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Description
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 haltedSometimes 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
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System information
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