Question: bowtie2 error in mapping pair ended sample
gravatar for kkj3083
3.2 years ago by
kkj30830 wrote:

Hi all,

I'm trying to map pair ended sample on ERCC(External RNA Control Consortium)92+Human cDNA fasta file.

So, Indexing was done by

 bowtie2-2.2.6/bowtie2-build Ambion_92_ERCC_Concentration_cms_095047_plus_ERCC_vector.fasta,Homo_sapiens.GRCh38.cdna.all.fa ERCC_bt2

and then, mapped by

 bowtie2-2.2.6/bowtie2 -x ERCC_bt2 -1 Rapaport2013_SEQC_A3.untie_1.fastq -2 Rapaport2013_SEQC_A3.untie_2.fastq -S ERCC_bt2.sam

After mapping I got error message like this

(ERR): bowtie2-align died with signal 15 (TERM)
61754424 reads; of these:
  61754424 (100.00%) were paired; of these:
    18726733 (30.32%) aligned concordantly 0 times
    7967420 (12.90%) aligned concordantly exactly 1 time
    35060271 (56.77%) aligned concordantly >1 times
    18726733 pairs aligned concordantly 0 times; of these:
      269850 (1.44%) aligned discordantly 1 time
    18456883 pairs aligned 0 times concordantly or discordantly; of these:
      36913766 mates make up the pairs; of these:
        32282274 (87.45%) aligned 0 times
        643672 (1.74%) aligned exactly 1 time
        3987820 (10.80%) aligned >1 times
73.86% overall alignment rate

I can not figure out exactly why this error was made. 

Actually, I got sam file (Not sure it is right), but does it matter?

bowtie2 err • 1.4k views
ADD COMMENTlink modified 3.2 years ago by Devon Ryan88k • written 3.2 years ago by kkj30830
gravatar for Devon Ryan
3.2 years ago by
Devon Ryan88k
Freiburg, Germany
Devon Ryan88k wrote:

SAM is the expected output format. The error is due to someone or something killing the process on the server you ran it on. As for why that happened, we can't say.

ADD COMMENTlink written 3.2 years ago by Devon Ryan88k

Maybe mapping with nohup Linux command (due to long running time) makes it happened


ADD REPLYlink written 3.2 years ago by kkj30830
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