Dependency conflicts and "NameError: name 'var' is not defined" error with biastools --analyze command

[g0ddengr]

I was unable to install the required dependency bcftools=1.9 because of the following conflicts. Instead, bcftools=1.10.2 was installed instead. This may or may not relate to the error that follows.

Could not solve for environment specs
The following packages are incompatible
├─ bcftools =1.9 * is installable with the potential options
│ ├─ bcftools 1.9 would require
│ │ └─ htslib >=1.9,<1.10.0a0 * with the potential options
│ │ ├─ htslib 1.9, which can be installed;
│ │ └─ htslib 1.9 would require
│ │ └─ libdeflate >=1.0,<1.1.0a0 *, which conflicts with any installable versions previously reported;
│ └─ bcftools 1.9 would require
│ └─ libdeflate >=1.0,<1.1.0a0 *, which conflicts with any installable versions previously reported;
└─ samtools =1.11 * is not installable because it requires
└─ htslib >=1.11,<1.22.0a0 *, which conflicts with any installable versions previously reported.

I encountered errors when running the biastools --analyze command with tutorial data. All other commands in the run.sh tutorial script worked. How can I fix this?

$ biastools --analyze -g grch38_chr20_part.fa -v HG002.chr20.part.vcf.gz -s HG002_part -r tutorial
[Biastools] Analyze and plot...
[Biastools] Intersect the bam file and vcf file
[Biastools] Reference bias analysis
start initializing chr20
INFO:main:Start building the variant maps...
INFO:main:Start comparing reads to the variant map...
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/apps/biastools/0.2.0/lib/python3.9/multiprocessing/pool.py", line 125, in worker
result = (True, func(*args, **kwds))
File "/apps/biastools/0.2.0/lib/python3.9/multiprocessing/pool.py", line 48, in mapstar
return list(map(*args))
File "/apps/biastools/0.2.0/lib/python3.9/site-packages/biastools/ref_bi_context.py", line 736, in analyze_read
return analyzer.analyze()
File "/apps/biastools/0.2.0/lib/python3.9/site-packages/biastools/ref_bi_context.py", line 46, in analyze
self.compare_reads_to_variants()
File "/apps/biastools/0.2.0/lib/python3.9/site-packages/biastools/ref_bi_context.py", line 287, in compare_reads_to_variants
self.process_read(segment)
File "/apps/biastools/0.2.0/lib/python3.9/site-packages/biastools/ref_bi_context.py", line 394, in process_read
if (seq_name, flag_read_n) in self.dict_ref_var_name[ref_name][var.start][1]: # check if the read name is in the golden set
NameError: name 'var' is not defined
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File "/apps/biastools/0.2.0/lib/python3.9/site-packages/biastools/ref_bi_context.py", line 805, in
main()
File "/apps/biastools/0.2.0/lib/python3.9/site-packages/biastools/ref_bi_context.py", line 799, in main
result = pool.map(analyze_read, list_info)
File "/apps/biastools/0.2.0/lib/python3.9/multiprocessing/pool.py", line 364, in map
return self._map_async(func, iterable, mapstar, chunksize).get()
File "/apps/biastools/0.2.0/lib/python3.9/multiprocessing/pool.py", line 771, in get
raise self._value
NameError: name 'var' is not defined
Traceback (most recent call last):
File "/apps/biastools/0.2.0/lib/python3.9/site-packages/biastools/golden_graph_report.py", line 190, in
df_use = pd.read_csv(fn_bias, sep='\t')
File "/apps/biastools/0.2.0/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1026, in read_csv
return _read(filepath_or_buffer, kwds)
File "/apps/biastools/0.2.0/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 620, in _read
parser = TextFileReader(filepath_or_buffer, **kwds)
File "/apps/biastools/0.2.0/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1620, in init
self._engine = self._make_engine(f, self.engine)
File "/apps/biastools/0.2.0/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1880, in _make_engine
self.handles = get_handle(
File "/apps/biastools/0.2.0/lib/python3.9/site-packages/pandas/io/common.py", line 873, in get_handle
handle = open(
FileNotFoundError: [Errno 2] No such file or directory: 'out_dir/tutorial_report/HG002_part.tutorial.sim.bias.SNP'
Traceback (most recent call last):
File "/apps/biastools/0.2.0/lib/python3.9/site-packages/biastools/golden_graph_report.py", line 190, in
df_use = pd.read_csv(fn_bias, sep='\t')
File "/apps/biastools/0.2.0/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1026, in read_csv
return _read(filepath_or_buffer, kwds)
File "/apps/biastools/0.2.0/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 620, in _read
parser = TextFileReader(filepath_or_buffer, **kwds)
File "/apps/biastools/0.2.0/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1620, in init
self._engine = self._make_engine(f, self.engine)
File "/apps/biastools/0.2.0/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1880, in _make_engine
self.handles = get_handle(
File "/apps/biastools/0.2.0/lib/python3.9/site-packages/pandas/io/common.py", line 873, in get_handle
handle = open(
FileNotFoundError: [Errno 2] No such file or directory: 'out_dir/tutorial_report/HG002_part.tutorial.sim.bias.gap'
Traceback (most recent call last):
File "/apps/biastools/0.2.0/lib/python3.9/site-packages/biastools/golden_graph.py", line 296, in
df_use = pd.read_csv(fn_bias, sep='\t')
File "/apps/biastools/0.2.0/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1026, in read_csv
return _read(filepath_or_buffer, kwds)
File "/apps/biastools/0.2.0/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 620, in _read
parser = TextFileReader(filepath_or_buffer, **kwds)
File "/apps/biastools/0.2.0/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1620, in init
self._engine = self._make_engine(f, self.engine)
File "/apps/biastools/0.2.0/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1880, in _make_engine
self.handles = get_handle(
File "/apps/biastools/0.2.0/lib/python3.9/site-packages/pandas/io/common.py", line 873, in get_handle
handle = open(
FileNotFoundError: [Errno 2] No such file or directory: 'out_dir/tutorial_report/HG002_part.tutorial.sim.bias.SNP'
Traceback (most recent call last):
File "/apps/biastools/0.2.0/lib/python3.9/site-packages/biastools/golden_graph.py", line 296, in
df_use = pd.read_csv(fn_bias, sep='\t')
File "/apps/biastools/0.2.0/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1026, in read_csv
return _read(filepath_or_buffer, kwds)
File "/apps/biastools/0.2.0/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 620, in _read
parser = TextFileReader(filepath_or_buffer, **kwds)
File "/apps/biastools/0.2.0/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1620, in init
self._engine = self._make_engine(f, self.engine)
File "/apps/biastools/0.2.0/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1880, in _make_engine
self.handles = get_handle(
File "/apps/biastools/0.2.0/lib/python3.9/site-packages/pandas/io/common.py", line 873, in get_handle
handle = open(
FileNotFoundError: [Errno 2] No such file or directory: 'out_dir/tutorial_report/HG002_part.tutorial.sim.bias.gap'
Traceback (most recent call last):
File "/apps/biastools/0.2.0/lib/python3.9/site-packages/biastools/indel_balance_plot.py", line 178, in
assign_report = read_bias_report(fn_assign_report)
File "/apps/biastools/0.2.0/lib/python3.9/site-packages/biastools/indel_balance_plot.py", line 14, in read_bias_report
f = open(fn_bias_report, 'r')
FileNotFoundError: [Errno 2] No such file or directory: 'out_dir/tutorial_report/HG002_part.tutorial.sim.bias.all'

[maojanlin]

Hi @g0ddengr , thanks for catching this. It was a bug in the script ref_bi_context.py, which I've now fixed in both GitHub and PyPi package. Please try the updated version--it should work as expected. Also, bcftools version 1.10.2 should work fine. Let me know if you run into other issues!

[g0ddengr]

Thank you for the quick work and update. I ran the tutorial data with the new installation (v.0.2.1) and generated the expected output.