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qiime2 / q2-dada2

QIIME 2 plugin wrapping DADA2
BSD 3-Clause "New" or "Revised" License
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Error in isBimeraDenovoTable(unqs[[i]], ..., verbose = verbose) : Input must be a valid sequence table. #90

Closed bassio closed 6 years ago

bassio commented 6 years ago

Hello, I got the error below at the step of chimera detection. I wonder if this is that there were no sequences left for chimera detection at the end of that stage. Running qiime 2 Feb 2018 version. Let me know if you need any further info

See below for error report:

Running external command line application(s). This may print messages to stdout and/or stderr. The command(s) being run are below. These commands cannot be manually re-run as they will depend on temporary files that no longer exist.

Command: run_dada_paired.R /tmp/tmps4hlcnk7/forward /tmp/tmps4hlcnk7/reverse /tmp/tmps4hlcnk7/output.tsv.biom /tmp/tmps4hlcnk7/filt_f /tmp/tmps4hlcnk7/filt_r 260 260 0 0 2.0 2 consensus 1.0 1 1000000

R version 3.4.1 (2017-06-30) Loading required package: Rcpp DADA2 R package version: 1.6.0 1) Filtering ... 2) Learning Error Rates 2a) Forward Reads Initializing error rates to maximum possible estimate. Sample 1 - 2656 reads in 1987 unique sequences. Sample 2 - 6060 reads in 2150 unique sequences. Sample 3 - 11141 reads in 3185 unique sequences. selfConsist step 2 selfConsist step 3 selfConsist step 4 selfConsist step 5 Convergence after 5 rounds. 2b) Reverse Reads Initializing error rates to maximum possible estimate. Sample 1 - 2656 reads in 1987 unique sequences. Sample 2 - 6060 reads in 2150 unique sequences. Sample 3 - 11141 reads in 3185 unique sequences. selfConsist step 2 selfConsist step 3 selfConsist step 4 selfConsist step 5 Convergence after 5 rounds.

3) Denoise remaining samples 4) Remove chimeras (method = consensus) Error in isBimeraDenovoTable(unqs[[i]], ..., verbose = verbose) : Input must be a valid sequence table. Calls: removeBimeraDenovo -> isBimeraDenovoTable In addition: Warning message: In is.na(colnames(unqs[[i]])) : is.na() applied to non-(list or vector) of type 'NULL' Execution halted

thermokarst commented 6 years ago

Hi @bassio - can you please post this question to the QIIME 2 Forum, at https://forum.qiime2.org? That is where we provide user support for QIIME 2. Thanks for your understanding!