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Help understanding json config for basic demultiplexing #32

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jcmcnch opened this issue Nov 30, 2021 · 2 comments
Closed

Help understanding json config for basic demultiplexing #32

jcmcnch opened this issue Nov 30, 2021 · 2 comments
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@moonwatcher
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@jcmcnch
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jcmcnch commented Nov 30, 2021

Hi,

I'm wondering if you'd be able to help me understand how to construct a correct JSON config file. My goal is to demultiplex based on 6bp I1 indices from 4 files provided by our sequencing center (we have I2, but it's meaningless in this case).

What I've tried:

  • Constructing a json file based on the templates you had in the documentation, and then running it through the python script you provided:

pheniqs/tool/pheniqs-io-api.py -c 211123_run064_pheniqs_test.json -LS -F fastq --compression gz > 211129_run064_pheniqs_post-io-api.json.

Where I'm confused

When I try to run pheniqs as follows pheniqs mux -F fastq --compression gz -c 211129_run064_pheniqs_post-io-api.json, it just prints the gzip-compressed output to standard out. Yet in the config JSON produced using your python script there are filenames as output. When I run the validate step, it also specifies output will be put to stdout which is a bit confusing to me. I've provided both configs in plaintext below.

Please accept my apologies for the vague query, but I am a bit stumped. I'm unfamiliar with JSON-formatted configs and used to providing this info in a TSV/CSV and am not quite sure where to start in troubleshooting this. Even if you can tell me this must be due to some stray punctuation / a missing section in my original config or some such issue that would be really helpful for me to understand how pheniqs works.

Thanks a lot for your help,
Jesse

Original JSON file I constructed with your template:

{
	"PL" : "ILLUMINA",
	"PM" : "NovaSeq_2x250_UCDavis_run064",
        "base input url": ".",
	"filter incoming qc fail" : true,
	"flowcell id" : "JMSNRSCF",
	"report url" : "211123_JMSNRSCF_demux_sample_report.json",
	"input" : [
		"JMSNRSCF_S1_L001_R1_001.fastq.gz",
		"JMSNRSCF_S1_L001_I1_001.fastq.gz",
		"JMSNRSCF_S1_L001_I2_001.fastq.gz",
		"JMSNRSCF_S1_L001_R2_001.fastq.gz"
	],
	"template" : {
		"transform" : {
			"token" : [ "0::", "3::" ]
		}
	},
	"sample" : {
		"transform" : {
			"token" : [ "1::6" ]
		},
		"algorithm" : "pamld",
		"confidence threshold" : 0.95,
		"noise" : 0.05,
		"codec" : {
            "@11_15": {
                "LB": "11_15",
                "barcode": [
                    "AGTCAA"
                ],
                "output": [
                    "JMSNRSCF_11_15_s01.fastq.gz",
                    "JMSNRSCF_11_15_s02.fastq.gz",
                    "JMSNRSCF_11_15_s03.fastq.gz",
                    "JMSNRSCF_11_15_s04.fastq.gz"
                ]
            },
            "@11_200": {
                "LB": "11_200",
                "barcode": [
                    "ATGTCA"
                ],
                "output": [
                    "JMSNRSCF_11_200_s01.fastq.gz",
                    "JMSNRSCF_11_200_s02.fastq.gz",
                    "JMSNRSCF_11_200_s03.fastq.gz",
                    "JMSNRSCF_11_200_s04.fastq.gz"
                ]
            },
            "@11_25": {
                "LB": "11_25",
                "barcode": [
                    "CGTACG"
                ],
                "output": [
                    "JMSNRSCF_11_25_s01.fastq.gz",
                    "JMSNRSCF_11_25_s02.fastq.gz",
                    "JMSNRSCF_11_25_s03.fastq.gz",
                    "JMSNRSCF_11_25_s04.fastq.gz"
                ]
            },
            "@2_120": {
                "LB": "2_120",
                "barcode": [
                    "AGTCAA"
                ],
                "output": [
                    "JMSNRSCF_2_120_s01.fastq.gz",
                    "JMSNRSCF_2_120_s02.fastq.gz",
                    "JMSNRSCF_2_120_s03.fastq.gz",
                    "JMSNRSCF_2_120_s04.fastq.gz"
                ]
            },
            "@2_400": {
                "LB": "2_400",
                "barcode": [
                    "ATCTCA"
                ],
                "output": [
                    "JMSNRSCF_2_400_s01.fastq.gz",
                    "JMSNRSCF_2_400_s02.fastq.gz",
                    "JMSNRSCF_2_400_s03.fastq.gz",
                    "JMSNRSCF_2_400_s04.fastq.gz"
                ]
            },
            "@2_45": {
                "LB": "2_45",
                "barcode": [
                    "AGGAAT"
                ],
                "output": [
                    "JMSNRSCF_2_45_s01.fastq.gz",
                    "JMSNRSCF_2_45_s02.fastq.gz",
                    "JMSNRSCF_2_45_s03.fastq.gz",
                    "JMSNRSCF_2_45_s04.fastq.gz"
                ]
            },
            "@7_120": {
                "LB": "7_120",
                "barcode": [
                    "ATTCCT"
                ],
                "output": [
                    "JMSNRSCF_7_120_s01.fastq.gz",
                    "JMSNRSCF_7_120_s02.fastq.gz",
                    "JMSNRSCF_7_120_s03.fastq.gz",
                    "JMSNRSCF_7_120_s04.fastq.gz"
                ]
            },
            "@7_200": {
                "LB": "7_200",
                "barcode": [
                    "GTGGCC"
                ],
                "output": [
                    "JMSNRSCF_7_200_s01.fastq.gz",
                    "JMSNRSCF_7_200_s02.fastq.gz",
                    "JMSNRSCF_7_200_s03.fastq.gz",
                    "JMSNRSCF_7_200_s04.fastq.gz"
                ]
            },
            "@7_25": {
                "LB": "7_25",
                "barcode": [
                    "GTGAAA"
                ],
                "output": [
                    "JMSNRSCF_7_25_s01.fastq.gz",
                    "JMSNRSCF_7_25_s02.fastq.gz",
                    "JMSNRSCF_7_25_s03.fastq.gz",
                    "JMSNRSCF_7_25_s04.fastq.gz"
                ]
            },
            "@7_45": {
                "LB": "7_45",
                "barcode": [
                    "ATGAGC"
                ],
                "output": [
                    "JMSNRSCF_7_45_s01.fastq.gz",
                    "JMSNRSCF_7_45_s02.fastq.gz",
                    "JMSNRSCF_7_45_s03.fastq.gz",
                    "JMSNRSCF_7_45_s04.fastq.gz"
                ]
            },
            "@8_200": {
                "LB": "8_200",
                "barcode": [
                    "ATGAGC"
                ],
                "output": [
                    "JMSNRSCF_8_200_s01.fastq.gz",
                    "JMSNRSCF_8_200_s02.fastq.gz",
                    "JMSNRSCF_8_200_s03.fastq.gz",
                    "JMSNRSCF_8_200_s04.fastq.gz"
                ]
            },
            "@8_800": {
                "LB": "8_800",
                "barcode": [
                    "CCGTCC"
                ],
                "output": [
                    "JMSNRSCF_8_800_s01.fastq.gz",
                    "JMSNRSCF_8_800_s02.fastq.gz",
                    "JMSNRSCF_8_800_s03.fastq.gz",
                    "JMSNRSCF_8_800_s04.fastq.gz"
                ]
            },
            "@9_200": {
                "LB": "9_200",
                "barcode": [
                    "ACTTCC"
                ],
                "output": [
                    "JMSNRSCF_9_200_s01.fastq.gz",
                    "JMSNRSCF_9_200_s02.fastq.gz",
                    "JMSNRSCF_9_200_s03.fastq.gz",
                    "JMSNRSCF_9_200_s04.fastq.gz"
                ]
            },
            "@BGT_PL01_rev11": {
                "LB": "BGT_PL01_rev11",
                "barcode": [
                    "GCGGAC"
                ],
                "output": [
                    "JMSNRSCF_BGT_PL01_rev11_s01.fastq.gz",
                    "JMSNRSCF_BGT_PL01_rev11_s02.fastq.gz",
                    "JMSNRSCF_BGT_PL01_rev11_s03.fastq.gz",
                    "JMSNRSCF_BGT_PL01_rev11_s04.fastq.gz"
                ]
            },
            "@BGT_PL01_rev12": {
                "LB": "BGT_PL01_rev12",
                "barcode": [
                    "TTTCAC"
                ],
                "output": [
                    "JMSNRSCF_BGT_PL01_rev12_s01.fastq.gz",
                    "JMSNRSCF_BGT_PL01_rev12_s02.fastq.gz",
                    "JMSNRSCF_BGT_PL01_rev12_s03.fastq.gz",
                    "JMSNRSCF_BGT_PL01_rev12_s04.fastq.gz"
                ]
            },
            "@BGT_PL01_rev13": {
                "LB": "BGT_PL01_rev13",
                "barcode": [
                    "CCGGTG"
                ],
                "output": [
                    "JMSNRSCF_BGT_PL01_rev13_s01.fastq.gz",
                    "JMSNRSCF_BGT_PL01_rev13_s02.fastq.gz",
                    "JMSNRSCF_BGT_PL01_rev13_s03.fastq.gz",
                    "JMSNRSCF_BGT_PL01_rev13_s04.fastq.gz"
                ]
            },
            "@BGT_PL01_rev14": {
                "LB": "BGT_PL01_rev14",
                "barcode": [
                    "ATCGTG"
                ],
                "output": [
                    "JMSNRSCF_BGT_PL01_rev14_s01.fastq.gz",
                    "JMSNRSCF_BGT_PL01_rev14_s02.fastq.gz",
                    "JMSNRSCF_BGT_PL01_rev14_s03.fastq.gz",
                    "JMSNRSCF_BGT_PL01_rev14_s04.fastq.gz"
                ]
            },
            "@BGT_PL02_rev15": {
                "LB": "BGT_PL02_rev15",
                "barcode": [
                    "TGAGTG"
                ],
                "output": [
                    "JMSNRSCF_BGT_PL02_rev15_s01.fastq.gz",
                    "JMSNRSCF_BGT_PL02_rev15_s02.fastq.gz",
                    "JMSNRSCF_BGT_PL02_rev15_s03.fastq.gz",
                    "JMSNRSCF_BGT_PL02_rev15_s04.fastq.gz"
                ]
            },
            "@BGT_PL02_rev16": {
                "LB": "BGT_PL02_rev16",
                "barcode": [
                    "CGCCTG"
                ],
                "output": [
                    "JMSNRSCF_BGT_PL02_rev16_s01.fastq.gz",
                    "JMSNRSCF_BGT_PL02_rev16_s02.fastq.gz",
                    "JMSNRSCF_BGT_PL02_rev16_s03.fastq.gz",
                    "JMSNRSCF_BGT_PL02_rev16_s04.fastq.gz"
                ]
            },
            "@CAP_PL01_rev01": {
                "LB": "CAP_PL01_rev01",
                "barcode": [
                    "CGTGAT"
                ],
                "output": [
                    "JMSNRSCF_CAP_PL01_rev01_s01.fastq.gz",
                    "JMSNRSCF_CAP_PL01_rev01_s02.fastq.gz",
                    "JMSNRSCF_CAP_PL01_rev01_s03.fastq.gz",
                    "JMSNRSCF_CAP_PL01_rev01_s04.fastq.gz"
                ]
            },
            "@CAP_PL01_rev02": {
                "LB": "CAP_PL01_rev02",
                "barcode": [
                    "ACATCG"
                ],
                "output": [
                    "JMSNRSCF_CAP_PL01_rev02_s01.fastq.gz",
                    "JMSNRSCF_CAP_PL01_rev02_s02.fastq.gz",
                    "JMSNRSCF_CAP_PL01_rev02_s03.fastq.gz",
                    "JMSNRSCF_CAP_PL01_rev02_s04.fastq.gz"
                ]
            },
            "@CAP_PL01_rev03": {
                "LB": "CAP_PL01_rev03",
                "barcode": [
                    "GCCTAA"
                ],
                "output": [
                    "JMSNRSCF_CAP_PL01_rev03_s01.fastq.gz",
                    "JMSNRSCF_CAP_PL01_rev03_s02.fastq.gz",
                    "JMSNRSCF_CAP_PL01_rev03_s03.fastq.gz",
                    "JMSNRSCF_CAP_PL01_rev03_s04.fastq.gz"
                ]
            },
            "@CAP_PL01_rev04": {
                "LB": "CAP_PL01_rev04",
                "barcode": [
                    "TGGTCA"
                ],
                "output": [
                    "JMSNRSCF_CAP_PL01_rev04_s01.fastq.gz",
                    "JMSNRSCF_CAP_PL01_rev04_s02.fastq.gz",
                    "JMSNRSCF_CAP_PL01_rev04_s03.fastq.gz",
                    "JMSNRSCF_CAP_PL01_rev04_s04.fastq.gz"
                ]
            },
            "@Colette_rev21": {
                "LB": "Colette_rev21",
                "barcode": [
                    "TTCGTC"
                ],
                "output": [
                    "JMSNRSCF_Colette_rev21_s01.fastq.gz",
                    "JMSNRSCF_Colette_rev21_s02.fastq.gz",
                    "JMSNRSCF_Colette_rev21_s03.fastq.gz",
                    "JMSNRSCF_Colette_rev21_s04.fastq.gz"
                ]
            },
            "@Colette_rev22": {
                "LB": "Colette_rev22",
                "barcode": [
                    "CCAACT"
                ],
                "output": [
                    "JMSNRSCF_Colette_rev22_s01.fastq.gz",
                    "JMSNRSCF_Colette_rev22_s02.fastq.gz",
                    "JMSNRSCF_Colette_rev22_s03.fastq.gz",
                    "JMSNRSCF_Colette_rev22_s04.fastq.gz"
                ]
            },
            "@Colette_rev23": {
                "LB": "Colette_rev23",
                "barcode": [
                    "TCAGTT"
                ],
                "output": [
                    "JMSNRSCF_Colette_rev23_s01.fastq.gz",
                    "JMSNRSCF_Colette_rev23_s02.fastq.gz",
                    "JMSNRSCF_Colette_rev23_s03.fastq.gz",
                    "JMSNRSCF_Colette_rev23_s04.fastq.gz"
                ]
            },
            "@Colette_rev24": {
                "LB": "Colette_rev24",
                "barcode": [
                    "CTGACC"
                ],
                "output": [
                    "JMSNRSCF_Colette_rev24_s01.fastq.gz",
                    "JMSNRSCF_Colette_rev24_s02.fastq.gz",
                    "JMSNRSCF_Colette_rev24_s03.fastq.gz",
                    "JMSNRSCF_Colette_rev24_s04.fastq.gz"
                ]
            },
            "@Delaney_rev19": {
                "LB": "Delaney_rev19",
                "barcode": [
                    "GGAACT"
                ],
                "output": [
                    "JMSNRSCF_Delaney_rev19_s01.fastq.gz",
                    "JMSNRSCF_Delaney_rev19_s02.fastq.gz",
                    "JMSNRSCF_Delaney_rev19_s03.fastq.gz",
                    "JMSNRSCF_Delaney_rev19_s04.fastq.gz"
                ]
            },
            "@Delaney_rev20": {
                "LB": "Delaney_rev20",
                "barcode": [
                    "CGAAAC"
                ],
                "output": [
                    "JMSNRSCF_Delaney_rev20_s01.fastq.gz",
                    "JMSNRSCF_Delaney_rev20_s02.fastq.gz",
                    "JMSNRSCF_Delaney_rev20_s03.fastq.gz",
                    "JMSNRSCF_Delaney_rev20_s04.fastq.gz"
                ]
            },
            "@Rae_rev05": {
                "LB": "Rae_rev05",
                "barcode": [
                    "CACTGT"
                ],
                "output": [
                    "JMSNRSCF_Rae_rev05_s01.fastq.gz",
                    "JMSNRSCF_Rae_rev05_s02.fastq.gz",
                    "JMSNRSCF_Rae_rev05_s03.fastq.gz",
                    "JMSNRSCF_Rae_rev05_s04.fastq.gz"
                ]
            },
            "@mystery12264": {
                "LB": "mystery12264",
                "barcode": [
                    "ACTGAT"
                ],
                "output": [
                    "JMSNRSCF_mystery12264_s01.fastq.gz",
                    "JMSNRSCF_mystery12264_s02.fastq.gz",
                    "JMSNRSCF_mystery12264_s03.fastq.gz",
                    "JMSNRSCF_mystery12264_s04.fastq.gz"
                ]
            },
            "@mystery17075": {
                "LB": "mystery17075",
                "barcode": [
                    "GTGGCC"
                ],
                "output": [
                    "JMSNRSCF_mystery17075_s01.fastq.gz",
                    "JMSNRSCF_mystery17075_s02.fastq.gz",
                    "JMSNRSCF_mystery17075_s03.fastq.gz",
                    "JMSNRSCF_mystery17075_s04.fastq.gz"
                ]
            },
            "@mystery4368": {
                "LB": "mystery4368",
                "barcode": [
                    "CGCCTG"
                ],
                "output": [
                    "JMSNRSCF_mystery4368_s01.fastq.gz",
                    "JMSNRSCF_mystery4368_s02.fastq.gz",
                    "JMSNRSCF_mystery4368_s03.fastq.gz",
                    "JMSNRSCF_mystery4368_s04.fastq.gz"
                ]
            },
            "@mystery4895": {
                "LB": "mystery4895",
                "barcode": [
                    "GGGGGG"
                ],
                "output": [
                    "JMSNRSCF_mystery4895_s01.fastq.gz",
                    "JMSNRSCF_mystery4895_s02.fastq.gz",
                    "JMSNRSCF_mystery4895_s03.fastq.gz",
                    "JMSNRSCF_mystery4895_s04.fastq.gz"
                ]
            },
            "@mystery8619": {
                "LB": "mystery8619",
                "barcode": [
                    "AGTTCC"
                ],
                "output": [
                    "JMSNRSCF_mystery8619_s01.fastq.gz",
                    "JMSNRSCF_mystery8619_s02.fastq.gz",
                    "JMSNRSCF_mystery8619_s03.fastq.gz",
                    "JMSNRSCF_mystery8619_s04.fastq.gz"
                ]
            },
            "@mystery9788": {
                "LB": "mystery9788",
                "barcode": [
                    "CCGTCC"
                ],
                "output": [
                    "JMSNRSCF_mystery9788_s01.fastq.gz",
                    "JMSNRSCF_mystery9788_s02.fastq.gz",
                    "JMSNRSCF_mystery9788_s03.fastq.gz",
                    "JMSNRSCF_mystery9788_s04.fastq.gz"
                ]
            }      
        
		}
	}
}

The output of your python processing script:

{
    "PL": "ILLUMINA",
    "PM": "NovaSeq_2x250_UCDavis_run064",
    "base input url": ".",
    "filter incoming qc fail": true,
    "flowcell id": "JMSNRSCF",
    "input": [
        "JMSNRSCF_S1_L001_R1_001.fastq.gz",
        "JMSNRSCF_S1_L001_I1_001.fastq.gz",
        "JMSNRSCF_S1_L001_I2_001.fastq.gz",
        "JMSNRSCF_S1_L001_R2_001.fastq.gz"
    ],
    "report url": "211123_JMSNRSCF_demux_sample_report.json",
    "sample": {
        "algorithm": "pamld",
        "codec": {
            "@11_15": {
                "LB": "11_15",
                "barcode": [
                    "AGTCAA"
                ],
                "output": [
                    "JMSNRSCF_11_15_s01.fastq.gz",
                    "JMSNRSCF_11_15_s02.fastq.gz",
                    "JMSNRSCF_11_15_s03.fastq.gz",
                    "JMSNRSCF_11_15_s04.fastq.gz"
                ]
            },
            "@11_200": {
                "LB": "11_200",
                "barcode": [
                    "ATGTCA"
                ],
                "output": [
                    "JMSNRSCF_11_200_s01.fastq.gz",
                    "JMSNRSCF_11_200_s02.fastq.gz",
                    "JMSNRSCF_11_200_s03.fastq.gz",
                    "JMSNRSCF_11_200_s04.fastq.gz"
                ]
            },
            "@11_25": {
                "LB": "11_25",
                "barcode": [
                    "CGTACG"
                ],
                "output": [
                    "JMSNRSCF_11_25_s01.fastq.gz",
                    "JMSNRSCF_11_25_s02.fastq.gz",
                    "JMSNRSCF_11_25_s03.fastq.gz",
                    "JMSNRSCF_11_25_s04.fastq.gz"
                ]
            },
            "@2_120": {
                "LB": "2_120",
                "barcode": [
                    "AGTCAA"
                ],
                "output": [
                    "JMSNRSCF_2_120_s01.fastq.gz",
                    "JMSNRSCF_2_120_s02.fastq.gz",
                    "JMSNRSCF_2_120_s03.fastq.gz",
                    "JMSNRSCF_2_120_s04.fastq.gz"
                ]
            },
            "@2_400": {
                "LB": "2_400",
                "barcode": [
                    "ATCTCA"
                ],
                "output": [
                    "JMSNRSCF_2_400_s01.fastq.gz",
                    "JMSNRSCF_2_400_s02.fastq.gz",
                    "JMSNRSCF_2_400_s03.fastq.gz",
                    "JMSNRSCF_2_400_s04.fastq.gz"
                ]
            },
            "@2_45": {
                "LB": "2_45",
                "barcode": [
                    "AGGAAT"
                ],
                "output": [
                    "JMSNRSCF_2_45_s01.fastq.gz",
                    "JMSNRSCF_2_45_s02.fastq.gz",
                    "JMSNRSCF_2_45_s03.fastq.gz",
                    "JMSNRSCF_2_45_s04.fastq.gz"
                ]
            },
            "@7_120": {
                "LB": "7_120",
                "barcode": [
                    "ATTCCT"
                ],
                "output": [
                    "JMSNRSCF_7_120_s01.fastq.gz",
                    "JMSNRSCF_7_120_s02.fastq.gz",
                    "JMSNRSCF_7_120_s03.fastq.gz",
                    "JMSNRSCF_7_120_s04.fastq.gz"
                ]
            },
            "@7_200": {
                "LB": "7_200",
                "barcode": [
                    "GTGGCC"
                ],
                "output": [
                    "JMSNRSCF_7_200_s01.fastq.gz",
                    "JMSNRSCF_7_200_s02.fastq.gz",
                    "JMSNRSCF_7_200_s03.fastq.gz",
                    "JMSNRSCF_7_200_s04.fastq.gz"
                ]
            },
            "@7_25": {
                "LB": "7_25",
                "barcode": [
                    "GTGAAA"
                ],
                "output": [
                    "JMSNRSCF_7_25_s01.fastq.gz",
                    "JMSNRSCF_7_25_s02.fastq.gz",
                    "JMSNRSCF_7_25_s03.fastq.gz",
                    "JMSNRSCF_7_25_s04.fastq.gz"
                ]
            },
            "@7_45": {
                "LB": "7_45",
                "barcode": [
                    "ATGAGC"
                ],
                "output": [
                    "JMSNRSCF_7_45_s01.fastq.gz",
                    "JMSNRSCF_7_45_s02.fastq.gz",
                    "JMSNRSCF_7_45_s03.fastq.gz",
                    "JMSNRSCF_7_45_s04.fastq.gz"
                ]
            },
            "@8_200": {
                "LB": "8_200",
                "barcode": [
                    "ATGAGC"
                ],
                "output": [
                    "JMSNRSCF_8_200_s01.fastq.gz",
                    "JMSNRSCF_8_200_s02.fastq.gz",
                    "JMSNRSCF_8_200_s03.fastq.gz",
                    "JMSNRSCF_8_200_s04.fastq.gz"
                ]
            },
            "@8_800": {
                "LB": "8_800",
                "barcode": [
                    "CCGTCC"
                ],
                "output": [
                    "JMSNRSCF_8_800_s01.fastq.gz",
                    "JMSNRSCF_8_800_s02.fastq.gz",
                    "JMSNRSCF_8_800_s03.fastq.gz",
                    "JMSNRSCF_8_800_s04.fastq.gz"
                ]
            },
            "@9_200": {
                "LB": "9_200",
                "barcode": [
                    "ACTTCC"
                ],
                "output": [
                    "JMSNRSCF_9_200_s01.fastq.gz",
                    "JMSNRSCF_9_200_s02.fastq.gz",
                    "JMSNRSCF_9_200_s03.fastq.gz",
                    "JMSNRSCF_9_200_s04.fastq.gz"
                ]
            },
            "@BGT_PL01_rev11": {
                "LB": "BGT_PL01_rev11",
                "barcode": [
                    "GCGGAC"
                ],
                "output": [
                    "JMSNRSCF_BGT_PL01_rev11_s01.fastq.gz",
                    "JMSNRSCF_BGT_PL01_rev11_s02.fastq.gz",
                    "JMSNRSCF_BGT_PL01_rev11_s03.fastq.gz",
                    "JMSNRSCF_BGT_PL01_rev11_s04.fastq.gz"
                ]
            },
            "@BGT_PL01_rev12": {
                "LB": "BGT_PL01_rev12",
                "barcode": [
                    "TTTCAC"
                ],
                "output": [
                    "JMSNRSCF_BGT_PL01_rev12_s01.fastq.gz",
                    "JMSNRSCF_BGT_PL01_rev12_s02.fastq.gz",
                    "JMSNRSCF_BGT_PL01_rev12_s03.fastq.gz",
                    "JMSNRSCF_BGT_PL01_rev12_s04.fastq.gz"
                ]
            },
            "@BGT_PL01_rev13": {
                "LB": "BGT_PL01_rev13",
                "barcode": [
                    "CCGGTG"
                ],
                "output": [
                    "JMSNRSCF_BGT_PL01_rev13_s01.fastq.gz",
                    "JMSNRSCF_BGT_PL01_rev13_s02.fastq.gz",
                    "JMSNRSCF_BGT_PL01_rev13_s03.fastq.gz",
                    "JMSNRSCF_BGT_PL01_rev13_s04.fastq.gz"
                ]
            },
            "@BGT_PL01_rev14": {
                "LB": "BGT_PL01_rev14",
                "barcode": [
                    "ATCGTG"
                ],
                "output": [
                    "JMSNRSCF_BGT_PL01_rev14_s01.fastq.gz",
                    "JMSNRSCF_BGT_PL01_rev14_s02.fastq.gz",
                    "JMSNRSCF_BGT_PL01_rev14_s03.fastq.gz",
                    "JMSNRSCF_BGT_PL01_rev14_s04.fastq.gz"
                ]
            },
            "@BGT_PL02_rev15": {
                "LB": "BGT_PL02_rev15",
                "barcode": [
                    "TGAGTG"
                ],
                "output": [
                    "JMSNRSCF_BGT_PL02_rev15_s01.fastq.gz",
                    "JMSNRSCF_BGT_PL02_rev15_s02.fastq.gz",
                    "JMSNRSCF_BGT_PL02_rev15_s03.fastq.gz",
                    "JMSNRSCF_BGT_PL02_rev15_s04.fastq.gz"
                ]
            },
            "@BGT_PL02_rev16": {
                "LB": "BGT_PL02_rev16",
                "barcode": [
                    "CGCCTG"
                ],
                "output": [
                    "JMSNRSCF_BGT_PL02_rev16_s01.fastq.gz",
                    "JMSNRSCF_BGT_PL02_rev16_s02.fastq.gz",
                    "JMSNRSCF_BGT_PL02_rev16_s03.fastq.gz",
                    "JMSNRSCF_BGT_PL02_rev16_s04.fastq.gz"
                ]
            },
            "@CAP_PL01_rev01": {
                "LB": "CAP_PL01_rev01",
                "barcode": [
                    "CGTGAT"
                ],
                "output": [
                    "JMSNRSCF_CAP_PL01_rev01_s01.fastq.gz",
                    "JMSNRSCF_CAP_PL01_rev01_s02.fastq.gz",
                    "JMSNRSCF_CAP_PL01_rev01_s03.fastq.gz",
                    "JMSNRSCF_CAP_PL01_rev01_s04.fastq.gz"
                ]
            },
            "@CAP_PL01_rev02": {
                "LB": "CAP_PL01_rev02",
                "barcode": [
                    "ACATCG"
                ],
                "output": [
                    "JMSNRSCF_CAP_PL01_rev02_s01.fastq.gz",
                    "JMSNRSCF_CAP_PL01_rev02_s02.fastq.gz",
                    "JMSNRSCF_CAP_PL01_rev02_s03.fastq.gz",
                    "JMSNRSCF_CAP_PL01_rev02_s04.fastq.gz"
                ]
            },
            "@CAP_PL01_rev03": {
                "LB": "CAP_PL01_rev03",
                "barcode": [
                    "GCCTAA"
                ],
                "output": [
                    "JMSNRSCF_CAP_PL01_rev03_s01.fastq.gz",
                    "JMSNRSCF_CAP_PL01_rev03_s02.fastq.gz",
                    "JMSNRSCF_CAP_PL01_rev03_s03.fastq.gz",
                    "JMSNRSCF_CAP_PL01_rev03_s04.fastq.gz"
                ]
            },
            "@CAP_PL01_rev04": {
                "LB": "CAP_PL01_rev04",
                "barcode": [
                    "TGGTCA"
                ],
                "output": [
                    "JMSNRSCF_CAP_PL01_rev04_s01.fastq.gz",
                    "JMSNRSCF_CAP_PL01_rev04_s02.fastq.gz",
                    "JMSNRSCF_CAP_PL01_rev04_s03.fastq.gz",
                    "JMSNRSCF_CAP_PL01_rev04_s04.fastq.gz"
                ]
            },
            "@Colette_rev21": {
                "LB": "Colette_rev21",
                "barcode": [
                    "TTCGTC"
                ],
                "output": [
                    "JMSNRSCF_Colette_rev21_s01.fastq.gz",
                    "JMSNRSCF_Colette_rev21_s02.fastq.gz",
                    "JMSNRSCF_Colette_rev21_s03.fastq.gz",
                    "JMSNRSCF_Colette_rev21_s04.fastq.gz"
                ]
            },
            "@Colette_rev22": {
                "LB": "Colette_rev22",
                "barcode": [
                    "CCAACT"
                ],
                "output": [
                    "JMSNRSCF_Colette_rev22_s01.fastq.gz",
                    "JMSNRSCF_Colette_rev22_s02.fastq.gz",
                    "JMSNRSCF_Colette_rev22_s03.fastq.gz",
                    "JMSNRSCF_Colette_rev22_s04.fastq.gz"
                ]
            },
            "@Colette_rev23": {
                "LB": "Colette_rev23",
                "barcode": [
                    "TCAGTT"
                ],
                "output": [
                    "JMSNRSCF_Colette_rev23_s01.fastq.gz",
                    "JMSNRSCF_Colette_rev23_s02.fastq.gz",
                    "JMSNRSCF_Colette_rev23_s03.fastq.gz",
                    "JMSNRSCF_Colette_rev23_s04.fastq.gz"
                ]
            },
            "@Colette_rev24": {
                "LB": "Colette_rev24",
                "barcode": [
                    "CTGACC"
                ],
                "output": [
                    "JMSNRSCF_Colette_rev24_s01.fastq.gz",
                    "JMSNRSCF_Colette_rev24_s02.fastq.gz",
                    "JMSNRSCF_Colette_rev24_s03.fastq.gz",
                    "JMSNRSCF_Colette_rev24_s04.fastq.gz"
                ]
            },
            "@Delaney_rev19": {
                "LB": "Delaney_rev19",
                "barcode": [
                    "GGAACT"
                ],
                "output": [
                    "JMSNRSCF_Delaney_rev19_s01.fastq.gz",
                    "JMSNRSCF_Delaney_rev19_s02.fastq.gz",
                    "JMSNRSCF_Delaney_rev19_s03.fastq.gz",
                    "JMSNRSCF_Delaney_rev19_s04.fastq.gz"
                ]
            },
            "@Delaney_rev20": {
                "LB": "Delaney_rev20",
                "barcode": [
                    "CGAAAC"
                ],
                "output": [
                    "JMSNRSCF_Delaney_rev20_s01.fastq.gz",
                    "JMSNRSCF_Delaney_rev20_s02.fastq.gz",
                    "JMSNRSCF_Delaney_rev20_s03.fastq.gz",
                    "JMSNRSCF_Delaney_rev20_s04.fastq.gz"
                ]
            },
            "@Rae_rev05": {
                "LB": "Rae_rev05",
                "barcode": [
                    "CACTGT"
                ],
                "output": [
                    "JMSNRSCF_Rae_rev05_s01.fastq.gz",
                    "JMSNRSCF_Rae_rev05_s02.fastq.gz",
                    "JMSNRSCF_Rae_rev05_s03.fastq.gz",
                    "JMSNRSCF_Rae_rev05_s04.fastq.gz"
                ]
            },
            "@mystery12264": {
                "LB": "mystery12264",
                "barcode": [
                    "ACTGAT"
                ],
                "output": [
                    "JMSNRSCF_mystery12264_s01.fastq.gz",
                    "JMSNRSCF_mystery12264_s02.fastq.gz",
                    "JMSNRSCF_mystery12264_s03.fastq.gz",
                    "JMSNRSCF_mystery12264_s04.fastq.gz"
                ]
            },
            "@mystery17075": {
                "LB": "mystery17075",
                "barcode": [
                    "GTGGCC"
                ],
                "output": [
                    "JMSNRSCF_mystery17075_s01.fastq.gz",
                    "JMSNRSCF_mystery17075_s02.fastq.gz",
                    "JMSNRSCF_mystery17075_s03.fastq.gz",
                    "JMSNRSCF_mystery17075_s04.fastq.gz"
                ]
            },
            "@mystery4368": {
                "LB": "mystery4368",
                "barcode": [
                    "CGCCTG"
                ],
                "output": [
                    "JMSNRSCF_mystery4368_s01.fastq.gz",
                    "JMSNRSCF_mystery4368_s02.fastq.gz",
                    "JMSNRSCF_mystery4368_s03.fastq.gz",
                    "JMSNRSCF_mystery4368_s04.fastq.gz"
                ]
            },
            "@mystery4895": {
                "LB": "mystery4895",
                "barcode": [
                    "GGGGGG"
                ],
                "output": [
                    "JMSNRSCF_mystery4895_s01.fastq.gz",
                    "JMSNRSCF_mystery4895_s02.fastq.gz",
                    "JMSNRSCF_mystery4895_s03.fastq.gz",
                    "JMSNRSCF_mystery4895_s04.fastq.gz"
                ]
            },
            "@mystery8619": {
                "LB": "mystery8619",
                "barcode": [
                    "AGTTCC"
                ],
                "output": [
                    "JMSNRSCF_mystery8619_s01.fastq.gz",
                    "JMSNRSCF_mystery8619_s02.fastq.gz",
                    "JMSNRSCF_mystery8619_s03.fastq.gz",
                    "JMSNRSCF_mystery8619_s04.fastq.gz"
                ]
            },
            "@mystery9788": {
                "LB": "mystery9788",
                "barcode": [
                    "CCGTCC"
                ],
                "output": [
                    "JMSNRSCF_mystery9788_s01.fastq.gz",
                    "JMSNRSCF_mystery9788_s02.fastq.gz",
                    "JMSNRSCF_mystery9788_s03.fastq.gz",
                    "JMSNRSCF_mystery9788_s04.fastq.gz"
                ]
            }
        },
        "confidence threshold": 0.95,
        "noise": 0.05,
        "transform": {
            "token": [
                "1::6"
            ]
        },
        "undetermined": {
            "output": [
                "JMSNRSCF_undetermined_s01.fastq.gz",
                "JMSNRSCF_undetermined_s02.fastq.gz",
                "JMSNRSCF_undetermined_s03.fastq.gz",
                "JMSNRSCF_undetermined_s04.fastq.gz"
            ]
        }
    },
    "template": {
        "transform": {
            "token": [
                "0::",
                "3::"
            ]
        }
    }
}
@moonwatcher
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Contributor

Hi @jcmcnch

First, welcome and thank you for using Pheniqs. Now about your config files...

  1. You can always validate your JSON to see that it is syntactically correct. I provide a simple wrapper for the python validator with Pheniqs. You can just download json_lint.py and use it to lint your json. That will give you a very clear error if something is wrong, i.e. what line and what is the problems. To use it do something like original_config.json|./json_lint.py. You should also use some text editor that can provide highlighting and collapsing of JSON documents (like Atom . It will make inspecting the document much easier.

  2. You don't really need the pheniqs-io-api.py with your config. The purpose of this api is to add the individual output directives to each barcode when you want to split the output into files by barcode. since you already did that, the only thing the api added is the undetermined class, which is implicitly added anyway if you didn't specify it. I linted both files and ran a diff

>         },
>         "undetermined": {
>             "output": [
>                 "JMSNRSCF_undetermined_s01.fastq.gz",
>                 "JMSNRSCF_undetermined_s02.fastq.gz",
>                 "JMSNRSCF_undetermined_s03.fastq.gz",
>                 "JMSNRSCF_undetermined_s04.fastq.gz"
>             ]

linting the files sorts the JSON dictionaries which makes comparing two files much easier.

  1. You also don't really need -F fastq --compression gz this will only provide a default output format for outputs that are not explicitly specified. Since you already added the fastq.gz extensions it is unnecessary.

  2. if you try and validate your config file you will notice you get an error.

pheniqs mux --config original.json --validate
Configuration error : sample decoder : duplicate barcode sequence AGTCAA

if you search for AGTCAA in your file you will notice it shows up twice. once in @11_15 and once in @2_120. You can't specify the same barcode sequence for two classes since that would be ambiguous. same for ATGAGC, GTGGCC, CGCCTG, CCGTCC. Once we remove those offending classes (again, barcode sequence must be unique per decoder, it is identifying the class), your next problems is

pheniqs mux --config original.json --validate
Configuration error : incorrect number of output URLs in channel

Your config file specifies the output template has 2 tokens 0:: and 3::, basically the complete first and 4th input segments.

"template" : {
	"transform" : {
		"token" : [ "0::", "3::" ]
	}
},

but in all your output directives you specify 4 output files. The number of output files in the output directive must be the number of segments you specify in your template.

  1. Once all those problems have been corrected your config file validated. I will provide the adjusted file and the validation report at the end of this reply but to answer your question about the output please notice the following lines from the validation report:
    Barcode undetermined
        ID : JMSNRSCF:undetermined
        PU : JMSNRSCF:undetermined
        PL : ILLUMINA
        PM : NovaSeq_2x250_UCDavis_run064
        Segment No.0  : /dev/stdout?format=fastq&compression=gz&level=5
        Segment No.1  : /dev/stdout?format=fastq&compression=gz&level=5

the output directive in pheniqs config files is cascaded. That means that if you specify it in the root of the document it will provide the default for anything further deeper. Since you explicitly provided the output directive for each barcode that leaves only the undetermined class to inherit the default. You didn't provide an output directive in the document root so it reverted to the global default which is SAM format to stdout. Since you provided the -F fastq --compression gz command line parameters that switched to gzip compressed FASTQ format. What you got over stdout are the unclassified reads. if you look at the folder where you executed this you will probably find the multiple fastq files for the individual barcodes. Notice you can specify /dev/null as output if you want to discard a certain output so you can specify the undetermined to have an output with /dev/null if you are not interested in it.

  1. One last comment. If you run pheniqs with --compile it will output your compiled config file. That is a config file where all the implicit runtime parameters have been computed and added. It might be a little big but it allows you to see exactly what pheniqs understood from your instruction and what will be executed. To compile your config file use pheniqs mux --config original.json --compile

If you still have questions, please don't hesitate to ask. We appreciate your feedback and are here to help.

Regards
Lior.

{
    "PL": "ILLUMINA",
    "PM": "NovaSeq_2x250_UCDavis_run064",
    "base input url": ".",
    "filter incoming qc fail": true,
    "flowcell id": "JMSNRSCF",
    "input": [
        "JMSNRSCF_S1_L001_R1_001.fastq.gz",
        "JMSNRSCF_S1_L001_I1_001.fastq.gz",
        "JMSNRSCF_S1_L001_I2_001.fastq.gz",
        "JMSNRSCF_S1_L001_R2_001.fastq.gz"
    ],
    "report url": "211123_JMSNRSCF_demux_sample_report.json",
    "sample": {
        "algorithm": "pamld",
        "codec": {
            "@11_15": {
                "LB": "11_15",
                "barcode": [
                    "AGTCAA"
                ],
                "output": [
                    "JMSNRSCF_11_15_s01.fastq.gz",
                    "JMSNRSCF_11_15_s02.fastq.gz"
                ]
            },
            "@11_200": {
                "LB": "11_200",
                "barcode": [
                    "ATGTCA"
                ],
                "output": [
                    "JMSNRSCF_11_200_s01.fastq.gz",
                    "JMSNRSCF_11_200_s02.fastq.gz"
                ]
            },
            "@11_25": {
                "LB": "11_25",
                "barcode": [
                    "CGTACG"
                ],
                "output": [
                    "JMSNRSCF_11_25_s01.fastq.gz",
                    "JMSNRSCF_11_25_s02.fastq.gz"
                ]
            },
            "@2_400": {
                "LB": "2_400",
                "barcode": [
                    "ATCTCA"
                ],
                "output": [
                    "JMSNRSCF_2_400_s01.fastq.gz",
                    "JMSNRSCF_2_400_s02.fastq.gz"
                ]
            },
            "@2_45": {
                "LB": "2_45",
                "barcode": [
                    "AGGAAT"
                ],
                "output": [
                    "JMSNRSCF_2_45_s01.fastq.gz",
                    "JMSNRSCF_2_45_s02.fastq.gz"
                ]
            },
            "@7_120": {
                "LB": "7_120",
                "barcode": [
                    "ATTCCT"
                ],
                "output": [
                    "JMSNRSCF_7_120_s01.fastq.gz",
                    "JMSNRSCF_7_120_s02.fastq.gz"
                ]
            },
            "@7_200": {
                "LB": "7_200",
                "barcode": [
                    "GTGGCC"
                ],
                "output": [
                    "JMSNRSCF_7_200_s01.fastq.gz",
                    "JMSNRSCF_7_200_s02.fastq.gz"
                ]
            },
            "@7_25": {
                "LB": "7_25",
                "barcode": [
                    "GTGAAA"
                ],
                "output": [
                    "JMSNRSCF_7_25_s01.fastq.gz",
                    "JMSNRSCF_7_25_s02.fastq.gz"
                ]
            },
            "@8_200": {
                "LB": "8_200",
                "barcode": [
                    "ATGAGC"
                ],
                "output": [
                    "JMSNRSCF_8_200_s01.fastq.gz",
                    "JMSNRSCF_8_200_s02.fastq.gz"
                ]
            },
            "@8_800": {
                "LB": "8_800",
                "barcode": [
                    "CCGTCC"
                ],
                "output": [
                    "JMSNRSCF_8_800_s01.fastq.gz",
                    "JMSNRSCF_8_800_s02.fastq.gz"
                ]
            },
            "@9_200": {
                "LB": "9_200",
                "barcode": [
                    "ACTTCC"
                ],
                "output": [
                    "JMSNRSCF_9_200_s01.fastq.gz",
                    "JMSNRSCF_9_200_s02.fastq.gz"
                ]
            },
            "@BGT_PL01_rev11": {
                "LB": "BGT_PL01_rev11",
                "barcode": [
                    "GCGGAC"
                ],
                "output": [
                    "JMSNRSCF_BGT_PL01_rev11_s01.fastq.gz",
                    "JMSNRSCF_BGT_PL01_rev11_s02.fastq.gz"
                ]
            },
            "@BGT_PL01_rev12": {
                "LB": "BGT_PL01_rev12",
                "barcode": [
                    "TTTCAC"
                ],
                "output": [
                    "JMSNRSCF_BGT_PL01_rev12_s01.fastq.gz",
                    "JMSNRSCF_BGT_PL01_rev12_s02.fastq.gz"
                ]
            },
            "@BGT_PL01_rev13": {
                "LB": "BGT_PL01_rev13",
                "barcode": [
                    "CCGGTG"
                ],
                "output": [
                    "JMSNRSCF_BGT_PL01_rev13_s01.fastq.gz",
                    "JMSNRSCF_BGT_PL01_rev13_s02.fastq.gz"
                ]
            },
            "@BGT_PL01_rev14": {
                "LB": "BGT_PL01_rev14",
                "barcode": [
                    "ATCGTG"
                ],
                "output": [
                    "JMSNRSCF_BGT_PL01_rev14_s01.fastq.gz",
                    "JMSNRSCF_BGT_PL01_rev14_s02.fastq.gz"
                ]
            },
            "@BGT_PL02_rev15": {
                "LB": "BGT_PL02_rev15",
                "barcode": [
                    "TGAGTG"
                ],
                "output": [
                    "JMSNRSCF_BGT_PL02_rev15_s01.fastq.gz",
                    "JMSNRSCF_BGT_PL02_rev15_s02.fastq.gz"
                ]
            },
            "@BGT_PL02_rev16": {
                "LB": "BGT_PL02_rev16",
                "barcode": [
                    "CGCCTG"
                ],
                "output": [
                    "JMSNRSCF_BGT_PL02_rev16_s01.fastq.gz",
                    "JMSNRSCF_BGT_PL02_rev16_s02.fastq.gz"
                ]
            },
            "@CAP_PL01_rev01": {
                "LB": "CAP_PL01_rev01",
                "barcode": [
                    "CGTGAT"
                ],
                "output": [
                    "JMSNRSCF_CAP_PL01_rev01_s01.fastq.gz",
                    "JMSNRSCF_CAP_PL01_rev01_s02.fastq.gz"
                ]
            },
            "@CAP_PL01_rev02": {
                "LB": "CAP_PL01_rev02",
                "barcode": [
                    "ACATCG"
                ],
                "output": [
                    "JMSNRSCF_CAP_PL01_rev02_s01.fastq.gz",
                    "JMSNRSCF_CAP_PL01_rev02_s02.fastq.gz"
                ]
            },
            "@CAP_PL01_rev03": {
                "LB": "CAP_PL01_rev03",
                "barcode": [
                    "GCCTAA"
                ],
                "output": [
                    "JMSNRSCF_CAP_PL01_rev03_s01.fastq.gz",
                    "JMSNRSCF_CAP_PL01_rev03_s02.fastq.gz"
                ]
            },
            "@CAP_PL01_rev04": {
                "LB": "CAP_PL01_rev04",
                "barcode": [
                    "TGGTCA"
                ],
                "output": [
                    "JMSNRSCF_CAP_PL01_rev04_s01.fastq.gz",
                    "JMSNRSCF_CAP_PL01_rev04_s02.fastq.gz"
                ]
            },
            "@Colette_rev21": {
                "LB": "Colette_rev21",
                "barcode": [
                    "TTCGTC"
                ],
                "output": [
                    "JMSNRSCF_Colette_rev21_s01.fastq.gz",
                    "JMSNRSCF_Colette_rev21_s02.fastq.gz"
                ]
            },
            "@Colette_rev22": {
                "LB": "Colette_rev22",
                "barcode": [
                    "CCAACT"
                ],
                "output": [
                    "JMSNRSCF_Colette_rev22_s01.fastq.gz",
                    "JMSNRSCF_Colette_rev22_s02.fastq.gz"
                ]
            },
            "@Colette_rev23": {
                "LB": "Colette_rev23",
                "barcode": [
                    "TCAGTT"
                ],
                "output": [
                    "JMSNRSCF_Colette_rev23_s01.fastq.gz",
                    "JMSNRSCF_Colette_rev23_s02.fastq.gz"
                ]
            },
            "@Colette_rev24": {
                "LB": "Colette_rev24",
                "barcode": [
                    "CTGACC"
                ],
                "output": [
                    "JMSNRSCF_Colette_rev24_s01.fastq.gz",
                    "JMSNRSCF_Colette_rev24_s02.fastq.gz"
                ]
            },
            "@Delaney_rev19": {
                "LB": "Delaney_rev19",
                "barcode": [
                    "GGAACT"
                ],
                "output": [
                    "JMSNRSCF_Delaney_rev19_s01.fastq.gz",
                    "JMSNRSCF_Delaney_rev19_s02.fastq.gz"
                ]
            },
            "@Delaney_rev20": {
                "LB": "Delaney_rev20",
                "barcode": [
                    "CGAAAC"
                ],
                "output": [
                    "JMSNRSCF_Delaney_rev20_s01.fastq.gz",
                    "JMSNRSCF_Delaney_rev20_s02.fastq.gz"
                ]
            },
            "@Rae_rev05": {
                "LB": "Rae_rev05",
                "barcode": [
                    "CACTGT"
                ],
                "output": [
                    "JMSNRSCF_Rae_rev05_s01.fastq.gz",
                    "JMSNRSCF_Rae_rev05_s02.fastq.gz"
                ]
            },
            "@mystery12264": {
                "LB": "mystery12264",
                "barcode": [
                    "ACTGAT"
                ],
                "output": [
                    "JMSNRSCF_mystery12264_s01.fastq.gz",
                    "JMSNRSCF_mystery12264_s02.fastq.gz"
                ]
            },
            "@mystery4895": {
                "LB": "mystery4895",
                "barcode": [
                    "GGGGGG"
                ],
                "output": [
                    "JMSNRSCF_mystery4895_s01.fastq.gz",
                    "JMSNRSCF_mystery4895_s02.fastq.gz"
                ]
            },
            "@mystery8619": {
                "LB": "mystery8619",
                "barcode": [
                    "AGTTCC"
                ],
                "output": [
                    "JMSNRSCF_mystery8619_s01.fastq.gz",
                    "JMSNRSCF_mystery8619_s02.fastq.gz"
                ]
            }
        },
        "confidence threshold": 0.95,
        "noise": 0.05,
        "transform": {
            "token": [
                "1::6"
            ]
        }
    },
    "template": {
        "transform": {
            "token": [
                "0::",
                "3::"
            ]
        }
    }
}
rick:jcmcnch lg% pheniqs mux --config original.json -F fastq --compression gz --validate
Environment

    Base input URL                              .
    Base output URL                             .
    Platform                                    ILLUMINA
    Quality tracking                            disabled
    Filter incoming QC failed reads             enabled
    Filter outgoing QC failed reads             disabled
    Input Phred offset                          33
    Output Phred offset                         33
    Leading segment index                       0
    Default output format                       fastq
    Default output compression                  gz
    Default output compression level            5
    Feed buffer capacity                        2048
    Threads                                     8
    Decoding threads                            2
    HTSLib threads                              8

Input

    Input segment cardinality                   4

    Input segment No.0 : ./JMSNRSCF_S1_L001_R1_001.fastq.gz?format=fastq&compression=gz
    Input segment No.1 : ./JMSNRSCF_S1_L001_I1_001.fastq.gz?format=fastq&compression=gz
    Input segment No.2 : ./JMSNRSCF_S1_L001_I2_001.fastq.gz?format=fastq&compression=gz
    Input segment No.3 : ./JMSNRSCF_S1_L001_R2_001.fastq.gz?format=fastq&compression=gz

    Input feed No.0
        Type : fastq
        Compression : gz
        Resolution : 1
        Phred offset : 33
        Platform : ILLUMINA
        Buffer capacity : 2048
        URL : ./JMSNRSCF_S1_L001_R1_001.fastq.gz?format=fastq&compression=gz

    Input feed No.1
        Type : fastq
        Compression : gz
        Resolution : 1
        Phred offset : 33
        Platform : ILLUMINA
        Buffer capacity : 2048
        URL : ./JMSNRSCF_S1_L001_I1_001.fastq.gz?format=fastq&compression=gz

    Input feed No.2
        Type : fastq
        Compression : gz
        Resolution : 1
        Phred offset : 33
        Platform : ILLUMINA
        Buffer capacity : 2048
        URL : ./JMSNRSCF_S1_L001_I2_001.fastq.gz?format=fastq&compression=gz

    Input feed No.3
        Type : fastq
        Compression : gz
        Resolution : 1
        Phred offset : 33
        Platform : ILLUMINA
        Buffer capacity : 2048
        URL : ./JMSNRSCF_S1_L001_R2_001.fastq.gz?format=fastq&compression=gz

Output transform

    Output segment cardinality                  2

    Token No.0
        Length        variable
        Pattern       0::
        Description   cycles 0 to end of input segment 0

    Token No.1
        Length        variable
        Pattern       3::
        Description   cycles 0 to end of input segment 3

    Assembly instruction
        Append token 0 of input segment 0 to output segment 0
        Append token 1 of input segment 3 to output segment 1

Sample decoding

    Decoding algorithm                          pamld
    Shannon bound                               0
    Noise                                       0.05
    Confidence threshold                        0.95
    Segment cardinality                         1
    Nucleotide cardinality                      6

    Transform

        Token No.0
            Length        6
            Pattern       1::6
            Description   cycles 0 to 6 of input segment 1

        Assembly instruction
            Append token 0 of input segment 1 to output segment 0


    Barcode undetermined
        ID : JMSNRSCF:undetermined
        PU : JMSNRSCF:undetermined
        PL : ILLUMINA
        PM : NovaSeq_2x250_UCDavis_run064
        Segment No.0  : /dev/stdout?format=fastq&compression=gz&level=5
        Segment No.1  : /dev/stdout?format=fastq&compression=gz&level=5

    Barcode @11_15
        ID : JMSNRSCF:AGTCAA
        PU : JMSNRSCF:AGTCAA
        LB : 11_15
        PL : ILLUMINA
        PM : NovaSeq_2x250_UCDavis_run064
        Concentration : 0.0306451612903226
        Barcode       : AGTCAA
        Segment No.0  : /Users/lg/Desktop/jcmcnch/JMSNRSCF_11_15_s01.fastq.gz?format=fastq&compression=gz&level=5
        Segment No.1  : /Users/lg/Desktop/jcmcnch/JMSNRSCF_11_15_s02.fastq.gz?format=fastq&compression=gz&level=5

    Barcode @11_200
        ID : JMSNRSCF:ATGTCA
        PU : JMSNRSCF:ATGTCA
        LB : 11_200
        PL : ILLUMINA
        PM : NovaSeq_2x250_UCDavis_run064
        Concentration : 0.0306451612903226
        Barcode       : ATGTCA
        Segment No.0  : /Users/lg/Desktop/jcmcnch/JMSNRSCF_11_200_s01.fastq.gz?format=fastq&compression=gz&level=5
        Segment No.1  : /Users/lg/Desktop/jcmcnch/JMSNRSCF_11_200_s02.fastq.gz?format=fastq&compression=gz&level=5

    Barcode @11_25
        ID : JMSNRSCF:CGTACG
        PU : JMSNRSCF:CGTACG
        LB : 11_25
        PL : ILLUMINA
        PM : NovaSeq_2x250_UCDavis_run064
        Concentration : 0.0306451612903226
        Barcode       : CGTACG
        Segment No.0  : /Users/lg/Desktop/jcmcnch/JMSNRSCF_11_25_s01.fastq.gz?format=fastq&compression=gz&level=5
        Segment No.1  : /Users/lg/Desktop/jcmcnch/JMSNRSCF_11_25_s02.fastq.gz?format=fastq&compression=gz&level=5

    Barcode @2_400
        ID : JMSNRSCF:ATCTCA
        PU : JMSNRSCF:ATCTCA
        LB : 2_400
        PL : ILLUMINA
        PM : NovaSeq_2x250_UCDavis_run064
        Concentration : 0.0306451612903226
        Barcode       : ATCTCA
        Segment No.0  : /Users/lg/Desktop/jcmcnch/JMSNRSCF_2_400_s01.fastq.gz?format=fastq&compression=gz&level=5
        Segment No.1  : /Users/lg/Desktop/jcmcnch/JMSNRSCF_2_400_s02.fastq.gz?format=fastq&compression=gz&level=5

    Barcode @2_45
        ID : JMSNRSCF:AGGAAT
        PU : JMSNRSCF:AGGAAT
        LB : 2_45
        PL : ILLUMINA
        PM : NovaSeq_2x250_UCDavis_run064
        Concentration : 0.0306451612903226
        Barcode       : AGGAAT
        Segment No.0  : /Users/lg/Desktop/jcmcnch/JMSNRSCF_2_45_s01.fastq.gz?format=fastq&compression=gz&level=5
        Segment No.1  : /Users/lg/Desktop/jcmcnch/JMSNRSCF_2_45_s02.fastq.gz?format=fastq&compression=gz&level=5

    Barcode @7_120
        ID : JMSNRSCF:ATTCCT
        PU : JMSNRSCF:ATTCCT
        LB : 7_120
        PL : ILLUMINA
        PM : NovaSeq_2x250_UCDavis_run064
        Concentration : 0.0306451612903226
        Barcode       : ATTCCT
        Segment No.0  : /Users/lg/Desktop/jcmcnch/JMSNRSCF_7_120_s01.fastq.gz?format=fastq&compression=gz&level=5
        Segment No.1  : /Users/lg/Desktop/jcmcnch/JMSNRSCF_7_120_s02.fastq.gz?format=fastq&compression=gz&level=5

    Barcode @7_200
        ID : JMSNRSCF:GTGGCC
        PU : JMSNRSCF:GTGGCC
        LB : 7_200
        PL : ILLUMINA
        PM : NovaSeq_2x250_UCDavis_run064
        Concentration : 0.0306451612903226
        Barcode       : GTGGCC
        Segment No.0  : /Users/lg/Desktop/jcmcnch/JMSNRSCF_7_200_s01.fastq.gz?format=fastq&compression=gz&level=5
        Segment No.1  : /Users/lg/Desktop/jcmcnch/JMSNRSCF_7_200_s02.fastq.gz?format=fastq&compression=gz&level=5

    Barcode @7_25
        ID : JMSNRSCF:GTGAAA
        PU : JMSNRSCF:GTGAAA
        LB : 7_25
        PL : ILLUMINA
        PM : NovaSeq_2x250_UCDavis_run064
        Concentration : 0.0306451612903226
        Barcode       : GTGAAA
        Segment No.0  : /Users/lg/Desktop/jcmcnch/JMSNRSCF_7_25_s01.fastq.gz?format=fastq&compression=gz&level=5
        Segment No.1  : /Users/lg/Desktop/jcmcnch/JMSNRSCF_7_25_s02.fastq.gz?format=fastq&compression=gz&level=5

    Barcode @8_200
        ID : JMSNRSCF:ATGAGC
        PU : JMSNRSCF:ATGAGC
        LB : 8_200
        PL : ILLUMINA
        PM : NovaSeq_2x250_UCDavis_run064
        Concentration : 0.0306451612903226
        Barcode       : ATGAGC
        Segment No.0  : /Users/lg/Desktop/jcmcnch/JMSNRSCF_8_200_s01.fastq.gz?format=fastq&compression=gz&level=5
        Segment No.1  : /Users/lg/Desktop/jcmcnch/JMSNRSCF_8_200_s02.fastq.gz?format=fastq&compression=gz&level=5

    Barcode @8_800
        ID : JMSNRSCF:CCGTCC
        PU : JMSNRSCF:CCGTCC
        LB : 8_800
        PL : ILLUMINA
        PM : NovaSeq_2x250_UCDavis_run064
        Concentration : 0.0306451612903226
        Barcode       : CCGTCC
        Segment No.0  : /Users/lg/Desktop/jcmcnch/JMSNRSCF_8_800_s01.fastq.gz?format=fastq&compression=gz&level=5
        Segment No.1  : /Users/lg/Desktop/jcmcnch/JMSNRSCF_8_800_s02.fastq.gz?format=fastq&compression=gz&level=5

    Barcode @9_200
        ID : JMSNRSCF:ACTTCC
        PU : JMSNRSCF:ACTTCC
        LB : 9_200
        PL : ILLUMINA
        PM : NovaSeq_2x250_UCDavis_run064
        Concentration : 0.0306451612903226
        Barcode       : ACTTCC
        Segment No.0  : /Users/lg/Desktop/jcmcnch/JMSNRSCF_9_200_s01.fastq.gz?format=fastq&compression=gz&level=5
        Segment No.1  : /Users/lg/Desktop/jcmcnch/JMSNRSCF_9_200_s02.fastq.gz?format=fastq&compression=gz&level=5

    Barcode @BGT_PL01_rev11
        ID : JMSNRSCF:GCGGAC
        PU : JMSNRSCF:GCGGAC
        LB : BGT_PL01_rev11
        PL : ILLUMINA
        PM : NovaSeq_2x250_UCDavis_run064
        Concentration : 0.0306451612903226
        Barcode       : GCGGAC
        Segment No.0  : /Users/lg/Desktop/jcmcnch/JMSNRSCF_BGT_PL01_rev11_s01.fastq.gz?format=fastq&compression=gz&level=5
        Segment No.1  : /Users/lg/Desktop/jcmcnch/JMSNRSCF_BGT_PL01_rev11_s02.fastq.gz?format=fastq&compression=gz&level=5

    Barcode @BGT_PL01_rev12
        ID : JMSNRSCF:TTTCAC
        PU : JMSNRSCF:TTTCAC
        LB : BGT_PL01_rev12
        PL : ILLUMINA
        PM : NovaSeq_2x250_UCDavis_run064
        Concentration : 0.0306451612903226
        Barcode       : TTTCAC
        Segment No.0  : /Users/lg/Desktop/jcmcnch/JMSNRSCF_BGT_PL01_rev12_s01.fastq.gz?format=fastq&compression=gz&level=5
        Segment No.1  : /Users/lg/Desktop/jcmcnch/JMSNRSCF_BGT_PL01_rev12_s02.fastq.gz?format=fastq&compression=gz&level=5

    Barcode @BGT_PL01_rev13
        ID : JMSNRSCF:CCGGTG
        PU : JMSNRSCF:CCGGTG
        LB : BGT_PL01_rev13
        PL : ILLUMINA
        PM : NovaSeq_2x250_UCDavis_run064
        Concentration : 0.0306451612903226
        Barcode       : CCGGTG
        Segment No.0  : /Users/lg/Desktop/jcmcnch/JMSNRSCF_BGT_PL01_rev13_s01.fastq.gz?format=fastq&compression=gz&level=5
        Segment No.1  : /Users/lg/Desktop/jcmcnch/JMSNRSCF_BGT_PL01_rev13_s02.fastq.gz?format=fastq&compression=gz&level=5

    Barcode @BGT_PL01_rev14
        ID : JMSNRSCF:ATCGTG
        PU : JMSNRSCF:ATCGTG
        LB : BGT_PL01_rev14
        PL : ILLUMINA
        PM : NovaSeq_2x250_UCDavis_run064
        Concentration : 0.0306451612903226
        Barcode       : ATCGTG
        Segment No.0  : /Users/lg/Desktop/jcmcnch/JMSNRSCF_BGT_PL01_rev14_s01.fastq.gz?format=fastq&compression=gz&level=5
        Segment No.1  : /Users/lg/Desktop/jcmcnch/JMSNRSCF_BGT_PL01_rev14_s02.fastq.gz?format=fastq&compression=gz&level=5

    Barcode @BGT_PL02_rev15
        ID : JMSNRSCF:TGAGTG
        PU : JMSNRSCF:TGAGTG
        LB : BGT_PL02_rev15
        PL : ILLUMINA
        PM : NovaSeq_2x250_UCDavis_run064
        Concentration : 0.0306451612903226
        Barcode       : TGAGTG
        Segment No.0  : /Users/lg/Desktop/jcmcnch/JMSNRSCF_BGT_PL02_rev15_s01.fastq.gz?format=fastq&compression=gz&level=5
        Segment No.1  : /Users/lg/Desktop/jcmcnch/JMSNRSCF_BGT_PL02_rev15_s02.fastq.gz?format=fastq&compression=gz&level=5

    Barcode @BGT_PL02_rev16
        ID : JMSNRSCF:CGCCTG
        PU : JMSNRSCF:CGCCTG
        LB : BGT_PL02_rev16
        PL : ILLUMINA
        PM : NovaSeq_2x250_UCDavis_run064
        Concentration : 0.0306451612903226
        Barcode       : CGCCTG
        Segment No.0  : /Users/lg/Desktop/jcmcnch/JMSNRSCF_BGT_PL02_rev16_s01.fastq.gz?format=fastq&compression=gz&level=5
        Segment No.1  : /Users/lg/Desktop/jcmcnch/JMSNRSCF_BGT_PL02_rev16_s02.fastq.gz?format=fastq&compression=gz&level=5

    Barcode @CAP_PL01_rev01
        ID : JMSNRSCF:CGTGAT
        PU : JMSNRSCF:CGTGAT
        LB : CAP_PL01_rev01
        PL : ILLUMINA
        PM : NovaSeq_2x250_UCDavis_run064
        Concentration : 0.0306451612903226
        Barcode       : CGTGAT
        Segment No.0  : /Users/lg/Desktop/jcmcnch/JMSNRSCF_CAP_PL01_rev01_s01.fastq.gz?format=fastq&compression=gz&level=5
        Segment No.1  : /Users/lg/Desktop/jcmcnch/JMSNRSCF_CAP_PL01_rev01_s02.fastq.gz?format=fastq&compression=gz&level=5

    Barcode @CAP_PL01_rev02
        ID : JMSNRSCF:ACATCG
        PU : JMSNRSCF:ACATCG
        LB : CAP_PL01_rev02
        PL : ILLUMINA
        PM : NovaSeq_2x250_UCDavis_run064
        Concentration : 0.0306451612903226
        Barcode       : ACATCG
        Segment No.0  : /Users/lg/Desktop/jcmcnch/JMSNRSCF_CAP_PL01_rev02_s01.fastq.gz?format=fastq&compression=gz&level=5
        Segment No.1  : /Users/lg/Desktop/jcmcnch/JMSNRSCF_CAP_PL01_rev02_s02.fastq.gz?format=fastq&compression=gz&level=5

    Barcode @CAP_PL01_rev03
        ID : JMSNRSCF:GCCTAA
        PU : JMSNRSCF:GCCTAA
        LB : CAP_PL01_rev03
        PL : ILLUMINA
        PM : NovaSeq_2x250_UCDavis_run064
        Concentration : 0.0306451612903226
        Barcode       : GCCTAA
        Segment No.0  : /Users/lg/Desktop/jcmcnch/JMSNRSCF_CAP_PL01_rev03_s01.fastq.gz?format=fastq&compression=gz&level=5
        Segment No.1  : /Users/lg/Desktop/jcmcnch/JMSNRSCF_CAP_PL01_rev03_s02.fastq.gz?format=fastq&compression=gz&level=5

    Barcode @CAP_PL01_rev04
        ID : JMSNRSCF:TGGTCA
        PU : JMSNRSCF:TGGTCA
        LB : CAP_PL01_rev04
        PL : ILLUMINA
        PM : NovaSeq_2x250_UCDavis_run064
        Concentration : 0.0306451612903226
        Barcode       : TGGTCA
        Segment No.0  : /Users/lg/Desktop/jcmcnch/JMSNRSCF_CAP_PL01_rev04_s01.fastq.gz?format=fastq&compression=gz&level=5
        Segment No.1  : /Users/lg/Desktop/jcmcnch/JMSNRSCF_CAP_PL01_rev04_s02.fastq.gz?format=fastq&compression=gz&level=5

    Barcode @Colette_rev21
        ID : JMSNRSCF:TTCGTC
        PU : JMSNRSCF:TTCGTC
        LB : Colette_rev21
        PL : ILLUMINA
        PM : NovaSeq_2x250_UCDavis_run064
        Concentration : 0.0306451612903226
        Barcode       : TTCGTC
        Segment No.0  : /Users/lg/Desktop/jcmcnch/JMSNRSCF_Colette_rev21_s01.fastq.gz?format=fastq&compression=gz&level=5
        Segment No.1  : /Users/lg/Desktop/jcmcnch/JMSNRSCF_Colette_rev21_s02.fastq.gz?format=fastq&compression=gz&level=5

    Barcode @Colette_rev22
        ID : JMSNRSCF:CCAACT
        PU : JMSNRSCF:CCAACT
        LB : Colette_rev22
        PL : ILLUMINA
        PM : NovaSeq_2x250_UCDavis_run064
        Concentration : 0.0306451612903226
        Barcode       : CCAACT
        Segment No.0  : /Users/lg/Desktop/jcmcnch/JMSNRSCF_Colette_rev22_s01.fastq.gz?format=fastq&compression=gz&level=5
        Segment No.1  : /Users/lg/Desktop/jcmcnch/JMSNRSCF_Colette_rev22_s02.fastq.gz?format=fastq&compression=gz&level=5

    Barcode @Colette_rev23
        ID : JMSNRSCF:TCAGTT
        PU : JMSNRSCF:TCAGTT
        LB : Colette_rev23
        PL : ILLUMINA
        PM : NovaSeq_2x250_UCDavis_run064
        Concentration : 0.0306451612903226
        Barcode       : TCAGTT
        Segment No.0  : /Users/lg/Desktop/jcmcnch/JMSNRSCF_Colette_rev23_s01.fastq.gz?format=fastq&compression=gz&level=5
        Segment No.1  : /Users/lg/Desktop/jcmcnch/JMSNRSCF_Colette_rev23_s02.fastq.gz?format=fastq&compression=gz&level=5

    Barcode @Colette_rev24
        ID : JMSNRSCF:CTGACC
        PU : JMSNRSCF:CTGACC
        LB : Colette_rev24
        PL : ILLUMINA
        PM : NovaSeq_2x250_UCDavis_run064
        Concentration : 0.0306451612903226
        Barcode       : CTGACC
        Segment No.0  : /Users/lg/Desktop/jcmcnch/JMSNRSCF_Colette_rev24_s01.fastq.gz?format=fastq&compression=gz&level=5
        Segment No.1  : /Users/lg/Desktop/jcmcnch/JMSNRSCF_Colette_rev24_s02.fastq.gz?format=fastq&compression=gz&level=5

    Barcode @Delaney_rev19
        ID : JMSNRSCF:GGAACT
        PU : JMSNRSCF:GGAACT
        LB : Delaney_rev19
        PL : ILLUMINA
        PM : NovaSeq_2x250_UCDavis_run064
        Concentration : 0.0306451612903226
        Barcode       : GGAACT
        Segment No.0  : /Users/lg/Desktop/jcmcnch/JMSNRSCF_Delaney_rev19_s01.fastq.gz?format=fastq&compression=gz&level=5
        Segment No.1  : /Users/lg/Desktop/jcmcnch/JMSNRSCF_Delaney_rev19_s02.fastq.gz?format=fastq&compression=gz&level=5

    Barcode @Delaney_rev20
        ID : JMSNRSCF:CGAAAC
        PU : JMSNRSCF:CGAAAC
        LB : Delaney_rev20
        PL : ILLUMINA
        PM : NovaSeq_2x250_UCDavis_run064
        Concentration : 0.0306451612903226
        Barcode       : CGAAAC
        Segment No.0  : /Users/lg/Desktop/jcmcnch/JMSNRSCF_Delaney_rev20_s01.fastq.gz?format=fastq&compression=gz&level=5
        Segment No.1  : /Users/lg/Desktop/jcmcnch/JMSNRSCF_Delaney_rev20_s02.fastq.gz?format=fastq&compression=gz&level=5

    Barcode @Rae_rev05
        ID : JMSNRSCF:CACTGT
        PU : JMSNRSCF:CACTGT
        LB : Rae_rev05
        PL : ILLUMINA
        PM : NovaSeq_2x250_UCDavis_run064
        Concentration : 0.0306451612903226
        Barcode       : CACTGT
        Segment No.0  : /Users/lg/Desktop/jcmcnch/JMSNRSCF_Rae_rev05_s01.fastq.gz?format=fastq&compression=gz&level=5
        Segment No.1  : /Users/lg/Desktop/jcmcnch/JMSNRSCF_Rae_rev05_s02.fastq.gz?format=fastq&compression=gz&level=5

    Barcode @mystery12264
        ID : JMSNRSCF:ACTGAT
        PU : JMSNRSCF:ACTGAT
        LB : mystery12264
        PL : ILLUMINA
        PM : NovaSeq_2x250_UCDavis_run064
        Concentration : 0.0306451612903226
        Barcode       : ACTGAT
        Segment No.0  : /Users/lg/Desktop/jcmcnch/JMSNRSCF_mystery12264_s01.fastq.gz?format=fastq&compression=gz&level=5
        Segment No.1  : /Users/lg/Desktop/jcmcnch/JMSNRSCF_mystery12264_s02.fastq.gz?format=fastq&compression=gz&level=5

    Barcode @mystery4895
        ID : JMSNRSCF:GGGGGG
        PU : JMSNRSCF:GGGGGG
        LB : mystery4895
        PL : ILLUMINA
        PM : NovaSeq_2x250_UCDavis_run064
        Concentration : 0.0306451612903226
        Barcode       : GGGGGG
        Segment No.0  : /Users/lg/Desktop/jcmcnch/JMSNRSCF_mystery4895_s01.fastq.gz?format=fastq&compression=gz&level=5
        Segment No.1  : /Users/lg/Desktop/jcmcnch/JMSNRSCF_mystery4895_s02.fastq.gz?format=fastq&compression=gz&level=5

    Barcode @mystery8619
        ID : JMSNRSCF:AGTTCC
        PU : JMSNRSCF:AGTTCC
        LB : mystery8619
        PL : ILLUMINA
        PM : NovaSeq_2x250_UCDavis_run064
        Concentration : 0.0306451612903226
        Barcode       : AGTTCC
        Segment No.0  : /Users/lg/Desktop/jcmcnch/JMSNRSCF_mystery8619_s01.fastq.gz?format=fastq&compression=gz&level=5
        Segment No.1  : /Users/lg/Desktop/jcmcnch/JMSNRSCF_mystery8619_s02.fastq.gz?format=fastq&compression=gz&level=5

    Output feed No.62
        Type : fastq
        Compression : gz@5
        Resolution : 1
        Phred offset : 33
        Platform : ILLUMINA
        Buffer capacity : 2048
        URL : /Users/lg/Desktop/jcmcnch/JMSNRSCF_CAP_PL01_rev02_s01.fastq.gz?format=fastq&compression=gz&level=5

    Output feed No.61
        Type : fastq
        Compression : gz@5
        Resolution : 1
        Phred offset : 33
        Platform : ILLUMINA
        Buffer capacity : 2048
        URL : /Users/lg/Desktop/jcmcnch/JMSNRSCF_11_200_s01.fastq.gz?format=fastq&compression=gz&level=5

    Output feed No.60
        Type : fastq
        Compression : gz@5
        Resolution : 1
        Phred offset : 33
        Platform : ILLUMINA
        Buffer capacity : 2048
        URL : /Users/lg/Desktop/jcmcnch/JMSNRSCF_BGT_PL02_rev15_s02.fastq.gz?format=fastq&compression=gz&level=5

    Output feed No.59
        Type : fastq
        Compression : gz@5
        Resolution : 1
        Phred offset : 33
        Platform : ILLUMINA
        Buffer capacity : 2048
        URL : /Users/lg/Desktop/jcmcnch/JMSNRSCF_11_25_s01.fastq.gz?format=fastq&compression=gz&level=5

    Output feed No.58
        Type : fastq
        Compression : gz@5
        Resolution : 1
        Phred offset : 33
        Platform : ILLUMINA
        Buffer capacity : 2048
        URL : /Users/lg/Desktop/jcmcnch/JMSNRSCF_CAP_PL01_rev03_s01.fastq.gz?format=fastq&compression=gz&level=5

    Output feed No.57
        Type : fastq
        Compression : gz@5
        Resolution : 1
        Phred offset : 33
        Platform : ILLUMINA
        Buffer capacity : 2048
        URL : /Users/lg/Desktop/jcmcnch/JMSNRSCF_8_200_s02.fastq.gz?format=fastq&compression=gz&level=5

    Output feed No.56
        Type : fastq
        Compression : gz@5
        Resolution : 1
        Phred offset : 33
        Platform : ILLUMINA
        Buffer capacity : 2048
        URL : /Users/lg/Desktop/jcmcnch/JMSNRSCF_8_800_s01.fastq.gz?format=fastq&compression=gz&level=5

    Output feed No.55
        Type : fastq
        Compression : gz@5
        Resolution : 1
        Phred offset : 33
        Platform : ILLUMINA
        Buffer capacity : 2048
        URL : /Users/lg/Desktop/jcmcnch/JMSNRSCF_CAP_PL01_rev01_s02.fastq.gz?format=fastq&compression=gz&level=5

    Output feed No.54
        Type : fastq
        Compression : gz@5
        Resolution : 1
        Phred offset : 33
        Platform : ILLUMINA
        Buffer capacity : 2048
        URL : /Users/lg/Desktop/jcmcnch/JMSNRSCF_2_400_s01.fastq.gz?format=fastq&compression=gz&level=5

    Output feed No.53
        Type : fastq
        Compression : gz@5
        Resolution : 1
        Phred offset : 33
        Platform : ILLUMINA
        Buffer capacity : 2048
        URL : /Users/lg/Desktop/jcmcnch/JMSNRSCF_mystery4895_s01.fastq.gz?format=fastq&compression=gz&level=5

    Output feed No.52
        Type : fastq
        Compression : gz@5
        Resolution : 1
        Phred offset : 33
        Platform : ILLUMINA
        Buffer capacity : 2048
        URL : /Users/lg/Desktop/jcmcnch/JMSNRSCF_2_400_s02.fastq.gz?format=fastq&compression=gz&level=5

    Output feed No.51
        Type : fastq
        Compression : gz@5
        Resolution : 1
        Phred offset : 33
        Platform : ILLUMINA
        Buffer capacity : 2048
        URL : /Users/lg/Desktop/jcmcnch/JMSNRSCF_2_45_s01.fastq.gz?format=fastq&compression=gz&level=5

    Output feed No.50
        Type : fastq
        Compression : gz@5
        Resolution : 1
        Phred offset : 33
        Platform : ILLUMINA
        Buffer capacity : 2048
        URL : /Users/lg/Desktop/jcmcnch/JMSNRSCF_Rae_rev05_s01.fastq.gz?format=fastq&compression=gz&level=5

    Output feed No.49
        Type : fastq
        Compression : gz@5
        Resolution : 1
        Phred offset : 33
        Platform : ILLUMINA
        Buffer capacity : 2048
        URL : /Users/lg/Desktop/jcmcnch/JMSNRSCF_11_15_s01.fastq.gz?format=fastq&compression=gz&level=5

    Output feed No.48
        Type : fastq
        Compression : gz@5
        Resolution : 1
        Phred offset : 33
        Platform : ILLUMINA
        Buffer capacity : 2048
        URL : /Users/lg/Desktop/jcmcnch/JMSNRSCF_2_45_s02.fastq.gz?format=fastq&compression=gz&level=5

    Output feed No.47
        Type : fastq
        Compression : gz@5
        Resolution : 1
        Phred offset : 33
        Platform : ILLUMINA
        Buffer capacity : 2048
        URL : /Users/lg/Desktop/jcmcnch/JMSNRSCF_9_200_s02.fastq.gz?format=fastq&compression=gz&level=5

    Output feed No.46
        Type : fastq
        Compression : gz@5
        Resolution : 1
        Phred offset : 33
        Platform : ILLUMINA
        Buffer capacity : 2048
        URL : /Users/lg/Desktop/jcmcnch/JMSNRSCF_11_15_s02.fastq.gz?format=fastq&compression=gz&level=5

    Output feed No.41
        Type : fastq
        Compression : gz@5
        Resolution : 1
        Phred offset : 33
        Platform : ILLUMINA
        Buffer capacity : 2048
        URL : /Users/lg/Desktop/jcmcnch/JMSNRSCF_mystery12264_s01.fastq.gz?format=fastq&compression=gz&level=5

    Output feed No.43
        Type : fastq
        Compression : gz@5
        Resolution : 1
        Phred offset : 33
        Platform : ILLUMINA
        Buffer capacity : 2048
        URL : /Users/lg/Desktop/jcmcnch/JMSNRSCF_8_200_s01.fastq.gz?format=fastq&compression=gz&level=5

    Output feed No.42
        Type : fastq
        Compression : gz@5
        Resolution : 2
        Phred offset : 33
        Platform : ILLUMINA
        Buffer capacity : 4096
        URL : /dev/stdout?format=fastq&compression=gz&level=5

    Output feed No.38
        Type : fastq
        Compression : gz@5
        Resolution : 1
        Phred offset : 33
        Platform : ILLUMINA
        Buffer capacity : 2048
        URL : /Users/lg/Desktop/jcmcnch/JMSNRSCF_7_25_s02.fastq.gz?format=fastq&compression=gz&level=5

    Output feed No.36
        Type : fastq
        Compression : gz@5
        Resolution : 1
        Phred offset : 33
        Platform : ILLUMINA
        Buffer capacity : 2048
        URL : /Users/lg/Desktop/jcmcnch/JMSNRSCF_BGT_PL01_rev13_s02.fastq.gz?format=fastq&compression=gz&level=5

    Output feed No.34
        Type : fastq
        Compression : gz@5
        Resolution : 1
        Phred offset : 33
        Platform : ILLUMINA
        Buffer capacity : 2048
        URL : /Users/lg/Desktop/jcmcnch/JMSNRSCF_Delaney_rev19_s01.fastq.gz?format=fastq&compression=gz&level=5

    Output feed No.35
        Type : fastq
        Compression : gz@5
        Resolution : 1
        Phred offset : 33
        Platform : ILLUMINA
        Buffer capacity : 2048
        URL : /Users/lg/Desktop/jcmcnch/JMSNRSCF_11_25_s02.fastq.gz?format=fastq&compression=gz&level=5

    Output feed No.33
        Type : fastq
        Compression : gz@5
        Resolution : 1
        Phred offset : 33
        Platform : ILLUMINA
        Buffer capacity : 2048
        URL : /Users/lg/Desktop/jcmcnch/JMSNRSCF_9_200_s01.fastq.gz?format=fastq&compression=gz&level=5

    Output feed No.31
        Type : fastq
        Compression : gz@5
        Resolution : 1
        Phred offset : 33
        Platform : ILLUMINA
        Buffer capacity : 2048
        URL : /Users/lg/Desktop/jcmcnch/JMSNRSCF_7_120_s01.fastq.gz?format=fastq&compression=gz&level=5

    Output feed No.32
        Type : fastq
        Compression : gz@5
        Resolution : 1
        Phred offset : 33
        Platform : ILLUMINA
        Buffer capacity : 2048
        URL : /Users/lg/Desktop/jcmcnch/JMSNRSCF_CAP_PL01_rev04_s01.fastq.gz?format=fastq&compression=gz&level=5

    Output feed No.30
        Type : fastq
        Compression : gz@5
        Resolution : 1
        Phred offset : 33
        Platform : ILLUMINA
        Buffer capacity : 2048
        URL : /Users/lg/Desktop/jcmcnch/JMSNRSCF_BGT_PL01_rev11_s01.fastq.gz?format=fastq&compression=gz&level=5

    Output feed No.29
        Type : fastq
        Compression : gz@5
        Resolution : 1
        Phred offset : 33
        Platform : ILLUMINA
        Buffer capacity : 2048
        URL : /Users/lg/Desktop/jcmcnch/JMSNRSCF_BGT_PL01_rev11_s02.fastq.gz?format=fastq&compression=gz&level=5

    Output feed No.28
        Type : fastq
        Compression : gz@5
        Resolution : 1
        Phred offset : 33
        Platform : ILLUMINA
        Buffer capacity : 2048
        URL : /Users/lg/Desktop/jcmcnch/JMSNRSCF_BGT_PL01_rev12_s01.fastq.gz?format=fastq&compression=gz&level=5

    Output feed No.27
        Type : fastq
        Compression : gz@5
        Resolution : 1
        Phred offset : 33
        Platform : ILLUMINA
        Buffer capacity : 2048
        URL : /Users/lg/Desktop/jcmcnch/JMSNRSCF_CAP_PL01_rev01_s01.fastq.gz?format=fastq&compression=gz&level=5

    Output feed No.26
        Type : fastq
        Compression : gz@5
        Resolution : 1
        Phred offset : 33
        Platform : ILLUMINA
        Buffer capacity : 2048
        URL : /Users/lg/Desktop/jcmcnch/JMSNRSCF_Colette_rev21_s02.fastq.gz?format=fastq&compression=gz&level=5

    Output feed No.22
        Type : fastq
        Compression : gz@5
        Resolution : 1
        Phred offset : 33
        Platform : ILLUMINA
        Buffer capacity : 2048
        URL : /Users/lg/Desktop/jcmcnch/JMSNRSCF_BGT_PL02_rev15_s01.fastq.gz?format=fastq&compression=gz&level=5

    Output feed No.40
        Type : fastq
        Compression : gz@5
        Resolution : 1
        Phred offset : 33
        Platform : ILLUMINA
        Buffer capacity : 2048
        URL : /Users/lg/Desktop/jcmcnch/JMSNRSCF_CAP_PL01_rev03_s02.fastq.gz?format=fastq&compression=gz&level=5

    Output feed No.19
        Type : fastq
        Compression : gz@5
        Resolution : 1
        Phred offset : 33
        Platform : ILLUMINA
        Buffer capacity : 2048
        URL : /Users/lg/Desktop/jcmcnch/JMSNRSCF_BGT_PL02_rev16_s02.fastq.gz?format=fastq&compression=gz&level=5

    Output feed No.18
        Type : fastq
        Compression : gz@5
        Resolution : 1
        Phred offset : 33
        Platform : ILLUMINA
        Buffer capacity : 2048
        URL : /Users/lg/Desktop/jcmcnch/JMSNRSCF_7_200_s01.fastq.gz?format=fastq&compression=gz&level=5

    Output feed No.4
        Type : fastq
        Compression : gz@5
        Resolution : 1
        Phred offset : 33
        Platform : ILLUMINA
        Buffer capacity : 2048
        URL : /Users/lg/Desktop/jcmcnch/JMSNRSCF_Delaney_rev20_s01.fastq.gz?format=fastq&compression=gz&level=5

    Output feed No.20
        Type : fastq
        Compression : gz@5
        Resolution : 1
        Phred offset : 33
        Platform : ILLUMINA
        Buffer capacity : 2048
        URL : /Users/lg/Desktop/jcmcnch/JMSNRSCF_11_200_s02.fastq.gz?format=fastq&compression=gz&level=5

    Output feed No.21
        Type : fastq
        Compression : gz@5
        Resolution : 1
        Phred offset : 33
        Platform : ILLUMINA
        Buffer capacity : 2048
        URL : /Users/lg/Desktop/jcmcnch/JMSNRSCF_BGT_PL02_rev16_s01.fastq.gz?format=fastq&compression=gz&level=5

    Output feed No.15
        Type : fastq
        Compression : gz@5
        Resolution : 1
        Phred offset : 33
        Platform : ILLUMINA
        Buffer capacity : 2048
        URL : /Users/lg/Desktop/jcmcnch/JMSNRSCF_Delaney_rev20_s02.fastq.gz?format=fastq&compression=gz&level=5

    Output feed No.17
        Type : fastq
        Compression : gz@5
        Resolution : 1
        Phred offset : 33
        Platform : ILLUMINA
        Buffer capacity : 2048
        URL : /Users/lg/Desktop/jcmcnch/JMSNRSCF_CAP_PL01_rev02_s02.fastq.gz?format=fastq&compression=gz&level=5

    Output feed No.16
        Type : fastq
        Compression : gz@5
        Resolution : 1
        Phred offset : 33
        Platform : ILLUMINA
        Buffer capacity : 2048
        URL : /Users/lg/Desktop/jcmcnch/JMSNRSCF_7_25_s01.fastq.gz?format=fastq&compression=gz&level=5

    Output feed No.12
        Type : fastq
        Compression : gz@5
        Resolution : 1
        Phred offset : 33
        Platform : ILLUMINA
        Buffer capacity : 2048
        URL : /Users/lg/Desktop/jcmcnch/JMSNRSCF_BGT_PL01_rev14_s02.fastq.gz?format=fastq&compression=gz&level=5

    Output feed No.13
        Type : fastq
        Compression : gz@5
        Resolution : 1
        Phred offset : 33
        Platform : ILLUMINA
        Buffer capacity : 2048
        URL : /Users/lg/Desktop/jcmcnch/JMSNRSCF_Colette_rev22_s01.fastq.gz?format=fastq&compression=gz&level=5

    Output feed No.14
        Type : fastq
        Compression : gz@5
        Resolution : 1
        Phred offset : 33
        Platform : ILLUMINA
        Buffer capacity : 2048
        URL : /Users/lg/Desktop/jcmcnch/JMSNRSCF_Colette_rev21_s01.fastq.gz?format=fastq&compression=gz&level=5

    Output feed No.11
        Type : fastq
        Compression : gz@5
        Resolution : 1
        Phred offset : 33
        Platform : ILLUMINA
        Buffer capacity : 2048
        URL : /Users/lg/Desktop/jcmcnch/JMSNRSCF_Colette_rev22_s02.fastq.gz?format=fastq&compression=gz&level=5

    Output feed No.5
        Type : fastq
        Compression : gz@5
        Resolution : 1
        Phred offset : 33
        Platform : ILLUMINA
        Buffer capacity : 2048
        URL : /Users/lg/Desktop/jcmcnch/JMSNRSCF_Delaney_rev19_s02.fastq.gz?format=fastq&compression=gz&level=5

    Output feed No.1
        Type : fastq
        Compression : gz@5
        Resolution : 1
        Phred offset : 33
        Platform : ILLUMINA
        Buffer capacity : 2048
        URL : /Users/lg/Desktop/jcmcnch/JMSNRSCF_mystery8619_s01.fastq.gz?format=fastq&compression=gz&level=5

    Output feed No.45
        Type : fastq
        Compression : gz@5
        Resolution : 1
        Phred offset : 33
        Platform : ILLUMINA
        Buffer capacity : 2048
        URL : /Users/lg/Desktop/jcmcnch/JMSNRSCF_7_120_s02.fastq.gz?format=fastq&compression=gz&level=5

    Output feed No.44
        Type : fastq
        Compression : gz@5
        Resolution : 1
        Phred offset : 33
        Platform : ILLUMINA
        Buffer capacity : 2048
        URL : /Users/lg/Desktop/jcmcnch/JMSNRSCF_BGT_PL01_rev13_s01.fastq.gz?format=fastq&compression=gz&level=5

    Output feed No.2
        Type : fastq
        Compression : gz@5
        Resolution : 1
        Phred offset : 33
        Platform : ILLUMINA
        Buffer capacity : 2048
        URL : /Users/lg/Desktop/jcmcnch/JMSNRSCF_mystery12264_s02.fastq.gz?format=fastq&compression=gz&level=5

    Output feed No.10
        Type : fastq
        Compression : gz@5
        Resolution : 1
        Phred offset : 33
        Platform : ILLUMINA
        Buffer capacity : 2048
        URL : /Users/lg/Desktop/jcmcnch/JMSNRSCF_Colette_rev23_s01.fastq.gz?format=fastq&compression=gz&level=5

    Output feed No.6
        Type : fastq
        Compression : gz@5
        Resolution : 1
        Phred offset : 33
        Platform : ILLUMINA
        Buffer capacity : 2048
        URL : /Users/lg/Desktop/jcmcnch/JMSNRSCF_Colette_rev24_s02.fastq.gz?format=fastq&compression=gz&level=5

    Output feed No.9
        Type : fastq
        Compression : gz@5
        Resolution : 1
        Phred offset : 33
        Platform : ILLUMINA
        Buffer capacity : 2048
        URL : /Users/lg/Desktop/jcmcnch/JMSNRSCF_Colette_rev23_s02.fastq.gz?format=fastq&compression=gz&level=5

    Output feed No.8
        Type : fastq
        Compression : gz@5
        Resolution : 1
        Phred offset : 33
        Platform : ILLUMINA
        Buffer capacity : 2048
        URL : /Users/lg/Desktop/jcmcnch/JMSNRSCF_mystery4895_s02.fastq.gz?format=fastq&compression=gz&level=5

    Output feed No.37
        Type : fastq
        Compression : gz@5
        Resolution : 1
        Phred offset : 33
        Platform : ILLUMINA
        Buffer capacity : 2048
        URL : /Users/lg/Desktop/jcmcnch/JMSNRSCF_8_800_s02.fastq.gz?format=fastq&compression=gz&level=5

    Output feed No.7
        Type : fastq
        Compression : gz@5
        Resolution : 1
        Phred offset : 33
        Platform : ILLUMINA
        Buffer capacity : 2048
        URL : /Users/lg/Desktop/jcmcnch/JMSNRSCF_Colette_rev24_s01.fastq.gz?format=fastq&compression=gz&level=5

    Output feed No.24
        Type : fastq
        Compression : gz@5
        Resolution : 1
        Phred offset : 33
        Platform : ILLUMINA
        Buffer capacity : 2048
        URL : /Users/lg/Desktop/jcmcnch/JMSNRSCF_7_200_s02.fastq.gz?format=fastq&compression=gz&level=5

    Output feed No.25
        Type : fastq
        Compression : gz@5
        Resolution : 1
        Phred offset : 33
        Platform : ILLUMINA
        Buffer capacity : 2048
        URL : /Users/lg/Desktop/jcmcnch/JMSNRSCF_BGT_PL01_rev12_s02.fastq.gz?format=fastq&compression=gz&level=5

    Output feed No.23
        Type : fastq
        Compression : gz@5
        Resolution : 1
        Phred offset : 33
        Platform : ILLUMINA
        Buffer capacity : 2048
        URL : /Users/lg/Desktop/jcmcnch/JMSNRSCF_CAP_PL01_rev04_s02.fastq.gz?format=fastq&compression=gz&level=5

    Output feed No.3
        Type : fastq
        Compression : gz@5
        Resolution : 1
        Phred offset : 33
        Platform : ILLUMINA
        Buffer capacity : 2048
        URL : /Users/lg/Desktop/jcmcnch/JMSNRSCF_Rae_rev05_s02.fastq.gz?format=fastq&compression=gz&level=5

    Output feed No.39
        Type : fastq
        Compression : gz@5
        Resolution : 1
        Phred offset : 33
        Platform : ILLUMINA
        Buffer capacity : 2048
        URL : /Users/lg/Desktop/jcmcnch/JMSNRSCF_BGT_PL01_rev14_s01.fastq.gz?format=fastq&compression=gz&level=5

    Output feed No.0
        Type : fastq
        Compression : gz@5
        Resolution : 1
        Phred offset : 33
        Platform : ILLUMINA
        Buffer capacity : 2048
        URL : /Users/lg/Desktop/jcmcnch/JMSNRSCF_mystery8619_s02.fastq.gz?format=fastq&compression=gz&level=5

@moonwatcher moonwatcher self-assigned this Dec 17, 2021
@jcmcnch
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jcmcnch commented Jun 22, 2022

Hi Lior,

Thank you so much for your detailed reply, and I'm sorry I never replied. This will be a great reference going forward, and I hope using your explanations I can now figure out how to construct the json config. If I'm still running into issues, I'll be sure to reach out.

Jesse

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