Is there any other possible explanation as to why it's stuck on this specific line?
It has completed that line, so it is stuck on what comes next. Here are all
bwa index lines when indexing a small file:
[bwa_index] Pack FASTA... 0.01 sec
[bwa_index] Construct BWT for the packed sequence...
[BWTIncCreate] textLength=3718406, availableWord=4724070
[bwt_gen] Finished constructing BWT in 5 iterations.
[bwa_index] 1.11 seconds elapse.
[bwa_index] Update BWT... 0.01 sec
[bwa_index] Pack forward-only FASTA... 0.01 sec
[bwa_index] Construct SA from BWT and Occ... 0.20 sec
[main] Version: 0.7.17-r1188
[main] CMD: bwa index -a bwtsw group_00.fa
[main] Real time: 1.638 sec; CPU: 1.342 sec
Since the first
bwa index line in my file took about 1s (total time was 1.6s) and yours was >3500, by extrapolation the whole process in your case should take about 1.5 hours. This is assuming that indexing time is linear - don't know if that's true - and that you have enough RAM to index this file in memory - don't know if that's true either. If your computer is short on memory, it may be swapping which can take very long time.
I suggest you find out how much your computer is swapping during this indexing operation:
This is what my computer shows at the moment:
Filename Type Size Used Priority
/dev/sda1 partition 97654780 280576 -2
As you can see, swap disk utilization here is less than 1% and I suspect yours will be much higher. Or try
free -m which will show both RAM and swap usage:
total used free shared buff/cache available
Mem: 257873 139270 54222 8 64380 116872
Swap: 95365 274 95091