Answers.Body: <p>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.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-02-05T05:03:54.737Z
Answers.LastActivityDate: 2021-02-05T05:03:54.737Z
Answers.UserDisplayName: Liam McIntyre
Body: <p>I tried running this command <code>python blastp.py CmydPro tlr TLR.txt</code> 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.</p>
  <p>This is the error I keep getting:</p>
  <pre class="lang-py prettyprint-override"><code>Traceback (most recent call last):
  File &quot;blastp.py&quot;, line 53, in
  blastp_scout = subprocess.Popen(['blastp', '-db', organism_db, '-query', 'temp.fa', '-out', 'blast', '-num_descriptions', '5', '-num_alignments', '0'])
  File &quot;/home/dylan_w190/miniconda3/lib/python3.8/subprocess.py&quot;, line 854, in __init__
  self._execute_child(args, executable, preexec_fn, close_fds,
  File &quot;/home/dylan_w190/miniconda3/lib/python3.8/subprocess.py&quot;, line 1702, in _execute_child
  raise child_exception_type(errno_num, err_msg, err_filename)
  FileNotFoundError: [Errno 2] No such file or directory: 'blastp'
  </code></pre>
  <p>These are all the files I have stored in my directory:</p>
  <pre><code>'$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'
  </code></pre>
  <p>There is a windows version. It seems that I already downloaded blast but I need to do this now:</p>
  <p><code>Command 'blastp' not found, but can be installed with: sudo apt install ncbi-blast+</code></p>
  <p>Do you have any idea how to might download this?</p>
  <p>I already downloaded blast as a tar file and the 2.11.0+ version. I'm just not sure how to download just ncbi-blast+ on its own.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-02-05T15:25:17.530Z
Comments.Text: That looks like you are using Windows. have you asked the developers if the script you are trying to run is even supposed to work on Windows? Is there a Windows version of blast? That can be launched from the command line?
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-07-06T01:45:40.613Z
Comments.Text: Could you please tell us what operating system you're running (e.g. Windows, Mac, Linux)? If Linux, could you please show the output of the command `uname -a`?
Comments.UserDisplayName: gringer
Tags: <file-formats>
Title: blast p-error with making directory
ThreadText: # blast p-error with making directory
  
  (Asked by: username_0 on 2021-02-05)
  
  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:
  
  ```py
  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'
  
  ```
  
  There is a windows version. It seems that I already downloaded blast but I need to do this now:
  
  `Command 'blastp' not found, but can be installed with: sudo apt install ncbi-blast+`
  
  Do you have any idea how to might download this?
  
  I already downloaded blast as a tar file and the 2.11.0+ version. I'm just not sure how to download just ncbi-blast+ on its own.
  
  **Tags:** file-formats
  
  > **Comments:**
  > **username_1**: That looks like you are using Windows. have you asked the developers if the script you are trying to run is even supposed to work on Windows? Is there a Windows version of blast? That can be launched from the command line?  
  > **username_2**: Could you please tell us what operating system you're running (e.g. Windows, Mac, Linux)? If Linux, could you please show the output of the command `uname -a`?  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_3 on 2021-02-05. Score: 1
  
  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.
  
  
  ---
  
  