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a2iEditing / RNAEditingIndexer

A tool for the calculation of RNA-editing index for RNA seq data
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AssertionError: Strand Calling In Stranded Library is Ambiguous! Skipping This Sample #31

Open sgomez0328 opened 2 years ago

sgomez0328 commented 2 years ago

I have run this pipeline on internally-generated RNA-seq libraries with no issue (and also the sample data), but when running it on TCGA datasets, I run into this issue when I also try to run the "stranded" flag. The libraries are indeed stranded...I'm not sure what the issue could be.

[21-08-26 22:07:49] EditingIndexProcessingSubprocessTCGA-13-0725-01A. CountPileupCoverter INFO Found 166181 regions, 13784044 coverages in chromosomes: ['chrY', 'chrX', 'chr13', 'chr12', 'chr11', 'chr10', 'chr17', 'chr16', 'chr15', 'chr14', 'chr19', 'chr18', 'chr22', 'chr20', 'chr21', 'chr7', 'chr6', 'chr5', 'chr4', 'chr3', 'chr2', 'chr1', 'chr9', 'chr8'] [21-08-26 22:07:49] EditingIndexProcessingSubprocessTCGA-13-0725-01A. A2IEditingIndex INFO Done Loading Second Strand Coverage Data of TCGA-13-0725-01A. [21-08-26 22:07:50] EditingIndexProcessingSubprocessTCGA-13-0725-01A. A2IEditingIndex ERROR Failed Processing of TCGA-13-0725-01A.! Traceback (most recent call last): File "Tools/EditingIndex/A2IEditingIndex.py", line 793, in load_and_process_sample File "Tools/EditingIndex/A2IEditingIndex.py", line 927, in get_stranded_strands_and_counts AssertionError: Strand Calling In Stranded Library is Ambiguous! Skipping This Sample [21-08-26 22:07:50] MainProcess A2IEditingIndex DEBUG Acquired Semaphore, left 0

ryrl9703 commented 2 years ago

I have the same problem, have you solved it?

umasstr commented 2 years ago

Same issue here. Also concerning is that their test data reproducibly fails to run in the docker container.

zhongzheng1999 commented 1 year ago

@umasstr @ryrl9703 @sgomez0328 I have the same problem, have you solved it?

umasstr commented 1 year ago

No unfortunately never got a response. The web tool also won't upload. Package is likely not maintained anymore...