Cannot run xtract from entrez direct
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3.9 years ago
rabio ▴ 10

I have been unable to use xtract function from EDirect, as I get the following message simply by typing "xtract" into terminal:

Unable to locate xtract executable. Please execute the following: ftp-cp ftp.ncbi.nlm.nih.gov /entrez/entrezdirect xtract.Darwin.gz gunzip -f xtract.Darwin.gz chmod +x xtract.Darwin

I ran this, but it does not solve the problem. I have tried reinstalling EDirect and changing the xtract.Darwin file name to just xtract as well, but to no success. Any suggestions would be much appreciated.

xtract entrez edirect • 2.6k views
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3.9 years ago
GenoMax 110k

Did you follow the instructions given on this page. Last step of running setup.sh from the edirect directory is important to get this working right.

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Yes! And in the directory ~/edirect the following files exist: xtract, xtract.Darwin, and xtract.go. And giving all permissions (chmod 777) does not help either.

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Is that directory in your $PATH?

export PATH=$PATH: ~/edirect

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echo $PATH returns the following:

/Users/username/src/edirect:/Users/username/Documents/SeniorPt1/Lab/miniconda3/bin:/Users/username/miniconda3/bin:/Library/Frameworks/Python.framework/Versions/2.7/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/username/edirect:/Users/username/edirect:/Users/username/edirect:/Users/username/edirect::/edirect:
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Are you using an account called username? Or did you just replace the real name with a dummy word? I assume the path is not permanently set like that. Can you open a new terminal window and do export PATH=$PATH: ~/edirect to see if that fixes the strange multiple entry path above?

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Yes, just replacing it with a dummy word.

Thank you so much, that fixed the problem! It works now!

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Hi, I'm having the exact same issue but having trouble understanding your proposed solution.

echo $PATH returns:

/Users/luke/src/edirect:/Users/luke/perl5/perlbrew/bin:/Users/luke/perl5/perlbrew/perls/perl-5.28.0/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Users/luke/edirect:/Users/luke

Opening a new terminal and executing:

export PATH=$PATH: ~/edirect

returns:

-bash: export: `/Users/luke/edirect': not a valid identifier

Any help is appreciated!

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That probably means the last step I mentioned in the original answer has not been executed.

What do you see when you do ls -lh ~/edirect?

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total 18192
-rw-r--r--  1 luke  staff   149K Aug 24 15:21 Mozilla-CA.tar.gz
-rw-r--r--  1 luke  staff   2.5K Oct 22  2016 README
-rwxr-xr-x  1 luke  staff   526B Oct 24  2016 amino-acid-composition
-rwxr-xr-x  1 luke  staff   1.5K Jul 27 12:50 archive-pubmed
-rwxr-xr-x  1 luke  staff   2.3K Aug 12  2017 asp-cp
-rwxr-xr-x  1 luke  staff   647B Jan 16  2018 asp-ls
drwxr-xr-x  5 luke  staff   160B Sep  1 19:29 aux
-rwxr-xr-x  1 luke  staff    88B Oct 24  2016 between-two-genes
-rw-r--r--  1 luke  staff    85K Aug 20 11:25 common.go
-rwxr-xr-x  1 luke  staff   742B Feb 18  2018 download-pubmed
-rwxr-xr-x  1 luke  staff   533B Oct 24  2017 download-sequence
-rwxr-xr-x  1 luke  staff   265B Jan  8  2015 eaddress
-rwxr-xr-x  1 luke  staff   263B Aug  5 14:00 eblast
-rwxr-xr-x  1 luke  staff   266B Oct 29  2016 ecitmatch
-rwxr-xr-x  1 luke  staff   265B Mar 20  2013 econtact
-rwxr-xr-x  1 luke  staff   117K Aug 16 12:50 edirect.pl
-rwxr-xr-x  1 luke  staff   2.6K Jan 16  2018 edirutil
-rwxr-xr-x  1 luke  staff   263B Mar 20  2013 efetch
-rwxr-xr-x  1 luke  staff   264B Mar 20  2013 efilter
-rwxr-xr-x  1 luke  staff   262B Mar 20  2013 einfo
-rwxr-xr-x  1 luke  staff   262B Mar 20  2013 elink
-rwxr-xr-x  1 luke  staff   264B Mar 20  2013 enotify
-rwxr-xr-x  1 luke  staff   3.4K May 17  2017 entrez-phrase-search
-rwxr-xr-x  1 luke  staff   262B Mar 20  2013 epost
-rwxr-xr-x  1 luke  staff   263B Mar 20  2013 eproxy
-rwxr-xr-x  1 luke  staff   264B Mar 20  2013 esearch
-rwxr-xr-x  1 luke  staff   263B Sep  8  2014 espell
-rwxr-xr-x  1 luke  staff   278B Feb 10  2014 esummary
-rwxr-xr-x  1 luke  staff   1.2K Jun  5 21:25 fetch-pubmed
-rwxr-xr-x  1 luke  staff   903B Nov 21  2016 filter-stop-words
-rwxr-xr-x  1 luke  staff   955B Jan 16  2018 ftp-cp
-rwxr-xr-x  1 luke  staff   637B Jan 16  2018 ftp-ls
-rwxr-xr-x  1 luke  staff    13K Jan 16  2018 gbf2xml
-rwxr-xr-x  1 luke  staff   1.1K Aug 12  2017 has-asp
-rwxr-xr-x  1 luke  staff   2.0K Jul 27 12:50 index-pubmed
-rwxr-xr-x  1 luke  staff   112B May 24 11:50 intersect-uid-lists
-rwxr-xr-x  1 luke  staff    45B Aug 31  2014 join-into-groups-of
-rwxr-xr-x  1 luke  staff   2.5K Aug 21 16:50 local-phrase-search
-rwxr-xr-x  1 luke  staff    10K Jan 16  2018 nquire
-rwxr-xr-x  1 luke  staff   331B Jun 21 19:50 pm-clean
-rwxr-xr-x  1 luke  staff   493B Jul 28 21:25 pm-current
-rwxr-xr-x  1 luke  staff   187B Mar 18 21:01 pm-erase
-rwxr-xr-x  1 luke  staff   371B Jul 13 20:00 pm-index
-rwxr-xr-x  1 luke  staff   393B Aug 20 11:25 pm-invert
-rwxr-xr-x  1 luke  staff   525B Feb 17  2018 pm-log
-rwxr-xr-x  1 luke  staff   446B Aug 20 11:25 pm-merge
-rwxr-xr-x  1 luke  staff   1.8K Jul 19 17:50 pm-prepare
-rwxr-xr-x  1 luke  staff   479B Aug 20 11:25 pm-promote
-rwxr-xr-x  1 luke  staff   959B Jun 25 12:00 pm-refresh
-rwxr-xr-x  1 luke  staff   643B Apr  3 03:00 pm-repack
-rwxr-xr-x  1 luke  staff   1.6K Aug  7 15:00 pm-stash
-rwxr-xr-x  1 luke  staff   188B Mar 18 21:01 pm-uids
-rwxr-xr-x  1 luke  staff    89B Apr 24 13:25 pm-verify
-rwxr-xr-x  1 luke  staff   107B Aug  5 15:00 protein-neighbors
-rwxr-xr-x  1 luke  staff   690B Apr  2 14:50 rchive
-rwxr-xr-x  1 luke  staff   4.5M Sep  1 23:35 rchive.Darwin
-rw-r--r--  1 luke  staff   129K Aug 24 14:00 rchive.go
-rwxr-xr-x  1 luke  staff   173B Jan 14  2015 reorder-columns
-rwxr-xr-x  1 luke  staff   2.6K Jan 16  2018 run-ncbi-converter
-rw-r--r--  1 luke  staff    51K Sep  1 23:35 setup-deps.log
-rwxr-xr-x  1 luke  staff   2.4K Jan 16  2018 setup-deps.pl
-rwxr-xr-x@ 1 luke  staff   2.6K Apr  2 14:50 setup.sh
-rwxr-xr-x  1 luke  staff   200B Oct 27  2016 sort-uniq-count
-rwxr-xr-x  1 luke  staff   249B Apr 16 13:00 sort-uniq-count-rank
-rwxr-xr-x  1 luke  staff   1.0K Jun  5 21:25 stream-pubmed
-rwxr-xr-x  1 luke  staff    80B Jul 14  2015 word-at-a-time
-rwxr-xr-x  1 luke  staff   690B Apr  2 14:50 xtract
-rwxr-xr-x  1 luke  staff   3.3M Sep  1 23:35 xtract.Darwin
-rw-r--r--  1 luke  staff   203K Aug 21 12:50 xtract.go
-rwxr-xr-x  1 luke  staff   1.3K Apr 15 15:25 xy-plot
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1
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Make sure there is no space between $PATH: and directory name.

export PATH=$PATH:~/edirect
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Progress.

It did not return:

-bash: export: `/Users/luke/edirect': not a valid identifier.

However, I still get the original error message from the OP and myself:

Unable to locate xtract executable. Please execute the following:

  ftp-cp ftp.ncbi.nlm.nih.gov /entrez/entrezdirect xtract.Darwin.gz
  gunzip -f xtract.Darwin.gz
  chmod +x xtract.Darwin

And executing this does not seem to fix the problem.

echo $PATH returns:

/Users/luke/src/edirect:/Users/luke/perl5/perlbrew/bin:/Users/luke/perl5/perlbrew/perls/perl-5.28.0/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Users/luke/edirect:/Users/luke:/Users/luke/edirect

@genomax, I can't thank you enough for helping me work through this!

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Just to confirm. You are using macOS? These executables are for macOS.

What do you get from which xtract and xtract -h or --help?

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Correct. macOS High Sierra 10.13.6

which xtract returns:

/Users/luke/src/edirect/xtract

xtract -h returns:

Unable to locate xtract executable. Please execute the following:

  ftp-cp ftp.ncbi.nlm.nih.gov /entrez/entrezdirect xtract.Darwin.gz
  gunzip -f xtract.Darwin.gz
  chmod +x xtract.Darwin
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Did you ever manage to get xtract working?

I am running into the exact same problem.

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I just followed the directions on same OS version and I am able to use xtract fine.

I get a warning about perl version of xtract being obsolete (if I run xtract -h) but it works.

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