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Are there any plans for updating MISQ to output TPM values instead of FPKM values (as TPM are much nicer for comparing across samples - see fx this blog post) ?

Hi,

I received an error message during the FPKM calculation step. I successfully get the gene_models.RData file in the msiq_result folder, but nothing else. Below is my code, error output, and session info:

library(MSIQ)
D=26 # number of samples
gtf_path="/u/project/butlersj/jbuth/RefGenome/homo_sapiens/Annotation/gencode.v28.annotation.gtf"
bam_path=as.vector(Sys.glob("*.bam"))
result=msiq(D, gtf_path, bam_path, ncores=5)

[1] "/u/home/j/jbuth/R/x86_64-pc-linux-gnu-library/3.5/MSIQ/exec/Gibbs_functions.py"
Import genomic features from the file as a GRanges object ... Found more than one class "file" in cache; using the first, from namespace 'RJSONIO'
Also defined by ‘BiocGenerics’
OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
[1] 1000
[1] 2000
...
[1] 56000
[1] 57000
[1] 58000
[1] "extarct basic statistics from bam files ..."
[1] "get FPKMs for replicate 1"
[1] "get FPKMs for replicate 2"
[1] "get FPKMs for replicate 3"
[1] "get FPKMs for replicate 4"
[1] "get FPKMs for replicate 5"
Error: $ operator is invalid for atomic vectors
In addition: Warning messages:
1: In .get_cds_IDX(type, phase) :
The "phase" metadata column contains non-NA values for features of type stop_codon. This
information was ignored.
2: In mclapply(1:D, function(d) { :
all scheduled cores encountered errors in user code

sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS release 6.9 (Final)

Matrix products: default
BLAS/LAPACK: /u/local/compilers/intel/17.0.1/compilers_and_libraries_2017.1.132/linux/mkl/lib/intel64_lin/libmkl_gf_lp64.so

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets
[8] methods base

other attached packages:
[1] MSIQ_0.0.1 GenomicAlignments_1.16.0
[3] Rsamtools_1.32.0 Biostrings_2.48.0
[5] XVector_0.20.0 SummarizedExperiment_1.10.1
[7] DelayedArray_0.6.1 BiocParallel_1.14.1
[9] matrixStats_0.53.1 GenomicFeatures_1.32.0
[11] AnnotationDbi_1.42.1 Biobase_2.40.0
[13] GenomicRanges_1.32.3 GenomeInfoDb_1.16.0
[15] IRanges_2.14.10 S4Vectors_0.18.3
[17] BiocGenerics_0.26.0 rbamtools_2.16.11
[19] refGenome_1.7.3 RSQLite_2.1.1
[21] doBy_4.6-1 rPython_0.0-6
[23] RJSONIO_1.3-0 devtools_1.13.5

loaded via a namespace (and not attached):
[1] progress_1.2.0 gtools_3.8.1 tidyselect_0.2.4
[4] purrr_0.2.5 lattice_0.20-35 rtracklayer_1.40.3
[7] blob_1.1.1 XML_3.98-1.11 rlang_0.2.1
[10] pillar_1.2.3 glue_1.2.0 withr_2.1.2
[13] DBI_1.0.0 bit64_0.9-7 bindrcpp_0.2.2
[16] GenomeInfoDbData_1.1.0 bindr_0.1.1 plyr_1.8.4
[19] stringr_1.3.1 zlibbioc_1.26.0 memoise_1.1.0
[22] biomaRt_2.36.1 Rcpp_0.12.17 bit_1.1-14
[25] hms_0.4.2 digest_0.6.15 stringi_1.2.3
[28] dplyr_0.7.5 grid_3.5.0 bitops_1.0-6
[31] tools_3.5.0 magrittr_1.5 RCurl_1.95-4.10
[34] tibble_1.4.2 crayon_1.3.4 pkgconfig_2.0.1
[37] MASS_7.3-50 Matrix_1.2-14 prettyunits_1.0.2
[40] assertthat_0.2.0 httr_1.3.1 R6_2.2.2
[43] compiler_3.5.0