IndexError: string index out of range

[robinycfang]

Hi

I was running ConsensusCeuncher to collapse UMIs. It seems to output some results:

├── sscs
│   ├── sscs.sorted.bam (.bai)                     
│   ├── singleton.sorted.bam (.bai)                
├── sscs_SC
|   ├── sscs.sc.sorted.bam (.bai)              
├── dcs
│   ├── dcs.sorted.bam (.bai)
├── dcs_SC
│   ├── dcs.sc.sorted.bam(.bai)
│   ├── all.unique.dcs.sorted.bam(.bai)
├── read_families.txt                       Family size and frequency
├── stats.txt                               Consensus sequence formation metrics
├── tag_fam_size.png                        Distribution of reads across family size

However, when I checked on the log, I found an error:

# === DCS ===
SSCS - Total reads: 26020276
SSCS - Unmapped reads: 0
SSCS - Secondary/Supplementary reads: 0
DCS reads: 89306
SSCS singletons: 25841664 

[bam_sort_core] merging from 6 files and 1 in-memory blocks...
Traceback (most recent call last):
  File "/ConsensusCruncher/singleton_correction.py", line 320, in <module>
    main()
  File "/ConsensusCruncher/singleton_correction.py", line 268, in main
    corrected_read = strand_correction(tag, duplex, query_name, singleton_dict)
  File "/ConsensusCruncher/singleton_correction.py", line 101, in strand_correction
    dcs = duplex_consensus(read, complement_read)
  File "/ConsensusCruncher/singleton_correction.py", line 71, in duplex_consensus
    if read1.query_sequence[i] == read2.query_sequence[i] and \
IndexError: string index out of range
[bam_sort_core] merging from 6 files and 1 in-memory blocks...
# === DCS - Singleton Correction ===
SSCS SC - Total reads: 26023245
SSCS SC - Unmapped reads: 0

It looks like DCS was not properly performed? For my experiments, I might just need to use sscs.sc.sorted.bam. Are these final bam files still safe to use? The following is my commands. Thanks!
python3 ConsensusCruncher.py fastq2bam --fastq1 sample_R1.fastq --fastq2 sample_R2.fastq -o out_dir -b bwa -g /picard/2.10.9/picard.jar -r hg38.fasta -s samtools -l umilist.txt

python3 ConsensusCruncher.py consensus -i sample.sorted.bam -o out_dir -s samtools -b cytoBand.txt -g hg38 --cleanup True --scorrect True