no reduction when using --minimap2reduce

[pwkooij]

First of all thanks for creating redundans, I have been working with it for several years now.

However, I've noticed something that I don't know how to solve. I am analyzing fungal datasets from ONT data and since the help tells me --minimap2reduce Use minimap2 for the initial and final Reduction step. Recommended for input assembled contigs from long reads using --preset[asm5] by default. By default LASTal is used for Reduction. I have been trying to use redundans with --minimap2reduce in the command.
I tried this for an ONT only dataset as well as a hybrid ONT/Illumina dataset and for both I get the following warning in the reduction and final reduction steps: [WARNING] Nothing reduced!
When I run redundans without this option it runs normally (with LASTal) and does perform reduction, however, this might not be optimal due to the data. Any suggestions?

Command and run output with --minimap2reduce:

redundans -v -l /home/pepijn/Documents/genomics/Ac200942/fastq/porechop/ont_porechop_all.fastq.gz -f /home/pepijn/Documents/genomics/Ac200942/fastq/medaka/default/consensus.fasta -o /home/pepijn/Documents/genomics/Ac200942/redundans/git_tests/with_minimap2reduce --populateScaffolds --minimap2scaffold -t 10 -m 100 --minimap2reduce

Options: Namespace(verbose=True, fastq=[], fasta='/home/pepijn/Documents/genomics/Ac200942/fastq/medaka/default/consensus.fasta', outdir='/home/pepijn/Documents/genomics/Ac200942/redundans/git_tests/with_minimap2reduce', threads=10, resume=False, log=<_io.TextIOWrapper name='<stderr>' mode='w' encoding='utf-8'>, nocleaning=True, mem=100, tmp='/tmp', identity=0.51, overlap=0.8, minLength=200, minimap2reduce=True, index='4G', noreduction=True, joins=5, linkratio=0.7, limit=0.2, mapq=10, iters=2, noscaffolding=True, usebwa=False, longreads=['/home/pepijn/Documents/genomics/Ac200942/fastq/porechop/ont_porechop_all.fastq.gz'], populateScaffolds=True, minimap2scaffold=True, reference='', norearrangements=False, preset='asm5', nogapclosing=True, runmerqury=False, kmer=21)

##################################################
[Wed Jan  8 10:20:05 2025] Reduction...
#file name      genome size     contigs heterozygous size       [%]     heterozygous contigs    [%]     identity [%]    possible joins  homozygous size [%]     homozygous contigs      [%]
[WARNING] Nothing reduced!
/home/pepijn/Documents/genomics/Ac200942/redundans/git_tests/with_minimap2reduce/contigs.fa     123360206       1113    0       0.00    0       0.00    0.000   0       123360206       100.00  1113    100.00

##################################################
[Wed Jan  8 10:20:37 2025] Using populateScaffolds mode for long read scaffolding mode...
 iteration 1...
Using minimap2 aligner preset map-ont for file /home/pepijn/Documents/genomics/Ac200942/fastq/porechop/ont_porechop_all.fastq.gz...

##################################################
[Wed Jan  8 10:21:20 2025] Final reduction...
#file name      genome size     contigs heterozygous size       [%]     heterozygous contigs    [%]     identity [%]    possible joins  homozygous size [%]     homozygous contigs      [%]
[WARNING] Nothing reduced!
/home/pepijn/Documents/genomics/Ac200942/redundans/git_tests/with_minimap2reduce/scaffolds.longreads.fa 123360206       1113    0       0.00    0       0.00    0.000   0       123360206       100.00  1113    100.00

##################################################
[Wed Jan  8 10:22:23 2025] Reporting statistics...
#fname  contigs bases   GC [%]  contigs >1kb    bases in contigs >1kb   N50     N90     Ns      longest
/home/pepijn/Documents/genomics/Ac200942/fastq/medaka/default/consensus.fasta   1113    123360206       36.809  1113    123360206       199353  47379   0       1247514
/home/pepijn/Documents/genomics/Ac200942/redundans/git_tests/with_minimap2reduce/contigs.fa     1113    123360206       36.809  1113    123360206       199353  47379   0       1247514
/home/pepijn/Documents/genomics/Ac200942/redundans/git_tests/with_minimap2reduce/contigs.reduced.fa     1113    123360206       36.809  1113    123360206       199353  47379   0       1247514
/home/pepijn/Documents/genomics/Ac200942/redundans/git_tests/with_minimap2reduce/scaffolds.longreads.1.fa       1113    123360206       36.809  1113    123360206       199353  47379   0       1247514
/home/pepijn/Documents/genomics/Ac200942/redundans/git_tests/with_minimap2reduce/scaffolds.longreads.fa 1113    123360206       36.809  1113    123360206       199353  47379   0       1247514
/home/pepijn/Documents/genomics/Ac200942/redundans/git_tests/with_minimap2reduce/scaffolds.reduced.fa   1113    123360206       36.809  1113    123360206       199353  47379   0       1247514  

##################################################
[Wed Jan  8 10:23:23 2025] Cleaning-up...
Finished cleaning up /home/pepijn/Documents/genomics/Ac200942/redundans/git_tests/with_minimap2reduce#Time elapsed: 0:03:18.445951

Command and run output without --minimap2reduce:

redundans -v -l /home/pepijn/Documents/genomics/Ac200942/fastq/porechop/ont_porechop_all.fastq.gz -f /home/pepijn/Documents/genomics/Ac200942/fastq/medaka/default/consensus.fasta -o /home/pepijn/Documents/genomics/Ac200942/redundans/git_tests/without_minimap2reduce --populateScaffolds --minimap2scaffold -t 10 -m 100

Options: Namespace(verbose=True, fastq=[], fasta='/home/pepijn/Documents/genomics/Ac200942/fastq/medaka/default/consensus.fasta', outdir='/home/pepijn/Documents/genomics/Ac200942/redundans/git_tests/without_minimap2reduce', threads=10, resume=False, log=<_io.TextIOWrapper name='<stderr>' mode='w' encoding='utf-8'>, nocleaning=True, mem=100, tmp='/tmp', identity=0.51, overlap=0.8, minLength=200, minimap2reduce=False, index='4G', noreduction=True, joins=5, linkratio=0.7, limit=0.2, mapq=10, iters=2, noscaffolding=True, usebwa=False, longreads=['/home/pepijn/Documents/genomics/Ac200942/fastq/porechop/ont_porechop_all.fastq.gz'], populateScaffolds=True, minimap2scaffold=True, reference='', norearrangements=False, preset='asm5', nogapclosing=True, runmerqury=False, kmer=21)

##################################################
[Wed Jan  8 10:31:04 2025] Reduction...
#file name      genome size     contigs heterozygous size       [%]     heterozygous contigs    [%]     identity [%]    possible joins  homozygous size [%]     homozygous contigs      [%]
/home/pepijn/Documents/genomics/Ac200942/redundans/git_tests/without_minimap2reduce/contigs.fa  123360206       1113    20316067        16.47   468     42.05   83.031  0       103044139       83.53   645     57.95

##################################################
[Wed Jan  8 10:49:05 2025] Using populateScaffolds mode for long read scaffolding mode...
 iteration 1...
Using minimap2 aligner preset map-ont for file /home/pepijn/Documents/genomics/Ac200942/fastq/porechop/ont_porechop_all.fastq.gz...

##################################################
[Wed Jan  8 10:49:31 2025] Final reduction...
#file name      genome size     contigs heterozygous size       [%]     heterozygous contigs    [%]     identity [%]    possible joins  homozygous size [%]     homozygous contigs      [%]
/home/pepijn/Documents/genomics/Ac200942/redundans/git_tests/without_minimap2reduce/scaffolds.longreads.fa      103044139       645     2826794 2.74    28      4.34    78.819  0       100217345       97.26   617     95.66

##################################################
[Wed Jan  8 11:02:44 2025] Reporting statistics...
#fname  contigs bases   GC [%]  contigs >1kb    bases in contigs >1kb   N50     N90     Ns      longest
/home/pepijn/Documents/genomics/Ac200942/fastq/medaka/default/consensus.fasta   1113    123360206       36.809  1113    123360206       199353  47379   0       1247514
/home/pepijn/Documents/genomics/Ac200942/redundans/git_tests/without_minimap2reduce/contigs.fa  1113    123360206       36.809  1113    123360206       199353  47379   0       1247514
/home/pepijn/Documents/genomics/Ac200942/redundans/git_tests/without_minimap2reduce/contigs.reduced.fa  645     103044139       36.723  645     103044139       242918  79884   0       1247514
/home/pepijn/Documents/genomics/Ac200942/redundans/git_tests/without_minimap2reduce/scaffolds.longreads.1.fa    645     103044139       36.723  645     103044139       242918  79884   0       1247514
/home/pepijn/Documents/genomics/Ac200942/redundans/git_tests/without_minimap2reduce/scaffolds.longreads.fa      645     103044139       36.723  645     103044139       242918  79884   0       1247514
/home/pepijn/Documents/genomics/Ac200942/redundans/git_tests/without_minimap2reduce/scaffolds.reduced.fa        617     100217345       36.754  617     100217345       244287  80982   0       1247514

##################################################
[Wed Jan  8 11:03:06 2025] Cleaning-up...
Finished cleaning up /home/pepijn/Documents/genomics/Ac200942/redundans/git_tests/without_minimap2reduce#Time elapsed: 0:32:02.742873

I do notice in these output that the noreduction=True is used, but this seems the case for both runs. Is there way to put noreduction=FALSE in the command to test if that might be the issue?