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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
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