Not results generating?

Open sekhwal opened this issue 4 years ago • 4 comments

I am following these commands. However, I am getting blank output file.

minimap2/minimap2 -x ava-pb -t8 pb-reads.fq pb-reads.fq | gzip -1 > reads.paf.gz

Layout

miniasm/miniasm -f reads.fq reads.paf.gz > reads.gfa

Command Message:

$./miniasm -f ../reference-e.coli.fasta ../overlaps.paf > ../Assembly.fasta

[M::main] ===> Step 1: reading read mappings <=== [M::ma_hit_read::0.0351.05] read 29586 hits; stored 45892 hits and 22946 sequences (165435970 bp) [M::main] ===> Step 2: 1-pass (crude) read selection <=== [M::ma_hit_sub::0.0421.04] 3 query sequences remain after sub [M::ma_hit_cut::0.0421.04] 0 hits remain after cut [M::ma_hit_flt::0.0421.04] 0 hits remain after filtering; crude coverage after filtering: -nan [M::main] ===> Step 3: 2-pass (fine) read selection <=== [M::ma_hit_sub::0.0421.04] 0 query sequences remain after sub [M::ma_hit_cut::0.0421.04] 0 hits remain after cut [M::ma_hit_contained::0.043*1.04] 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 /home/kumarm/RNA-Seq/e-coli-data/e.coli-reads.fasta /home/kumarm/RNA-Seq/e-coli-data/overlaps.paf [M::main] Real time: 0.351 sec; CPU: 0.353 sec /RNA-Seq/MinION-data/miniasm$