Closed luolab-cuhk closed 2 years ago
@luolab-cuhk, I seriously apologize for the delay in my response. I have never observed this error before personally, but I believe the error is indicating that the reference sequence information potentially was not parsed from one or more lines from the problematic BAM files. The "overlapchunks" function accepts a stored index of the reference name as its second parameter, which was not passed. Is it possible for you to confirm this.
I got this error when I was accidentally used an .faa (not .fna) file for HISAT2 prior to using FADU.
@Emay222 Thanks for pointing this out. This weekend, I will try to write a catch for when the user passes in a .faa file instead of an .fna file.
Found this was addressed in https://github.com/BioJulia/XAM.jl/issues/11
Pushed a commit to address this and will tag as release v1.8.3
Hi,
Thanks for developing FADU! I processed transcriptomic data of some isolates by following the steps in /FADU/benchmark_scripts/. My align and sort steps are as follows:
In total, I have 40 samples subjected to the above processing. 35 of them finished with no errors, but 5 of them report the following errors when doing counts
The difference between problematic samples and normal ones is the log of
samtools sort
step. The former showed[bam_sort_core] merging from 0 files
, while the latter showed[bam_sort_core] merging from 4 files
, the 4 can be any number larger than 0. I am not sure if this is related to the error, could you please help me to solve this problem? Thanks a lot.