Unrecognized value for mode flag. Running with default parameters

[dupuquan]

I met a problem using 3D-DNA after using juicer to assemble my contigs.

:( Unrecognized value for mode flag. Running with default parameters (--mode haploid).
:| WARNING: GNU Parallel version 20150322 or later not installed. We highly recommend to install it to increase performance. Starting pipeline without parallelization!
/public/home/pqdu/software/3d-dna/run-asm-pipeline.sh: line 656: [: too many arguments
:( Please remove or rename files contigs_mature3..cprops contigs_mature3.mnd..txt. Exiting!

list below is my 3D-DNA folder:
33114779.err h.scaffolds.original.notation.step.65.txt
33114779.out h.scaffolds.original.notation.step.66.txt
3D-DNA.lsf h.scaffolds.original.notation.step.67.txt
archive.contigs_mature3.edits.at.step.1.txt h.scaffolds.original.notation.step.68.txt
contigs_mature3.0.asm h.scaffolds.original.notation.step.69.txt
contigs_mature3.0_asm.scaffold_track.txt h.scaffolds.original.notation.step.6.txt
contigs_mature3.0_asm.superscaf_track.txt h.scaffolds.original.notation.step.70.txt
contigs_mature3.0.assembly h.scaffolds.original.notation.step.71.txt
contigs_mature3.0.cprops h.scaffolds.original.notation.step.72.txt
contigs_mature3.0.hic h.scaffolds.original.notation.step.73.txt
contigs_mature3.1.asm h.scaffolds.original.notation.step.74.txt
contigs_mature3.1_asm.scaffold_track.txt h.scaffolds.original.notation.step.75.txt
contigs_mature3.1_asm.superscaf_track.txt h.scaffolds.original.notation.step.76.txt
contigs_mature3.1.assembly h.scaffolds.original.notation.step.77.txt
contigs_mature3.1.cprops h.scaffolds.original.notation.step.78.txt
contigs_mature3.1.hic h.scaffolds.original.notation.step.79.txt
contigs_mature3.2.asm h.scaffolds.original.notation.step.7.txt
contigs_mature3.2_asm.scaffold_track.txt h.scaffolds.original.notation.step.80.txt
contigs_mature3.2_asm.superscaf_track.txt h.scaffolds.original.notation.step.81.txt
contigs_mature3.2.assembly h.scaffolds.original.notation.step.82.txt
contigs_mature3.2.cprops h.scaffolds.original.notation.step.83.txt
contigs_mature3.2.hic h.scaffolds.original.notation.step.84.txt
contigs_mature3.cprops h.scaffolds.original.notation.step.85.txt
contigs_mature3.edits.txt h.scaffolds.original.notation.step.86.txt
contigs_mature3.mnd.0.txt h.scaffolds.original.notation.step.87.txt
contigs_mature3.mnd.txt h.scaffolds.original.notation.step.88.txt
contigs_mature3.polished.asm h.scaffolds.original.notation.step.89.txt
contigs_mature3.polished_asm.scaffold_track.txt h.scaffolds.original.notation.step.8.txt
contigs_mature3.polished_asm.superscaf_track.txt h.scaffolds.original.notation.step.90.txt
contigs_mature3.polished.cprops h.scaffolds.original.notation.step.91.txt
contigs_mature3.polished.depletion_score_narrow.wig h.scaffolds.original.notation.step.92.txt
contigs_mature3.polished.depletion_score_wide.wig h.scaffolds.original.notation.step.93.txt
contigs_mature3.polished.edits_2D.txt h.scaffolds.original.notation.step.94.txt
contigs_mature3.polished.hic h.scaffolds.original.notation.step.95.txt
contigs_mature3.polished.mismatches_2D.txt h.scaffolds.original.notation.step.96.txt
contigs_mature3.polished.mismatch_narrow.bed h.scaffolds.original.notation.step.97.txt
contigs_mature3.polished.mismatch_wide.bed h.scaffolds.original.notation.step.98.txt
contigs_mature3.polished.split.assembly h.scaffolds.original.notation.step.99.txt
contigs_mature3.polished.split.depletion_score_narrow.wig h.scaffolds.original.notation.step.9.txt
contigs_mature3.polished.split.depletion_score_wide.wig h.scaffolds.step.100.txt
contigs_mature3.polished.split.edits_2D.txt h.scaffolds.step.101.txt
contigs_mature3.polished.split.mismatches_2D.txt h.scaffolds.step.102.txt
contigs_mature3.polished.split.mismatch_narrow.bed h.scaffolds.step.103.txt
contigs_mature3.polished.split.mismatch_wide.bed h.scaffolds.step.104.txt
contigs_mature3.polished.split.suspicious_2D.txt h.scaffolds.step.105.txt
contigs_mature3.polished.suspect_2D.txt h.scaffolds.step.106.txt
contigs_mature3.rawchrom.asm h.scaffolds.step.107.txt
contigs_mature3.rawchrom_asm.scaffold_track.txt h.scaffolds.step.108.txt
contigs_mature3.rawchrom_asm.superscaf_track.txt h.scaffolds.step.109.txt
contigs_mature3.rawchrom.assembly h.scaffolds.step.10.txt
contigs_mature3.rawchrom.cprops h.scaffolds.step.110.txt
contigs_mature3.rawchrom.fasta h.scaffolds.step.111.txt
contigs_mature3.rawchrom.hic h.scaffolds.step.112.txt
contigs_mature3.resolved.asm h.scaffolds.step.113.txt
contigs_mature3.resolved_asm.scaffold_track.txt h.scaffolds.step.114.txt
contigs_mature3.resolved_asm.superscaf_track.txt h.scaffolds.step.115.txt
contigs_mature3.resolved.cprops h.scaffolds.step.116.txt
contigs_mature3.resolved.hic h.scaffolds.step.117.txt
contigs_mature3.resolved.polish.assembly h.scaffolds.step.118.txt
contigs_mature3.split.asm h.scaffolds.step.119.txt
contigs_mature3.split_asm.scaffold_track.txt h.scaffolds.step.11.txt
contigs_mature3.split_asm.superscaf_track.txt h.scaffolds.step.120.txt
contigs_mature3.split.assembly h.scaffolds.step.121.txt
contigs_mature3.split.cprops h.scaffolds.step.122.txt
contigs_mature3.split.hic h.scaffolds.step.123.txt
coverage_wide.at.step.0.wig h.scaffolds.step.124.txt
coverage_wide.at.step.1.wig h.scaffolds.step.125.txt
depletion_score_narrow.at.step.0.wig h.scaffolds.step.126.txt
depletion_score_narrow.at.step.1.wig h.scaffolds.step.127.txt
depletion_score_wide.at.step.0.wig h.scaffolds.step.128.txt
depletion_score_wide.at.step.1.wig h.scaffolds.step.129.txt
edits.for.step.1.txt h.scaffolds.step.12.txt
edits.for.step.2.txt h.scaffolds.step.130.txt
h.double.sorted.confidence.step.100.txt h.scaffolds.step.131.txt
h.double.sorted.confidence.step.101.txt h.scaffolds.step.132.txt
h.double.sorted.confidence.step.102.txt h.scaffolds.step.133.txt
h.double.sorted.confidence.step.103.txt h.scaffolds.step.134.txt
h.double.sorted.confidence.step.104.txt h.scaffolds.step.135.txt
h.double.sorted.confidence.step.105.txt h.scaffolds.step.136.txt
h.double.sorted.confidence.step.106.txt h.scaffolds.step.137.txt
h.double.sorted.confidence.step.107.txt h.scaffolds.step.138.txt
h.double.sorted.confidence.step.108.txt h.scaffolds.step.139.txt
h.double.sorted.confidence.step.109.txt h.scaffolds.step.13.txt
h.double.sorted.confidence.step.10.txt h.scaffolds.step.140.txt
h.double.sorted.confidence.step.110.txt h.scaffolds.step.141.txt
h.double.sorted.confidence.step.111.txt h.scaffolds.step.142.txt
h.double.sorted.confidence.step.112.txt h.scaffolds.step.143.txt
h.double.sorted.confidence.step.113.txt h.scaffolds.step.144.txt
h.double.sorted.confidence.step.114.txt h.scaffolds.step.145.txt
h.double.sorted.confidence.step.115.txt h.scaffolds.step.146.txt
h.double.sorted.confidence.step.116.txt h.scaffolds.step.147.txt
h.double.sorted.confidence.step.117.txt h.scaffolds.step.148.txt
h.double.sorted.confidence.step.118.txt h.scaffolds.step.149.txt
h.double.sorted.confidence.step.119.txt h.scaffolds.step.14.txt
h.double.sorted.confidence.step.11.txt h.scaffolds.step.150.txt
h.double.sorted.confidence.step.120.txt h.scaffolds.step.151.txt
h.double.sorted.confidence.step.121.txt h.scaffolds.step.152.txt
h.double.sorted.confidence.step.122.txt h.scaffolds.step.153.txt
h.double.sorted.confidence.step.123.txt h.scaffolds.step.154.txt
h.double.sorted.confidence.step.124.txt h.scaffolds.step.155.txt
h.double.sorted.confidence.step.125.txt h.scaffolds.step.156.txt
h.double.sorted.confidence.step.126.txt h.scaffolds.step.157.txt
h.double.sorted.confidence.step.127.txt h.scaffolds.step.158.txt
h.double.sorted.confidence.step.128.txt h.scaffolds.step.159.txt
h.double.sorted.confidence.step.129.txt h.scaffolds.step.15.txt
h.double.sorted.confidence.step.12.txt h.scaffolds.step.160.txt
h.double.sorted.confidence.step.130.txt h.scaffolds.step.161.txt
h.double.sorted.confidence.step.131.txt h.scaffolds.step.162.txt
h.double.sorted.confidence.step.132.txt h.scaffolds.step.163.txt
h.double.sorted.confidence.step.133.txt h.scaffolds.step.164.txt
h.double.sorted.confidence.step.134.txt h.scaffolds.step.165.txt
h.double.sorted.confidence.step.135.txt h.scaffolds.step.166.txt
h.double.sorted.confidence.step.136.txt h.scaffolds.step.167.txt
h.double.sorted.confidence.step.137.txt h.scaffolds.step.168.txt
h.double.sorted.confidence.step.138.txt h.scaffolds.step.169.txt
h.double.sorted.confidence.step.139.txt h.scaffolds.step.16.txt
h.double.sorted.confidence.step.13.txt h.scaffolds.step.170.txt
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h.double.sorted.confidence.step.149.txt h.scaffolds.step.17.txt
h.double.sorted.confidence.step.14.txt h.scaffolds.step.180.txt
h.double.sorted.confidence.step.150.txt h.scaffolds.step.181.txt
h.double.sorted.confidence.step.151.txt h.scaffolds.step.182.txt
h.double.sorted.confidence.step.152.txt h.scaffolds.step.183.txt
h.double.sorted.confidence.step.153.txt h.scaffolds.step.184.txt
h.double.sorted.confidence.step.154.txt h.scaffolds.step.18.txt
h.double.sorted.confidence.step.155.txt h.scaffolds.step.19.txt
h.double.sorted.confidence.step.156.txt h.scaffolds.step.1.txt
h.double.sorted.confidence.step.157.txt h.scaffolds.step.20.txt
h.double.sorted.confidence.step.158.txt h.scaffolds.step.21.txt
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h.double.sorted.confidence.step.15.txt h.scaffolds.step.23.txt
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h.double.sorted.confidence.step.161.txt h.scaffolds.step.25.txt
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h.double.sorted.confidence.step.164.txt h.scaffolds.step.28.txt
h.double.sorted.confidence.step.165.txt h.scaffolds.step.29.txt
h.double.sorted.confidence.step.166.txt h.scaffolds.step.2.txt
h.double.sorted.confidence.step.167.txt h.scaffolds.step.30.txt
h.double.sorted.confidence.step.168.txt h.scaffolds.step.31.txt
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h.double.sorted.confidence.step.16.txt h.scaffolds.step.33.txt
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h.double.sorted.confidence.step.19.txt h.scaffolds.step.4.txt
h.double.sorted.confidence.step.1.txt h.scaffolds.step.50.txt
h.double.sorted.confidence.step.20.txt h.scaffolds.step.51.txt
h.double.sorted.confidence.step.21.txt h.scaffolds.step.52.txt
h.double.sorted.confidence.step.22.txt h.scaffolds.step.53.txt
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h.double.sorted.confidence.step.24.txt h.scaffolds.step.55.txt
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h.double.sorted.confidence.step.27.txt h.scaffolds.step.58.txt
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h.double.sorted.confidence.step.2.txt h.scaffolds.step.60.txt
h.double.sorted.confidence.step.30.txt h.scaffolds.step.61.txt
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h.double.sorted.confidence.step.32.txt h.scaffolds.step.63.txt
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h.double.sorted.confidence.step.35.txt h.scaffolds.step.66.txt
h.double.sorted.confidence.step.36.txt h.scaffolds.step.67.txt
h.double.sorted.confidence.step.37.txt h.scaffolds.step.68.txt
h.double.sorted.confidence.step.38.txt h.scaffolds.step.69.txt
h.double.sorted.confidence.step.39.txt h.scaffolds.step.6.txt
h.double.sorted.confidence.step.3.txt h.scaffolds.step.70.txt
h.double.sorted.confidence.step.40.txt h.scaffolds.step.71.txt
h.double.sorted.confidence.step.41.txt h.scaffolds.step.72.txt
h.double.sorted.confidence.step.42.txt h.scaffolds.step.73.txt
h.double.sorted.confidence.step.43.txt h.scaffolds.step.74.txt
h.double.sorted.confidence.step.44.txt h.scaffolds.step.75.txt
h.double.sorted.confidence.step.45.txt h.scaffolds.step.76.txt
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h.double.sorted.confidence.step.49.txt h.scaffolds.step.7.txt
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h.double.sorted.confidence.step.50.txt h.scaffolds.step.81.txt
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h.double.sorted.confidence.step.67.txt h.scaffolds.step.98.txt
h.double.sorted.confidence.step.68.txt h.scaffolds.step.99.txt
h.double.sorted.confidence.step.69.txt h.scaffolds.step.9.txt
h.double.sorted.confidence.step.6.txt h.scores.step.100.txt
h.double.sorted.confidence.step.70.txt h.scores.step.101.txt
h.double.sorted.confidence.step.71.txt h.scores.step.102.txt
h.double.sorted.confidence.step.72.txt h.scores.step.103.txt
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h.double.sorted.confidence.step.74.txt h.scores.step.105.txt
h.double.sorted.confidence.step.75.txt h.scores.step.106.txt
h.double.sorted.confidence.step.76.txt h.scores.step.107.txt
h.double.sorted.confidence.step.77.txt h.scores.step.108.txt
h.double.sorted.confidence.step.78.txt h.scores.step.109.txt
h.double.sorted.confidence.step.79.txt h.scores.step.10.txt
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h.double.sorted.confidence.step.99.txt h.scores.step.12.txt
h.double.sorted.confidence.step.9.txt h.scores.step.130.txt
h.dropouts.step.0.txt h.scores.step.131.txt
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h.dropouts.step.125.txt h.scores.step.134.txt
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h.dropouts.step.145.txt h.scores.step.136.txt
h.dropouts.step.149.txt h.scores.step.137.txt
h.dropouts.step.155.txt h.scores.step.138.txt
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h.dropouts.step.159.txt h.scores.step.13.txt
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h.dropouts.step.181.txt h.scores.step.144.txt
h.dropouts.step.56.txt h.scores.step.145.txt
h.dropouts.step.79.txt h.scores.step.146.txt
h.edits.txt h.scores.step.147.txt
h.scaffolds.original.notation.step.0.txt h.scores.step.148.txt
h.scaffolds.original.notation.step.100.txt h.scores.step.149.txt
h.scaffolds.original.notation.step.101.txt h.scores.step.14.txt
h.scaffolds.original.notation.step.102.txt h.scores.step.150.txt
h.scaffolds.original.notation.step.103.txt h.scores.step.151.txt
h.scaffolds.original.notation.step.104.txt h.scores.step.152.txt
h.scaffolds.original.notation.step.105.txt h.scores.step.153.txt
h.scaffolds.original.notation.step.106.txt h.scores.step.154.txt
h.scaffolds.original.notation.step.107.txt h.scores.step.155.txt
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h.scaffolds.original.notation.step.109.txt h.scores.step.157.txt
h.scaffolds.original.notation.step.10.txt h.scores.step.158.txt
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h.scaffolds.original.notation.step.118.txt h.scores.step.166.txt
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