Firstly, i was install shortbred by conda Shortbred :: Anaconda.org. we also installed by biobakery, but return the same error.
(1) i run the following command, it same the usearch path is not right
(shortbred) dell@dell-PowerEdge-R720:~$ shortbred_quantify.py --markers /home/dell/raw_data/amrfinder/amrfinder.fa --wgs /home/dell/raw_data/rmhg19fastqcat/H1.rmhg19.fastp.fastq --results /home/dell/raw_data/shortbred/H1_results.txt --tmp /home/dell/raw_data/shortbred/H1_quantify
Traceback (most recent call last):
File “/home/dell/miniconda3/envs/shortbred/bin/shortbred_quantify.py”, line 139, in
src.CheckDependency(args.strUSEARCH,"",“usearch”)
File “/home/dell/miniconda3/envs/shortbred/lib/python2.7/site-packages/shortbred_src/ init .py”, line 36, in CheckDependency
raise IOError("\nShortBRED was unable to find " + strIntendedProgram + " at the path " + strCmd + " \nPlease check that the program is installed and the path is correct. Please note that ShortBRED will not be able to use the unix alias for the program.")
IOError:
ShortBRED was unable to find usearch at the path usearch
Please check that the program is installed and the path is correct. Please note that ShortBRED will not be able to use the unix alias for the program.
(2)so i used --usearch to note the path, but it still return error, i wonder how to resove it.
(shortbred) dell@dell-PowerEdge-R720:~$ shortbred_quantify.py --markers /home/dell/raw_data/amrfinder/amrfinder.fa --usearch /home/dell/bioinfo/usearch11.0.667_i86linux32 --wgs /home/dell/raw_data/rmhg19fastqcat/H1.rmhg19.fastp.fastq --results /home/dell/raw_data/shortbred/H1_results.txt --tmp /home/dell/raw_data/shortbred/H1_quantify
Traceback (most recent call last):
File “/home/dell/miniconda3/envs/shortbred/bin/shortbred_quantify.py”, line 139, in
src.CheckDependency(args.strUSEARCH,"",“usearch”)
File “/home/dell/miniconda3/envs/shortbred/lib/python2.7/site-packages/shortbred_src/ init .py”, line 43, in CheckDependency
pCmd = subprocess.Popen([strCmd],stdout=subprocess.PIPE,stderr=subprocess.PIPE)
File “/home/dell/miniconda3/envs/shortbred/lib/python2.7/subprocess.py”, line 710, in init
errread, errwrite)
File “/home/dell/miniconda3/envs/shortbred/lib/python2.7/subprocess.py”, line 1335, in _execute_child
raise child_exception
OSError: [Errno 13] Permission denied
thanks.
Qiang