sleuth fails with unusual error

Question

[arunprasanna83]

Hi,

I ran the RNA-seq pipeline as follows in my workstation with 128GB RAM and several TBs storage:

RNA-seq -i FASTQ/ -o DEG -j 10 --DAG --local -m 'alignment-free,deepTools_qc' --aligner 'HISAT2' --sampleSheet samplesheet1.tsv Cv2

The pipeline keeps failing at sleuth with the following error:

summarizing bootstraps
................................Error in sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) : 
  write error, closing pipe to the master
Calls: sleuth_prep ... apply_function -> <Anonymous> -> lapply -> FUN -> sendMaster
Error in identical(indices, order(indices)) : 
  unimplemented type 'list' in 'orderVector1'
Calls: sleuth_prep ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted

My sample sheet is:

name    time    condition
C1t25D0 DH0 Control
C2t25D0 DH0 Control
C3t25D0 DH0 Control
C4t25D0 DH0 Control
C6t25D0 DH0 Control
C7t25L0 LH0 Control
C10t25L0    LH0 Control
C11t25L0    LH0 Control
C12t25L0    LH0 Control
C13t32L0    LH0 Stress
C14t32L0    LH0 Stress
C15t32L0    LH0 Stress
C16t32L0    LH0 Stress
C17t32L0    LH0 Stress
C19t32L24   LH24    Stress
C20t32L24   LH24    Stress
C22t32L24   LH24    Stress
C23t32L24   LH24    Stress
C24t32L24   LH24    Stress
C25t32D36   DH36    Stress
C26t32D36   DH36    Stress
C29t32D36   DH36    Stress
C30t32D36   DH36    Stress
C31t32L72   LH72    Stress
C32t32L72   LH72    Stress
C34t32L72   LH72    Stress
C36t32L72   LH72    Stress
C37t32L120  LH120   Stress
C39t32L120  LH120   Stress
C40t32L120  LH120   Stress
C41t32L120  LH120   Stress
C42t32L120  LH120   Stress

However, the sleuth.out shows that there are 32 levels. I am not sure if this correct ?. When I check few threads, it shows about memory, but I do not see peak memory crossing more than 10G. Is there any problem with my sample sheet?

Thanks in advance.

[Devon Ryan]

This looks like a bug in Sleuth, though your design is such that you can't discriminate between things like stress and control and some of the time points (e.g., LH120).