I used the parameter --bed with circAtlas bed file, the outputs are always "KeyError: '[circAtlas ID]'"

[DooYal]

Though I deleted the record as the bug report mentioned, it always interrupts with error report like the image, so how should I do can quantify the sequence with circAtlas ID.

[DooYal]

我的输入是====================================
CIRIquant -t 20
-1 $out_prefix.qc.1.fastq.gz
-2 $out_prefix.qc.2.fastq.gz
--bam $out_prefix.tp2.fusion/accepted_hits.bam
--config ${config_yml}
--bed ~/transcirc/human_circ_v3.0.bed
-o $out_prefix.ciriquant
-p $sample.ciriquant

config_yml===================================
tools:
bwa:~/miniconda3/envs/circ/bin/bwa
hisat2: ~/miniconda3/envs/circ/bin/hisat2
stringtie: ~/miniconda3/envs/circ/bin/stringtie
samtools: ~/program/samtools-1.19.2/bin/samtools
reference:
fasta: ~/humandb/G38.p14.fasta
gtf: ~/humandb/gencode.v44.annotation.gtf
bwa_index: ~/humandb/G38.p14.bwa
hisat_index: ~/humandb/G38.p14.hs2

[Kevinzjy]

Hi @DooYal , the input file should be converted to standard bed format, for example:

chrom    start    end    circRNA_ID    .    strand

[DooYal]

Hi @DooYal , the input file should be converted to standard bed format, for example:

chrom    start    end    circRNA_ID    .    strand

是这种格式的，也是制表符分割，但是总会在一个点报错，去查了一下报错的地方和其它行文本没有区别