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bioinfo-biols / CIRIquant

circular RNA quantification tools
https://sourceforge.net/projects/ciri/files/CIRIquant
MIT License
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KeyError #58

Closed stefanerb89 closed 9 months ago

stefanerb89 commented 9 months ago

Hello, i started my analysis in CiriQuant and got the following error: What did that mean? Is the library type correct? We used Illumina Truseq stranded library kit.

CIRIquant -t 10 -1 SID14749_R1_001.fastq.gz -2 SID14749_R2_001.fastq.gz --config /home//Documents/circRNA/config.yml -o /home/Documents/circRNA -p SID14749_R1_001.fastq.gz --library-type 2
[Tue 2023-09-26 10:56:58] [INFO ] Input reads: SID14749_R1_001.fastq.gz,SID14749_R2_001.fastq.gz
[Tue 2023-09-26 10:56:58] [INFO ] Library type: TAKARA SMARTer
[Tue 2023-09-26 10:56:58] [INFO ] Output directory: /home//Documents/circRNA, Output prefix: SID14749_R1_001.fastq.gz
[Tue 2023-09-26 10:56:58] [INFO ] Config: hg38 Loaded
[Tue 2023-09-26 10:56:58] [INFO ] 32 CPU cores availble, using 10
[Tue 2023-09-26 10:56:58] [INFO ] Align RNA-seq reads to reference genome ..
[Tue 2023-09-26 11:02:39] [INFO ] Estimate gene abundance ..
[Tue 2023-09-26 11:03:14] [INFO ] No circRNA information provided, run CIRI2 for junction site prediction ..
[Tue 2023-09-26 11:03:14] [INFO ] Running BWA-mem mapping candidate reads ..
[Tue 2023-09-26 11:21:05] [INFO ] Running CIRI2 for circRNA detection ..
[Tue 2023-09-26 11:22:07] [INFO ] Extract circular sequence
[Tue 2023-09-26 11:22:07] [100% ] [##################################################]
[Tue 2023-09-26 11:22:07] [INFO ] Building circular index ..
[Tue 2023-09-26 11:22:07] [INFO ] De novo alignment for circular RNAs ..
[Tue 2023-09-26 11:28:05] [INFO ] Detecting reads containing Back-splicing signals
Traceback (most recent call last):
  File "/home/anaconda3/envs/CIRI/bin/CIRIquant", line 8, in <module>
    sys.exit(main())
  File "/home/anaconda3/envs/CIRI/lib/python2.7/site-packages/CIRIquant/main.py", line 192, in main
    args.no_fsj, args.bsj_read_file)
  File "/home/anaconda3/envs/CIRI/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/anaconda3/envs/CIRI/lib/python2.7/site-packages/CIRIquant/circ.py", line 320, in proc_denovo_bam
    tmp_cand = job.get()
  File "/home/anaconda3/envs/CIRI/lib/python2.7/multiprocessing/pool.py", line 572, in get
    raise self._value
KeyError: '1:193150304|193152585'