Answers.Body: <p>The issue here was I was using an older version of eDirect. There is no command to check version or updates. Your best bet is if you experience problems uninstall and reinstall. </p>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-12-08T09:13:21.787Z
Answers.LastActivityDate: 2017-12-08T09:13:21.787Z
Answers.UserDisplayName: AudileF
Answers.Body: <p>If you want to find version info you can either :</p>
  
  <p>Ask for another edirect tool version (it will be the same version for edirect) :</p>
  
  <pre><code>efetch -version
  </code></pre>
  
  <blockquote>
    <p>6.80</p>
  </blockquote>
  
  <p>Check the info contained in the edirect.pl script :</p>
  
  <pre><code>grep -i 'version = ' edirect.pl
  </code></pre>
  
  <blockquote>
    <p>$version = "6.80";</p>
  </blockquote>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-12-12T11:02:00.980Z
Answers.LastActivityDate: 2017-12-12T11:02:00.980Z
Answers.UserDisplayName: Erwan SCAON
Body: <p>Not sure if this is allowed but I cannot think of a better place to ask. I am attempting to download all genomic sequences from refseq associated with the query Peptostreptococcaceae. I have been been using the following command (based on some reading of the <a href="https://www.ncbi.nlm.nih.gov/books/NBK179288/" rel="nofollow noreferrer">manual</a>):</p>
  
  <pre><code>esearch -db nuccore -query "Peptostreptococcaceae" | efilter -molecule genomic -source refseq | efetch -format fasta
  </code></pre>
  
  <p>But I keep getting the following error</p>
  
  <pre><code>Unknown option: molecule   
  Unknown option: source   
  Must supply -query or -days or -mindate and -maxdate arguments on command 
  line Db value not found in fetch input No do_post output returned from 
  'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=nuccore&amp;term=Peptostreptococcaceae&amp;retmax=0&amp;usehistory=y&amp;edirect=3.80&amp;tool=edirect&amp;email=lgunn@sonic15' Result of do_post http request is .............
  (a lot of text which I assume is .html or .xml related)
  </code></pre>
  
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-12-07T17:19:24.763Z
Comments.Text: What operating system are you using? I just installed edirect using the instructions you linked to, then ran the exact command you show and it seems to be working fine. Could you be using an older version of `edirect` that doesn't support these options?
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-12-07T17:22:17.763Z
Comments.Text: Quite possible. I tried looking up versions but could not find the info. Ill remove it and reinstall it. Fingers crossed.
Comments.UserDisplayName: AudileF
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-12-07T17:30:26.547Z
Comments.Text: That was it @terdon. Thanks. Theres no mention of updates or versions so I assumed the one I had would work fine.
Comments.UserDisplayName: AudileF
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-12-07T17:32:46.003Z
Comments.Text: Great! Could you please post a quick answer (and then accept it when the system lets you—you need to wait a bit) explaining this? That way, the question can be marked as solved.
Comments.UserDisplayName: terdon
Tags: <data-retrieval><edirect>
Title: NCBI - edirect suite to download all genome sequences associated with a query - troubleshooting
ThreadText: # NCBI - edirect suite to download all genome sequences associated with a query - troubleshooting
  
  (Asked by: username_0 on 2017-12-07)
  
  Not sure if this is allowed but I cannot think of a better place to ask. I am attempting to download all genomic sequences from refseq associated with the query Peptostreptococcaceae. I have been been using the following command (based on some reading of the [manual](https://www.ncbi.nlm.nih.gov/books/NBK179288/)):
  
  ```
  esearch -db nuccore -query "Peptostreptococcaceae" | efilter -molecule genomic -source refseq | efetch -format fasta
  
  ```
  
  But I keep getting the following error
  
  ```
  Unknown option: molecule   
  Unknown option: source   
  Must supply -query or -days or -mindate and -maxdate arguments on command 
  line Db value not found in fetch input No do_post output returned from 
  'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=nuccore&term=Peptostreptococcaceae&retmax=0&usehistory=y&edirect=3.80&tool=edirect&email=lgunn@sonic15' Result of do_post http request is .............
  (a lot of text which I assume is .html or .xml related)
  
  ```
  
  **Tags:** data-retrieval, edirect
  
  > **Comments:**
  > **username_1**: What operating system are you using? I just installed edirect using the instructions you linked to, then ran the exact command you show and it seems to be working fine. Could you be using an older version of `edirect` that doesn't support these options?  
  > **username_0**: Quite possible. I tried looking up versions but could not find the info. Ill remove it and reinstall it. Fingers crossed.  
  > **username_0**: That was it @username_1. Thanks. Theres no mention of updates or versions so I assumed the one I had would work fine.  
  > **username_1**: Great! Could you please post a quick answer (and then accept it when the system lets you—you need to wait a bit) explaining this? That way, the question can be marked as solved.  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_0 on 2017-12-08. Score: 1 | Accepted answer
  
  The issue here was I was using an older version of eDirect. There is no command to check version or updates. Your best bet is if you experience problems uninstall and reinstall.
  
  
  ---
  
  ### Answer by username_2 on 2017-12-12. Score: 1
  
  If you want to find version info you can either :
  
  Ask for another edirect tool version (it will be the same version for edirect) :
  
  ```
  efetch -version
  
  ```
  
  > 6.80
  
  Check the info contained in the edirect.pl script :
  
  ```
  grep -i 'version = ' edirect.pl
  
  ```
  
  > $version = "6.80";
  
  
  ---
  
  