groHMM fails with CHM13 occasionally

[edmundmiller]

Description of the bug

Details

Command output:
  
  Returning to R Enivorment :)
  $c.UTS..1.UTS...1.
  [1] 45.00000000  0.02222222 -1.00000000
  
  $c.0.5..10...1.
  [1]   0.2564279 264.2384571  -1.0000000
  
  $c.log.1...exp.LtProbA....LtProbA.
  [1] -0.006589323 -5.025597509
  
  $c.LtProbB..log.1...exp.LtProbB...
  [1] -100    0
  
  [1] "Input transcript annotations"
  [1] "Printing kg_tx......."
  GRanges object with 181708 ranges and 3 metadata columns:
             seqnames            ranges strand |         gene_id     tx_id
                <Rle>         <IRanges>  <Rle> | <CharacterList> <integer>
         [1]     chr1       15080-21429      + |  LOC124905335_1         1
         [2]     chr1     205295-214212      + |       LINC01409         2
         [3]     chr1     205329-214212      + |       LINC01409         3
         [4]     chr1     220504-227987      + |    LOC124903817         4
         [5]     chr1     246378-248841      + |          FAM87B         5
         ...      ...               ...    ... .             ...       ...
    [181704]     chrY 26841747-26844871      - |    LOC107987352    181704
    [181705]     chrY 27005778-27047281      - |         REREP2Y    181705
    [181706]     chrY 27213049-27221044      - |    LOC105377244    181706
    [181707]     chrY 62439553-62441822      - |        WASIR1_1    181707
    [181708]     chrY 62449384-62451910      - |      DDX11L16_1    181708
                 tx_name
             <character>
         [1]        <NA>
         [2]        <NA>
         [3]        <NA>
         [4]        <NA>
         [5]        <NA>
         ...         ...
    [181704]        <NA>
    [181705]        <NA>
    [181706]        <NA>
    [181707]        <NA>
    [181708]        <NA>
    -------
    seqinfo: 24 sequences from an unspecified genome; no seqlengths
  [1] "Collapse annotations in preparation for overlap"
  [1] "Finished consensus annotations"
  [1] "repairing with annotations"
  564  transcripts are broken into  1269 
  548  transcripts are broken into  1252 

Command error:
  Warning message:
  'memory.limit()' is Windows-specific 
  Import genomic features from the file as a GRanges object ... OK
  Prepare the 'metadata' data frame ... OK
  Make the TxDb object ... OK
  Warning messages:
  1: In .extract_transcripts_from_GRanges(tx_IDX, gr, mcols0$type, mcols0$ID,  :
    some transcripts have no "transcript_id" attribute ==> their name
    ("tx_name" column in the TxDb object) was set to NA
  2: In .extract_transcripts_from_GRanges(tx_IDX, gr, mcols0$type, mcols0$ID,  :
    the transcript names ("tx_name" column in the TxDb object) imported
    from the "transcript_id" attribute are not unique
  3: In .find_exon_cds(exons, cds) :
    The following transcripts have exons that contain more than one CDS
    (only the first CDS was kept for each exon): NM_001134939.1,
    NM_001172437.2, NM_001184961.1, NM_001301020.1, NM_001301302.1,
    NM_001301371.1, NM_002537.3, NM_004152.3, NM_015068.3, NM_016178.2
  Reduce isoforms(22385) ... OK
  Truncate overlapped ranges ... OK
  Error in h(simpleError(msg, call)) : 
    error in evaluating the argument 'x' in selecting a method for function 'end': subscript contains NAs
  Calls: combineTranscripts ... normalizeSingleBracketSubscript -> NSBS -> NSBS -> .subscript_error
  Execution halted

Sometimes it works, sometimes it doesn't.

Don't want this edge case to hold up merging #165

Command used and terminal output

No response

Relevant files

No response

System information

No response