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maiziex / Aquila

Diploid personal genome assembly and comprehensive variant detection based on linked-reads
MIT License
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Ran out of input error #2

Open LucaBertoli opened 2 years ago

LucaBertoli commented 2 years ago

Hello, I am testing Aquila on a bam file produced with longranger. I am struggling with this error that I can not adress during Aquila_step1. 

Traceback (most recent call last):
  File "/opt/Aquila/bin/Generate_highconf_cut_profile_v2.py", line 185, in <module>
    Run_all(bam_file,chr_start,chr_end,mbq_threshold,mmq_threshold,out_dir,uniq_map_dir)
  File "/opt/Aquila/bin/Generate_highconf_cut_profile_v2.py", line 161, in Run_all
    uniq_map_dict = pickle.load(open(uniq_map_file,"rb"))

EOFError: Ran out of input
/home/lucab/miniconda3/envs/env/lib/python3.9/site-packages/numpy/core/fromnumeric.py:3440: RuntimeWarning: Mean of empty slice.
  return _methods._mean(a, axis=axis, dtype=dtype,
/home/lucab/miniconda3/envs/env/lib/python3.9/site-packages/numpy/core/_methods.py:189: RuntimeWarning: invalid value encountered in double_scalars
  ret = ret.dtype.type(ret / rcount)
/home/lucab/miniconda3/envs/env/lib/python3.9/site-packages/numpy/core/fromnumeric.py:3440: RuntimeWarning: Mean of empty slice.
  return _methods._mean(a, axis=axis, dtype=dtype,
/home/lucab/miniconda3/envs/env/lib/python3.9/site-packages/numpy/core/_methods.py:189: RuntimeWarning: invalid value encountered in double_scalars
  ret = ret.dtype.type(ret / rcount)
/home/lucab/miniconda3/envs/env/lib/python3.9/site-packages/numpy/core/fromnumeric.py:3440: RuntimeWarning: Mean of empty slice.
  return _methods._mean(a, axis=axis, dtype=dtype,
/home/lucab/miniconda3/envs/env/lib/python3.9/site-packages/numpy/core/_methods.py:189: RuntimeWarning: invalid value encountered in double_scalars
  ret = ret.dtype.type(ret / rcount)
/home/lucab/miniconda3/envs/env/lib/python3.9/site-packages/numpy/core/fromnumeric.py:3440: RuntimeWarning: Mean of empty slice.
  return _methods._mean(a, axis=axis, dtype=dtype,
/home/lucab/miniconda3/envs/env/lib/python3.9/site-packages/numpy/core/_methods.py:189: RuntimeWarning: invalid value encountered in double_scalars
  ret = ret.dtype.type(ret / rcount)
/home/lucab/miniconda3/envs/env/lib/python3.9/site-packages/numpy/core/fromnumeric.py:3440: RuntimeWarning: Mean of empty slice.
  return _methods._mean(a, axis=axis, dtype=dtype,
/home/lucab/miniconda3/envs/env/lib/python3.9/site-packages/numpy/core/_methods.py:189: RuntimeWarning: invalid value encountered in double_scalars
  ret = ret.dtype.type(ret / rcount)
/home/lucab/miniconda3/envs/env/lib/python3.9/site-packages/numpy/core/fromnumeric.py:3440: RuntimeWarning: Mean of empty slice.
  return _methods._mean(a, axis=axis, dtype=dtype,
/home/lucab/miniconda3/envs/env/lib/python3.9/site-packages/numpy/core/_methods.py:189: RuntimeWarning: invalid value encountered in double_scalars
  ret = ret.dtype.type(ret / rcount)
/home/lucab/miniconda3/envs/env/lib/python3.9/site-packages/numpy/core/fromnumeric.py:3440: RuntimeWarning: Mean of empty slice.
  return _methods._mean(a, axis=axis, dtype=dtype,
/home/lucab/miniconda3/envs/env/lib/python3.9/site-packages/numpy/core/_methods.py:189: RuntimeWarning: invalid value encountered in double_scalars
  ret = ret.dtype.type(ret / rcount)
/home/lucab/miniconda3/envs/env/lib/python3.9/site-packages/numpy/core/fromnumeric.py:3440: RuntimeWarning: Mean of empty slice.
  return _methods._mean(a, axis=axis, dtype=dtype,
/home/lucab/miniconda3/envs/env/lib/python3.9/site-packages/numpy/core/_methods.py:189: RuntimeWarning: invalid value encountered in double_scalars
  ret = ret.dtype.type(ret / rcount)
/home/lucab/miniconda3/envs/env/lib/python3.9/site-packages/numpy/core/fromnumeric.py:3440: RuntimeWarning: Mean of empty slice.
  return _methods._mean(a, axis=axis, dtype=dtype,
/home/lucab/miniconda3/envs/env/lib/python3.9/site-packages/numpy/core/_methods.py:189: RuntimeWarning: invalid value encountered in double_scalars
  ret = ret.dtype.type(ret / rcount)
/home/lucab/miniconda3/envs/env/lib/python3.9/site-packages/numpy/core/fromnumeric.py:3440: RuntimeWarning: Mean of empty slice.
  return _methods._mean(a, axis=axis, dtype=dtype,
/home/lucab/miniconda3/envs/env/lib/python3.9/site-packages/numpy/core/_methods.py:189: RuntimeWarning: invalid value encountered in double_scalars
  ret = ret.dtype.type(ret / rcount)
/home/lucab/miniconda3/envs/env/lib/python3.9/site-packages/numpy/core/fromnumeric.py:3440: RuntimeWarning: Mean of empty slice.
  return _methods._mean(a, axis=axis, dtype=dtype,
/home/lucab/miniconda3/envs/env/lib/python3.9/site-packages/numpy/core/_methods.py:189: RuntimeWarning: invalid value encountered in double_scalars
  ret = ret.dtype.type(ret / rcount)
/home/lucab/miniconda3/envs/env/lib/python3.9/site-packages/numpy/core/fromnumeric.py:3440: RuntimeWarning: Mean of empty slice.
  return _methods._mean(a, axis=axis, dtype=dtype,
/home/lucab/miniconda3/envs/env/lib/python3.9/site-packages/numpy/core/_methods.py:189: RuntimeWarning: invalid value encountered in double_scalars
  ret = ret.dtype.type(ret / rcount)
/home/lucab/miniconda3/envs/env/lib/python3.9/site-packages/numpy/core/fromnumeric.py:3440: RuntimeWarning: Mean of empty slice.
  return _methods._mean(a, axis=axis, dtype=dtype,
/home/lucab/miniconda3/envs/env/lib/python3.9/site-packages/numpy/core/_methods.py:189: RuntimeWarning: invalid value encountered in double_scalars
  ret = ret.dtype.type(ret / rcount)
[]

I am running it on a conda enviroment with this command line: nohup /opt/Aquila/bin/Aquila_step1.py --bam_file possorted_bam.bam --vcf_file XXXXXX_freebayes_10xreference.vcf --sample_name XXXXXX --out_dir Assembly_results_XXXXXX --uniq_map_dir /opt/Aquila/Uniqness_map --num_threads 8 &

Does someone have any idea of why is it happening?

Thanks in advance, Luca

maiziex commented 2 years ago

Can you send me (maizie.zhou@vanderbilt.edu) a few lines of your bam and vcf files? and what reference do you use? hg38?