I tried running this command
python blastp.py CmydPro tlr TLR.txt to extract the query sequence for the target species I’m looking at. However, whenever I try running it always comes up as a blast p error and says there’s no directory. I downloaded blastp.py as a file made from my lab’s GitHub but I have no idea how to troubleshoot the error since it’s not a required directory. I made sure all my directories were correct and that all my files were intact. Any help with this would be greatly appreciated.
This is the error I keep getting:
Traceback (most recent call last): File "blastp.py", line 53, in blastp_scout = subprocess.Popen(['blastp', '-db', organism_db, '-query', 'temp.fa', '-out', 'blast', '-num_descriptions', '5', '-num_alignments', '0']) File "/home/dylan_w190/miniconda3/lib/python3.8/subprocess.py", line 854, in __init__ self._execute_child(args, executable, preexec_fn, close_fds, File "/home/dylan_w190/miniconda3/lib/python3.8/subprocess.py", line 1702, in _execute_child raise child_exception_type(errno_num, err_msg, err_filename) FileNotFoundError: [Errno 2] No such file or directory: 'blastp'
These are all the files I have stored in my directory:
'$RECYCLE.BIN' 'Genome Files' TLR.txt 'ASM 28112' 'Genome Files (1)' Tham 'ASM 28964' 'Genome Files (2)' Vim 'ASM 3597' 'Genome Files (3)' Xenopus 'ASM 45574' 'Genome Files (4)' blast-2.11.0+ AnoCar Git blastp.py Chrysemys GopAga get-pip.py Cliv GopAga2.0-Genome human CmydPro Halia ls CmydPro_results.txt LICENCE mouse Config.Msi Lib ncbi-blast-2.6.0+ CroPor Miniconda3-latest-Linux-x86_64.sh ncbi-blast-2.6.0+-win64.exe 'FASTAs (2)' OpenSSH-Win64 pip Format Ornitho pvi GCF_015237465.1_rCheMyd1.pri_genomic.fna PelSin pyzo GFFs Python setup.py 'GFFs (2)' PythonX temp.fa GRCh38 README.txt tlr_CmydPro.fa GRCm38 Rnor tlr_ref.fasta Gallus 'Rnor - Copy' vs_buildtools__576366542.1609221376.exe GavGan Scripts vs_community__576366542.1609221376.exe Gekko 'System Volume Information'
You don't have blastp in your path. Blast is either not installed on your system or it's just not been added to path right.
Answered by Liam McIntyre on May 3, 2021
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