Skip to content

invalid literal for int() with base error #3

@LHG-GG

Description

@LHG-GG

Hi,
Great work on automated centromere annotation. the tool works well with the testdataset.

But I encountered the "invalid literal for int() with base" error while running hicat on chm13 chr18 centromere region. below is the command:
hicat -i chr18.fa -t AlphaSat.fa -th 50

the full error is:

Run stringdecomposer

python /home/sarashettp/miniforge3/envs/hica/bin/stringdecomposer/bin/stringdecomposer chr18.fa AlphaSat.fa -o ./HiCAT_out
2023-11-30 11:15:24,490 - StringDecomposer - INFO - cmd: ['/home/sarashettp/miniforge3/envs/hica/bin/stringdecomposer/bin/stringdecomposer', 'chr18.fa', '/home/sarashettp/scratch/tools/HORmon/test_data/AlphaSat.fa', '-o', './HiCAT_out']
2023-11-30 11:15:24,491 - StringDecomposer - INFO - Run /home/sarashettp/miniforge3/envs/hica/bin/stringdecomposer/stringdecomposer/build/bin/dp with parameters chr18.fa /home/sarashettp/scratch/tools/HORmon/test_data/AlphaSat.fa 1 5000 500 -1,-1,-1,1
Scores: insertion=-1 deletion=-1 mismatch=-1 match=1
Prepared reads
100%: Aligned chr18_15965700-20933550:._us:2000_ds:2000
2023-11-30 11:15:46,877 - StringDecomposer - INFO - Saved raw decomposition to ./HiCAT_out/final_decomposition_raw.tsv
2023-11-30 11:15:46,946 - StringDecomposer - INFO - Transforming raw alignments...
2023-11-30 11:15:49,917 - StringDecomposer - INFO - Transformation finished. Results can be found in ./HiCAT_out/final_decomposition.tsv
2023-11-30 11:15:49,918 - StringDecomposer - INFO - Thank you for using StringDecomposer!
Run HiCAT HOR

python /home/sarashettp/miniforge3/envs/hica/bin/HiCAT_HOR.py -d ./HiCAT_out/final_decomposition.tsv -b ./HiCAT_out/input_fasta.1.fa -o ./HiCAT_out -s 0.94 -st 0.005 -m 40 -sp 5 -sn 10 -t 50
start
build block sequence and read base sequence
calculate ed distance
ed distance thread: 50
Traceback (most recent call last):
  File "/home/sarashettp/miniforge3/envs/hica/bin/HiCAT_HOR.py", line 1589, in <module>
    main()
  File "/home/sarashettp/miniforge3/envs/hica/bin/HiCAT_HOR.py", line 1495, in main
    edit_distance_matrix, block_name_index = calculateED(block_sequence, base_sequence,thread)
  File "/home/sarashettp/miniforge3/envs/hica/bin/HiCAT_HOR.py", line 62, in calculateED
    split_base_sequence = base_sequence[int(items[1]):int(items[2])]
ValueError: invalid literal for int() with base 10: '15965700-20933550:.'

Please let me know if you need any additional information. I have attached the input file used.
chr18.txt

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions