Output problem from 'qiime vsearch cluster-feature-closed-reference'

[SLee (Sunghee Lee)]

Dear All,

I encountered an unexpected problem regarding output of ‘cluster-features-closed-reference’ a few days ago.
My command line is as follows,

(qiime2-2018.6) slee@ubuntu-1710:~/ID_server/vaginal_microbiome/vag2$ qiime vsearch cluster-features-closed-reference --i-table vag2_dereplicate_table.qza --i-sequences vag2_dereplicate_seqs.qza --i-reference-sequences …/…/…/DB/eztaxon/eztaxon_qiime_full_V3-V4_ref.qza --p-perc-identity 0.97 --output-dir ./vag2_cluster_closed_97 --o-unmatched-sequences vag2_unmatched.qza --p-threads 30

I expected 3 output from this command.

1. ./vag2_cluster_closed_97/clustered_table.qza
2. ./vag2_cluster_closed_97/clustered_seqs.qza
3. vag2_unmatched.qza

However I just got a ‘clustered_table.qza’ file. I don’t know why .seq.qza and unmatched.qza files did not show in output folder. Actually, this is not the first time. I have had similar situation several times.
Have you had a similar experience? or do you have any ideas about this?

Thanks,
SL

[thermokarst]

Hey there @SLee!

I just tried to reproduce, using the OTU Clustering test data:

qiime vsearch cluster-features-closed-reference \
  --i-table table.qza \
  --i-sequences rep-seqs.qza \
  --i-reference-sequences 85_otus.qza \
  --p-perc-identity 0.85 \
  --output-dir closed_ref \
  --o-unmatched-sequences unmatched.qza

The command successfully ran, and printed the following:

Saved FeatureTable[Frequency] to: closed_ref/clustered_table.qza
Saved FeatureData[Sequence] to: closed_ref/clustered_sequences.qza
Saved FeatureData[Sequence] to: unmatched.qza

If I run a tree in my current directory:

tree
.
├── 85_otus.qza
├── closed_ref
│   ├── clustered_sequences.qza
│   └── clustered_table.qza
├── rep-seqs.qza
├── seqs.fna
├── seqs.qza
├── table.qza
└── unmatched.qza

Looks like all three artifacts are there, where they should be!

@SLee

I have had similar situation several times.

Is it possible you lost track of which file is which? Maybe try again, but specify all new locations, somewhere that is a brand-new working environment, just to keep things straight. If that doesn't help, please send us the files necessary for us to re-run the command you provided above.

Thanks!

[SLee (Sunghee Lee)]

Hi Matthew,

Thank you for your kindly response.
As you mentioned, I tried to rerun example set using OTU Clustering test data.
I could see the result ‘Saved Feature…’ of 3 lines.
And then I obtained 2 output files in ‘closed_ref’ folder likewise you.

I could not see the ‘Saved Feature…’ printed text when I analyzed before.
I had added ‘&’ in the end of command, and then I took off the terminal.
As your comment, I will rerun by specify all new locations.

Many thanks,
SL