refine assembly fails

[antoine4ucsd]

Hello I am trying to apply the de novo assemble pipeline on HIV WGS data but always fails at the refine assembly step

hp_refine_assembly --ncpu 1 --fq1 mysample_outdir/corrected_1.fastq --fq2 mysample_outdir/corrected_2.fastq --ref_fa mysample_outdir/amplicon_assembly.fna --sample_id mysample --max_step 5 --quiet --logfile mysample_outdir/haphpipe.out --outdir mysample_outdir

Traceback (most recent call last):
  File "mypath/opt/miniconda3/envs/haphpipe/bin/hp_refine_assembly", line 10, in <module>
    sys.exit(console())
  File "mypath/opt/miniconda3/envs/haphpipe/lib/python3.10/site-packages/haphpipe/stages/refine_assembly.py", line 310, in console
    args.func(**sysutils.args_params(args))
  File "mypath/opt/miniconda3/envs/haphpipe/lib/python3.10/site-packages/haphpipe/stages/refine_assembly.py", line 106, in refine_assembly
    return progressive_refine_assembly(**kwargs)
  File "mypath/opt/miniconda3/envs/haphpipe/lib/python3.10/site-packages/haphpipe/stages/refine_assembly.py", line 194, in progressive_refine_assembly
    tmp_refined, tmp_bt2 = refine_assembly_step(
  File "mypath/opt/miniconda3/envs/haphpipe/lib/python3.10/site-packages/haphpipe/stages/refine_assembly.py", line 128, in refine_assembly_step
    tmp_aligned, tmp_bt2 = align_reads.align_reads(
  File "mypath/opt/miniconda3/envs/haphpipe/lib/python3.10/site-packages/haphpipe/stages/align_reads.py", line 257, in align_reads
    sysutils.command_runner(
  File "mypath/opt/miniconda3/envs/haphpipe/lib/python3.10/site-packages/haphpipe/utils/sysutils.py", line 160, in command_runner
    raise PipelineStepError(
haphpipe.utils.sysutils.PipelineStepError: 
[--- FAILED: align_reads:realign ---]
Command:
_JAVA_OPTIONS="-Xmx32g" gatk -T RealignerTargetCreator -I /var/folders/r3/y359df552hg8krxm_3lr1f1r0000gr/T/tmpHP_align_readscfzw_7qu/rmdup.bam -R /var/folders/r3/y359df552hg8krxm_3lr1f1r0000gr/T/tmpHP_align_readscfzw_7qu/initial.fasta -o /var/folders/r3/y359df552hg8krxm_3lr1f1r0000gr/T/tmpHP_align_readscfzw_7qu/tmp.intervals && _JAVA_OPTIONS="-Xmx32g" gatk -T IndelRealigner --use_jdk_deflater --use_jdk_inflater -maxReads 1000000 -dt NONE -I /var/folders/r3/y359df552hg8krxm_3lr1f1r0000gr/T/tmpHP_align_readscfzw_7qu/rmdup.bam -R /var/folders/r3/y359df552hg8krxm_3lr1f1r0000gr/T/tmpHP_align_readscfzw_7qu/initial.fasta -targetIntervals /var/folders/r3/y359df552hg8krxm_3lr1f1r0000gr/T/tmpHP_align_readscfzw_7qu/tmp.intervals -o /var/folders/r3/y359df552hg8krxm_3lr1f1r0000gr/T/tmpHP_align_readscfzw_7qu/realign.bam
returncode: 1
[---haphpipe_assemble_01---] (Tue Oct  4 09:53:33 PDT 2022) FAILED: refine_assembly

[---haphpipe_assemble_01---] (Tue Oct  4 09:53:33 PDT 2022) Stage: finalize_assembly
[---haphpipe_assemble_01---] (Tue Oct  4 09:53:33 PDT 2022) finalize_assembly command:

any suggestions on how to fix it? I am also attaching the log for this sample

thank you! haphpipe.out.txt