search

xjtu-omics / HiCAT

HiCAT new project
Other
25 stars 2 forks source link

invalid literal for int() with base error #10

Closed LHG-GG closed 6 months ago

LHG-GG commented 9 months ago

Hi,

could you help with https://github.com/865699871/HiCAT/issues/3

865699871 commented 7 months ago

You can rename the input sequence and don't use :: or -.

LHG-GG commented 7 months ago

I have removed everything like you said, the error still remains

Prepared reads
100%: Aligned chr22_Mat
2024-02-22 13:04:50,343 - StringDecomposer - INFO - Saved raw decomposition to ./HiCAT_out/final_decomposition_raw.tsv
2024-02-22 13:04:50,542 - StringDecomposer - INFO - Transforming raw alignments...
2024-02-22 13:05:15,755 - StringDecomposer - INFO - Transformation finished. Results can be found in ./HiCAT_out/final_decomposition.tsv
2024-02-22 13:05:15,758 - 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: 'Mat'
865699871 commented 7 months ago

I guess may be '_'. If there is still problem you can send us your input fa file. E-mail is zym81666881@stu.xjtu.edu.cn.