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I am trying to run metamap, but I keep getting "fgets: No such file or directory" when I try to test it with echo "lung cancer" | ./bin/metamap -I. I downloaded the public_mm directory from one of our servers and had to use dos2unix to get it to work on Ubuntu locally to test new code that uses metamap, so I think that is part of the problem, but its hard to tell what it is trying to find. Everything is running though.

deasc:/mnt/c/public_mm$ ps -ef | grep java
deasc      741     1  0 Nov23 tty1     00:07:10 java -Dtaggerserver.port=1795 -DlexFile=/mnt/c/public_mm/MedPost-SKR/data/lexDB.serial -DngramOne=/mnt/c/public_mm/MedPost-SKR/data/ngramOne.serial -cp /mnt/c/public_mm/MedPost-SKR/Tagger_server/lib/taggerServer.jar:/mnt/c/public_mm/MedPost-SKR/Tagger_server/lib/mps.jar taggerServer
deasc      767     1  0 Nov23 tty1     00:09:18 java -Xmx2g -Dserver.config.file=/mnt/c/public_mm/WSD_Server/config/disambServer.cfg -classpath /mnt/c/public_mm/WSD_Server/lib/metamapwsd.jar:/mnt/c/public_mm/WSD_Server/lib/utils.jar:/mnt/c/public_mm/WSD_Server/lib/lucene-core-3.0.1.jar:/mnt/c/public_mm/WSD_Server/lib/monq-1.1.1.jar:/mnt/c/public_mm/WSD_Server/lib/wsd.jar:/mnt/c/public_mm/WSD_Server/lib/kss-api.jar:/mnt/c/public_mm/WSD_Server/lib/thirdparty.jar:/mnt/c/public_mm/WSD_Server/lib/db.jar:/mnt/c/public_mm/WSD_Server/lib/log4j-1.2.8.jar wsd.server.DisambiguatorServer
deasc     1377   440  0 13:48 tty1     00:00:00 grep --color=auto java

deasc:/mnt/c/public_mm$ /bin/bash bin/mmserver16
/mnt/c/public_mm/bin/SKRrun.16 /mnt/c/public_mm/bin/mmserver16.BINARY.Linux --lexicon db -Z 2016AA
Server options: [port(8066),accepted_hosts(['127.0.0.1'])]
Established connection $stream(140265336584736) to TAGGER Server on localhost.
Options:[lexicon,'Z']
Args:[db,'2016AA']
port:8066

deasc:/mnt/c/public_mm$ echo "lung cancer" | ./bin/metamap -I
/mnt/c/public_mm/bin/SKRrun.16 /mnt/c/public_mm/bin/metamap16.BINARY.Linux --lexicon db -Z 2016AA -I
fgets: No such file or directory

Everyone that originally set all this up is no longer here to help and I can't find anyone that's had the same issue. Any suggestions on what the problem is/what path its looking for?

The result should be

Berkeley DB databases (USAbase 2016AA strict model) are open.
Static variants will come from table varsan in /data/metamap/public_mm/DB/DB.USAbase.2016AA.strict.
Derivational Variants: Adj/noun ONLY.
Variant generation mode: static.
Established connection $stream(139692534873008) to TAGGER Server on localhost.

metamap16.BINARY.Linux (2016)

Control options:
  composite_phrases=4
  lexicon=db
  mm_data_year=2016AA
  show_cuis
Processing 00000000.tx.1: lung cancer
Callie Deas
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1 Answers1

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Based on the prompt, it appears this is being run on Ubuntu on WSL. If so, I suspect that the bzip archive was unpacked under Windows which failed to create the symbolic links. Try unpacking within Ubuntu using something like:

tar xvfj /mnt/c/downloads/public_mm_linux_main_2016.tar.bz2

You can find the complete installation steps here: https://lhncbc.nlm.nih.gov/ii/tools/MetaMap/documentation/Installation.html#org402dbaf.

David C
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