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I can not assembly this fasta file
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12 months ago
apl00028 • 20

I am trying to asembly several fasta files following the same steps but one of them I can not. The steps that I followed are:

I removed no mapped reads of my fastq files:

  python fastqcombinepairedendnew.py PV003_1_trim.fq PV003_2_trim.fq

I combined both parts of my fastq files and I converted it in fasta file:

  fq2fa --merge PV003_1_trim.fq_pairs_R1.fastq PV003_2_trim.fq_pairs_R2.fastq PV003_cmv3.fa

after that I assembled it:

idba_ud -r /PV003_cmv3.fa --num_threads 8 -o /PV003_trim.out

I get this error:

          number of threads 8
          Killed

I do not understand why I get this error, because I did the same process with other files and I do not get this error message. However, I see a difference among the size files, this file is heavier than the others (8 gbs).

How can I solve this error?

Thanks in advantage.

assembly ngs • 204 views
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If you suspect that the file is too big, try to see if it works on a subset of your fasta file. It might be that the specs of your hardware are not sufficient for that file.

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But a lab mate have done the same process with other heavy file and he got the assembly, so I would like to know if there is an alternative way to assembly or change same paramether

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Check the memory usage, for example using htop during the assembly and see if it's full. We have no idea how large your genome is, and how many reads you have. See also Brief Reminder On How To Ask A Good Question

You are also using a lot of tools I never heard of, so I'm not sure if the assembler is the best for the job.

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Thanks!, I guess it was the mistake, because if I filter this file:

        /./seqtk/seqtk subseq /PV003_cmv3.fa all_qseqid.txt > PV003.v_cmv3.fa

It generates a fasta file less heavy than the previous (only 65.4 Mb), so I tried to assemble it again and ¡It works!

Thanks

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I'll try next time to elaborate more my question.

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Okay I thought you said that this file was bigger (heavier) than the rest, must have read it wrong sorry. My advice is to ask your lab mate for help!

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