No output in GFA file after miniasm run.

[tayabsoomro]

I did a MinION run of some plant pathogen, followed it by canu correction script. I then ran minimap2 to map against the host to exclude the host reads. Now, I need to do an assembly using Miniasm and polishing using Racon.

I am following this procedure for miniasm.

I did all against all overlap with minimap2:

minimap2 -t 20 $DIR/asm20.unmapped.fasta $DIR/asm20.unmapped.fasta | gzip -1 > asm20.minimap2.paf.gz
and this faithfully generates PAF file of around ~ 3Gb in size.

But during the assembly with miniasm step, it results in a GFA file with no content. There are no apparent errors in the log file to hint as to what might be the issue.

Here is the command I am running:

miniasm -f $DIR/asm20.unmapped.fastq $DIR/asm20.minimap2.paf.gz >$DIR/asm20.miniasm.gfa

NOTE: I generated asm20.unmapped.fastq file from the asm20.unmapped.fasta file to figure out if the file format was the issue, but apparently not.

Here is the relevent log:

...

[M::main] ===> Step 1: reading read mappings <===
[M::ma_hit_read::49.688*1.00] read 18714458 hits; stored 35645910 hits and 822072 sequences (12781243018 bp)
[M::main] ===> Step 2: 1-pass (crude) read selection <===
[M::ma_hit_sub::61.441*1.00] 810473 query sequences remain after sub
[M::ma_hit_cut::67.730*1.00] 35395033 hits remain after cut
[M::ma_hit_flt::71.654*1.00] 35114675 hits remain after filtering; crude coverage after filtering: 36.91
[M::main] ===> Step 3: 2-pass (fine) read selection <===
[M::ma_hit_sub::73.627*1.00] 809731 query sequences remain after sub
[M::ma_hit_cut::74.754*1.00] 35105421 hits remain after cut
[M::ma_hit_contained::76.821*1.00] 110 sequences and 57 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 110 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 -f /isilon/saskatoon-rdc/users/soomrot/Canu_results/Canu_run_4/pb3-ont/miniasm/asm20.unmapped.fastq /isilon/saskatoon-rdc/users/soomrot/Canu_results/Canu_run_4/pb3-ont/miniasm/asm20.minimap2.paf.gz
[M::main] Real time: 121.952 sec; CPU: 120.127 sec

Any ideas?

[tayabsoomro]

Still waiting for a response...

[lh3]

You need to use -x map-ont1 or -x map-pb`, or choose another assembler like flye, wtdbg2 or shasta.

[lh3]

Sorry, should be -x ava-ont or -x ava-pb.

[tayabsoomro]

That worked! Thanks! :)