Question: Tadpole error correction error killed:9
0
gravatar for djackso
21 months ago by
djackso0
djackso0 wrote:

Hi all,

I'm also using tadpole.sh 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 reformat.sh vpair and all is well.

Here's a copy of the error message:

/usr/local/bin/bbmap/tadpole.sh: 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 • 450 views
ADD COMMENTlink written 21 months ago by djackso0

Tagging Brian Bushnell.

ADD REPLYlink written 21 months ago by h.mon28k
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