BAM as input

[RViuj]

Hi,

After I unsuccessfully trying to run paired end FASTQ files on a local machine, I created the BAM files to run TRUST4 on the local machine.

However,
1 - TRUST4 did not recognise the BAM files. To make sure the BAM file is correct:

a - Checked the BAM file and confirmed it was valid using samtools quickcheck.

b - Ensured that the BAM file was indexed correctly with the samtools index command.

c - Verified that the BAM file had read groups (@rg).

d - Despite all these checks, TRUST4 kept returning the help menu.

Then I checked it the TRUST4 was complied with BAM Support, I checked for HTSlib (which I thought is required for BAM file processing).
a - TRUST4 returned no link to HTSlib

b - I modified the Makefile to explicitly link TRUST4 with HTSlib using -L$(brew --prefix htslib)/lib -lhts.

c - Tried forcing HTSlib during compilation with specific paths.

d - Despite these changes, otool (which shows the linked libraries) never showed libhts.dylib, indicating BAM support was not enabled during the build process.


When I ran "ls /opt/homebrew/lib | grep libhts" and "ls /opt/homebrew/include | grep hts" it returned;

libhts.1.21.dylib
libhts.3.dylib
libhts.a
libhts.dylib
htslib

However, when I ran "ls /opt/homebrew/lib | grep libbam" it returned blank.

I understand that "libbam/libbam.a" file is not built when samtools is installed either from the sourcecode (https://github.com/samtools/samtools/releases) or using Homebrew. May I know how I could make this to run TRUST4 using BAM as input?

I even tried to reinstall TRUST4 via CONDA, Samtools from the Source Code and also from Homebrew. Even then TRUST4 failed to recognise BAM input.

While TRUST4 was recognising FASTQ files, due to the storage/memory, it never finished the run. When the BAM file was used as the input, it is not recognising. I am not sure how I can fix it. Your expert syggestion will be helpful.

Thank you.

[mourisl]

What was your running command and how did you download and compile TRUST4? The "samtools" package is in the github repo, so you don't need to compile that through htslib.

[RViuj]

Thank you. I used "./run-trust4 -f /Users/rv/TRUST4/human_IMGT+C.fa -b /Users/rv/Desktop/BAM/D001_BAM_sorted.bam -o /Users/rv/Desktop/BAM/TRUST4_results"

[mourisl]

What was your error message? Did you see any compilation errors when compiling TRUST4?

[RViuj]

Thank you. Couple of errors I came across are "Missing BAM library (libbam)" and "Undefined symbols for architecture arm64".