Cannot even pass the example test

[YuanfengZhang]

LiBis installed in a new and clean conda env.

❯ LiBis -n sample1_mate1.fq.gz,sample1_mate2.fq.gz sample2_mate1.fq.gz,sample2_mate2.fq.gz -r /opt/ref/custom_genome/BL.fa
[ 2025-04-01 17:03:54.902335 ]  Running Alignment for samples...
[ 2025-04-01 17:03:54.916018 ]  Temprary files cleaning...
[ 2025-04-01 17:03:54.916052 ]  Begin the alignment process with clipping.
[ 2025-04-01 17:03:54.916075 ]  Begin the 1st round full reads mapping.
[ 2025-04-01 17:03:55.509017 ]  Filtering and clipping unmapped reads.
Temporary file doesn't exist: sample1_mate1.unmapped.fastq !
[E::hts_open_format] Failed to open file "sample1_mate1.bam" : No such file or directory
Traceback (most recent call last):
  File "/home/zhangyuanfeng/mambaforge/envs/libis/bin/LiBis", line 215, in <module>
    main()
  File "/home/zhangyuanfeng/mambaforge/envs/libis/bin/LiBis", line 212, in main
    computeProcess(input_args())
  File "/home/zhangyuanfeng/mambaforge/envs/libis/lib/python3.9/site-packages/LiBis/computeProcess.py", line 136, in computeProcess
    name,bsmapresult = computeBsmap(name,bsmap,param) 
  File "/home/zhangyuanfeng/mambaforge/envs/libis/lib/python3.9/site-packages/LiBis/computeProcess.py", line 76, in computeBsmap
    newname,logname = bsmap.clipping(n,param,given_bam,given_label)
  File "/home/zhangyuanfeng/mambaforge/envs/libis/lib/python3.9/site-packages/LiBis/moabs.py", line 134, in clipping
    newname,log = clipmode(filenames,param, given_bam_file,given_label)
  File "/home/zhangyuanfeng/mambaforge/envs/libis/lib/python3.9/site-packages/LiBis/clipmode.py", line 406, in clipmode
    newn,originallog,splitlog,cleanname=clip_process(name,param, given_bam_file,given_label)
  File "/home/zhangyuanfeng/mambaforge/envs/libis/lib/python3.9/site-packages/LiBis/clipmode.py", line 271, in clip_process
    bam_file = pysam.AlignmentFile(bam_file_name,'rb')
  File "pysam/libcalignmentfile.pyx", line 751, in pysam.libcalignmentfile.AlignmentFile.__cinit__
  File "pysam/libcalignmentfile.pyx", line 950, in pysam.libcalignmentfile.AlignmentFile._open
FileNotFoundError: [Errno 2] could not open alignment file `sample1_mate1.bam`: No such file or directory