Plugin error from vsearch: Incorrect number of fields detected on line 2. Should be exactly 18

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1

Hi, Im studying microbial community in the Korea. When I following this pipe line(GitHub - shu251/V4_tagsequencing_18Sdiversity_qiime2: Pipeline for sequence QC and analysis in qiime2 - specific for 18S diversity), I am confronting this problem.

(qiime2-2018.6) LabOfMarineProtistanEcophysioloygy:test lompe$ qiime vsearch uchime-ref \
 --i-table closedref/table_closed_97.qza \
 --i-sequences closedref/rep-seqs_closed_97.qza \
 --i-reference-sequences /Users/lompe/test/pr2.qza \
 --p-threads 8 \
 --output-dir chimera_ref_dir

Plugin error from vsearch:

  /var/folders/kv/pkjw8_2d2_x9ydbtrbt_ns9c0000gn/T/q2-UchimeStatsFmt-2t6ckkl5 is not a(n) UchimeStatsFmt file:

  Incorrect number of fields detected on line 2. Should be exactly 18.

Debug info has been saved to /var/folders/kv/pkjw8_2d2_x9ydbtrbt_ns9c0000gn/T/qiime2-q2cli-err-6lm2mq6p.log

How can I fixed it? please give me a hand.

4

Hey there @Don!

I'm not too sure what is going wrong here --- would you be able to provide the files necessary for us to rerun this command? If not, can you at least try re-running with the --verbose flag? Please copy and paste all results. Thanks! :qiime2: :t_rex:

6

Thanks for your reply. I solve it changing threads number(8 -> 1).

But this command was working well(see below).

qiime feature-classifier classify-consensus-vsearch
--i-query rep-seqs_ref_nc.qza
--i-reference-reads v4_extracts.qza
--i-reference-taxonomy pr2_tax.qza
--p-perc-identity 0.9
--p-threads 8
--o-classification tax_vsearch.qza

I dont know why I need to changing threads number

8

Thanks for sharing, @Don. I'm not sure what the problem was, so will file this away under "weird" for a later date.

Thanks! :qiime2:

10

@Don - would you be willing to share:

  • closedref/table_closed_97.qza
  • closedref/rep-seqs_closed_97.qza
  • /Users/lompe/test/pr2.qza

with us? We would like to see if we can recreate this error. You can send a download link in a private message to me if you don't want to share publicly. Thanks!

13

@Don - I received the files you sent me, unfortunately they aren't the files I requested, so I can't use them for any debugging purposes. I need the three files that you used to run the command above, that way I can reproduce the error locally. Thanks!