Why cnvkit run with output error

Question

[gaihua559]

I install cnvkit recently and try to fun it, my command is:

python2.7 /Software/cnvkit/cnvkit.py batch /Projects/P46-tumor.sorted.bam --normal /Projects/P46-blood.sorted.bam \ --processes 0 --targets /APP/Panel2.bed --fasta /Data/HG19/hg19.fa \ --split --access /Software/cnvkit/data/access-5k-mappable.hg19.bed \ --output-reference /Work/P46/varscan0/tumor_blood.cnn --output-dir /Work/diagnosis2/P46/varscan0/

Then several minutes later, it show me following reports and I don't know why. Could any one help me? Thanks very much!

Traceback (most recent call last): File "Software/cnvkit/cnvkit.py", line 11, in <module> args.func(args) File "/Software/cnvkit/cnvlib/commands.py", line 97, in _cmd_batch args.processes, args.count_reads) File "/Software/cnvkit/cnvlib/commands.py", line 182, in batch_make_reference male_reference) File "/Software/cnvkit/cnvlib/commands.py", line 522, in do_reference do_gc, do_edge, False) File "/Software/cnvkit/cnvlib/reference.py", line 40, in combine_probes cnarr1 = CNA.read(filenames[0]) File "/Software/cnvkit/cnvlib/gary.py", line 460, in read dtype={'chromosome': 'string'}, File "/usr/local/lib/python2.7/dist-packages/pandas/io/parsers.py", line 529, in parser_f return _read(filepath_or_buffer, kwds) File "/usr/local/lib/python2.7/dist-packages/pandas/io/parsers.py", line 295, in _read parser = TextFileReader(filepath_or_buffer, *kwds) File "/usr/local/lib/python2.7/dist-packages/pandas/io/parsers.py", line 612, in __init__ self._make_engine(self.engine) File "/usr/local/lib/python2.7/dist-packages/pandas/io/parsers.py", line 747, in _make_engine self._engine = CParserWrapper(self.f, *self.options) File "/usr/local/lib/python2.7/dist-packages/pandas/io/parsers.py", line 1119, in __init__ self._reader = _parser.TextReader(src, **kwds) File "pandas/parser.pyx", line 353, in pandas.parser.TextReader.__cinit__ (pandas/parser.c:3246) File "pandas/parser.pyx", line 591, in pandas.parser.TextReader._setup_parser_source (pandas/parser.c:6111) IOError: File varscan0/P46-blood.targetcoverage.cnn does not exist

Answer 1

[Sandeep]

The error as I see is because the output.cnn is not found. Try creating the same in the working directory. I have modified the command, paste it directly and check if the error appears. I have also removed the process argument as it was 0.

python2.7 /Software/cnvkit/cnvkit.py batch /Projects/P46-tumor.sorted.bam --normal /Projects/P46-blood.sorted.bam --targets /APP/Panel2.bed --fasta /Data/HG19/hg19.fa --split --access /Software/cnvkit/data/access-5k-mappable.hg19.bed --output-reference tumor_blood.cnn --output-dir /Work/diagnosis2/P46/varscan0/

Hope this works.