Not results generating?

[sekhwal]

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$

[ouyang-lang]

Has this problem been solved? I also met to

[libingtju]

I met it, Show this problem"Command terminated by signal 9", the memory is not enough. But I don’t know how miniasm uses multithreading

[vebaev]

It generate empty file, even on Galaxy EU/ORG platforms?

[Lucas-Ripoll]

I have the same issue.... do you have some solution to it?

[USMortality]

You may want to adjust your settings, as the tool seems to be expecting long reads by default and does some filtering...
e.g.: miniasm -1 -2 -m 30 -s 50 -o 50 -I 0.5 -f hq.fastq hq.paf.gz > hq.gfa for pretty loose settings...