No output of Minisam?

[HuJane]

Hi lh3,
I have minimap output, but no minisam output. The error may be because the first step of minisam: read 0 hits; stored 0 hits and 0 sequences.
Can you help to figure out the problem? Thank you!

[hujie@YanfaCenter01 miniasm]$ minimap2 --cs=long -w5 -L100 -m0 -t8 /home/hujie/nanopore/albacore/micro-S9/workspace/pass/barcode01/.fastq /home/hujie/nanopore/albacore/micro-S9/workspace/pass/barcode01/.fastq | gzip -1 > micro-bc1.paf.gz
[M::mm_idx_gen::1.2161.00] collected minimizers
[M::mm_idx_gen::1.4771.65] sorted minimizers
[M::main::1.4771.65] loaded/built the index for 4000 target sequence(s)
[M::mm_mapopt_update::1.5721.61] mid_occ = 24
[M::mm_idx_stat] kmer size: 15; skip: 5; is_hpc: 0; #seq: 4000
[M::mm_idx_stat::1.6391.58] distinct minimizers: 3219472 (79.81% are singletons); average occurrences: 1.354; average spacing: 2.949
[M::worker_pipeline::8.4365.45] mapped 4000 sequences
[M::worker_pipeline::16.5626.01] mapped 4000 sequences
[M::worker_pipeline::24.8736.23] mapped 4000 sequences
[M::worker_pipeline::29.1506.21] mapped 2033 sequences
[M::worker_pipeline::31.3966.20] mapped 4000 sequences
[M::worker_pipeline::37.8926.28] mapped 4000 sequences
[M::worker_pipeline::45.9146.35] mapped 4000 sequences
[M::worker_pipeline::53.7966.37] mapped 4000 sequences
[M::worker_pipeline::57.9586.35] mapped 2033 sequences
[M::main] Version: 2.10-r770-dirty
[M::main] CMD: minimap2 --cs=long -w5 -L100 -m0 -t8 /home/hujie/nanopore/albacore/micro-S9/workspace/pass/barcode01/fastq_runid_9d4de8c78879334fb7318ec861eb6d27b74228c6_0.fastq /home/hujie/nanopore/albacore/micro-S9/workspace/pass/barcode01/fastq_runid_9d4de8c78879334fb7318ec861eb6d27b74228c6_1.fastq /home/hujie/nanopore/albacore/micro-S9/workspace/pass/barcode01/fastq_runid_9d4de8c78879334fb7318ec861eb6d27b74228c6_2.fastq /home/hujie/nanopore/albacore/micro-S9/workspace/pass/barcode01/fastq_runid_9d4de8c78879334fb7318ec861eb6d27b74228c6_3.fastq /home/hujie/nanopore/albacore/micro-S9/workspace/pass/barcode01/fastq_runid_9d4de8c78879334fb7318ec861eb6d27b74228c6_4.fastq /home/hujie/nanopore/albacore/micro-S9/workspace/pass/barcode01/fastq_runid_9d4de8c78879334fb7318ec861eb6d27b74228c6_0.fastq /home/hujie/nanopore/albacore/micro-S9/workspace/pass/barcode01/fastq_runid_9d4de8c78879334fb7318ec861eb6d27b74228c6_1.fastq /home/hujie/nanopore/albacore/micro-S9/workspace/pass/barcode01/fastq_runid_9d4de8c78879334fb7318ec861eb6d27b74228c6_2.fastq /home/hujie/nanopore/albacore/micro-S9/workspace/pass/barcode01/fastq_runid_9d4de8c78879334fb7318ec861eb6d27b74228c6_3.fastq /home/hujie/nanopore/albacore/micro-S9/workspace/pass/barcode01/fastq_runid_9d4de8c78879334fb7318ec861eb6d27b74228c6_4.fastq
[M::main] Real time: 57.998 sec; CPU: 368.039 sec

[hujie@YanfaCenter01 miniasm]$ miniasm -f /home/hujie/nanopore/albacore/micro-S9/workspace/pass/barcode01/.fastq micro-bc1.paf.gz > micro-bc1.gfa
[M::main] ===> Step 1: reading read mappings <===
[M::ma_hit_read::0.1761.00] read 0 hits; stored 0 hits and 0 sequences (0 bp)
[M::main] ===> Step 2: 1-pass (crude) read selection <===
[M::ma_hit_sub::0.1761.00] 0 query sequences remain after sub
[M::ma_hit_cut::0.1761.00] 0 hits remain after cut
[M::ma_hit_flt::0.1761.00] 0 hits remain after filtering; crude coverage after filtering: -nan
[M::main] ===> Step 3: 2-pass (fine) read selection <===
[M::ma_hit_sub::0.1761.00] 0 query sequences remain after sub
[M::ma_hit_cut::0.1761.00] 0 hits remain after cut
[M::ma_hit_contained::0.1761.00] 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: 0.2-r168-dirty
[M::main] CMD: miniasm -f /home/hujie/nanopore/albacore/micro-S9/workspace/pass/barcode01/fastq_runid_9d4de8c78879334fb7318ec861eb6d27b74228c6_0.fastq /home/hujie/nanopore/albacore/micro-S9/workspace/pass/barcode01/fastq_runid_9d4de8c78879334fb7318ec861eb6d27b74228c6_1.fastq /home/hujie/nanopore/albacore/micro-S9/workspace/pass/barcode01/fastq_runid_9d4de8c78879334fb7318ec861eb6d27b74228c6_2.fastq /home/hujie/nanopore/albacore/micro-S9/workspace/pass/barcode01/fastq_runid_9d4de8c78879334fb7318ec861eb6d27b74228c6_3.fastq /home/hujie/nanopore/albacore/micro-S9/workspace/pass/barcode01/fastq_runid_9d4de8c78879334fb7318ec861eb6d27b74228c6_4.fastq micro-bc1.paf.gz
[M::main] Real time: 0.240 sec; CPU: 0.241 sec

[RxLoutre]

Hello there,

I had the exact same issue. Minimap2 worked fine but miniasm does not produce any output for some particular fastq file without any further indications. Did you solved your problem in the mean time ?

Cheers,

Roxane

[shehongbing]

Hi, there,
I had the same issue. I could get the results when I used the test data. But it does not work when I used my own data. maybe it's too large? I do not know why?, Did you solved the problem
?

Popeye

[sarahbonnin]

Hi,
did any of you manage to solve this issue?
Thanks

[shehongbing]

NO, thanks

…

在 2020年3月19日，上午12:40，Sarah Bonnin ***@***.***> 写道： Hi, did any of you manage to solve this issue? Thanks — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#50 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ALZETBJAOGAAA5ULSRL2TODRID2QVANCNFSM4FINGIQA>.

[abattenhouse]

I'm having the same issue. Ran minimap2 -x ava-ont on my sequences and got what look like lots of good alignments. But nothing from miniasm. Log below. Any ideas?

[M::main] ===> Step 1: reading read mappings <===
[M::ma_hit_read::2.2090.87] read 1903412 hits; stored 585 hits and 266 sequences (838205 bp)
[M::main] ===> Step 2: 1-pass (crude) read selection <===
[M::ma_hit_sub::2.2100.87] 35 query sequences remain after sub
[M::ma_hit_cut::2.2100.87] 271 hits remain after cut
[M::ma_hit_flt::2.2100.87] 271 hits remain after filtering; crude coverage after filtering: 5.96
[M::main] ===> Step 3: 2-pass (fine) read selection <===
[M::ma_hit_sub::2.2100.87] 30 query sequences remain after sub
[M::ma_hit_cut::2.2100.87] 253 hits remain after cut
[M::ma_hit_contained::2.210*0.87] 2 sequences and 5 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 1 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: ../../bin/miniasm-0.3/miniasm -f raw/A_sample02_barcode02.fastq overlap_A02_1.paf.gz
[M::main] Real time: 2.210 sec; CPU: 1.928 sec

[Emi273-max]

Hello there,
yesterday I tried to run miniasm after minimap but I didn't have any output.
-minimap2/minimap2 -map-ont file.fasta PROVA.fastq > prova_mapping.paf
-miniasm/miniasm -f PROVA.fastq prova_mapping.paf > output.gfa
These are the commands that I used.
I had a paf file from minimap command. Miniasm worked but I didn't have gfa output
Do you know how to solve this issue?
Thanks

[zhaoxvwahaha]

Same problem, still waiting for answer, Dr Li, could you please give some suggestion? @lh3

[Emi273-max]

Hi,
I solved the issue with a change in minimap command. I changed command with:
minimap2 -ax ava-ont file1.fastq file1.fastq > overlapped_reads.paf
This is the correct output from Minimap to successfully run Miniasm because you need to create overlapped reads in paf format.