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Error in Platanus assembly? #111

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sanalbert opened this issue Oct 17, 2024 · 0 comments
Open

Error in Platanus assembly? #111

sanalbert opened this issue Oct 17, 2024 · 0 comments

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@sanalbert
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Hello, thanks for the great tool!

I am working on a ~200Mb size insect genomic data, sequenced with Illumina short reads (150bp PE).
Using redundans, I came upon this error message, of which I could not find any information online.

[ERROR] Couldn't guess handle for redundans/denovo/out_contig.fa

What may be the problem, and how could it be solved?

The log file (redundans/denovo/out.log) stopped at this:

Platanus version: 1.2.4
platanus assemble -tmp /tmp -t 16 -m 32 -o redundans/denovo/out -f /tmp/redundans_mnu1nhf8 

K = 32, saving kmers from reads...
AVE_READ_LEN=150.273

KMER_EXTENSION:
K=32, KMER_COVERAGE=330.239 (>= 25), COVERAGE_CUTOFF=25
K=42, KMER_COVERAGE=302.552, COVERAGE_CUTOFF=25, PROB_SPLIT=10e-inf
K=52, KMER_COVERAGE=274.864, COVERAGE_CUTOFF=25, PROB_SPLIT=10e-inf
K=62, KMER_COVERAGE=247.176, COVERAGE_CUTOFF=25, PROB_SPLIT=10e-inf
K=72, KMER_COVERAGE=219.488, COVERAGE_CUTOFF=25, PROB_SPLIT=10e-inf
K=82, KMER_COVERAGE=191.801, COVERAGE_CUTOFF=25, PROB_SPLIT=10e-inf
K=92, KMER_COVERAGE=164.113, COVERAGE_CUTOFF=25, PROB_SPLIT=10e-inf
K=102, KMER_COVERAGE=136.425, COVERAGE_CUTOFF=25, PROB_SPLIT=10e-inf
K=112, KMER_COVERAGE=108.737, COVERAGE_CUTOFF=25, PROB_SPLIT=10e-inf
K=122, KMER_COVERAGE=81.0496, COVERAGE_CUTOFF=25, PROB_SPLIT=10e-11.9912
K=132, KMER_COVERAGE=53.3619, COVERAGE_CUTOFF=12, PROB_SPLIT=10e-10.6372
K=139, KMER_COVERAGE=33.9805, COVERAGE_CUTOFF=4, PROB_SPLIT=10e-10
K=141, KMER_COVERAGE=28.4429, COVERAGE_CUTOFF=2, PROB_SPLIT=10e-10.4065
loading kmers...
connecting kmers...
removing branches...
BRANCH_DELETE_THRESHOLD=0.5
NUM_CUT=40201
NUM_CUT=83
NUM_CUT=0
TOTAL_NUM_CUT=40284
mapping reads on de Bruijn Graph nodes...
TOTAL_MAPPED_READS=343484481
TOTAL_UNMAPPED_READS=41379413
TOTAL_SHORT_READS(<32)=0
NUM_DELETE_NODE(reads are unmapped)=36666
NUM_CUT_NODE=7269
extracting reads (containing kmer used in contig assemble)...
K = 42, loading kmers from contigs...
K = 42, saving additional kmers(not found in contigs) from reads...
COVERAGE_CUTOFF = 25
loading kmers...
connecting kmers...

Any advice would be greatly appreciated. Thank you in advance for all your support!

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