Can miniasm be used for contigs

[SilasK]

I like to combine different metagenome-assembled genomes (contigs) into one.

I tried to use miniasmwith:

cat all_genomes/*.fasta > x.fasta

minimap2 -x asm10 -t4 x.fasta x.fasta | gzip -1 > x.paf.gz
miniasm -i 0.9 -o 200 -c 1 -f x.fasta x.paf.gz > x.gfa

The gfa file is empty and I get the following log.

[M::main] ===> Step 1: reading read mappings <===
[M::ma_hit_read::0.416*1.00] read 398828 hits; stored 575002 hits and 9518 sequences (312118248 bp)
[M::main] ===> Step 2: 1-pass (crude) read selection <===
[M::ma_hit_sub::0.497*1.00] 7429 query sequences remain after sub
[M::ma_hit_cut::0.505*1.00] 569351 hits remain after cut
[M::ma_hit_flt::0.511*1.00] 563681 hits remain after filtering; crude coverage after filtering: 56.25
[M::main] ===> Step 3: 2-pass (fine) read selection <===
[M::ma_hit_sub::0.532*1.00] 7400 query sequences remain after sub
[M::ma_hit_cut::0.542*1.00] 561656 hits remain after cut
[M::ma_hit_contained::0.551*1.00] 0 sequences and 0 hits remain after containment removal
[M::main] ===> Step 4: graph cleaning <===
[M::ma_sg_gen] read 0 arcs
[M::main] ===> Step 4.1: transitive reduction <===
[M::asg_arc_del_trans] transitively reduced 0 arcs
[M::main] ===> Step 4.2: initial tip cutting and bubble popping <===
[M::asg_cut_tip] cut 0 tips
[M::asg_arc_del_multi] removed 0 multi-arcs
[M::asg_arc_del_asymm] removed 0 asymmetric arcs
[M::asg_pop_bubble] popped 0 bubbles and trimmed 0 tips
[M::main] ===> Step 4.3: cutting short overlaps (3 rounds in total) <===
[M::asg_arc_del_short] removed 0 short overlaps
[M::asg_arc_del_short] removed 0 short overlaps
[M::asg_arc_del_short] removed 0 short overlaps
[M::main] ===> Step 4.4: removing short internal sequences and bi-loops <===
[M::asg_cut_internal] cut 0 internal sequences
[M::asg_cut_biloop] cut 0 small bi-loops
[M::asg_cut_tip] cut 0 tips
[M::asg_pop_bubble] popped 0 bubbles and trimmed 0 tips
[M::main] ===> Step 4.5: aggressively cutting short overlaps <===
[M::asg_arc_del_short] removed 0 short overlaps
[M::main] ===> Step 5: generating unitigs <===
[M::main] Version: 0.3-r179
[M::main] CMD: miniasm -i 0.9 -o 200 -c 1 -f x.fasta x.paf.gz
[M::main] Real time: 0.965 sec; CPU: 0.964 sec

[lh3]

Miniasm is designed for reads. It filters out reads with low coverage. You can see all input sequences are dropped at step 4. You may try to add option -1 -2 (or just -2). I don't know if that helps, though.