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!