BSJ_DETECTION:CIRIQUANT:MAIN - No such file or directory .sorted.bam.bai

### Description of the bug Hi all, I was running the pipeline already back in March and CIRIquant never made an issue. But since a few weeks, I am getting the error below. I cloned the newest repo and ran the test,full which replicated the error. Interestingly, while running the same test,full on an old cloned repo from March, suddenly CIRIquant succeeded. Was there something changed within ciriquant_main? Thanks! ### Command used and terminal output ```console nextflow run \ ${LOCAL_PATH} \ -profile company,cluster,test,full \ -resume Command exit status: 1 Command output: (empty) Command error: [Tue 2025-07-29 18:34:32] [INFO ] Input reads: fust1_3_1_val_1.fq.gz,fust1_3_2_val_2.fq.gz [Tue 2025-07-29 18:34:32] [INFO ] Library type: unstranded [Tue 2025-07-29 18:34:32] [INFO ] Output directory: fust1_3, Output prefix: fust1_3 [Tue 2025-07-29 18:34:32] [INFO ] Config: ciriquant Loaded [Tue 2025-07-29 18:34:32] [INFO ] 40 CPU cores availble, using 4 [Tue 2025-07-29 18:34:32] [INFO ] Align RNA-seq reads to reference genome .. Traceback (most recent call last): File "/opt/conda/bin/CIRIquant", line 8, in <module> sys.exit(main()) ^^^^^^ File "/opt/conda/lib/python3.12/site-packages/CIRIquant/main.py", line 165, in main hisat_bam = pipeline.align_genome(log_file, thread, reads, outdir, prefix) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/opt/conda/lib/python3.12/site-packages/CIRIquant/pipeline.py", line 40, in align_genome if os.path.getsize(sorted_bam + '.bai') <= 16: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "<frozen genericpath>", line 62, in getsize FileNotFoundError: [Errno 2] No such file or directory: 'fust1_3/align/fust1_3.sorted.bam.bai' ``` ### Relevant files _No response_ ### System information _No response_