Empty gfa file after miniasm run

[aastha-v]

Hello, I have run the following commands:

minimap2 -x ava-ont -t32 reads.fastq reads.fastq -K5M | gzip -1 > n_reads.paf.gz [M::mm_idx_gen::0.7540.99] collected minimizers [M::mm_idx_gen::0.8582.63] sorted minimizers [M::main::0.8582.63] loaded/built the index for 20814 target sequence(s) [M::mm_mapopt_update::0.8822.59] mid_occ = 1971 [M::mm_idx_stat] kmer size: 15; skip: 5; is_hpc: 0; #seq: 20814 [M::mm_idx_stat::0.8982.56] distinct minimizers: 925688 (78.09% are singletons); average occurrences: 5.356; average spacing: 2.977 [M::worker_pipeline::46.2509.91] mapped 7168 sequences [M::worker_pipeline::68.9709.32] mapped 7007 sequences [M::worker_pipeline::86.2197.52] mapped 6639 sequences [M::main] Version: 2.17-r941 [M::main] CMD: minimap2 -x ava-ont -t32 -K5M reads.fastq reads.fastq [M::main] Real time: 86.242 sec; CPU: 648.232 sec; Peak RSS: 1.735 GB

miniasm -f reads.fastq n_reads.paf.gz > n_reads.gfa [M::main] ===> Step 1: reading read mappings <=== [M::ma_hit_read::31.0881.00] read 24248695 hits; stored 3 hits and 3 sequences (8137 bp) [M::main] ===> Step 2: 1-pass (crude) read selection <=== [M::ma_hit_sub::31.1331.00] 0 query sequences remain after sub [M::ma_hit_cut::31.1331.00] 0 hits remain after cut [M::ma_hit_flt::31.1331.00] 0 hits remain after filtering; crude coverage after filtering: -nan [M::main] ===> Step 3: 2-pass (fine) read selection <=== [M::ma_hit_sub::31.1331.00] 0 query sequences remain after sub [M::ma_hit_cut::31.1331.00] 0 hits remain after cut [M::ma_hit_contained::31.133*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 -f reads.fastq n_reads.paf.gz [M::main] Real time: 31.292 sec; CPU: 31.089 sec

I have tried several variations of the miniasm command on two different datasets only to obtain empty .gfa files each time.

Could you please help me figure where I could be going wrong? Thanks!

[ouyang-lang]

请问这个问题解决了吗？

[zhaoxvwahaha]

I also had this problem，any one solve it?

[yusator]

I have also been having the same issue

[tweilin]

I have facing this issue, any clues?