IndexError encountered while running the sample data

[luckyvivi]

Hi there,
Thank you so much for providing this useful software.
However, while running the sample data, I encountered an issue that made the interrupt.
Blow is the log:
INFO:root:[Sun Sep 8 23:40:46 2024] rG4-seeker: Pre-computing putative quadruplex sequences from reference genome and gene annotations
INFO:root:[Sun Sep 8 23:40:46 2024] Begin building whitelist for annotation ./gencode.v29.chr20.annotation.gff3.gz
INFO:root:[Sun Sep 8 23:40:53 2024] Completed building whitelist for annotation ./gencode.v29.chr20.annotation.gff3.gz
INFO:root:[Sun Sep 8 23:40:53 2024] Begin rG4 finding for annotation ./gencode.v29.chr20.annotation.gff3.gz
INFO:root:[Sun Sep 8 23:41:31 2024] Completed rG4 finding for annotation ./gencode.v29.chr20.annotation.gff3.gz
INFO:root:[Sun Sep 8 23:41:31 2024] Begin building whitelist for annotation ./GRCh38.chr20.refseq_annotation.gff.gz
INFO:root:[Sun Sep 8 23:41:39 2024] Completed building whitelist for annotation ./GRCh38.chr20.refseq_annotation.gff.gz
INFO:root:[Sun Sep 8 23:41:39 2024] Begin rG4 finding for annotation ./GRCh38.chr20.refseq_annotation.gff.gz
INFO:root:[Sun Sep 8 23:42:41 2024] Completed rG4 finding for annotation ./GRCh38.chr20.refseq_annotation.gff.gz
INFO:root:[Sun Sep 8 23:42:41 2024] rG4-seeker: Pre-processing input aligned reads
INFO:root:[Sun Sep 8 23:42:41 2024] Begin preprocessing BAM file ./HeLa-2016-Li-rep1.chr20.bam
INFO:root:[Sun Sep 8 23:43:18 2024] Completed preprocessing BAM file ./HeLa-2016-Li-rep1.chr20.bam
INFO:root:[Sun Sep 8 23:43:18 2024] Begin preprocessing BAM file ./HeLa-2016-K-rep1.chr20.bam
INFO:root:[Sun Sep 8 23:43:42 2024] Completed preprocessing BAM file ./HeLa-2016-K-rep1.chr20.bam
INFO:root:[Sun Sep 8 23:43:42 2024] Begin preprocessing BAM file ./HeLa-2016-KPDS-rep1.chr20.bam
INFO:root:[Sun Sep 8 23:44:03 2024] Completed preprocessing BAM file ./HeLa-2016-KPDS-rep1.chr20.bam
INFO:root:[Sun Sep 8 23:44:03 2024] Begin preprocessing BAM file ./HeLa-2016-Li-rep2.chr20.bam
INFO:root:[Sun Sep 8 23:44:29 2024] Completed preprocessing BAM file ./HeLa-2016-Li-rep2.chr20.bam
INFO:root:[Sun Sep 8 23:44:29 2024] Begin preprocessing BAM file ./HeLa-2016-K-rep2.chr20.bam
INFO:root:[Sun Sep 8 23:44:51 2024] Completed preprocessing BAM file ./HeLa-2016-K-rep2.chr20.bam
INFO:root:[Sun Sep 8 23:44:51 2024] Begin preprocessing BAM file ./HeLa-2016-KPDS-rep2.chr20.bam
INFO:root:[Sun Sep 8 23:45:14 2024] Completed preprocessing BAM file ./HeLa-2016-KPDS-rep2.chr20.bam
INFO:root:[Sun Sep 8 23:45:14 2024] Begin preprocessing BAM file ./HeLa-2016-Li-rep3.chr20.bam
INFO:root:[Sun Sep 8 23:45:38 2024] Completed preprocessing BAM file ./HeLa-2016-Li-rep3.chr20.bam
INFO:root:[Sun Sep 8 23:45:38 2024] Begin preprocessing BAM file ./HeLa-2016-K-rep3.chr20.bam
INFO:root:[Sun Sep 8 23:45:58 2024] Completed preprocessing BAM file ./HeLa-2016-K-rep3.chr20.bam
INFO:root:[Sun Sep 8 23:45:58 2024] Begin preprocessing BAM file ./HeLa-2016-KPDS-rep3.chr20.bam
INFO:root:[Sun Sep 8 23:46:21 2024] Completed preprocessing BAM file ./HeLa-2016-KPDS-rep3.chr20.bam
INFO:root:[Sun Sep 8 23:46:21 2024] Begin preprocessing BAM file ./HeLa-2016-Li-rep4.chr20.bam
INFO:root:[Sun Sep 8 23:47:00 2024] Completed preprocessing BAM file ./HeLa-2016-Li-rep4.chr20.bam
INFO:root:[Sun Sep 8 23:47:00 2024] Begin preprocessing BAM file ./HeLa-2016-K-rep4.chr20.bam
INFO:root:[Sun Sep 8 23:47:28 2024] Completed preprocessing BAM file ./HeLa-2016-K-rep4.chr20.bam
INFO:root:[Sun Sep 8 23:47:28 2024] Begin preprocessing BAM file ./HeLa-2016-KPDS-rep4.chr20.bam
INFO:root:[Sun Sep 8 23:47:51 2024] Completed preprocessing BAM file ./HeLa-2016-KPDS-rep4.chr20.bam
INFO:root:[Sun Sep 8 23:47:51 2024] rG4-seeker: Piling read coverage and 5' start site information
INFO:root:[Sun Sep 8 23:47:51 2024] Piling read coverage and 5' start site information for sample Li-rep1 in 8 CPU threads
INFO:root:[Sun Sep 8 23:48:25 2024] Piling read coverage and 5' start site information for sample K-rep1 in 8 CPU threads
INFO:root:[Sun Sep 8 23:48:47 2024] Piling read coverage and 5' start site information for sample KPDS-rep1 in 8 CPU threads
INFO:root:[Sun Sep 8 23:49:09 2024] Piling read coverage and 5' start site information for sample Li-rep2 in 8 CPU threads
INFO:root:[Sun Sep 8 23:49:34 2024] Piling read coverage and 5' start site information for sample K-rep2 in 8 CPU threads
INFO:root:[Sun Sep 8 23:49:54 2024] Piling read coverage and 5' start site information for sample KPDS-rep2 in 8 CPU threads
INFO:root:[Sun Sep 8 23:50:17 2024] Piling read coverage and 5' start site information for sample Li-rep3 in 8 CPU threads
INFO:root:[Sun Sep 8 23:50:40 2024] Piling read coverage and 5' start site information for sample K-rep3 in 8 CPU threads
INFO:root:[Sun Sep 8 23:50:58 2024] Piling read coverage and 5' start site information for sample KPDS-rep3 in 8 CPU threads
INFO:root:[Sun Sep 8 23:51:19 2024] Piling read coverage and 5' start site information for sample Li-rep4 in 8 CPU threads
INFO:root:[Sun Sep 8 23:51:57 2024] Piling read coverage and 5' start site information for sample K-rep4 in 8 CPU threads
INFO:root:[Sun Sep 8 23:52:24 2024] Piling read coverage and 5' start site information for sample KPDS-rep4 in 8 CPU threads
INFO:root:[Sun Sep 8 23:53:08 2024] rG4-seeker: Computing RSR peaks
INFO:root:[Sun Sep 8 23:53:08 2024] Computing RSR peaks for sample K-rep1
INFO:root:[Sun Sep 8 23:56:33 2024] Computing RSR peaks for sample KPDS-rep1
INFO:root:[Sun Sep 8 23:59:56 2024] Computing RSR peaks for sample K-rep2
INFO:root:[Mon Sep 9 00:02:42 2024] Computing RSR peaks for sample KPDS-rep2
INFO:root:[Mon Sep 9 00:05:31 2024] Computing RSR peaks for sample K-rep3
INFO:root:[Mon Sep 9 00:08:24 2024] Computing RSR peaks for sample KPDS-rep3
INFO:root:[Mon Sep 9 00:11:27 2024] Computing RSR peaks for sample K-rep4
INFO:root:[Mon Sep 9 00:15:14 2024] Computing RSR peaks for sample KPDS-rep4
INFO:root:[Mon Sep 9 00:18:56 2024] rG4-seeker: Determining per-replicate detection cutoffs
INFO:root:[Mon Sep 9 00:18:56 2024] Target cutoff at FDR=0.015
INFO:root:[Mon Sep 9 00:19:05 2024] rG4-seeker: Analyzing RTS sites
INFO:root:[Mon Sep 9 00:19:05 2024] Loading whitelists...
INFO:root:[Mon Sep 9 00:19:08 2024] Loading annotations...
INFO:root:[Mon Sep 9 00:19:12 2024] Loading RTS site data...
INFO:root:[Mon Sep 9 00:19:21 2024] Analyzing RTS combining all replicates...
Traceback (most recent call last):
File "/data/wxw/.local/bin/rG4-seeker", line 8, in <module>
sys.exit(main())
File "/data/wxw/.local/lib/python3.10/site-packages/rg4seeker/__main__.py", line 223, in main
main_driver(sys.argv[1])
File "/data/wxw/.local/lib/python3.10/site-packages/rg4seeker/__main__.py", line 215, in main_driver
apriori_rts_analysis.main(prefix, analysis_conditions, replicate_number, bootstrap_id, genome_fasta,
File "/data/wxw/.local/lib/python3.10/site-packages/rg4seeker/apriori_rts_analysis.py", line 929, in main
full_result = rts_analyze(full_valid_rts_sites, rg4_motif_information, rg4_threeprime_array, faidx_genome,
File "/data/wxw/.local/lib/python3.10/site-packages/rg4seeker/apriori_rts_analysis.py", line 808, in rts_analyze
coverage = _single_cond_rts_arrays[condition][replicate][
File "src/HTSeq/_HTSeq.pyx", line 696, in HTSeq._HTSeq.GenomicArray.__getitem__
File "src/HTSeq/_HTSeq.pyx", line 463, in HTSeq._HTSeq.ChromVector.__getitem__
IndexError

and my HTSeq version is 1.99.2
pip show HTSeq
Name: HTSeq
Version: 1.99.2
Summary: A framework to process and analyze data from high-throughput sequencing (HTS) assays
Home-page: https://github.com/htseq
Author: Simon Anders, Fabio Zanini
Author-email: [email protected]
License: GPL3
Location: /usr/local/lib/python3.10/dist-packages
Requires:
Required-by: #N/A