Issue with running LeafcutterMD.R

[looxon93]

Hi all,

I wanted to use LeafcutterMD.R script, with this command line: /opt/leafcutter/scripts/leafcutterMD.R --num_threads 4 clust_perind_numers.counts.gz

However it returned following error:

Loading counts from clust_perind_numers.counts.gz
Settings:
$output_prefix
[1] "leafcutter_outlier"

$max_cluster_size
[1] 50

$min_coverage
[1] 20

$timeout
[1] 30

$num_threads
[1] 4

$help
[1] FALSE

Running outlier splicing analysis...
Error in h(simpleError(msg, call)) :
  error in evaluating the argument 'x' in selecting a method for function 't': subscript out of bounds
Calls: processAllClusters ... write.table -> is.data.frame -> t -> .handleSimpleError -> h
Execution halted

I also tried this with number of threads=1, but always bump into the the same issue. Can someone help with this?

[kvn95ss]

Hello,

I'm facing the same issue, however with the test data set the command seems to be working fine. When I use my single, lone sample as input I get the same error. Would it be a good idea to take some publicly available RNA-seq data for controls?

Thanks

[pjewell-biociphers]

Hello,

I'm trying to run through the tutorial series at http://davidaknowles.github.io/leafcutter/articles/UsageLeafcutterMD.html using SRA data and when I get to the final state trying to run the leafcutter/scripts/leafcutterMD.R script, I receive exactly the same error as @looxon93 and @kvn95ss :

Running outlier splicing analysis...
Error in h(simpleError(msg, call)) :
  error in evaluating the argument 'x' in selecting a method for function 't': subscript out of bounds
Calls: processAllClusters ... write.table -> is.data.frame -> t -> .handleSimpleError -> h
Execution halted

Does anyone have an idea what causes this? The issue seems quite old at this point.

[jaicher]

This happens because:

• writeResToFile assumes that the results object has information about at least one cluster in it.
• There are no clusters in results.
  • this can happen if only one sample is passed in (as for @kvn95ss's case)

This could be fixed by:

• raising an informative error if count information doesn't have enough experiments in it
• raising an informative error if results are empty after iterating over clusters.

[asegarra22]

Hi all,

I am having the same error as @looxon93. `Settings: $output_prefix [1] "leafcutter_outlier"

$max_cluster_size [1] 50

$min_coverage [1] 20

$timeout [1] 30

$num_threads [1] 4

$help [1] FALSE

Running outlier splicing analysis... Error in results[[1]] : subscript out of bounds Calls: processAllClusters ... writeResToFile -> write.table -> is.data.frame -> t Execution halted`

I have checked the file "perind_numers.counts.gz" and I do have clusters. How did you fixed this?