Vivianstats
commented
4 years ago 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
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