Error in reading fastq files

[apcristi]

I'm having issues with a dada2 pipeline I have run successfully in the past and I believe it has to be with Biostrings

When I try to compute the number of paired reads using the function below:

df <- data.frame()

loop through all the R1 files (no need to go through R2 which should be the same)

for (i in 1:length(fns_R1)) {

#use the dada2 function fastq.geometry
geom <- fastq.geometry(fns_R1[i])

#extract the information on the number of sequences and file name
df_one_row <- data.frame(n_seq = geom[1], file_name = basename(fns[i]))

#add one line to a data frame
df <- bind_rows(df, df_one_row)

}

Display the number of sequences and write data to a small file

knitr::kable(df)

Error in .Call2("fastq_seqlengths", filexp_list, nrec, skip, seek.first.rec, : reading FASTQ file ./fastq/TAN2101-CTD01-DNA-3_CGAAGG-KGFBK_L001_R1.fastq.gz: "+" expected at beginning of line 26171.

I have reinstalled Biostrings and R Studio and it keeps happening. I tried the script with old fastq files that have been analysed before and got the same error, so the problem should not be with the files. The pipeline I use was adapted from https://vaulot.github.io/tutorials/R_dada2_tutorial.html

[hpages]

Can we have access to the file? It's hard to help you if we can't reproduce the problem.

Also please show your sessionInfo().

Thanks

[hpages]

Are you planning to follow up on this @apcristi?

[apcristi]

Hi, sorry. Tracked the issue back and there was an update on the server that corrupted the files, downloaded the fastq again and now it works!

[hpages]

Glad you solved the problem. Thanks for letting me know.