Hi,
I'm trying to align on myrna some human RNA seq, paired, illumina with Ensembl 58 reference as on the myrna manual.
This is my command:
I've tried with/without the --family gaussian option; however getting the same result.
And here I'm getting this error message:
The thing is, I'm getting the same error message on my local computer as well as on the web-based interface.
Do I need to provide at least 2 groups in the manifast file?
Maybe, I've totally misunderstood myrna - is the reference only used for aligning? Does the RNA seq not beeing compaired with the reference at all?
Thank you in advance,
Serena Rhie
I'm trying to align on myrna some human RNA seq, paired, illumina with Ensembl 58 reference as on the myrna manual.
This is my command:
Code:
$MYRNA_HOME/myrna_local --reference /home/Serena/myrna-1.0.9/reftools/human_ensembl_58 --input /media/SAMSUNG/Data/myrna/paired_8M_preprocess_only/paired_8M_preprocessed --output /media/SAMSUNG/Data/myrna/paired_8M_preprocess_only/output --family gaussian --quality solexa64 --keep-all --cpus 8 --bowtie-args "-m 1 -n 3 -l 10 -q -I 450 -X 550"
And here I'm getting this error message:
Code:
Pid 31271 reducing task task-00003 [4 of 32]... Pid 31268 reducing task task-00000 [1 of 32]... ****** * Aborting master loop because child 31275 failed * (other children may also have failed) * Input file or string was: * /tmp/myrna/intermediate/27481/stats.reduce.pre/reduce.stasks/stask-31275 * Error message is in file: /tmp/myrna/intermediate/27481/stats.reduce.pre/reduce.err/epart-31275, also printed below ****** * Stats.pl: Family: gaussian * Stats.pl: # nulls per gene: 0 * Stats.pl: seed (-1 = let R decide): -1 * Stats.pl: Bypass P-value calculation: 0 * Stats.pl: Profiling enabled: 0 * Stats.pl: Add fudge factor: 0 * Stats.pl: Samples are paired: 0 * Get.pm:lsDir: About to parse URL /tmp/myrna/intermediate/27481/globals/multiset/label/ * Get.pm:lsDir: About to handle local * ls -1 /tmp/myrna/intermediate/27481/globals/multiset/label/ * Result of get_mset_global('label'): 0 * /home/Serena/myrna-1.0.9/R/bin/Rscript --vanilla --default-packages=stats,zoo,grDevices,graphics,utils,methods,lmtest,MASS /home/Serena/myrna-1.0.9/Stats.R --args .tmp.Stats.pl.31279 0 gaussian 0 -1 0 0 0 0 * runAndWait: Child's PID is 31412 * Stats.R [10:55:35]: Called deTest(.tmp.Stats.pl.31279, 0, gaussian, FALSE, 0, FALSE) * Read 8065 records * Stats.R [10:55:35]: Processing batch of 8065 alignments * Stats.R [10:55:35]: Alignment batch has 205 genes * Stats.R [10:55:35]: Genes: ENSG00000003987G ENSG00000006015G ... ENSG00000243646G ENSG00000244509G * Stats.R [10:55:35]: Alignment batch has 1 distinct labels * Stats.R [10:55:35]: Labels: 0 * Stats.R [10:55:35]: Whole dataset has 1 distinct labels * Stats.R [10:55:35]: Labels: 0 * Stats.R [10:55:35]: Batch has 1 distinct groups * Stats.R [10:55:35]: Groups: 0 * Stats.R [10:55:35]: Whole dataset has 1 distinct groups * Stats.R [10:55:35]: Groups: 0 * Stats.R [10:55:35]: Factorizing label column * Stats.R [10:55:35]: Getting per-sample normalization factors * Stats.R [10:55:35]: Setting up data matrix * Stats.R [10:55:35]: Setting up output strings * Stats.R [10:55:35]: Calculating batch of 205 observed P-values * reporter:counter:Stats,Observed Pval batches calculated,1 * reporter:counter:Stats,Observed Pvals calculated,205 * Error in `contrasts<-`(`*tmp*`, value = "contr.treatment") : * contrasts can be applied only to factors with 2 or more levels * Calls: deTest ... model.matrix -> model.matrix.default -> contrasts<- * Execution halted * Waiting for R (it's been 5 secs)... * cp: cannot stat `*': No such file or directory * cp: omitting directory `.' * cp: omitting directory `..' * Exitlevel 256 from command /home/Serena/myrna-1.0.9/R/bin/Rscript --vanilla --default-packages=stats,zoo,grDevices,graphics,utils,methods,lmtest,MASS /home/Serena/myrna-1.0.9/Stats.R --args .tmp.Stats.pl.31279 0 gaussian 0 -1 0 0 0 0
Do I need to provide at least 2 groups in the manifast file?
Maybe, I've totally misunderstood myrna - is the reference only used for aligning? Does the RNA seq not beeing compaired with the reference at all?
Thank you in advance,
Serena Rhie
Comment