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DEBUG-lines in json-reports #11

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jonbra opened this issue Dec 8, 2024 · 1 comment
Open

DEBUG-lines in json-reports #11

jonbra opened this issue Dec 8, 2024 · 1 comment

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@jonbra
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jonbra commented Dec 8, 2024

Hi,
When I pull the latest images for running HCV-GLUE I now get a lot of lines starting with "DEBUG". But the rest of the json-report seems to be ok, and the corresponding html-report seems to be ok. Do I need to be worried about this? It breaks my downstream json-parser, but this I can fix by removing the DEBUG lines.

First lines of json file:

DEBUG   17336   [freemark] (): Couldn't find template in cache for "utils/glueDocUtils.ftlx"("en", UTF-8, parsed); will try to load it.
DEBUG   17336   [freemark] (): TemplateLoader.findTemplateSource("utils/glueDocUtils_en.ftlx"): Not found
DEBUG   17336   [freemark] (): TemplateLoader.findTemplateSource("utils/glueDocUtils.ftlx"): Found
DEBUG   17336   [freemark] (): Loading template for "utils/glueDocUtils.ftlx"("en", UTF-8, parsed) from "jar:file:/opt/gluetools/lib/gluetools-core.jar!/freemarker/utils/glueDocUtils.ftlx"
DEBUG   17336   [freemark] (): "utils/glueDocUtils.ftlx"("en", UTF-8, parsed) cached copy not yet stale; using cached.
DEBUG   17336   [freemark] (): "utils/glueDocUtils.ftlx"("en", UTF-8, parsed) cached copy not yet stale; using cached.
DEBUG   17336   [freemark] (): "utils/glueDocUtils.ftlx"("en", UTF-8, parsed) cached copy not yet stale; using cached.
DEBUG   17336   [freemark] (): "utils/glueDocUtils.ftlx"("en", UTF-8, parsed) cached copy not yet stale; using cached.
DEBUG   17336   [freemark] (): "utils/glueDocUtils.ftlx"("en", UTF-8, parsed) cached copy not yet stale; using cached.
DEBUG   17336   [freemark] (): "utils/glueDocUtils.ftlx"("en", UTF-8, parsed) cached copy not yet stale; using cached.
DEBUG   17336   [freemark] (): "utils/glueDocUtils.ftlx"("en", UTF-8, parsed) cached copy not yet stale; using cached.
DEBUG   17336   [freemark] (): "utils/glueDocUtils.ftlx"("en", UTF-8, parsed) cached copy not yet stale; using cached.
DEBUG   17336   [freemark] (): "utils/glueDocUtils.ftlx"("en", UTF-8, parsed) cached copy not yet stale; using cached.
DEBUG   17336   [freemark] (): "utils/glueDocUtils.ftlx"("en", UTF-8, parsed) cached copy not yet stale; using cached.
DEBUG   17336   [freemark] (): "utils/glueDocUtils.ftlx"("en", UTF-8, parsed) cached copy not yet stale; using cached.
DEBUG   17336   [freemark] (): "utils/glueDocUtils.ftlx"("en", UTF-8, parsed) cached copy not yet stale; using cached.
DEBUG   17336   [freemark] (): "utils/glueDocUtils.ftlx"("en", UTF-8, parsed) cached copy not yet stale; using cached.
DEBUG   17336   [freemark] (): "utils/glueDocUtils.ftlx"("en", UTF-8, parsed) cached copy not yet stale; using cached.
DEBUG   17336   [freemark] (): "utils/glueDocUtils.ftlx"("en", UTF-8, parsed) cached copy not yet stale; using cached.
DEBUG   17336   [freemark] (): "utils/glueDocUtils.ftlx"("en", UTF-8, parsed) cached copy not yet stale; using cached.
DEBUG   17336   [freemark] (): "utils/glueDocUtils.ftlx"("en", UTF-8, parsed) cached copy not yet stale; using cached.
DEBUG   17336   [freemark] (): "utils/glueDocUtils.ftlx"("en", UTF-8, parsed) cached copy not yet stale; using cached.
DEBUG   17336   [freemark] (): "utils/glueDocUtils.ftlx"("en", UTF-8, parsed) cached copy not yet stale; using cached.
DEBUG   17336   [freemark] (): "utils/glueDocUtils.ftlx"("en", UTF-8, parsed) cached copy not yet stale; using cached.
DEBUG   17336   [freemark] (): "utils/glueDocUtils.ftlx"("en", UTF-8, parsed) cached copy not yet stale; using cached.
DEBUG   17336   [freemark] (): "utils/glueDocUtils.ftlx"("en", UTF-8, parsed) cached copy not yet stale; using cached.
DEBUG   17336   [freemark] (): "utils/glueDocUtils.ftlx"("en", UTF-8, parsed) cached copy not yet stale; using cached.
DEBUG   17336   [freemark] (): "utils/glueDocUtils.ftlx"("en", UTF-8, parsed) cached copy not yet stale; using cached.
DEBUG   17336   [freemark] (): "utils/glueDocUtils.ftlx"("en", UTF-8, parsed) cached copy not yet stale; using cached.
DEBUG   17336   [freemark] (): "utils/glueDocUtils.ftlx"("en", UTF-8, parsed) cached copy not yet stale; using cached.
DEBUG   17336   [freemark] (): "utils/glueDocUtils.ftlx"("en", UTF-8, parsed) cached copy not yet stale; using cached.
DEBUG   17336   [freemark] (): "utils/glueDocUtils.ftlx"("en", UTF-8, parsed) cached copy not yet stale; using cached.
DEBUG   17336   [freemark] (): "utils/glueDocUtils.ftlx"("en", UTF-8, parsed) cached copy not yet stale; using cached.
DEBUG   17336   [freemark] (): "utils/glueDocUtils.ftlx"("en", UTF-8, parsed) cached copy not yet stale; using cached.
DEBUG   17336   [freemark] (): "utils/glueDocUtils.ftlx"("en", UTF-8, parsed) cached copy not yet stale; using cached.
DEBUG   17336   [freemark] (): "utils/glueDocUtils.ftlx"("en", UTF-8, parsed) cached copy not yet stale; using cached.
DEBUG   17336   [freemark] (): "utils/glueDocUtils.ftlx"("en", UTF-8, parsed) cached copy not yet stale; using cached.
DEBUG   17336   [freemark] (): "utils/glueDocUtils.ftlx"("en", UTF-8, parsed) cached copy not yet stale; using cached.
DEBUG   17336   [freemark] (): "utils/glueDocUtils.ftlx"("en", UTF-8, parsed) cached copy not yet stale; using cached.
DEBUG   17336   [freemark] (): "utils/glueDocUtils.ftlx"("en", UTF-8, parsed) cached copy not yet stale; using cached.
DEBUG   17336   [freemark] (): "utils/glueDocUtils.ftlx"("en", UTF-8, parsed) cached copy not yet stale; using cached.
DEBUG   17336   [freemark] (): "utils/glueDocUtils.ftlx"("en", UTF-8, parsed) cached copy not yet stale; using cached.
DEBUG   17336   [freemark] (): "utils/glueDocUtils.ftlx"("en", UTF-8, parsed) cached copy not yet stale; using cached.
DEBUG   17336   [freemark] (): "utils/glueDocUtils.ftlx"("en", UTF-8, parsed) cached copy not yet stale; using cached.
DEBUG   17336   [freemark] (): "utils/glueDocUtils.ftlx"("en", UTF-8, parsed) cached copy not yet stale; using cached.
DEBUG   17336   [freemark] (): "utils/glueDocUtils.ftlx"("en", UTF-8, parsed) cached copy not yet stale; using cached.
DEBUG   17336   [freemark] (): "utils/glueDocUtils.ftlx"("en", UTF-8, parsed) cached copy not yet stale; using cached.
DEBUG   17336   [freemark] (): "utils/glueDocUtils.ftlx"("en", UTF-8, parsed) cached copy not yet stale; using cached.
DEBUG   17336   [freemark] (): "utils/glueDocUtils.ftlx"("en", UTF-8, parsed) cached copy not yet stale; using cached.
DEBUG   17336   [freemark] (): "utils/glueDocUtils.ftlx"("en", UTF-8, parsed) cached copy not yet stale; using cached.
DEBUG   17336   [freemark] (): "utils/glueDocUtils.ftlx"("en", UTF-8, parsed) cached copy not yet stale; using cached.
DEBUG   17336   [freemark] (): "utils/glueDocUtils.ftlx"("en", UTF-8, parsed) cached copy not yet stale; using cached.
DEBUG   17336   [freemark] (): "utils/glueDocUtils.ftlx"("en", UTF-8, parsed) cached copy not yet stale; using cached.

{
    "phdrReport":{
        "sequenceDataFormat":"SAM/BAM",
        "filePath":"2173510-HCV.5a_AF064490_major.major.nodup.bam",
        "samReferenceResult":{
            "id":"5a_AF064490",
            "samReference":{
                "name":"5a_AF064490",
                "length":9408,
                "index":0,
                "species":null,
                "assembly":null
            },
            "isForwardHcv":true,
            "isReverseHcv":false,
            "placements":[
                {
                    "placementIndex":1,
                    "likeWeightRatio":1,
                    "edgeIndex":81,
                    "distalLength":0.022096,
                    "pendantLength":0.043364,
                    "logLikelihood":-717469.146241
                }
            ],
            "genotypingResult":{
                "queryName":"5a_AF064490",
                "queryCladeCategoryResult":[
                    {
....
@robjgiff
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robjgiff commented Dec 9, 2024

Hi Jon,
Thanks for letting me know - I will take a look and get back to you this week.
Cheers,
Rob

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