Software still supported?

[LucasMcNU]

Is CLAM still supported? I'm running into the following issue.

`CLAM peakcaller -i P1KO_P1AB_R1_S13_L005_filt.sort.bam -c P1KO_Input_S23_L005_filt.sort.bam -o /projects/b1042/BackmanLab/Lucas/022025_RIPseq/ --binsize 200 --gtf /projects/b1042/BackmanLab/Lucas/022025_RIPseq/genome/gtf/ensembl_gtf/Homo_sapiens.GRCh38.113.gtf
/home/lmc0633/.local/lib/python3.6/site-packages/pandas/compat/_optional.py:106: UserWarning: Pandas requires version '1.2.1' or newer of 'bottleneck' (version '1.2.0' currently installed).
warnings.warn(msg, UserWarning)
2025-02-25 23:07:17,567 - CLAM.Peakcaller - INFO -
start
2025-02-25 23:07:17,567 - CLAM.Peakcaller - INFO -
run info: /home/lmc0633/.local/bin/CLAM peakcaller -i P1KO_P1AB_R1_S13_L005_filt.sort.bam -c P1KO_Input_S23_L005_filt.sort.bam -o /projects/b1042/BackmanLab/Lucas/022025_RIPseq/ --binsize 200 --gtf /projects/b1042/BackmanLab/Lucas/022025_RIPseq/genome/gtf/ensembl_gtf/Homo_sapiens.GRCh38.113.gtf
2025-02-25 23:07:17,567 - CLAM.Peakcaller - INFO -
Params:
ip_bam_list = ['P1KO_P1AB_R1_S13_L005_filt.sort.bam']
gtf_fp = /projects/b1042/BackmanLab/Lucas/022025_RIPseq/genome/gtf/ensembl_gtf/Homo_sapiens.GRCh38.113.gtf
con_bam_list = ['P1KO_Input_S23_L005_filt.sort.bam']
nthread = 8
out_dir = /projects/b1042/BackmanLab/Lucas/022025_RIPseq/
binsize = 200
norm_lib = False
unique_only = False
unstranded = False
qval_cutoff = 0.05
fold_change = [2.0]
min_clip_cov = 4
pooling = False

2025-02-25 23:07:17,567 - CLAM.Peakcaller - INFO -
with only 1 bam file provided, i can only run --unique-only
2025-02-25 23:07:17,571 - CLAM.Peakcaller - INFO -
read GTF from "/projects/b1042/BackmanLab/Lucas/022025_RIPseq/genome/gtf/ensembl_gtf/Homo_sapiens.GRCh38.113.gtf"
Traceback (most recent call last):
File "/home/lmc0633/.local/bin/CLAM", line 326, in
main()
File "/home/lmc0633/.local/bin/CLAM", line 66, in main
peakcaller.parser( args )
File "/home/lmc0633/.local/lib/python3.6/site-packages/CLAM/peakcaller.py", line 648, in parser
pooling=pooling)
File "/home/lmc0633/.local/lib/python3.6/site-packages/CLAM/peakcaller.py", line 564, in peakcaller
gene_annot = read_gtf(gtf_fp)
File "/home/lmc0633/.local/lib/python3.6/site-packages/CLAM/peakcaller.py", line 72, in read_gtf
gene_id = re.findall(r"(\w+)", ele[-1])[1]
IndexError: list index out of range`

Any help would be appreciated!