ZERO length suplied to intervalList::add(), ignoring interval.

[JeWeizhong]

What does the output below mean.

 cd unitigging
    /public/canu_v2.0/Linux-amd64/bin/tgStoreDump \
      -S ../out.seqStore \
      -T ./out.ctgStore 2 \
      -sizes -s 1900000000 \
    > ./out.ctgStore/seqDB.v002.sizes.txt
sqStore_loadMetadata()-- Using 'corrected-trimmed' 0x10 reads.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.
ZERO length suplied to intervalList::add(), ignoring interval.

My program currently is running ,but it has no output so far

thanks

[skoren]

It's a warning which you can ignore as long as Canu doesn't stop with an error.

[JeWeizhong]

thanks. The cause of the previous problem is no storage space .

I find that alignGFA has always been stat D now, although the disks bas enough space.

public/canu_v2.0/Linux-amd64/bin/alignGFA -bed -T ../out.utgStore 2 -C ../out.ctgStore 2 -i ./out.unitigs.bed -o ./out.unitigs.aligned.bed -t 16

TAT START   TIME COMMAND
/4 D May21  42:10      \_ /public/canu_v2.0/Linux-amd64/bin/alignGFA -bed -T ../out.utgStore  2 -C ../out.ctgStore 2 -i ./out.unitigs.bed -o ./out.unitigs.aligned.bed -t 16

[skoren]

That may be OK assuming it's waiting for your disk to read/write. You could always kill that job and Canu will re-try alignGFA again in case this is an issue due to previously being out of space but I'm not sure it'd run any differently.

[skoren]

Idle