Error in order(indices)

[philge]

Hi

Following code is giving error

sample_to_condition <- METADATA %>% dplyr::rename(sample = ID) rownames(sample_to_condition) <- sample_to_condition$sample sample_to_condition <- sample_to_condition[sample_id,] s2c <- dplyr::mutate(sample_to_condition, path = kal_dirs)

so <- sleuth_prep(s2c, extra_bootstrap_summary = TRUE)

reading in kallisto results dropping unused factor levels ............................................................................................................................................................................................................................................................................ normalizing est_counts 100408 targets passed the filter normalizing tpm merging in metadata summarizing bootstraps .................................................... ............................................................................ ............................................... .............................................Error in order(indices) : unimplemented type 'list' in 'orderVector1'

Please help me to fix the issue.

Thanks Philge Philip

[philge]

Hi

I was running the code on Amazon EC2. It seems error is because of some broken parallel processing. When i re-run the code with parameter num_cores=2, code run without error.

Thanks Philge

[warrenmcg]

Hi @philge, if there are no more issues, I'm going to close this. If you experience a similar issue, please feel free to reopen the issue. Thanks!

[xqrongm]

I'm having the same problem as described in the original post. I tried several values of num_cores including 1, 2, 20, 28 (there are 28 cores available on my node), all gave me the same error.

@warrenmcg Should I open a new issue or someone can help me re-open this issue? Thanks!

[warrenmcg]

Hi @xqrongm,

Could you tell me what version of sleuth you are running (if you are running a devel version, please tell me which commit you are using)?

Also, you are getting the exact same error when you set num_cores = 1? If it's not exact same error, can you show what the precise error is.

Once you answer those questions, that will help us decide if this is a new issue or to re-open this old one. Thanks!

[xqrongm]

version 0.29.0

Yes, I'm getting the exact same error for num_cores = 1,2,20,28:

reading in kallisto results
dropping unused factor levels
.....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
normalizing est_counts
80030 targets passed the filter
normalizing tpm
merging in metadata
aggregating by column: ensembl_gene_id
21832 genes passed the filter
summarizing bootstraps
........................................................................
..............Error in order(indices) : unimplemented type 'list' in 'orderVector1'

Thanks!

[MDSharma]

Hi,

this issue seems closed but I seem to be getting it as well with the latest build, when using more than one factor in the model:

'''

so2 <- sleuth_prep(s2c, ~ population + day, num_cores = 1) reading in kallisto results dropping unused factor levels .................................. normalizing est_counts 66490 targets passed the filter normalizing tpm merging in metadata summarizing bootstraps ................................ . Error in identical(indices, order(indices)) : unimplemented type 'list' in 'orderVector1' '''