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DNA methylation analysis downstream to Nanopolish for Oxford Nanopore DNA sequencing datasets
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Comp_report exiting with invalid file input type from Interval_Aggregate #48

Closed dithiii closed 4 years ago

dithiii commented 4 years ago

Hi I'm getting an error with Comp_report not reading my Interval_Aggregate input file (looks fine in .tsv and .bed format). Not sure where the problem is. Here's the first 3 lines of the Interval_aggregate file, and then the error from Comp_report.

head -n 3 barcode01.Interval_Aggregate.tsv
chromosome  start   end num_motifs  median_llr  llr_list    pos_list
chr1    125175000   125180000   11  1.92    [1.92,5.855,4.945,5.065,1.1,0.385,1.79] [125179758,125179784,125179833,125179863,125179882,125179925,125179987]
chr1    125180000   125185000   43  3.11    [2.08,4.8,2.52,5.315,2.53,1.16,3.965,3.955,4.94,4.49,5.91,1.86,2.475,0.31,2.83,3.11,2.035,-0.24,2.895,3.65,4.39,6.54,-0.37,3.54,3.905]  [125180008,125180032,125180060,125180083,125180104,125180154,125180187,125180226,125180252,125180301,125180331,125180393,125180419,125180471,125180575,125180606,125180624,125180650,125180682,125180700,125180723,125180746,125180764,125180800,125180821]

Here's the error with Comp_report

pycoMeth Comp_Report -i barcode01.Interval_Aggregate.tsv -g ~/Desktop/genomes/Homo_sapiens.GRCh38.101.gff3 -f ~/Desktop/genomes/hg38softmasked/hg38softmasked.fa --report_non_significant --verbose
## Checking options and input files ##
    [DEBUG]: Options summary
    [DEBUG]:    Package name: pycoMeth
    [DEBUG]:    Package version: 0.4.25
    [DEBUG]:    Timestamp: 2020-11-02 15:43:48.841354
    [DEBUG]:    methcomp_fn: barcode01.Interval_Aggregate.tsv
    [DEBUG]:    gff3_fn: /home/cfaulk/Desktop/genomes/Homo_sapiens.GRCh38.101.gff3
    [DEBUG]:    ref_fasta_fn: /home/cfaulk/Desktop/genomes/hg38softmasked/hg38softmasked.fa
    [DEBUG]:    outdir: ./
    [DEBUG]:    n_top: 100
    [DEBUG]:    max_tss_distance: 100000
    [DEBUG]:    pvalue_threshold: 0.01
    [DEBUG]:    min_diff_llr: 1
    [DEBUG]:    n_len_bin: 500
    [DEBUG]:    api_mode: False
    [DEBUG]:    export_static_plots: False
    [DEBUG]:    report_non_significant: True
    [DEBUG]:    verbose: True
    [DEBUG]:    quiet: False
    [DEBUG]:    progress: False
    [DEBUG]:    kwargs
    [DEBUG]:        subcommands: Comp_Report
    [DEBUG]:        func: <function Comp_Report at 0x7fcecf1145f0>
## Loading and preparing data ##
    Loading Methcomp data from TSV file
Traceback (most recent call last):
  File "/home/cfaulk/miniconda3/envs/pycoMeth/bin/pycoMeth", line 8, in <module>
    sys.exit(main())
  File "/home/cfaulk/miniconda3/envs/pycoMeth/lib/python3.7/site-packages/pycoMeth/__main__.py", line 116, in main
    args.func(**vars(args))
  File "/home/cfaulk/miniconda3/envs/pycoMeth/lib/python3.7/site-packages/pycoMeth/Comp_Report.py", line 96, in Comp_Report
    raise pycoMethError ("Invalid input file type passed. Expecting Meth_Comp TSV file generated from samples processed with Interval_Aggregate")
pycoMeth.common.pycoMethError: Invalid input file type passed. Expecting Meth_Comp TSV file generated from samples processed with Interval_Aggregate
dithiii commented 4 years ago

Nevermind. I didn't read the instructions very well.