AssemblePairs.py sequential fails when input file lists are added under the '-1' and '-2' arguments.

When ordered file lists are added as inputs to AssemblePairs.py sequential under the ‘-1’ and ‘-2’ arguments, only the first file pair assembles successfully. Failure happens after initializing the second file pair. The failure is a result of the V gene reference file, specified by the ‘-r’ argument, not being parsed for the file pairs after the first. I worked around the issue by calling the AssemblePairs.py sequential function multiple times for individual file pairs. The downsampled FASTQ files used in the below example are attached.

AssemblePairs.py sequential --version
AssemblePairs.py sequential: 0.6.2.999 2021.08.08

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AssemblePairs.py sequential \
  -1 AA.R2.pRESTO.fastq   CC.R2.pRESTO.fastq  DD.R2.pRESTO.fastq \
  -2 AA.R1.pRESTO.fastq   CC.R1.pRESTO.fastq  DD.R1.pRESTO.fastq \
  -o AA.pRESTO.fastq      CC.pRESTO.fastq     DD.pRESTO.fastq \
  --coord illumina \
  --rc tail \
  --1f UMI \
  -r V_refs.fasta \
  --aligner usearch

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START> AssemblePairs
     COMMAND> sequential
       FILE1> AA.R2.pRESTO.fastq
       FILE2> AA.R1.pRESTO.fastq
  COORD_TYPE> illumina
     REFFILE> V_refs.fasta
       ALPHA> 1e-05
   MAX_ERROR> 0.3
     MIN_LEN> 8
     MAX_LEN> 1000
SCAN_REVERSE> False
   MIN_IDENT> 0.5
      EVALUE> 1e-05
    MAX_HITS> 100
        FILL> False
     ALIGNER> usearch
       NPROC> 24

PROGRESS> 20:07:08 |####################| 100% (494) 0.0 min

OUTPUT> AA.pRESTO.fastq
 PAIRS> 494
  PASS> 310
  FAIL> 184
   END> AssemblePairs

       START> AssemblePairs
     COMMAND> sequential
       FILE1> CC.R2.pRESTO.fastq
       FILE2> CC.R1.pRESTO.fastq
  COORD_TYPE> illumina
       ALPHA> 1e-05
   MAX_ERROR> 0.3
     MIN_LEN> 8
     MAX_LEN> 1000
SCAN_REVERSE> False
   MIN_IDENT> 0.5
      EVALUE> 1e-05
    MAX_HITS> 100
        FILL> False
     ALIGNER> usearch
       NPROC> 24

Traceback (most recent call last):
  File "/home/ubuntu/.local/bin/AssemblePairs.py", line 469, in <module>
    assemblePairs(**args_dict)
  File "/home/ubuntu/.local/bin/AssemblePairs.py", line 200, in assemblePairs
    ref_file = assemble_args.pop('ref_file')
KeyError: 'ref_file'

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