bowtie2 error in mapping pair ended sample

Question

[kkj3083]

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?

Answer 1

[Devon Ryan]

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.

[kkj3083]

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

Thanks!