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Hi,
I was trying to run the R2Dtool, the r2d liftover and r2d annotation work fine for me. However, when I try to run the r2d plotMetaTranscript script I get the following error: Command used:
./r2d plotMetaTranscript -i "/home/priyanka/R2D_m6a_Cheui_PvSal1/annotatetrial.bed" -o "/home/priyanka/R2D_m6a_Cheui_PvSal1/metatranscript_m6A.png" --filter-field "stoichiometry" --cutoff "1" --cutoff-type "lower" -l Error:
Arguments being passed to R2_plotMetaTranscript.R:
Rscript R2_plotMetaTranscript.R /home/priyanka/R2D_m6a_Cheui_PvSal1/annotatetrial.bed /home/priyanka/R2D_m6a_Cheui_PvSal1/metatranscript_m6A.png stoichiometry 1 lower -c loess -l
Executing R script: "/home/priyanka/R2Dtool/target/release/../../scripts/R2_plotMetaTranscript.R"
R script stdout:
[1] "Using loess method for confidence intervals."
R script stderr:
Parsed with column specification:
cols(
.default = col_double(),
transcript = col_character(),
name = col_character(),
score = col_character(),
strand = col_character(),
motif = col_character(),
gene_id = col_character(),
gene_name = col_logical(),
transcript_biotype = col_logical(),
cds_start = col_logical(),
cds_end = col_logical(),
tx_end = col_logical(),
transcript_metacoordinate = col_logical(),
abs_cds_start = col_logical(),
abs_cds_end = col_logical()
)
See spec(...) for full column specifications.
Warning message: guess_max is a very large value, setting to 21474836 to avoid exhausting memory
Error in mutate():
ℹ In argument: interval = cut(...).
Caused by error in cut.default():
! 'x' must be numeric
Backtrace:
▆
Hi,
I was trying to run the R2Dtool, the r2d liftover and r2d annotation work fine for me. However, when I try to run the r2d plotMetaTranscript script I get the following error:
Command used:
./r2d plotMetaTranscript -i "/home/priyanka/R2D_m6a_Cheui_PvSal1/annotatetrial.bed" -o "/home/priyanka/R2D_m6a_Cheui_PvSal1/metatranscript_m6A.png" --filter-field "stoichiometry" --cutoff "1" --cutoff-type "lower" -l
Error:
Arguments being passed to R2_plotMetaTranscript.R:
Rscript R2_plotMetaTranscript.R /home/priyanka/R2D_m6a_Cheui_PvSal1/annotatetrial.bed /home/priyanka/R2D_m6a_Cheui_PvSal1/metatranscript_m6A.png stoichiometry 1 lower -c loess -l
Executing R script: "/home/priyanka/R2Dtool/target/release/../../scripts/R2_plotMetaTranscript.R"
R script stdout:
[1] "Using loess method for confidence intervals."
R script stderr:
Parsed with column specification:
cols(
.default = col_double(),
transcript = col_character(),
name = col_character(),
score = col_character(),
strand = col_character(),
motif = col_character(),
gene_id = col_character(),
gene_name = col_logical(),
transcript_biotype = col_logical(),
cds_start = col_logical(),
cds_end = col_logical(),
tx_end = col_logical(),
transcript_metacoordinate = col_logical(),
abs_cds_start = col_logical(),
abs_cds_end = col_logical()
)
See spec(...) for full column specifications.
Warning message:
guess_max
is a very large value, setting to21474836
to avoid exhausting memoryError in
mutate()
:ℹ In argument:
interval = cut(...)
.Caused by error in
cut.default()
:! 'x' must be numeric
Backtrace:
▆
Execution halted
Error: R script exited with non-zero status: ExitStatus(unix_wait_status(256))
PlotMetaTranscript generation failed. Please check the error messages above.
Please let me know what could went wrong.
Thank you in advance.
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