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Error when running fastqPairedFilter #212
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Haven't seen that one before. Which package are you using to knit with, Can you report the output of the following:
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Yes, I should have included that information!
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Someone else has run into this same error with a different (QuasR) package: https://support.bioconductor.org/p/92701/ No answer there, though, either. My guess is that it's propagating out from a change in one of the dependencies. |
Ah that is a bummer :-( I will look into writing a regular R script to get around this. Thanks! |
The solution may be as easy as fully loading the package at the beginning of your Rmd... e.g. library("ShortRead") and so on, until the error goes away. I can't guarantee it will work, but it is one of the things I'd try if Rmd/HTML was a high priority. |
I did actually load it in the very beginning of my script. |
I'm getting this error as well, but on a Windows 7 operating system. At first, I thought this might be an RTools installation problem, but I've checked RTools and it is good to go. I'm also running the walkthrough demo successfully on a Windows 10 operating system. Is there a chance, this is an operating system specific error? My code and error result:
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I am not sure if this error is actually caused by knitr, as I had previously assumed. I specifically unloaded the knitr package and I still encounter the same error:
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The traceback for the error message:
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I strongly suspect this is an issue w/in the ShortRead package, and the fact that I haven't been able to reproduce it thus far makes things hard, but if multiple people are seeing it then we need to try to get to the bottom of it. @melindahiggins2000 Can you also post the |
@melindahiggins2000 and I were teaching the dada2 pipeline today. We asked everybody to come prepared with everything installed and downloaded and had them do so as homework that they posted to their class github repo. We had at least one other Windows10 user who had the same issue. I will ask for her sessionInfo as well. |
Here is our
I did not run the |
I cannot replicate this, but the Please reopen if this issue reappears in the newer versions of the package. |
This is still happening in dada2 version 1.2.2 and 1.5.0 on Win10 on both the command line and within markdown. Never happens with 1.2.1 on my Win10 laptop. |
Grumble. I am confused. @caledonius Can you report a |
Closing this in the absence of any further reports. I've never been able to reproduce this bug. |
Hi guys,
Any help on this? |
@frannasc Update your R to 3.4.2 and see if the same error occurs. |
Hello,
locale: attached base packages: other attached packages: loaded via a namespace (and not attached): |
The software versions you have are pretty old (~2 years) at this point. If you update to current versions this error will probably be resolved. I would recommend installing R 3.5, and then reinstalling dada2 via Bioconductor, which will update all the dependencies as well. If you can't update R, you can try installing the current version of dada2 via github: |
Thank you for the kind suggestion. |
I also have this issue
R version 3.3.3 (2017-03-06) -- "Another Canoe" packageVersion("dada2"): '1.2.2' |
If you upgrade to a recent version of the dada2 R package (1.6 or later) this issue will go away. The 1.2 version is almost 2 years old now. |
@benjjneb apologies for commenting on a closed issue. I'm encountering this same error when I run
My
What I have tried:
Notable package versions are as follows:
Lastly, my
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Thank you guys! was running into the same issue and resolved by matrix version issue! |
This should be fixed in the latest commit to the devel (master) branch. That is, it should work with Matrix 1.3.3. |
Downgraded Matrix to 1.3-2 and the issue was resolved. Thanks!! |
Hi,
Then I clicked on the adjacent X icon to Matrix package in the right bottom corner to remove it, and got this error: Updating HTML index of packages in '.Library' Any recommendations please? |
@emankhalaf
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Much thanks for your swift response. I did the following:
So, how could I figure it out? |
It seems you have multiple locations (paths) for your R libraries. You need to figure out where you have installed it.
At the very least it should have
and one other location
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I did this:
and when ran
I have no idea how to solve it. Actually, I ran the entire script last week successfully, but when I re-ran it today, I got this error. |
@emankhalaf When you input multiple paths to the Try These lines one at a time
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Yes, for sure. I tried each and got these:
So, I am not sure what should I do with HTML package? |
@emankhalaf I would consider installing the latest devel version of the dada2 R package as a fix here instead. It might be simpler, and solves the error a different way that is independent of the Matrix package version.
This latest devel version (1.19.2) will be the next release version of the package, and that release is imminent -- it should be out via BioConductor in a week or two. |
Hello, |
@emankhalaf No, that is version 1.2.2 and 3+ years old at this point. |
Thanks! My current installed version is 1.19.1, however, I will be waiting for the latest as you recommend. |
Hey All, Here is my info session for reference:
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Hello, The scriptlibrary(dada2); packageVersion("dada2")
args <- commandArgs(TRUE)
path <- args[[1]]
# Forward and reverse fastq filenames have format: SAMPLENAME_R1_001.fastq and SAMPLENAME_R2_001.fastq
fnFs <- sort(list.files(path, pattern="_R1_001.fastq", full.names = TRUE))
fnRs <- sort(list.files(path, pattern="_R2_001.fastq", full.names = TRUE))
# Extract sample names, assuming filenames have format: SAMPLENAME_XXX.fastq
sample.names <- sapply(strsplit(basename(fnFs), "_"), `[`, 1)
# Place filtered files in filtered/ subdirectory
filtFs <- file.path(path, "filtered", paste0(sample.names, "_F_filt.fastq.gz"))
filtRs <- file.path(path, "filtered", paste0(sample.names, "_R_filt.fastq.gz"))
out <- filterAndTrim(fnFs, filtFs, fnRs, filtRs, truncLen=c(240,160),
maxN=0, maxEE=c(2,2), truncQ=2, rm.phix=TRUE,
compress=TRUE, multithread=TRUE) System infoI initially had the problem in a Ubuntu box, but replicated it locally on my Mac (macOS 11.3.1) so I print here
Update: How it was fixedI tried to recreate the "new nonworking environment" by just adding I'm shocked by this instability in the dep tree! :) |
I'm glad people have been able to get their pipelines working again :) @benjjneb #212 (comment) above from @kalen-rasmussen notes updated dada2 which should have bypassed the Matrix function issue but seemingly is still present... Just want to make you aware of that.
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Glad it got fixed! Yeah, it is the same issue with the same fix. Unfortunate that this might be propagated to some Bioconda builds though, which we don't really have control over. |
I believe I should uninstall dada2_1.19.1 (the one I have currently) first, then install the new version (1.19.2), correct? |
It is working now! Thanks @benjjneb |
Hi all,
First of all, thanks for making dada2 available! I've only played with the tutorials (the miseq PE-read walkthrough) but the features and capabilities look great so far!
I ran into a strange error with
fastqPairedFilter()
that seems to occur when I try to run the sample walkthrough code in knitr.This did not occur when I ran the code manually on the command line however I can't imagine what would be different in the knitr environment (it sets up all the same libraries, etc). In fact, I set up my markdown document and copied and pasted into the command line from there while practicing. I am looking to automate basic processing of 16S data at some point, so being able to run it through knitr to produce a report that includes QC plots etc would be attractive.
Thanks for any suggestions or pointers to additional reading you might have!
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