Open HadleyKing opened 8 months ago
Validating the following object only returns "Bad request. BCO is not formatted correctly."
More detail should be included.
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"https://scihive.fda.gov/dna.cgi?cmd=objFile&ids=637703" }, { "uri": "https://scihive.fda.gov/dna.cgi?cmd=objFile&ids=637702" } ], "output_list": [ { "uri": "https://scihive.fda.gov/dna.cgi?cmd=objFile&ids=843914&filename=dna-alignx_screenResult.csv" }, { "uri": "https://scihive.fda.gov/dna.cgi?cmd=objFile&ids=843914&filename=dna-alignx_screenShannon.csv" }, { "uri": "https://scihive.fda.gov/dna.cgi?cmd=objFile&ids=843914&filename=dna-alignx_acclist.csv" }, { "uri": "https://scihive.fda.gov/dna.cgi?cmd=objFile&ids=843914&filename=coverage_dict" }, { "uri": "https://scihive.fda.gov/dna.cgi?cmd=objFile&ids=843914&filename=_.progress.json" } ] }, { "step_number": 2, "name": "HIVE-Hexagon", "description": "HIVE hexagon alignment engine optimized for HIVE cloud performance on Next Generation data", "input_list": [ { "uri": "https://scihive.fda.gov/dna.cgi?cmd=objFile&ids=20607" }, { "uri": "https://scihive.fda.gov/dna.cgi?cmd=objFile&ids=637703" }, { "uri": "https://scihive.fda.gov/dna.cgi?cmd=objFile&ids=637702" } ], "output_list": [ { "uri": "https://scihive.fda.gov/dna.cgi?cmd=objFile&ids=843915&filename=coverage_dict" }, { "uri": "https://scihive.fda.gov/dna.cgi?cmd=objFile&ids=843915&filename=alignment.hiveal" }, { "uri": "https://scihive.fda.gov/dna.cgi?cmd=objFile&ids=843915&filename=histogram.csv" }, { "uri": "https://scihive.fda.gov/dna.cgi?cmd=objFile&ids=843915&filename=_.progress.json" } ] } ] }, "execution_domain": { "script": [ { "uri": { "uri": "" } } ], "script_driver": "", "software_prerequisites": [ { "name": "", "version": "", "uri": { "uri": "" } } ], "external_data_endpoints": [ { "name": "HIVE", "url": "https://scihive.fda.gov/dna.cgi?cmd=login" } ], "environment_variables": { } }, "parametric_domain": [ { "param": "_type", "value": "svc-dna-screening", "step": "1" }, { "param": "name", "value": "Patient_205_R1_fastq", "step": "1" }, { "param": "CensusIterations", "value": "1", "step": "1" }, { "param": "CensuslimitIterations", "value": "50", "step": "1" }, { "param": "chunk_size", "value": "4000", "step": "1" }, { "param": "cutOffvalue", "value": "0.0005", "step": "1" }, { "param": "filterNs", "value": "true", "step": "1" }, { "param": "random_seed", "value": "0", "step": "1" }, { "param": "Sample", "value": "10", "step": "1" }, { "param": "slice", "value": "0", "step": "1" }, { "param": "alignSelector", "value": "svc-align-blast", "step": "1" }, { "param": "automanual", "value": "0", "step": "1" }, { "param": "taxDepth", "value": "species", "step": "1" }, { "param": "subject", "value": "653801", "step": "1" }, { "param": "resultInQueryDir", "value": "0", "step": "1" }, { "param": "selfStopping", "value": "true", "step": "1" }, { "param": "storeAlignments", "value": "false", "step": "1" }, { "param": "blastparams", "value": "{\"blastWordSize\":28,\"blastMegablast\":true,\"blastevalue\":0.000001}", "step": "1" }, { "param": "censusScope_otherInput", "value": 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"mismatches", "value": "{\"13.0\":{\"maxMissQueryPercent\":3,\"considerGoodSubalignments\":1}}", "step": "2" }, { "param": "computeDiagonalWidth", "value": "auto", "step": "2" }, { "param": "doubleHash", "value": "false", "step": "2" }, { "param": "doubleStagePerfect", "value": "1", "step": "2" }, { "param": "hashCompileStp", "value": "2", "step": "2" }, { "param": "hashStp", "value": "auto", "step": "2" }, { "param": "isbackward", "value": "1", "step": "2" }, { "param": "isextendtails", "value": "0", "step": "2" }, { "param": "isoptimize", "value": "1", "step": "2" }, { "param": "keepAllMatches", "value": "0", "step": "2" }, { "param": "looseExtenderMinimumLengthPercent", "value": "66", "step": "2" }, { "param": "looseExtenderMismatchesPercent", "value": "15", "step": "2" }, { "param": "maxExtensionGaps", "value": "0", "step": "2" }, { "param": "maxHashBin", "value": "50", "step": "2" }, { "param": "maxHitsPerRead", "value": "50", "step": "2" }, { "param": "maxNumberQuery", "value": "all", "step": "2" }, { "param": "random_seed", "value": "0", "step": "2" }, { "param": "readconflicts", "value": "{\"resolveConfictsUnique\":false}", "step": "2" }, { "param": "reverseEngine", "value": "0", "step": "2" }, { "param": "scoreFilter", "value": "None", "step": "2" }, { "param": "selfQueryPosJumpInNonPerfectAlignment", "value": "1", "step": "2" }, { "param": "trimLowScoreEnds", "value": "{\"44.0\":{\"trimLowScoreEndsWindow\":0}}", "step": "2" }, { "param": "useRedundSim", "value": "1", "step": "2" }, { "param": "alignSelector", "value": "622206", "step": "2" }, { "param": "force_reindex", "value": "false", "step": "2" } ], "io_domain": { "input_subdomain": [ { "uri": { "uri": "https://scihive.fda.gov/dna.cgi?cmd=objFile&ids=637703" } }, { "uri": { "uri": "https://scihive.fda.gov/dna.cgi?cmd=objFile&ids=637702" } } ], "output_subdomain": [ { "mediatype": "application/octet-stream", "uri": { "uri": "https://scihive.fda.gov/dna.cgi?cmd=objFile&ids=843915&filename=coverage_dict" } }, { "mediatype": "application/octet-stream", "uri": { "uri": "https://scihive.fda.gov/dna.cgi?cmd=objFile&ids=843915&filename=alignment.hiveal" } }, { "mediatype": "application/octet-stream", "uri": { "uri": "https://scihive.fda.gov/dna.cgi?cmd=objFile&ids=843915&filename=histogram.csv" } }, { "mediatype": "application/octet-stream", "uri": { "uri": "https://scihive.fda.gov/dna.cgi?cmd=objFile&ids=843915&filename=_.progress.json" } } ] }, "error_domain": { "algorithmic_error": { "text": "v" }, "empirical_error": { "text": "not required" } }, "checksum": "079470722b296d2ad3bb880f46c444cb72eb8741" }```
Validating the following object only returns "Bad request. BCO is not formatted correctly."
More detail should be included.