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hifiasm-meta exit! #31

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Giotto187 opened this issue Jan 1, 2024 · 1 comment
Open

hifiasm-meta exit! #31

Giotto187 opened this issue Jan 1, 2024 · 1 comment

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@Giotto187
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Giotto187 commented Jan 1, 2024

For assembly of metagenomic samples with HiFi reads, I ran hifiasm-meta with default parameters. The command line was as follow:
hifiasm_meta -t 32 -o asm hifi_reads.fastq.gz

But the process was exit in the step of "checkpoint: post-assembly". The log file showed:

********** checkpoint: post-assembly **********
[M::hamt_clean_graph] (peak RSS so far: 18.8 GB)
[M::hamt_ug_opportunistic_elementary_circuits] collected 0 circuits, used 0.00s
[M::hamt_ug_opportunistic_elementary_circuits] wrote all rescued circles, used 0.00s
[T::hamt_ug_opportunistic_elementary_circuits_helper_deduplicate_minhash] got the sequences, used 0.0s
[T::hamt_minhash_mashdist] sketched - 0.0s.
[T::hamt_minhash_mashdist] compared - 0.0s.
[T::hamt_ug_opportunistic_elementary_circuits_helper_deduplicate_minhash] collected mash distances for 0 seqs, used 0.0s
[M::hamt_ug_opportunistic_elementary_circuits_helper_deduplicate_minhash] had 0 paths, 0 remained (0 dropped by length diff, 0 by length abs),used 0.0s after sketching.
[M::hamt_ug_opportunistic_elementary_circuits] deduplicated rescued circles, used 0.01s
[M::hamt_ug_opportunistic_elementary_circuits] wrote deduplicated rescued circles, used 0.00s
[M::hamt_simple_binning] Will try to bin on 147 contigs (skipped 0 because blacklist).
Using random seed: 42
Perplexity too large for the number of data points!
################

How can I fix it? I'm looking for your reply. Thank you very much!

@xfengnefx
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Sorry for the delay. And sorry, the log is confusing, will fix soon. The assembly has finished. It has produced a contig graph with too few contigs, and the post-assembly genome binning stopped at clustering step.

The output: the assembly is asm.p_ctg.gfa, and the post-assembly binning is asm.rescue.fa (might be empty).

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