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pysam-developers / pysam

Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtools, bcftools, and tabix.
https://pysam.readthedocs.io/en/latest/
MIT License
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CIRIquant: Error #1285

Open atul2422 opened 3 months ago

atul2422 commented 3 months ago

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 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