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:hibiscus: reference-free transcriptome assembly for short and long reads
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Error occur during RNA-Bloom command #10

Closed aman21392 closed 3 years ago

aman21392 commented 4 years ago

I use this command-- java -jar RNA-Bloom.jar -long combined.fasta -stranded -ntcard -t 30 -outdir output

Counting Bloom filter FPR: 1.0123985 %

Stage 1 completed in 3m 35s

Stage 2: Correct long reads for "rnabloom" Parsing combined.fasta... Corrected Read Lengths Sampling Distribution (n=1000) min q1 med q3 max 200 423 671 1076 1895 Parsed 1,231,437 sequences. Kept: 1,146,017(93.063385%) Discarded: 85,420(6.9366117%) Artifacts: 3(2.4361782E-4%) Stage 2 completed in 11m 9s Stage 3: Assemble long reads for "rnabloom" Overlapped sequences: 261,062

  • discarded: 105,394
  • artifacts: 1
  • unique: 119,308
  • dovetail: 234 G: |V|=234 |E|=311 G: |V|=234 |E|=72 before: 1,146,004 after: 119,236 ERROR: Error assembling long reads!

See also rnabloom.longreads.assembly_map.paf.gz.log file result --- [M::mm_idx_gen::2.8941.35] collected minimizers [M::mm_idx_gen::3.0132.39] sorted minimizers [M::main::3.0132.39] loaded/built the index for 119236 target sequence(s) [M::mm_mapopt_update::3.0312.38] mid_occ = 61895 [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 119236 [M::mm_idx_stat::3.043*2.37] distinct minimizers: 787299 (67.99% are singletons); average occurrences: 34.539; average spacing: 5.415; total length: 147235275 Killed

See also rnabloom.transcripts.fa.log file result -- [racon::Polisher::initialize] loaded target sequences 0.707022 s [racon::Polisher::initialize] loaded sequences 6.976079 s [racon::Polisher::initialize] error: empty overlap set!

So please tell me there is no overlap set so the final output transcript file is empty. If any suggestion to get result please tell me. Thanks in advance

kmnip commented 4 years ago

Hi,

Several questions:

  1. Is this direct RNA-seq data?
  2. Can you please check the size of rnabloom.longreads.assembly_map.paf.gz?
  3. Can you please try again with the option --lrrd 1?

Thanks, Ka Ming