Hello,
I am processing my dataset and coming across this error when learning the error rates. My data is NextSeq PE 300 for V4-V5 region.
I initially tried this in dada2 on Qiime2 but it gave me errors discussing not able to estimate errors (I do not have an error message easily available). I then moved to dada2 in R. My filtered forward went through learnErrors() fine. Took a while on my laptop, but still went through using default learnErrors() parameters. However, I cannot get my reverse reads to go through. I have played around with different nbases and multithread., as well as trunclength() values for the reverse (180, 220, etc) when filtering. When I receive an error, it is within 4 min of my entering the code (see script below for examples). The only time it lasted longer than 4 min was when I tried nbases = 1e9, but R crashes on my laptop hours later (guessing due to memory issues). Currently, I am trying to move over to a super computer to try this but I don't know what is happening.
Any thoughts? I can provide the plotQualityProfile(filtFs[]) and plotQualityProfile(filtRs[]) , but I am currently filtering again. Notably, the quality is not bad ( the median quality line ranges from 30-40 through out) and the number of reads is not low after filtering (averaging 75 - 80% filtered paired-sequences (examples also shown below). Thank you for any help!
Read in 245228 paired-sequences, output 186666 (76.1%) filtered paired-sequences.
Read in 291754 paired-sequences, output 235653 (80.8%) filtered paired-sequences.
errR <- learnErrors(filtRs, multithread=TRUE)
120439440 total bases in 669108 reads from 3 samples will be used for learning the error rates.
Error rates could not be estimated (this is usually because of very few reads).
Error in getErrors(err, enforce = TRUE) : Error matrix is NULL.
errR <- learnErrors(filtRs,multithread = FALSE,nbases = 5e8)
501217920 total bases in 2784544 reads from 14 samples will be used for learning the error rates.
Error rates could not be estimated (this is usually because of very few reads).
Error in getErrors(err, enforce = TRUE) : Error matrix is NULL.
errR <- learnErrors(filtRs, multithread = FALSE,nbases = 1e8)
120439440 total bases in 669108 reads from 3 samples will be used for learning the error rates.
Error rates could not be estimated (this is usually because of very few reads).
Error in getErrors(err, enforce = TRUE) : Error matrix is NULL.
Hello,
I am processing my dataset and coming across this error when learning the error rates. My data is NextSeq PE 300 for V4-V5 region.
I initially tried this in dada2 on Qiime2 but it gave me errors discussing not able to estimate errors (I do not have an error message easily available). I then moved to dada2 in R. My filtered forward went through learnErrors() fine. Took a while on my laptop, but still went through using default learnErrors() parameters. However, I cannot get my reverse reads to go through. I have played around with different nbases and multithread., as well as trunclength() values for the reverse (180, 220, etc) when filtering. When I receive an error, it is within 4 min of my entering the code (see script below for examples). The only time it lasted longer than 4 min was when I tried nbases = 1e9, but R crashes on my laptop hours later (guessing due to memory issues). Currently, I am trying to move over to a super computer to try this but I don't know what is happening.
Any thoughts? I can provide the plotQualityProfile(filtFs[]) and plotQualityProfile(filtRs[]) , but I am currently filtering again. Notably, the quality is not bad ( the median quality line ranges from 30-40 through out) and the number of reads is not low after filtering (averaging 75 - 80% filtered paired-sequences (examples also shown below). Thank you for any help!
Read in 245228 paired-sequences, output 186666 (76.1%) filtered paired-sequences.
Read in 291754 paired-sequences, output 235653 (80.8%) filtered paired-sequences.