List index out of range during gc correction

[RSchwieger]

I am facing an issue with the GC correction. I created the gc-file using the instructions to create a gc-file and provided the file in ref_genome_conf.py.

When running the following command

cnvpytor -conf ref_genome_conf.py -root file.pytor -his 10000 100000

I get the error message:

2024-11-15 10:23:01,081 - cnvpytor.root - INFO - Chromosome 'CM020500.1' bin size 100 stat - RD unique distribution gaussian fit:  8.39 +- 4.84
2024-11-15 10:23:01,081 - cnvpytor.root - INFO - Calculating global statistics.
2024-11-15 10:23:01,414 - cnvpytor.root - INFO - Calculating GC corrected RD histogram using bin size 100 for chromosome 'CM020439.1'.
Traceback (most recent call last):
  File "/environment4CNVpytor/.pipeline-env/bin/cnvpytor", line 8, in <module>
    sys.exit(main())
             ^^^^^^
  File "/environment4CNVpytor/.pipeline-env/lib/python3.12/site-packages/cnvpytor/__main__.py", line 400, in main
    app.calculate_histograms(args.his, chroms=args.chrom, gc_auto=args.gc_auto, gc_corr_rm_ol=args.gc_corr_rm_ol)
  File "/environment4CNVpytor/.pipeline-env/lib/python3.12/site-packages/cnvpytor/root.py", line 1005, in calculate_histograms
    his_p_corr = his_p / np.array(list(map(lambda x: gc_corr[int(x)], gcp_decompress(gcat, bin_ratio))))
                                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

  File "/environment4CNVpytor/.pipeline-env/lib/python3.12/site-packages/cnvpytor/root.py", line 1005, in <lambda>
    his_p_corr = his_p / np.array(list(map(lambda x: gc_corr[int(x)], gcp_decompress(gcat, bin_ratio))))
                                                     ~~~~~~~^^^^^^^^
IndexError: list index out of range

And the output of

cnvpytor -conf ref_genome_conf.py -root file.pytor -ls

was

Error message:

File created: 2024-11-15 10:19 using CNVpytor ver 1.3.2

Chromosomes with RD signal: CM020439.1, CM020440.1, CM020441.1, CM020442.1, CM020443.1, CM020444.1, CM020445.1, CM020446.1, CM020447.1, CM020448.1, CM020449.1, CM020450.1, CM020451.1, CM020452.1, CM020453.1, CM020454.1, CM020455.1, CM020456.1, CM020457.1, CM020458.1, CM020459.1, CM020460.1, CM020461.1, CM020463.1, CM020462.1, CM020500.1

Chromosomes with SNP signal: 

Using reference genome: bSteHir1 [ GC: yes, mask: no ]

Chromosomes with RD histograms [bin sizes]:  []

Chromosomes with SNP histograms [bin sizes]:  []

[arpanda]

Hi @RSchwieger,
It seems there is an issue with your GC file or providing the path for GC file. Please ensure the following:

• The same FASTA file was used for both the alignment and the creation of the GC file.
• The full path to the GC file is correctly specified.

Thank you,
-Arijit