Hi there! Thanks for all your work on this pipeline. New user here with a question about the quantification workflow. I am getting the following error during

QUANTIFICATION:CIRIQUANT:MAIN

$ nextflow run $nfhome -profile test,singularity --tools ciriquant
$ cat work/00/e87601a183fb216db669f3d8e3acc9/.command.log
INFO:  Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred
INFO:  Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
INFO:  underlay of /etc/localtime required more than 50 (73) bind mounts
[Wed 2025-08-20 16:40:47] [INFO ] Input reads: fust1_1_1_val_1.fq.gz,fust1_1_2_val_2.fq.gz
[Wed 2025-08-20 16:40:47] [INFO ] Library type: unstranded
[Wed 2025-08-20 16:40:47] [INFO ] Output directory: /****/nf_circ_test/work/00/e87601a183fb216db669f3d8e3acc9/fust1_1, Output prefix: fust1_1
[Wed 2025-08-20 16:40:47] [INFO ] Config: ciriquant Loaded
[Wed 2025-08-20 16:40:47] [INFO ] 80 CPU cores availble, using 4
[Wed 2025-08-20 16:40:47] [INFO ] Align RNA-seq reads to reference genome ..
[Wed 2025-08-20 16:40:53] [INFO ] Estimate gene abundance ..
[Wed 2025-08-20 16:40:55] [INFO ] Using user-provided circRNA bed file: /****/nf_circ_test/work/00/e87601a183fb216db669f3d8e3acc9/all.annotated.bed12
[Wed 2025-08-20 16:40:55] [INFO ] Extract circular sequence
[Wed 2025-08-20 16:40:55] [100% ] [##################################################]
[Wed 2025-08-20 16:40:55] [INFO ] Building circular index ..
[Wed 2025-08-20 16:40:55] [INFO ] De novo alignment for circular RNAs ..
[Wed 2025-08-20 16:41:09] [INFO ] Detecting reads containing Back-splicing signals
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
 File "/opt/conda/lib/python3.12/multiprocessing/pool.py", line 125, in worker
  result = (True, func(*args, **kwds))
          ^^^^^^^^^^^^^^^^^^^
 File "/opt/conda/lib/python3.12/site-packages/CIRIquant/circ.py", line 364, in denovo_worker
  parser = CIRC[contig][circ_id]
       ~~~~~~~~~~~~^^^^^^^^^
KeyError: 'circ_chrI:1039055-1039884:+'
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
 File "/opt/conda/bin/CIRIquant", line 8, in <module>
  sys.exit(main())
       ^^^^^^
 File "/opt/conda/lib/python3.12/site-packages/CIRIquant/main.py", line 201, in main
  out_file = circ.proc(log_file, thread, bed_file, hisat_bam, rnaser_file, reads, outdir, prefix, anchor, lib_type,
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 File "/opt/conda/lib/python3.12/site-packages/CIRIquant/circ.py", line 659, in proc
  cand_bsj = proc_denovo_bam(denovo_bam, thread, circ_info, anchor, lib_type)
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 File "/opt/conda/lib/python3.12/site-packages/CIRIquant/circ.py", line 321, in proc_denovo_bam
  tmp_cand = job.get()
        ^^^^^^^^^
 File "/opt/conda/lib/python3.12/multiprocessing/pool.py", line 774, in get
  raise self._value
KeyError: 'circ_chrI:1039055-1039884:+'

1. Could somebody kindly confirm whether the following is the expected format of the circRNA ID (in the 4th column of the BED file called “`all.annotated.bed12`” —I think it is output by

NFCORE_CIRCRNA:CIRCRNA:BSJ_DETECTION:ANNOTATE_COMBINED:RENAME

)? Specifically the “circ_” prefix before “chrI”. I think the "chrI" in the first field being discrepant from the "circ_chrI" in the 4th field would cause problems in CIRIquant.

$ head work/67/9ea9165027dc485e9517f6eaa6016b/all.annotated.bed12

chrI  1039055 1039884 circ_chrI:1039055-1039884:+   0    +    1039055 1039055 0,0,0  3    120,80,544   0,162,285    0    circRNA Y34D9A.3    NM_001306323
  9,10,11 chrI:1037716-1039055|chrI:1039884-1040116
chrI  1056063 1060673 circ_chrI:1056063-1060673:-   0    -    1056063 1056063 0,0,0  4    145,219,164,221 0,1633,3319,4389    0    circRNA vps-4  NM_058415

1. Likewise, when running

NFCORE_CIRCRNA:CIRCRNA:QUANTIFICATION:CIRI_QUANT:MAIN

, is this the expected appearance of the circRNA ID’s appearing in the SN field of the header of “`*_denovo.sorted.bam`”?

Apptainer> samtools view -H test/circ/test_denovo.sorted.bam | head
@HD	VN:1.0	SO:coordinate
@SQ	SN:circ_chrI:1039055-1039884:+	    LN:1660
@SQ	SN:circ_chrI:1056063-1060673:-	    LN:9222
@SQ	SN:circ_chrI:1071472-1071936:+	    LN:930

Thank you!!

Hey, sorry for the issue, I just fixed this via this PR

That's awesome; will give it a try. Thank you!!