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No output of Minisam? #50
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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 |
Hi, there, Popeye |
Hi, |
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
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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 <=== |
Hello there, |
Same problem, still waiting for answer, Dr Li, could you please give some suggestion? @lh3 |
Hi, |
Hi lh3,
![image](https://user-images.githubusercontent.com/17492179/42305142-28cfadd4-805c-11e8-9a6e-b0a38f2eb786.png)
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
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