Error somewhere after fragment estimation

[alecbarrett]

Hello,

I'm running the AIDE package, which has worked well for 9 bam files, but on the 10th file I'm getting an error and halted execution that I don't fully understand.

Some milestones from outfile printed below.

[1] "extracting gene models from GTF ..."
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
... ... ...
[1] 46700
[bamCountAll] Counting XtDNA [ 7/7]
[bamCountAll] Finished.
[1] "estimating fragment length ..."
[1] "start estimating mean and sd of fragment length ..."
[1] "number of genes used: 0"
[1] "do not have enough reads for estimation ..."
[1] "using default values ..."
[1] 250
[1] 80
[1] 150 400
[1] "estimating bias ..."
[1] "number of genes with 1 tx: 15906"
... ... ...
[1] 15500
[1] 15000
Error in if (nrow(starts_data) < 1500 * 2) { : argument is of length zero
Calls: aide
In addition: Warning message:
In .get_cds_IDX(type, phase) :
The "phase" metadata column contains non-NA values for features of type
stop_codon. This information was ignored.
Execution halted

The BAM file contains about 8 million paired end reads, all 150nt long.

Any help that can be given would be really appreciated
Thank you!
-Alec

[Vivianstats]

Hi Alec,

I'm sorry about the late reply, as I didn't get a notification from Github about your post.

I wonder if you manage to find out the reason and solve the problem?

Vivian