I have seen this issue indicated several times here but I couldn’t find any clear solution. Hope anyone can help me.
I’m following the ITS DADA2 Pipeline Workflow to analyze my data: 36 paired fastqs files obtained using Illumina MiSeq. The input samples were fungal ITS amplicons. I followed the tutorial first in Galaxy and then in Rstudio and I run into the same problem. When assigning taxonomy this happens:
#Assign Taxonomy
path ← file.path(“UNITE_public_10.05.2021.fasta.gz”, “UNITE_public_10.05.2021.fasta”)
taxa ← assignTaxonomy(seqtab.nochim, path, multithread = TRUE, tryRC = TRUE,
taxLevels = c(“Kingdom”, “Phylum”, “Class”, “Order”, “Family”, “Genus”, “Species”),
verbose = FALSE)
Error in C_assign_taxonomy2(seqs, rc(seqs), refs, ref.to.genus, tax.mat.int, :
Memory allocation failed.
In addition: Warning message:
In .Call2(“fasta_index”, filexp_list, nrec, skip, seek.first.rec, :
reading FASTA file UNITE_public_10.05.2021.fasta.gz/UNITE_public_10.05.2021.fasta: ignored 8 invalid one-letter sequence codes
I tried to increase the memory limit and this is what I have
memory.size()
[1] 11921.24
memory.limit()
[1] 31975
These are the characteristics of my laptop:
Processor AMD Ryzen 7 PRO 4750U with Radeon Graphics 1.70 GHz
RAM 32.0 GB (31.2 GB utilizable)
System Sistema operativo de 64 bits, procesador x64
If necessary this is the step before the taxonomy assignment:
#Track reads through the pipeline
getN ← function(x) sum(getUniques(x))
track ← cbind(out, sapply(dadaFs, getN), sapply(dadaRs, getN), sapply(mergers, getN), rowSums(seqtab.nochim))
colnames(track) ← c(“input”, “filtered”, “denoisedF”, “denoisedR”, “merged”, “nonchim”)
rownames(track) ← sample.names
head(track)
input filtered denoisedF
1-01A_S63_L001_R1_001.fastq 39949 39663 37575
1-01B_S64_L001_R1_001.fastq 51059 50727 47766
1-01C_S65_L001_R1_001.fastq 71229 70897 68033
1-04A_S78_L001_R1_001.fastq 48126 47701 44850
1-04B_S79_L001_R1_001.fastq 78663 78350 75736
1-04C_S80_L001_R1_001.fastq 67420 67102 64241
denoisedR merged nonchim
1-01A_S63_L001_R1_001.fastq 34082 3900 3831
1-01B_S64_L001_R1_001.fastq 41556 4241 4139
1-01C_S65_L001_R1_001.fastq 54961 16499 16157
1-04A_S78_L001_R1_001.fastq 41881 13130 12954
1-04B_S79_L001_R1_001.fastq 69691 11161 11070
1-04C_S80_L001_R1_001.fastq 59966 25060 24773
Thank you very much in advance!