Open moniekvanselst opened 4 years ago
kbchoi-jax
commented
4 years ago Could you show me the first few lines of your bam file except the header please? It also helps if you give me some more info regarding the experimental settings and your goals. If you prefer to keep it confidencial, email me at kb.choi@jax.org.
nikhilmilind
commented
3 years ago Hello! Any fix for this yet? I have the same issue with a BAM file I generated using STAR...
kbchoi-jax
commented
3 years ago Hi NMilind, could you share your bam file? Please contact me at kb.choi@jax.org.
Hello,
I am trying to run alntools, because i want to use emase-zero afterwards. Unfortunately i keep getting this error, it said that the variable "chunks" is a NonType and gives an error for trying to calculate the length(see full error message below). Changing the -c (chunks) value does not seem to have any effect on the matter. I also tried running bam2emase, but this give me the same error. Further I tried running it with different bam files (that have been accepted by other, similar tools), this also gave the same error.
Do you have any suggestions on how to fix this error?
full error: Traceback (most recent call last): File "/opt/conda/bin/alntools", line 4, in
import('pkg_resources').run_script('alntools==0.1.1', 'alntools')
File "/opt/conda/lib/python2.7/site-packages/pkg_resources/init.py", line 666, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/opt/conda/lib/python2.7/site-packages/pkg_resources/init.py", line 1462, in run_script
exec(code, namespace, namespace)
File "/opt/conda/lib/python2.7/site-packages/alntools-0.1.1-py2.7.egg/EGG-INFO/scripts/alntools", line 29, in
cli()
File "/opt/conda/lib/python2.7/site-packages/click/core.py", line 764, in call
return self.main(args, kwargs)
File "/opt/conda/lib/python2.7/site-packages/click/core.py", line 717, in main
rv = self.invoke(ctx)
File "/opt/conda/lib/python2.7/site-packages/click/core.py", line 1137, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/opt/conda/lib/python2.7/site-packages/click/core.py", line 956, in invoke
return ctx.invoke(self.callback, ctx.params)
File "/opt/conda/lib/python2.7/site-packages/click/core.py", line 555, in invoke
return callback(args, **kwargs)
File "/opt/conda/lib/python2.7/site-packages/alntools-0.1.1-py2.7.egg/alntools/cli.py", line 75, in bam2ec
methods.bam2ec(bam_file, ec_file, chunks, directory, number_processes, rangefile, sample, targets)
File "/opt/conda/lib/python2.7/site-packages/alntools-0.1.1-py2.7.egg/alntools/methods.py", line 32, in bam2ec
bam_utils.convert(bam_filename, ec_filename, None, num_chunks=chunks, number_processes=number_processes, temp_dir=directory, range_filename=range_filename, sample=sample, target_filename=target_filename)
File "/opt/conda/lib/python2.7/site-packages/alntools-0.1.1-py2.7.egg/alntools/bam_utils.py", line 642, in convert
LOG.info("{:,} chunks calculated in {}, total time: {}".format(len(chunks),
TypeError: object of type 'NoneType' has no len()