Question: Tadpole error correction error killed:9
gravatar for djackso
2.8 years ago by
djackso0 wrote:

Hi all,

I'm also using to error correct some paired end reads. It runs very well on most files but there's a couple that it cannot seem to run through. Note that I have validated the pairing of the input files using vpair and all is well.

Here's a copy of the error message:

/usr/local/bin/bbmap/ line 221: 90936 Killed: 9 java -ea -Xmx55g -Xms55g -cp /usr/local/bin/bbmap/current/ assemble.Tadpole prealloc=t -Xmx55g in1=infile_R1.fastq.gz in2=infile_R2.fastq.gz out1=outfile_error_corrected_R1.fastq.gz out2=outfile_error_corrected_R2.fastq.gz mode=correct k=50

A little Googling tells me that "Killed: 9" is most likely a "SIGKILL" error.....

Any thoughts on why this is happening on a few of my files and not the others?

error correction tadpole • 634 views
ADD COMMENTlink written 2.8 years ago by djackso0

Tagging Brian Bushnell.

ADD REPLYlink written 2.8 years ago by h.mon31k
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