Closed StollML closed 3 years ago
benjjneb
commented
3 years ago Use saveRDS/readRDS to do this transfer of the sequence table.
That will get you back exactly what you had before. write.table/read.table will not, in particular as it relates to the variable types, like the integer type that dada2 is checking for and not finding in your re-read sequence table.
StollML
commented
3 years ago Thank you very much. Unfortunately, the cluster R version is older and is not recognizing the RDS file that I generated in the Windows R (version 4). Is there an easy fix for this (e.g. a way to save the file as an RDS that would be recognized by R 3.0, or do I just need for them to upgrade R?
Regards,
Matt
From: Benjamin Callahan [mailto:notifications@github.com] Sent: Tuesday, February 16, 2021 5:10 PM To: benjjneb/dada2 dada2@noreply.github.com Cc: Matthew Stoll, M.D. mstoll@peds.uab.edu; Author author@noreply.github.com Subject: [EXT] Re: [benjjneb/dada2] Problem going from Windows R to Unix R (#1274)
Use saveRDS/readRDS to do this transfer of the sequence table.
That will get you back exactly what you had before. write.table/read.table will not, in particular as it relates to the variable types, like the integer type that dada2 is checking for and not finding in your re-read sequence table.
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/benjjneb/dada2/issues/1274#issuecomment-780176809, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AGCV36XZ3TKB3M2N3VYDL4TS7L3MZANCNFSM4XWOM3UQ.
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benjjneb
commented
3 years ago If there is an easier method I don't know it. How out of date is their version of R? This is the first time I've heard that an RDS file using base R was rejected by another R installation.
On Tue, Feb 16, 2021 at 9:22 PM StollML notifications@github.com wrote:
Thank you very much. Unfortunately, the cluster R version is older and is not recognizing the RDS file that I generated in the Windows R (version 4). Is there an easy fix for this (e.g. a way to save the file as an RDS that would be recognized by R 3.0, or do I just need for them to upgrade R?
Regards,
Matt
From: Benjamin Callahan [mailto:notifications@github.com] Sent: Tuesday, February 16, 2021 5:10 PM To: benjjneb/dada2 dada2@noreply.github.com Cc: Matthew Stoll, M.D. mstoll@peds.uab.edu; Author < author@noreply.github.com> Subject: [EXT] Re: [benjjneb/dada2] Problem going from Windows R to Unix R (#1274)
Use saveRDS/readRDS to do this transfer of the sequence table.
That will get you back exactly what you had before. write.table/read.table will not, in particular as it relates to the variable types, like the integer type that dada2 is checking for and not finding in your re-read sequence table.
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub< https://github.com/benjjneb/dada2/issues/1274#issuecomment-780176809>, or unsubscribe< https://github.com/notifications/unsubscribe-auth/AGCV36XZ3TKB3M2N3VYDL4TS7L3MZANCNFSM4XWOM3UQ>.
WARNING: This email originated from outside UAB Pediatrics. Please be cautious of any links or e-mail replies.
— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/benjjneb/dada2/issues/1274#issuecomment-780250839, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABMHKVECNNCPXFLNS32D6VLS7MR5FANCNFSM4XWOM3UQ .
StollML
commented
3 years ago Here is the exact error message:
<<
Error in readRDS("seqtab.rds") : cannot read workspace version 3 written by R 4.0.3; need R 3.5.0 or newer Execution halted
Thanks,
Matt
From: Benjamin Callahan [notifications@github.com] Sent: Tuesday, February 16, 2021 8:55 PM To: benjjneb/dada2 Cc: Matthew Stoll, M.D.; Author Subject: [EXT] Re: [benjjneb/dada2] Problem going from Windows R to Unix R (#1274)
If there is an easier method I don't know it. How out of date is their version of R? This is the first time I've heard that an RDS file using base R was rejected by another R installation.
On Tue, Feb 16, 2021 at 9:22 PM StollML notifications@github.com wrote:
Thank you very much. Unfortunately, the cluster R version is older and is not recognizing the RDS file that I generated in the Windows R (version 4). Is there an easy fix for this (e.g. a way to save the file as an RDS that would be recognized by R 3.0, or do I just need for them to upgrade R?
Regards,
Matt
From: Benjamin Callahan [mailto:notifications@github.com] Sent: Tuesday, February 16, 2021 5:10 PM To: benjjneb/dada2 dada2@noreply.github.com Cc: Matthew Stoll, M.D. mstoll@peds.uab.edu; Author < author@noreply.github.com> Subject: [EXT] Re: [benjjneb/dada2] Problem going from Windows R to Unix R (#1274)
Use saveRDS/readRDS to do this transfer of the sequence table.
That will get you back exactly what you had before. write.table/read.table will not, in particular as it relates to the variable types, like the integer type that dada2 is checking for and not finding in your re-read sequence table.
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub< https://github.com/benjjneb/dada2/issues/1274#issuecomment-780176809>, or unsubscribe< https://github.com/notifications/unsubscribe-auth/AGCV36XZ3TKB3M2N3VYDL4TS7L3MZANCNFSM4XWOM3UQ>.
WARNING: This email originated from outside UAB Pediatrics. Please be cautious of any links or e-mail replies.
— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/benjjneb/dada2/issues/1274#issuecomment-780250839, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABMHKVECNNCPXFLNS32D6VLS7MR5FANCNFSM4XWOM3UQ .
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benjjneb
commented
3 years ago They need to update their version of R. 3.5.0 is three years old at this point.
StollML
commented
3 years ago Thanks.
Matt
Sent from my iPhone
On Feb 17, 2021, at 6:19 AM, Benjamin Callahan notifications@github.com wrote:
They need to update their version of R. 3.5.0 is three years old at this point.
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/benjjneb/dada2/issues/1274#issuecomment-780518941, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AGCV36W4FE36NIY2CCLCTR3S7OX5RANCNFSM4XWOM3UQ.
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I created a Seqtab in the Windows R environment, but need to do some downstream steps in our computing cluster due to memory issues.
I save the seqtab as a txt (or csv) table write.table(seqtab,file="seqtab.txt",quote=FALSE)
Import it into the Unix system and run dada2 from there. seqtab <- read.table("Seqtab.txt",header=TRUE,sep="")
However, this is not recognized as a Sequence table dada2:::is.sequence.table(seqtab) # FALSE
Even though the same code from the Windows R environment yielded # TRUE
taxa <- assignTaxonomy(seqtab, "silva_nr_v132_train_set.fa.gz") yielded the following error message
Error in getUniques(object, collapse = collapse, silence = silence) : Unrecognized format: Requires named integer vector, dada-class, derep-class, sequence matrix, or a data.frame with $sequence and $abundance columns. Calls: assignTaxonomy -> getSequences -> getUniques
To troubleshoot, I generated a file I called partial partial <- seqtab[1:3,1:3]
The assignTaxonomy script works just fine from the Windows environment. I am uploading the Partial.txt file.
Partial.txt
Thank you very much --
Matt