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nedialkova-lab / mim-tRNAseq

Modification-induced misincorporation tRNA sequencing
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Conda Installation - R version problem #26

Closed cyken6621 closed 2 years ago

cyken6621 commented 2 years ago

Hi Drew,

I have used previous version of mimseq 0.3.x and it worked for me except for some issue that I have reported here in GitHub.

Recently, I tried to install the ver 0.4 by creating another new conda env as your instruction. However, I found that R4.1.1 was installed in the new conda env. The modification analysis was interrupted with error

+------------------+ | Parsing new mods | +------------------+ 2021-12-15 16:15:54,622 [INFO ] 0 new predicted position 34 inosines 2021-12-15 16:15:54,624 [INFO ] 6 new predicted modifications 2021-12-15 16:15:54,675 [INFO ] 277 clusters filtered out according to minimum coverage threshold: 2000.0 total read coverage per isodecoder. 2021-12-15 16:16:09,646 [INFO ] Output final tables, counts and new mods... 2021-12-15 16:16:11,285 [INFO ] Read counts per anticodon saved to v4hg38_HEK239vsK562/counts/Anticodon_counts_raw.txt 2021-12-15 16:16:11,285 [INFO ] Read counts per isodecoder saved to v4hg38_HEK239vsK562/counts/Isodecoder_counts_raw.txt 2021-12-15 16:16:11,379 [INFO ] Plotting modification and RT stop data... Error in library(reshape2) : there is no package called ‘reshape2’ Calls: suppressMessages -> withCallingHandlers -> library Execution halted 2021-12-15 16:16:12,175 [INFO ]

Here is part of the message showed during the installation step of
(mimseq) ~$ mamba install -c bioconda mimseq ...

~$ conda activate mimseq (mimseq) ~$ which mimseq /home/yk/anaconda3/envs/mimseq/bin/mimseq (mimseq) ~$ which R /home/yk/anaconda3/envs/mimseq/bin/R (mimseq) ~$ R --version R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-conda-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under the terms of the GNU General Public License versions 2 or 3. For more information about these matters see https://www.gnu.org/licenses/.

(mimseq) ~$ mimseq --version

() __ | || | \ | | / \ _ | ' _ \| | '_ _ \ ___| | |) | | | / \ / |/ \/ ` | | | | | | | | | | | | |___| || <| |\ |/ \_ \ / (| | || || |||| || || \|| __| _// __/_|\, | |_|

Modification-induced misincorporation analysis of tRNA sequencing data

mimseq 0.4

drewjbeh commented 2 years ago

Hi there,

Thanks for reporting this! We are aware of the error and a new release will fix this. It is coming from from the reshape2 R dependency not being installed. For now, the simplest fix is to start R in you mimseq environment (by simply running R) and then installing the package with install.packages("reshape2"). You can then exit R and try rerunning your mimseq command.

Sorry for the inconvenience!

cyken6621 commented 2 years ago

Hi Drew,

Thank you for the reply. It is fine now after installing the reshape2.

One more error that may be specific to my data. I have a set of data containing 2 WT and 2 KO. The DESeq2 analysis is interrupted with error and there is no heatmap generated. The _diffexpr-countplot.pdf files showed only 1 DEG (triangle) in anticodon and 0 DEG in isodecoder.

Here is error message Error in unit(x0, default.units) : 'x' and 'units' must have length > 0 Calls: rowAnnotation ... do.call -> -> gList -> segmentsGrob -> unit In addition: Warning messages: 1: In DESeqDataSet(se, design = design, ignoreRank) : some variables in design formula are characters, converting to factors 2: In DESeqDataSet(se, design = design, ignoreRank) : some variables in design formula are characters, converting to factors 3: Transformation introduced infinite values in continuous x-axis 4: Transformation introduced infinite values in continuous y-axis 5: Transformation introduced infinite values in continuous x-axis 6: It is deprecated to specify guide = FALSE to remove a guide. Please use guide = "none" instead. 7: Transformation introduced infinite values in continuous x-axis 8: Transformation introduced infinite values in continuous y-axis 9: Transformation introduced infinite values in continuous x-axis 10: It is deprecated to specify guide = FALSE to remove a guide. Please use guide = "none" instead. Execution halted

From deseq.R in mimseq package, I guess the error is due to the low DEG numbers in generating the heatmap. Perhaps, you would be able to add some error-proof for this in the R script.

Thank you.