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nilesh-tawari / ChronQC

Manuscript describing ChronQC is now available online in Bioinformatics
https://doi.org/10.1093/bioinformatics/btx843
MIT License
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chronqc database showing usage info instead of creating database #1

Closed multimeric closed 5 years ago

multimeric commented 5 years ago

I have run the following command, and I'm getting the following output:

$ chronqc database --create --run-date-info chromqc/date_info.csv -o . multiqc/multiqc_data/multiqc_general_stats.txt AshTrio
Running ChronQC |############--------------------------------------| 25.0% usage: chronqc [-h] {database,plot,annotation,chrongen} ...

positional arguments:
  {database,plot,annotation,chrongen}
    database            Generate ChronQC database for ChronQC plots. Type
                        "chronqc database -h" for help on generating/updating
                        ChronQC database.
    plot                Generate ChronQC plots. Type "chronqc plot -h" for
                        help on generating ChronQC plots.
    annotation          Start connectivity for annotating plots. Type "chronqc
                        annotation -h" for help on starting ChronQC annotation
                        server.
    chrongen            Use this option for automating ChronQC plot
                        generation. Type "chronqc chrongen -h" for details on
                        required arguments.

optional arguments:
  -h, --help            show this help message and exit

I believe I'm running it in the exact same way as described in the documentation. My input files are:

multiqc_general_stats.txt:

Sample  FastQC_mqc-generalstats-fastqc-percent_duplicates       FastQC_mqc-generalstats-fastqc-percent_gc       FastQC_mqc-generalstats-fastqc-avg_sequence_length      FastQC_mqc-generalstats-fastqc-percent_fails        FastQC_mqc-generalstats-fastqc-total_sequences
TD06-GV1008_R1  23.583813895575773      48.0    126.0   16.666666666666664      75193388.0
TD06-GV1008_R2  23.55288528173324       48.0    126.0   16.666666666666664      75193388.0
TD06-GV1009_R1  21.13916226098023       48.0    126.0   16.666666666666664      64304319.0
TD06-GV1009_R2  21.362002911460763      48.0    126.0   16.666666666666664      64304319.0
TD06-GV1010_R1  22.371300749740257      48.0    126.0   16.666666666666664      73074989.0
TD06-GV1010_R2  22.501682511070243      48.0    126.0   16.666666666666664      73074989.0

chromqc/date_info.csv:

TD06-GV1008_R1,Run-1,01/01/2018
TD06-GV1008_R2,Run-1,01/01/2018
TD06-GV1009_R1,Run-1,01/02/2018
TD06-GV1009_R2,Run-1,01/02/2018
TD06-GV1010_R1,Run-1,01/03/2018
TD06-GV1010_R2,Run-1,01/03/2018

I also note that I don't have this issue if I use --multiqc-sources instead of --run-date-info.

multimeric commented 5 years ago

Oh, this might be because I was missing the header in my date_info file? This worked when I instead used:

Sample,Run,Date
TD06-GV1008_R1,Run-1,01/01/2018
TD06-GV1008_R2,Run-1,01/01/2018
TD06-GV1009_R1,Run-1,01/02/2018
TD06-GV1009_R2,Run-1,01/02/2018
TD06-GV1010_R1,Run-1,01/03/2018
TD06-GV1010_R2,Run-1,01/03/2018
nilesh-tawari commented 5 years ago

@TMiguelT Thanks for figuring it out, yes header is mandatory.