CIRIquant: ValueError: file has no sequences defined (mode='rb') - is it SAM/BAM format? Consider opening with check_sq=False
0
0
Entering edit mode
29 days ago
Atul K. • 0

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
Ciriquant • 161 views
ADD COMMENT

Login before adding your answer.

Traffic: 2084 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6