Running error

[hzlzldr]

hi,

I ran it according to your sample code in quick start, and the following error occurred. Have you run it by yourself?

Looking forward to your reply and code fixes!

genomedisco run_all --metadata_samples examples/metadata.samples --metadata_pairs examples/metadata.pairs --bins examples/Bins.w50000.bed.gz --outdir examples/output
Traceback (most recent call last):
File "/data5/huanglu/miniconda3/bin/genomedisco", line 11, in
load_entry_point('genomedisco', 'console_scripts', 'genomedisco')()
File "/data4/lzl/genomedisco/genomedisco/main.py", line 17, in main
command_methodscommand
File "/data4/lzl/genomedisco/genomedisco/concordance_utils.py", line 847, in run_all
preprocess(metadata_samples,bins,re_fragments,methods,outdir,running_mode,subset_chromosomes,parameters_file,timing)
File "/data4/lzl/genomedisco/genomedisco/concordance_utils.py", line 150, in preprocess
write_resolution(nodes,resolution_file)
File "/data4/lzl/genomedisco/genomedisco/concordance_utils.py", line 115, in write_resolution
items=line.strip().split('\t')
TypeError: a bytes-like object is required, not 'str'

[oursu]

Hi! One suggestion I have is to make sure you are using python2, as recommended in the Readme. If that does not solve the issue, please let me know here and I am happy to continue helping to troubleshoot.

[hzlzldr]

it does not work with py2

---

(base) huanglu 22:46:00 /data4/lzl/genomedisco
python --version
Python 2.7.15+

(base) huanglu 22:46:00 /data4/lzl/genomedisco
$ genomedisco run_all --metadata_samples examples/metadata.samples --metadata_pairs examples/metadata.pairs --bins examples/Bins.w50000.bed.gz --outdir examples/output
Traceback (most recent call last):
File "/data5/huanglu/miniconda3/bin/genomedisco", line 11, in
load_entry_point('genomedisco', 'console_scripts', 'genomedisco')()
File "/data4/lzl/genomedisco/genomedisco/main.py", line 17, in main
command_methodscommand
File "/data4/lzl/genomedisco/genomedisco/concordance_utils.py", line 847, in run_all
preprocess(metadata_samples,bins,re_fragments,methods,outdir,running_mode,subset_chromosomes,parameters_file,timing)
File "/data4/lzl/genomedisco/genomedisco/concordance_utils.py", line 150, in preprocess
write_resolution(nodes,resolution_file)
File "/data4/lzl/genomedisco/genomedisco/concordance_utils.py", line 115, in write_resolution
items=line.strip().split('\t')
TypeError: a bytes-like object is required, not 'str'

[oursu-broad]

I'm still worried it calls the python3 version because of /data5/huanglu/miniconda3/bin/genomedisco

[QichenFU]

Hi! One suggestion I have is to make sure you are using python2, as recommended in the Readme. If that does not solve the issue, please let me know here and I am happy to continue helping to troubleshoot.

May I ask how to run the command using python2 rather than python3 since it calls python3 by default?