error occur when run human species test_dataset

[yxian9]

Hi,

The beditor is really helpful! Would you please take a look on one error which occured when I run the test dataset?

First of all, The test_datasets.py run perfectly. I assumed the software has been successfully installed on our server.

Then when I try make_datasets.py , and use source activate beditor;cd test_beditor/dataset_homo_sapiens; beditor --cfg mutation_format_nucleotide_mutation_mutations_for.yml. I get the error as following:

logfile: .log_beditor_2018_10_11_13_20_33_179487_mutation_format_nucleotide_mutation_mutations_for.yml_None_None_False_False.log 2018_10_11_13_20_35_241797: processing: mutation_format_nucleotide_mutation_mutations_for 2018_10_11_13_20_36_760623: processing: 5 chunks. 2018_10_11_13_20_36_829145: processing: chunk00000003 2018_10_11_13_20_36_834763: processing: chunk00000001 2018_10_11_13_20_36_829236: processing: chunk00000004 multiprocessing.pool.RemoteTraceback: """ Traceback (most recent call last): File "/mnt/silencer2/home/ydiao/Oct4/Software/miniconda/envs/beditor/lib/python3.6/multiprocessing/pool.py", line 119, in worker result = (True, func(*args, *kwds)) File "/mnt/silencer2/home/ydiao/Oct4/Software/miniconda/envs/beditor/lib/python3.6/multiprocessing/pool.py", line 44, in mapstar return list(map(args)) File "/mnt/silencer2/home/ydiao/Oct4/Software/miniconda/envs/beditor/lib/python3.6/site-packages/beditor/pipeline.py", line 106, in pipeline_chunks dguides2offtargets(cfg) File "/mnt/silencer2/home/ydiao/Oct4/Software/miniconda/envs/beditor/lib/python3.6/site-packages/beditor/lib/get_specificity.py", line 465, in dguides2offtargets cfg=dannots2dalignbed2dannotsagg(cfg) File "/mnt/silencer2/home/ydiao/Oct4/Software/miniconda/envs/beditor/lib/python3.6/site-packages/beditor/lib/get_specificity.py", line 281, in dannots2dalignbed2dannotsagg to_colns=['gene name','gene id','transcript id','protein id','exon id']) File "/mnt/silencer2/home/ydiao/Oct4/Software/miniconda/envs/beditor/lib/python3.6/site-packages/beditor/lib/io_dfs.py", line 196, in lambda2cols axis=1).apply(pd.Series) File "/mnt/silencer2/home/ydiao/Oct4/Software/miniconda/envs/beditor/lib/python3.6/site-packages/pandas/core/frame.py", line 6014, in apply return op.get_result() File "/mnt/silencer2/home/ydiao/Oct4/Software/miniconda/envs/beditor/lib/python3.6/site-packages/pandas/core/apply.py", line 142, in get_result return self.apply_standard() File "/mnt/silencer2/home/ydiao/Oct4/Software/miniconda/envs/beditor/lib/python3.6/site-packages/pandas/core/apply.py", line 248, in apply_standard self.apply_series_generator() File "/mnt/silencer2/home/ydiao/Oct4/Software/miniconda/envs/beditor/lib/python3.6/site-packages/pandas/core/apply.py", line 277, in apply_series_generator results[i] = self.f(v) File "/mnt/silencer2/home/ydiao/Oct4/Software/miniconda/envs/beditor/lib/python3.6/site-packages/beditor/lib/iodfs.py", line 195, in df=df.apply(lambda x: lambdaf(x[in_coln]), File "/mnt/silencer2/home/ydiao/Oct4/Software/miniconda/envs/beditor/lib/python3.6/site-packages/beditor/lib/io_seqs.py", line 105, in gffatributes2ids if '=' in s: TypeError: ("argument of type 'float' is not iterable", 'occurred at index 1|+120558086|22M|2') """

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

Traceback (most recent call last): File "/mnt/silencer2/home/ydiao/Oct4/Software/miniconda/envs/beditor/bin/beditor", line 11, in sys.exit(main()) File "/mnt/silencer2/home/ydiao/Oct4/Software/miniconda/envs/beditor/lib/python3.6/site-packages/beditor/pipeline.py", line 491, in main test=args.test,force=args.force) File "/mnt/silencer2/home/ydiao/Oct4/Software/miniconda/envs/beditor/lib/python3.6/site-packages/beditor/pipeline.py", line 425, in pipeline pool.map(pipeline_chunks, chunkcfgps) File "/mnt/silencer2/home/ydiao/Oct4/Software/miniconda/envs/beditor/lib/python3.6/multiprocessing/pool.py", line 266, in map return self._map_async(func, iterable, mapstar, chunksize).get() File "/mnt/silencer2/home/ydiao/Oct4/Software/miniconda/envs/beditor/lib/python3.6/multiprocessing/pool.py", line 644, in get raise self._value TypeError: ("argument of type 'float' is not iterable", 'occurred at index 1|+120558086|22M|2') (beditor)

Similar error also show when test danio_rerio species:

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

Traceback (most recent call last):
  File "/mnt/silencer2/home/ydiao/Oct4/Software/miniconda/envs/beditor/bin/beditor", line 11, in <module>
    sys.exit(main())
  File "/mnt/silencer2/home/ydiao/Oct4/Software/miniconda/envs/beditor/lib/python3.6/site-packages/beditor/pipeline.py", line 491, in main
    test=args.test,force=args.force)
  File "/mnt/silencer2/home/ydiao/Oct4/Software/miniconda/envs/beditor/lib/python3.6/site-packages/beditor/pipeline.py", line 425, in pipeline
    pool.map(pipeline_chunks, chunkcfgps)
  File "/mnt/silencer2/home/ydiao/Oct4/Software/miniconda/envs/beditor/lib/python3.6/multiprocessing/pool.py", line 266, in map
    return self._map_async(func, iterable, mapstar, chunksize).get()
  File "/mnt/silencer2/home/ydiao/Oct4/Software/miniconda/envs/beditor/lib/python3.6/multiprocessing/pool.py", line 644, in get
    raise self._value
TypeError: ("argument of type 'float' is not iterable", 'occurred at index 1|-16522189|22M|2')
(beditor)

Thank you very much!

[rraadd88]

Hello @yuxuth , That is strange! Could you try the newest version of from git repo? Also can you post the mutation_format_nucleotide_mutation_mutations_for.yml file. Thanks.

[yxian9]

Hi @rraadd88 ,

Thank you for replying me! The beditor version I used is v1.1.1. I installed it using pip install beditor, following your installation manual. Is there a new version on git repo? I will try to install directly from git repo

The mutation_format_nucleotide_mutation_mutations_for.yml file is generated by make_datasets.py. I also post it here:

BEs:
- Target-AID
- ABE
chunksize: 200
cores: 6
dinp: input_nucleotide.tsv
dsubmap_preferred_path: null
genomeassembly: GRCh38
genomerelease: 92
host: homo_sapiens
max_subs_per_codon: 1
mimetism_level: medium
mutation_format: nucleotide
mutations: mutations
pams:
- NGG
- NG 

[rraadd88]

Hi again @yuxuth , Just curious to whether you tried the updated version (either from git or pypi (currently 1.1.3)). Also make sure that pyensembl (1.6.0) and other dependencies are installed through the conda-virtual-environment file as follows:

wget https://raw.githubusercontent.com/rraadd88/beditor/master/environment.yml
conda env create -f environment.yml

[yxian9]

It works on the latest version v1.1.3. Thank you very much!

[rraadd88]

You are welcome!