Solving the "Error: BiocParallel errors" (in almost every sample)

[Yoonseopark02]

Hi, I am an undergraduate studying bioinformatics in the microbiome analysis field, and I am having a BiocParallel Error every time I run my code for the ENA database datasets.
The same code worked well for NCBI datasets, and I kept on debugging but couldn't solve the problem.

Following is the code I used:

library(dada2)
library(ggplot2)
library(dplyr)

path <- "/Users/User/Documents/SeniorThesis/zebraENA/reads_fastq/PRJNA806371"
list.files(path)

#Assuming your forward and reverse fastq filenames have the format: SRRXXXXXXX_1.fastq and SRRXXXXXXX_2.fastq
fnFs <- sort(list.files(path, pattern="_1\.fastq.gz$", full.names = TRUE))
fnRs <- sort(list.files(path, pattern="2\.fastq.gz$", full.names = TRUE))
#Extract sample names, assuming filenames have the format: SRRXXXXXXX_X.fastq
sample.names <- sapply(strsplit(basename(fnFs), ""), [, 1)

#INSPECT READ QUALITY PROFILES
QPF <- plotQualityProfile(fnFs[1:2])

Error: BiocParallel errors
1 remote errors, element index: 1
0 unevaluated and other errors
first remote error:
Error in data.frame(sequence = names(freqtbl$top), count = as.integer(freqtbl$top), : arguments imply differing number of rows: 0, 1

I am getting this same error in almost every single public data I used..
Please give me comments how to solve this error.
Thanks so much in advance!

[benjjneb]

What is head(fnFs)?

What is the output of head(ShortRead::readFastq(fnFs[[1]]))?

[Yoonseopark02]

Thanks so much for the reply @benjjneb !!
It appears like this:

head(fnFs)
[1] "/Users/User/Documents/SeniorThesis/zebraENA/reads_fastq/PRJNA806371/SRR18030333_1.fastq.gz"
[2] "/Users/User/Documents/SeniorThesis/zebraENA/reads_fastq/PRJNA806371/SRR18030334_1.fastq.gz"
[3] "/Users/User/Documents/SeniorThesis/zebraENA/reads_fastq/PRJNA806371/SRR18030335_1.fastq.gz"
[4] "/Users/User/Documents/SeniorThesis/zebraENA/reads_fastq/PRJNA806371/SRR18030336_1.fastq.gz"
[5] "/Users/User/Documents/SeniorThesis/zebraENA/reads_fastq/PRJNA806371/SRR18030337_1.fastq.gz"
head(ShortRead::readFastq(fnFs[[1]]))
class: ShortReadQ
length: 6 reads; width: 151 cycles

[benjjneb]

Could there be any input files in your data that are empty (i.e. contain no sequences)? See this comment thread: #1503 (comment)

If there are, removing those before running plotQualityProfile should solve the issue.

[Yoonseopark02]

@benjjneb Thanks! I found that the input files had the error and solved it.

Sorry but can I ask one more thing, please?

I am having these errors in one large dataset when running the code
out <- filterAndTrim(fnFs, filtFs, fnRs, filtRs, truncLen=c(150,150), trimLeft = c(17, 21),
maxN=0, maxEE=c(2,2), truncQ=2, rm.phix=TRUE,
compress=TRUE, multithread=TRUE)

Error in filterAndTrim(fnFs, filtFs, fnRs, filtRs, truncLen = c(150, 150), :
These are the errors (up to 5) encountered in individual cores...
Error in (function (fn, fout, maxN = c(0, 0), truncQ = c(2, 2), truncLen = c(0, :
Mismatched forward and reverse sequence files: 0, 100000.
...
This error with multiple lines (please see the picture attached)
I often encounter this error too, and I tried to refer to #283 and ran this but couldn't find the problem.

Can you give me some advice on how to solve this?
Thank you so much!

[benjjneb]

The error messages indicate that for pairs of forward/reverse fastq files, one of the files has many reads (100k or 83.5k) while the other has zero reads. To troubleshoot, I would check that this error is caused by a single sample (i.e. fnFs[[1]] etc.), and then look at those individual files. Is one of them empty? Then it becomes a question of how these files were obtained. Did some pre-processing on your end lead to one of them being empty? Or did this discrepancy exist in the raw files you downloaded?