error while running RESCRIPt

[Birong]

Hi Mike,

Thanks so much for this tutorial! Learned a lot!

Everything went well with this:

qiime rescript dereplicate \
    --i-sequences trnL-ref-seqs.qza \
    --i-taxa trnL-ref-tax.qza \
    --p-mode 'uniq' \
    --p-threads 8 \
    --o-dereplicated-sequences trnL-ref-seqs-derep.qza \
    --o-dereplicated-taxa trnL-ref-tax-derep.qza

But then I get this error for the same function:

qiime rescript dereplicate \
    --i-sequences trnL-gh-seq-segments.qza \
    --i-taxa  trnL-ref-tax-derep.qza \
    --p-mode 'uniq' \
    --p-threads 8 \
    --o-dereplicated-sequences trnL-gh-seq-segments-derep.qza \
    --o-dereplicated-taxa trnL-gh-tax-segments-derep.qza

Here is the error:

Plugin error from rescript:

  'FN908487.1.1452'

Debug info has been saved to /tmp/qiime2-q2cli-err-vtou_205.log
[c.c2050857@cl2(hawk) taxonomy]$ cat /tmp/qiime2-q2cli-err-vtou_205.log
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command: vsearch --derep_fulllength /tmp/qiime2-archive-zlspfrjz/9421ff15-bc03-4737-ab63-71203be03c2c/data/dna-sequences.fasta --output /tmp/tmpmoglhdgj --uc /tmp/tmpluj4r3oc --qmask none --xsize --threads 8

vsearch v2.7.0_linux_x86_64, 125.8GB RAM, 32 cores
https://github.com/torognes/vsearch

Reading file /tmp/qiime2-archive-zlspfrjz/9421ff15-bc03-4737-ab63-71203be03c2c/data/dna-sequences.fasta 100%
70037271 nt in 241987 seqs, min 50, max 1939, avg 289
Dereplicating 100%
Sorting 100%
150411 unique sequences, avg cluster 1.6, median 1, max 2115
Writing output file 100%
Writing uc file, first part 100%
Writing uc file, second part 100%
Traceback (most recent call last):
  File "/apps/genomics/qiime2/2020.11-rescript/el7/AVX512/gnu-7.3/serial/qiime2-2020.11-rescript/lib/python3.6/site-packages/pandas/core/indexes/base.py", line 2898, in get_loc
    return self._engine.get_loc(casted_key)
  File "pandas/_libs/index.pyx", line 70, in pandas._libs.index.IndexEngine.get_loc
  File "pandas/_libs/index.pyx", line 101, in pandas._libs.index.IndexEngine.get_loc

Could you please help me to have a look at this? Many thanks!

Best regards,
Birong

[SoilRotifer (Mike Robeson)]

Hi @Birong,

It appears you are using a 2-year old version of / RESCRIPt.

@Birong

2020.11

RESCRIPt works best with the most recent versions of QIIME 2. I'd recommend running these RESCRIPt commands in the latest release of QIIME 2 as specified at the beginning of this tutorial (as of this date).

I just re-ran this entire pipeline in 2022.11 and was successful. Thus, I recommend simply installing the latest version of QIIME 2 and then install the latest version of RESCRIPt.