CIRIquant: ValueError: file has no sequences defined (mode='rb') - is it SAM/BAM format? Consider opening with check_sq=False

Question

[Atul K.]

While running the ciriquant, i came across this error, i tried twice, but the same error. How to figure out this... any suggestions?

(/home/akk/software_library/CIRIquant_env)
akk@kashyap:~/circ_analysis/new_analysis$ CIRIquant --config /home/akk/circ_analysis/new_analysis/config.yaml -1 /home/akk/circ_analysis/new_analysis/SRR14150856_1.fastq -2 /home/akk/circ_analysis/new_analysis/SRR14150856_2.fastq
[Fri 2024-04-19 16:40:07] [INFO ] Input reads: SRR14150856_1.fastq,SRR14150856_2.fastq
[Fri 2024-04-19 16:40:07] [INFO ] Library type: unstranded
[Fri 2024-04-19 16:40:07] [INFO ] Output directory: /home/akk/circ_analysis/new_analysis/SRR14150856, Output prefix: SRR14150856
[Fri 2024-04-19 16:40:07] [INFO ] Config: /home/akk/circ_analysis/new_analysis/config.yaml Loaded
[Fri 2024-04-19 16:40:07] [INFO ] 4 CPU cores availble, using 4
[Fri 2024-04-19 16:40:07] [INFO ] Align RNA-seq reads to reference genome ..
[Fri 2024-04-19 16:49:53] [INFO ] Estimate gene abundance ..
[Fri 2024-04-19 16:51:06] [INFO ] No circRNA information provided, run CIRI2 for junction site prediction ..
[Fri 2024-04-19 16:51:06] [INFO ] Running BWA-mem mapping candidate reads ..
[Fri 2024-04-19 17:23:23] [INFO ] Running CIRI2 for circRNA detection ..
[Sat 2024-04-20 06:28:11] [INFO ] Extract circular sequence
[Sat 2024-04-20 06:28:11] [100% ] [##################################################]
[Sat 2024-04-20 06:28:11] [INFO ] Building circular index ..
[Sat 2024-04-20 06:28:12] [INFO ] De novo alignment for circular RNAs ..
[Sat 2024-04-20 06:28:19] [INFO ] Detecting reads containing Back-splicing signals
Traceback (most recent call last):
  File "/home/akk/software_library/CIRIquant_env/bin/CIRIquant", line 8, in <module>
    sys.exit(main())
  File "/home/akk/software_library/CIRIquant_env/lib/python2.7/site-packages/CIRIquant/main.py", line 198, in main
    args.no_fsj, args.bsj_read_file)
  File "/home/akk/software_library/CIRIquant_env/lib/python2.7/site-packages/CIRIquant/circ.py", line 658, in proc
    cand_bsj = proc_denovo_bam(denovo_bam, thread, circ_info, anchor, lib_type)
  File "/home/akk/software_library/CIRIquant_env/lib/python2.7/site-packages/CIRIquant/circ.py", line 306, in proc_denovo_bam
    sam = pysam.AlignmentFile(bam_file, 'rb')
  File "pysam/libcalignmentfile.pyx", line 736, in pysam.libcalignmentfile.AlignmentFile.__cinit__
  File "pysam/libcalignmentfile.pyx", line 985, in pysam.libcalignmentfile.AlignmentFile._open
ValueError: file has no sequences defined (mode='rb') - is it SAM/BAM format? Consider opening with check_sq=False