Hi again, sorry to bother you all! Hope your holidays are going well.
I'm still trying to run DADA2 on my 53 unjoined, paired-end fastq files. The code I used is below. I added a --p-n-threads option to help with the processing speed:
$ qiime dada2 denoise-paired --i-demultiplexed-seqs demux-paired-end.qza --p-trim-left-f 0 --p-trunc-len-f 270 --p-trim-left-r 0 --p-trunc-len-r 120 --o-representative-sequences rep-seqs.qza --p-n-threads 0 --o-table table-dada2.qza
It came out with an error:
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 /var/folders/8x/rqqs6m296k7g3trbdz559cnm0000gp/T/tmp4oi35lem/forward /var/folders/8x/rqqs6m296k7g3trbdz559cnm0000gp/T/tmp4oi35lem/reverse /var/folders/8x/rqqs6m296k7g3trbdz559cnm0000gp/T/tmp4oi35lem/output.tsv.biom /var/folders/8x/rqqs6m296k7g3trbdz559cnm0000gp/T/tmp4oi35lem/filt_f /var/folders/8x/rqqs6m296k7g3trbdz559cnm0000gp/T/tmp4oi35lem/filt_r 270 120 0 0 2.0 2 consensus 1.0 0 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.
Sample 1 - 165126 reads in 46441 unique sequences.
*** caught segfault ***
address 0x8, cause 'memory not mapped'
Traceback:
1: .Call("_dada2_dada_uniques", PACKAGE = "dada2", seqs, abundances, err, quals, score, gap, use_kmers, kdist_cutoff, band_size, omegaA, max_clust, min_fold, min_hamming, min_abund, use_quals, final_consensus, vectorized_alignment, homo_gap, multithread, verbose, SSE)
2: dada_uniques(names(derep[[i]]$uniques), unname(derep[[i]]$uniques), err, qi, opts[["SCORE_MATRIX"]], opts[["GAP_PENALTY"]], opts[["USE_KMERS"]], opts[["KDIST_CUTOFF"]], opts[["BAND_SIZE"]], opts[["OMEGA_A"]], if (initializeErr) { 1 } else { opts[["MAX_CLUST"]] }, opts[["MIN_FOLD"]], opts[["MIN_HAMMING"]], opts[["MIN_ABUNDANCE"]], TRUE, FALSE, opts[["VECTORIZED_ALIGNMENT"]], opts[["HOMOPOLYMER_GAP_PENALTY"]], multithread, (verbose >= 2), opts[["SSE"]])
3: dada(drpsF, err = NULL, selfConsist = TRUE, multithread = multithread, VECTORIZED_ALIGNMENT = FALSE, SSE = 2)
An irrecoverable exception occurred. R is aborting now ...
Traceback (most recent call last):
File "/Users/sm939/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/q2_dada2/_denoise.py", line 179, in denoise_paired
run_commands([cmd])
File "/Users/sm939/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/q2_dada2/_denoise.py", line 35, in run_commands
subprocess.run(cmd, check=True)
File "/Users/sm939/miniconda3/envs/qiime2-2017.12/lib/python3.5/subprocess.py", line 398, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['run_dada_paired.R', '/var/folders/8x/rqqs6m296k7g3trbdz559cnm0000gp/T/tmp4oi35lem/forward', '/var/folders/8x/rqqs6m296k7g3trbdz559cnm0000gp/T/tmp4oi35lem/reverse', '/var/folders/8x/rqqs6m296k7g3trbdz559cnm0000gp/T/tmp4oi35lem/output.tsv.biom', '/var/folders/8x/rqqs6m296k7g3trbdz559cnm0000gp/T/tmp4oi35lem/filt_f', '/var/folders/8x/rqqs6m296k7g3trbdz559cnm0000gp/T/tmp4oi35lem/filt_r', '270', '120', '0', '0', '2.0', '2', 'consensus', '1.0', '0', '1000000']' returned non-zero exit status -11
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/Users/sm939/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/q2cli/commands.py", line 224, in call
results = action(**arguments)
File "", line 2, in denoise_paired
File "/Users/sm939/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/qiime2/sdk/action.py", line 228, in bound_callable
output_types, provenance)
File "/Users/sm939/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/qiime2/sdk/action.py", line 363, in callable_executor
output_views = self._callable(**view_args)
File "/Users/sm939/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/q2_dada2/_denoise.py", line 194, in denoise_paired
" and stderr to learn more." % e.returncode)
Exception: An error was encountered while running DADA2 in R (return code -11), please inspect stdout and stderr to learn more.
I'm not sure what the segfault is, or what "'memory not mapped'" means? If anyone can shed some light on this error and what I might be doing wrong I would be really appreciative. Thank you so much.
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