A5 Pipeline : Idba To Crash

Question

[HG]

Hi everyone, i am using A5 pipeline for Miseq 250bp pairend reads. Getting some error message like this :

1876358    Sequences
9744    Tags rejected (0.5%) at 29.0% coverage cutoff (0.010000 FDR).
    Elapsed time:
        131 seconds (130.77 CPU+SYS seconds)
[a5_s2] Building contigs from mygenome.ec.fastq with IDBA
[a5_s2] Building contigs from mygenome.ec.fastq with IDBA
[a5] idba -long mygenome.s2/mygenome.ec.fasta -o mygenome.s2/mygenome --mink 25 --maxk 90
terminate called after throwing an instance of 'std::logic_error'
  what():  SequenceReader::SequenceReader() istream is invalid
Aborted (core dumped)
[a5] Error building contigs with IDBA

Please help me out

[SES]

You should have added to your question or started a new post instead of editing the title and completely changing the question. Now, it is unclear what my answer is about (even though it solved your problem) and if someone else has this issue, it won't be as easy for them to find a solution.

Answer 1

[SES]

That message is saying the quality encoding of your data is not what is expected by the program. This could be do to not setting an argument to the program correctly, or it could be a bug. However, this message in the output:

"Check your data and re-run preprocess with the correct quality scaling flag."

seems to indicate it is the first of those two possible issues I mentioned. So, try to rerun the preprocess program with the appropriate settings. If that does not solve your problem, you may want to read the conversation about issue #5 reported to the mailing list. It appears similar issues have been seen in the past, and there are ways to solve them.

[HG]

Thank you for your suggestion now i have changed sub get_phred6. So far earlier issue solved but now problem with IDBA, i am using current version of IDBA V1.1.1

1876358    Sequences
9746    Tags rejected (0.5%) at 29.0% coverage cutoff (0.010000 FDR).


    Elapsed time:
        131 seconds (130.42 CPU+SYS seconds)
[a5_s2] Building contigs from mygenome.ec.fastq with IDBA
[a5_s2] Building contigs from mygenome.ec.fastq with IDBA
[a5] idba -long mygenome.s2/mygenome.ec.fasta -o mygenome.s2/mygenome --mink 10 --maxk 250
[a5] Error building contigs with IDBA