ialbert
commented
1 year ago the problem seems to be that you have python 3.6 installed
the install script should install python3.8 by default, so that needs to change, perhaps you are using an old version of the book
After I did conda activate bioinfo, I did this; doctor.py
Doctor! Doctor! Give me the news.
Checking symptoms ...
bwa ... OK
datamash ... OK
fastqc -h ... OK
hisat2 ... OK
seqret -h ... OK
featureCounts ... OK
efetch ... OK
esearch ... OK
samtools ... OK
fastq-dump ... OK
bowtie2 ... OK
bcftools ... OK
seqtk ... OK
seqkit ... OK
bio ... Traceback (most recent call last):
File "/home/davo/bin/doctor.py", line 125, in
health_check()
File "/home/davo/bin/doctor.py", line 105, in health_check
errors += tool_check(tools=TOOLS)
File "/home/davo/bin/doctor.py", line 69, in tool_check
res = subprocess.run(args, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
File "/home/davo/miniconda3/envs/bioinfo/lib/python3.6/subprocess.py", line 423, in run
with Popen(*popenargs, **kwargs) as process:
File "/home/davo/miniconda3/envs/bioinfo/lib/python3.6/subprocess.py", line 729, in init
restore_signals, start_new_session)
File "/home/davo/miniconda3/envs/bioinfo/lib/python3.6/subprocess.py", line 1364, in _execute_child
raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'bio': 'bio'
(bioinfo)
Since the bio seem to failed I decided to use "pip install bio --upgrade" I got a warning: the scripts f2py,, f2py3 and f2py3.8 are installed in '/home/davo/. local/bin hich is not on path consider adding this directory to path. the same thing goes for "tqdm", "bio" and fasta_filter.py
when I now ran a realistic analysis ith make command I got make Makefile:61: *** "Program: bio not found.". Stop. (bioinfo) Please kindly help.