Building a COI database from BOLD references

Community Contributions Tutorials
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3 off-topic replies have been merged into an existing topic: 12s database using rescript - australian taxa only?

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An off-topic reply has been split into a new topic: Merge CO1 artifacts

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An off-topic reply has been split into a new topic: Error following COI database tutorial

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I ran into the same issue and fixed it by following these commands:

  1. check the maximum allowed size of arguments: getconf ARG_MAX
  2. check myval length: echo ${#myval}
  3. write the contents of $myval into a separate .sed file. echo "$myval" > commands.sed
  4. Then, use sed with the -f (file) option: sed -f commands.sed bold_allrawSeqs.fasta > cleaned_bold_allrawSeqs.fasta

This last line takes a few minutes to run (~ 10 min)

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