Hi there! I still get an error in dada2. I run 20 samples with the following command:
(qiime2-2018.2) qiime2@qiime2core2018-2:~/MiSeqRun-180417-Pretest$ qiime dada2 denoise-paired \
--i-demultiplexed-seqs trimmed-seqs-180417_pretest.qza
--p-trim-left-f 0
--p-trim-left-r 0
--p-trunc-len-f 276
--p-trunc-len-r 260
--o-table table-dada2.qza
--o-representative-sequences rep-seqs-dada2.qza
--verbose
And it gives me out:
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/tmp5k2lifa7/forward /tmp/tmp5k2lifa7/reverse /tmp/tmp5k2lifa7/output.tsv.biom /tmp/tmp5k2lifa7/filt_f /tmp/tmp5k2lifa7/filt_r 276 260 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
- Filtering ....................
- Learning Error Rates
2a) Forward Reads
Initializing error rates to maximum possible estimate.
Error in dada_uniques(names(derep[[i]]$uniques), unname(derep[[i]]$uniques), :
Memory allocation failed.
Calls: dada -> dada_uniques -> .Call
Execution halted
Warning message:
system call failed: Cannot allocate memory
Plugin error from dada2:An error was encountered while running DADA2 in R (return code 1), please inspect stdout and stderr to learn more.
I split the 20 samples in packages of 5 - and it worked for each of the four five packs. So it cannot be the dada trimm of values. Could you give me a hint how to solve the problem. Tahnk you so much. -Jul
(Here are the data specifications: raw data demultiplexed paired-end reads; qiime2: data input with Casava, pre-trimming of sequencing artifacts (primers etc.) with cutadapt trim-paired
qiime cutadapt trim-paired
--i-demultiplexed-sequences demux-paired-end-180417_pretest.qza
--p-front-f CCTACGGGNGGCWGCAG
--p-front-r GACTACHVGGGTATCTAATCC
--p-error-rate 0
--o-trimmed-sequences trimmed-seqs-180417_pretest.qza
--verbose
)