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invalid literal for int() with base 10: 'START_A' #266

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valentinShimansky opened this issue May 20, 2024 · 0 comments
Open

invalid literal for int() with base 10: 'START_A' #266

valentinShimansky opened this issue May 20, 2024 · 0 comments

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@valentinShimansky
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Hello!
I've encountered this error

invalid literal for int() with base 10: 'START_A'

after using this command

metaquast -o ./spades_K11/quast_K11 -t 20 -1 A_Corrosion_K11_adapter_clear_1.fastq -2 A_Corrosion_K11_adapter_clear_2.fastq ./spades_K11/scaffolds_K11.fasta

full error message

invalid literal for int() with base 10: 'START_A'
Traceback (most recent call last):
  File "/raid/home/vasilchenko_ng/miniconda3/envs/quast/bin/metaquast", line 427, in <module>
    return_code = main(sys.argv[1:])
  File "/raid/home/vasilchenko_ng/miniconda3/envs/quast/bin/metaquast", line 296, in main
    _start_quast_main(quast_py_args + ambiguity_opts,
  File "/raid/home/vasilchenko_ng/miniconda3/envs/quast/bin/metaquast", line 72, in _start_quast_main
    return_code = quast.main(args)
  File "/raid/home/vasilchenko_ng/miniconda3/envs/quast/opt/quast-5.2.0/quast.py", line 118, in main
    bed_fpath, cov_fpath, physical_cov_fpath = reads_analyzer.do(ref_fpath, contigs_fpaths,
  File "/raid/home/vasilchenko_ng/miniconda3/envs/quast/opt/quast-5.2.0/quast_libs/reads_analyzer.py", line 951, in do
    bed_fpath, cov_fpath, physical_cov_fpath = run_processing_reads(contigs_fpaths, ref_fpath, meta_ref_fpaths, ref_labels_by_chromosomes,
  File "/raid/home/vasilchenko_ng/miniconda3/envs/quast/opt/quast-5.2.0/quast_libs/reads_analyzer.py", line 339, in run_processing_reads
    if not is_valid_bed(bed_fpath):
  File "/raid/home/vasilchenko_ng/miniconda3/envs/quast/opt/quast-5.2.0/quast_libs/ra_utils/misc.py", line 419, in is_valid_bed
    align1 = (int(fs[1]), int(fs[2]), correct_name(fs[0]), fs[6])
ValueError: invalid literal for int() with base 10: 'START_A'
ERROR! exception caught!

Is there a way to fix this error, or may be there is a problem with command/input files? Quast log attached.
metaquast.log

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