Closed choijamtsmunkhzul closed 1 year ago
Hello there, I had issue with CIRIquant function.
CIRIquant -t 16 -1 control_1_1.fastq -2 control_1_2.fastq --config CIRI_quant.yaml -o ./test -p test
[Sun 2023-02-12 22:06:55] [INFO ] Input reads: control_1_1.fastq,control_1_2.fastq [Sun 2023-02-12 22:06:55] [INFO ] Library type: unstranded [Sun 2023-02-12 22:06:55] [INFO ] Output directory: /home/choi/test, Output prefix: test [Sun 2023-02-12 22:06:55] [INFO ] Config: mm10 Loaded [Sun 2023-02-12 22:06:55] [INFO ] 16 CPU cores availble, using 16 [Sun 2023-02-12 22:06:55] [INFO ] Align RNA-seq reads to reference genome .. [Sun 2023-02-12 22:33:55] [INFO ] Estimate gene abundance .. [Sun 2023-02-12 22:36:05] [INFO ] No circRNA information provided, run CIRI2 for junction site prediction .. [Sun 2023-02-12 22:36:05] [INFO ] Running BWA-mem mapping candidate reads .. [Sun 2023-02-12 22:51:15] [INFO ] Running CIRI2 for circRNA detection .. [Sun 2023-02-12 23:00:34] [INFO ] Extract circular sequence [Sun 2023-02-12 23:00:34] [100% ] [##################################################] [Sun 2023-02-12 23:00:34] [INFO ] Building circular index .. [Sun 2023-02-12 23:00:36] [INFO ] De novo alignment for circular RNAs .. [Sun 2023-02-12 23:00:41] [INFO ] Detecting reads containing Back-splicing signals Traceback (most recent call last): File "/root/miniconda3/envs/CIRI/bin/CIRIquant", line 10, in <module> sys.exit(main()) File "/root/miniconda3/envs/CIRI/lib/python2.7/site-packages/CIRIquant/main.py", line 183, in main out_file = circ.proc(log_file, thread, bed_file, hisat_bam, rnaser_file, reads, outdir, prefix, anchor, lib_type) File "/root/miniconda3/envs/CIRI/lib/python2.7/site-packages/CIRIquant/circ.py", line 655, in proc cand_bsj = proc_denovo_bam(denovo_bam, thread, circ_info, anchor, lib_type) File "/root/miniconda3/envs/CIRI/lib/python2.7/site-packages/CIRIquant/circ.py", line 306, in proc_denovo_bam sam = pysam.AlignmentFile(bam_file, 'rb') File "pysam/calignmentfile.pyx", line 318, in pysam.calignmentfile.AlignmentFile.__cinit__ (pysam/calignmentfile.c:4730) File "pysam/calignmentfile.pyx", line 574, in pysam.calignmentfile.AlignmentFile._open (pysam/calignmentfile.c:7746) ValueError: file header is empty (mode='rb') - is it SAM/BAM format?
How can I fix above issue?
Thank you.
Hello there, I had issue with CIRIquant function.
CIRIquant -t 16 -1 control_1_1.fastq -2 control_1_2.fastq --config CIRI_quant.yaml -o ./test -p test
[Sun 2023-02-12 22:06:55] [INFO ] Input reads: control_1_1.fastq,control_1_2.fastq [Sun 2023-02-12 22:06:55] [INFO ] Library type: unstranded [Sun 2023-02-12 22:06:55] [INFO ] Output directory: /home/choi/test, Output prefix: test [Sun 2023-02-12 22:06:55] [INFO ] Config: mm10 Loaded [Sun 2023-02-12 22:06:55] [INFO ] 16 CPU cores availble, using 16 [Sun 2023-02-12 22:06:55] [INFO ] Align RNA-seq reads to reference genome .. [Sun 2023-02-12 22:33:55] [INFO ] Estimate gene abundance .. [Sun 2023-02-12 22:36:05] [INFO ] No circRNA information provided, run CIRI2 for junction site prediction .. [Sun 2023-02-12 22:36:05] [INFO ] Running BWA-mem mapping candidate reads .. [Sun 2023-02-12 22:51:15] [INFO ] Running CIRI2 for circRNA detection .. [Sun 2023-02-12 23:00:34] [INFO ] Extract circular sequence [Sun 2023-02-12 23:00:34] [100% ] [##################################################] [Sun 2023-02-12 23:00:34] [INFO ] Building circular index .. [Sun 2023-02-12 23:00:36] [INFO ] De novo alignment for circular RNAs .. [Sun 2023-02-12 23:00:41] [INFO ] Detecting reads containing Back-splicing signals Traceback (most recent call last): File "/root/miniconda3/envs/CIRI/bin/CIRIquant", line 10, in <module> sys.exit(main()) File "/root/miniconda3/envs/CIRI/lib/python2.7/site-packages/CIRIquant/main.py", line 183, in main out_file = circ.proc(log_file, thread, bed_file, hisat_bam, rnaser_file, reads, outdir, prefix, anchor, lib_type) File "/root/miniconda3/envs/CIRI/lib/python2.7/site-packages/CIRIquant/circ.py", line 655, in proc cand_bsj = proc_denovo_bam(denovo_bam, thread, circ_info, anchor, lib_type) File "/root/miniconda3/envs/CIRI/lib/python2.7/site-packages/CIRIquant/circ.py", line 306, in proc_denovo_bam sam = pysam.AlignmentFile(bam_file, 'rb') File "pysam/calignmentfile.pyx", line 318, in pysam.calignmentfile.AlignmentFile.__cinit__ (pysam/calignmentfile.c:4730) File "pysam/calignmentfile.pyx", line 574, in pysam.calignmentfile.AlignmentFile._open (pysam/calignmentfile.c:7746) ValueError: file header is empty (mode='rb') - is it SAM/BAM format?How can I fix above issue?
Thank you.