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stianlagstad / chimeraviz

chimeraviz is an R package that automates the creation of chimeric RNA visualizations.
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Failed to create reference fasta file #89

Closed ashishyeri closed 3 years ago

ashishyeri commented 3 years ago

Hi, I'm not able to create the reference fasta file to get a bam file for my fusion. I'm using STAR-fusion on a Linux operating system. The error I get is "Error in write_fusion_reference(fusion = a[[2]], filename = referenceFilename) : The fusion sequence length is zero, so the fusion reference sequence cannot be written."

My fusion is stored in a[[2]]. I'm not able to figure out where its trying to get the fusion reference sequence length from. Any help is greatly appreciated. Thanks!

Regards,

Ashish

Thank you for your interest in chimeraviz. To make it easier for me to help you, please provide this information in your submitted issue:

  1. The output of sessionInfo().
  2. Which fusion-finder tool you are using, and its version.
  3. Which operating system you are using, and its version.
  4. Example code leading to the error (if you're experiencing an error).
ashishyeri commented 3 years ago

R version 3.6.0 (2019-04-26) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 18.04.5 LTS

Matrix products: default BLAS: /usr/local/lib/R/lib/libRblas.so LAPACK: /usr/local/lib/R/lib/libRlapack.so

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

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

other attached packages: [1] chimeraviz_1.10.0 data.table_1.13.6 ensembldb_2.8.1
[4] AnnotationFilter_1.8.0 Gviz_1.28.3 gprofiler2_0.2.0
[7] BSgenome.Hsapiens.UCSC.hg38_1.4.1 BSgenome_1.52.0 rtracklayer_1.44.4
[10] TxDb.Hsapiens.UCSC.hg38.knownGene_3.4.6 vroom_1.4.0 COSMIC.67_1.20.0
[13] VariantAnnotation_1.30.1 Rsamtools_2.0.3 Biostrings_2.52.0
[16] XVector_0.24.0 SummarizedExperiment_1.14.1 DelayedArray_0.10.0
[19] BiocParallel_1.18.1 matrixStats_0.58.0 TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 [22] GenomicFeatures_1.36.4 AnnotationDbi_1.46.1 Biobase_2.44.0
[25] GenomicRanges_1.36.1 GenomeInfoDb_1.20.0 IRanges_2.18.3
[28] S4Vectors_0.22.1 BiocGenerics_0.30.0 TCGAretriever_1.5

loaded via a namespace (and not attached): [1] colorspace_2.0-0 ellipsis_0.3.1 biovizBase_1.32.0 htmlTable_2.1.0 ArgumentCheck_0.10.2
[6] base64enc_0.1-3 dichromat_2.0-0 rstudioapi_0.13 DT_0.17 bit64_4.0.5
[11] splines_3.6.0 cachem_1.0.4 knitr_1.31 Formula_1.2-4 jsonlite_1.7.2
[16] cluster_2.1.1 png_0.1-7 graph_1.62.0 BiocManager_1.30.10 compiler_3.6.0
[21] httr_1.4.2 backports_1.2.1 assertthat_0.2.1 Matrix_1.3-2 fastmap_1.1.0
[26] lazyeval_0.2.2 org.Mm.eg.db_3.8.2 htmltools_0.5.1.1 prettyunits_1.1.1 tools_3.6.0
[31] gtable_0.3.0 glue_1.4.2 GenomeInfoDbData_1.2.1 dplyr_1.0.4 Rcpp_1.0.6
[36] vctrs_0.3.6 xfun_0.21 stringr_1.4.0 lifecycle_1.0.0 gtools_3.8.2
[41] XML_3.99-0.3 org.Hs.eg.db_3.8.2 zlibbioc_1.30.0 RCircos_1.2.1 scales_1.1.1
[46] BiocStyle_2.12.0 hms_1.0.0 ProtGenerics_1.16.0 RColorBrewer_1.1-2 yaml_2.2.1
[51] curl_4.3 memoise_2.0.0 gridExtra_2.3 ggplot2_3.3.3 biomaRt_2.40.5
[56] rpart_4.1-15 latticeExtra_0.6-29 stringi_1.5.3 RSQLite_2.2.3 checkmate_2.0.0
[61] rlang_0.4.10 pkgconfig_2.0.3 bitops_1.0-6 evaluate_0.14 lattice_0.20-41
[66] purrr_0.3.4 GenomicAlignments_1.20.1 htmlwidgets_1.5.3 bit_4.0.4 tidyselect_1.1.0
[71] plyr_1.8.6 magrittr_2.0.1 R6_2.5.0 generics_0.1.0 Hmisc_4.4-2
[76] DBI_1.1.1 pillar_1.4.7 foreign_0.8-72 withr_2.4.1 survival_3.2-7
[81] RCurl_1.98-1.2 nnet_7.3-15 tibble_3.0.6 crayon_1.4.1 plotly_4.9.3
[86] rmarkdown_2.6 jpeg_0.1-8.1 progress_1.2.2 Rgraphviz_2.28.0 blob_1.2.1
[91] digest_0.6.27 tidyr_1.1.2 munsell_0.5.0 viridisLite_0.3.0

stianlagstad commented 3 years ago

Hi @ashishyeri! As far as I understand it, STAR-fusion does not include the fusion sequence in the result file by default, but:

STAR-fusion >= 1.2.0, when run with --denovo_reconstruct has a column FUSION_CDS in output file star-fusion.fusion_predictions.abridged.annotated.coding_effect.tsv which contains the fusion sequence.

(that's from here. See also: https://github.com/stianlagstad/chimeraviz/issues/24)

So, if you run a newer STAR-fusion version with the --denovo_reconstruct argument, the fusion sequence should be included and chimeraviz should import it. Let me know whether that solves the issue for you!

ashishyeri commented 3 years ago

Hi @stianlagstad, Thank you very much for your reply. I suspected this was the issue. I'm running star-fusion with the fusion-inspector and will report back soon. Thanks again!

Regards,

Ashish

stianlagstad commented 3 years ago

Hi @ashishyeri ! I'll close this, but feel free to open again if you still see this issue.