN onUpdateCheckComplete failed to parse update manifest: [Exception… “Update manifest is missing a required addons property.” nsresult: “0x80004005 (NS_ERROR_FAILURE)” location: “JS frame :: resource://gre/modules/addons/AddonUpdateChecker.jsm :: getRequiredProperty :: line 473” data: no] Stack trace: getRequiredProperty()@resource://gre/modules/addons/AddonUpdateChecker.jsm:473 < parseJSONManifest()@resource://gre/modules/addons/AddonUpdateChecker.jsm:483 < UpdateParser.prototype.onLoad/parser()@resource://gre/modules/addons/AddonUpdateChecker.jsm:655 < UpdateParser.prototype.onLoad()@resource://gre/modules/addons/AddonUpdateChecker.jsm:675 < UpdateParser/<()@resource://gre/modules/addons/AddonUpdateChecker.jsm:593
1572700179538 addons.update-checker WARN onUpdateCheckComplete failed to parse update manifest: [Exception… “Update manifest is missing a required addons property.” nsresult: “0x80004005 (NS_ERROR_FAILURE)” location: “JS frame :: resource://gre/modules/addons/AddonUpdateChecker.jsm :: getRequiredProperty :: line 473” data: no] Stack trace: getRequiredProperty()@resource://gre/modules/addons/AddonUpdateChecker.jsm:473 < parseJSONManifest()@resource://gre/modules/addons/AddonUpdateChecker.jsm:483 < UpdateParser.prototype.onLoad/parser()@resource://gre/modules/addons/AddonUpdateChecker.jsm:655 < UpdateParser.prototype.onLoad()@resource://gre/modules/addons/AddonUpdateChecker.jsm:675 < UpdateParser/<()@resource://gre/modules/addons/AddonUpdateChecker.jsm:593
console.error:
Message: Error: Error(s) encountered during statement execution: too many SQL variables
Stack:

Thank you very much.

Best regards,
Qianqian

2 Likes

Following that , I get the classification qza output and running the below command to get the visualized taxa_barplot successfully:
qiime taxa barplot --i-table pear-end-demux-filtered.table.qza --i-taxonomy vsearch_otu.qza --m-metadata-file metadata_1million.txt --o-visualization taxa_barplot.qzv.

However, when I imported the biom output into R, R crashed. I am wondering why it happens.
I am sure it is not my R problem becaue I imported the other biom output successfully.

I am thinking maybe the problem of output biom file should be result from the above warning.
Can anyone help me why it happens and how I can modify my biom output.

Thank you very much.

Best regards,
Qianqian

Hi @Qianqian!

This isn’t actually coming from QIIME 2, it appears to be logging output from Firefox, or perhaps some other tool installed in your environment. Either way, it looks like QIIME 2 ran successfully.

Are you sure it actually crashed, or is it just more noise from Firefox?

Dear @thermokarst,
Thanks for your quick reply. I am sure it is the noise from Firefox because I used R in my personal laptop not the server.
I used the qiime2R package in R to export otu table and taxonomy table from qza output in QIIME2. Then I imported the otu table, taxonomy table into R and built a phyloseq file. It worked.
I still had no clue why the biom file didn’t work.
Hope othe QIIME2 users leave their suggestions.
Thanks.
Best regards,
Qianqian

2 Likes

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