TobyBaril
commented
4 months ago Hi! In this case, your system killed the process (either taking too long, or using too many resources). This should have been retried automatically in this case, as well as continued into the next round so will not affect the final output. One way to avoid this in future runs is to ask for less threads or more memory (if available on the system). Generally, repeat annotation requires high-memory nodes if the genome is quite large or repeat-heavy!
I hope this helps!
mylena-s
Hello!
I am writing to ask you about an error that appeared during family consensus refinement:
mafft: line 2842: 2167931 Killed "$prefix/tbfast" -u $unalignlevel $localparam -C $numthreads $seqtype $model -g $lexp -f $lgop -Q $spfactor -h $laof -L $usenaivepairscore $focusarg -+ $iterate -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $termgapopt $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg $focusarg < infile > /dev/null 2>> "$progressfile"
The run continued with no clear error mesage. I wanted to ask you if it is safe to continue despite this error, or would be better to re run the pipeline? I guess is something related to resource allocation... Is there any way to just rerun that step? Thanks! Cheers