vg deconstruct error

[arslan9732]

Hi, I am running pggb with this command:

pggb -i ../Genomes/community/chr04.fa.gz \
     -o chr04 \
     -D chr04_tmp \
     --keep-temp-files \
     -n 11 \
     -t 200 \
     -p 90 \
     -s 5k \
     -V 'ref:1000' \
    --multiqc -S -r

But it gave this error:

Error [vg deconstruct]: No specified reference path or prefix found in graph
Command exited with non-zero status 1
vg deconstruct -P ref -H 1000 -e -a -t 200 chr04/chr04.fa.gz.3907ad6.417fcdf.c00ce9c.smooth.final.gfa

The fasta file headers are like this:

>Genome1#1#chr04
>Genome2#1#chr04
>Genome3#1#chr04
...
>Genome11#1#chr04

[AndreaGuarracino]

You have to specify the prefix of the genome you want to use as reference. For example, if Genome1#1#chr04 is your reference, you have to write -V Genome1:1000

pggb -i ../Genomes/community/chr04.fa.gz \
     -o chr04 \
     -D chr04_tmp \
     --keep-temp-files \
     -n 11 \
     -t 200 \
     -p 90 \
     -s 5k \
     -V 'Genome1:1000' \
    --multiqc -S -r

[arslan9732]

I ran it with your suggestion but it gave an empty vcf (except header lines), and didn't produce any error. Although it produced other files which seem to be fine.

[subwaystation]

Could you please post the name of your reference sequence in the graph and the actual command line?

[arslan9732]

I rerun it with 10 genomes (one genome is sequenced by short reads and the output graph is weird so I removed it). But when I look into the log file, it is stuck at vg deconstruct step.

odgi sort -P -p Ygs --temp-dir chr01-10_tmp -t 200 -i - -o chr01-10/chr01-10.fa.gz.3907ad6.417fcdf.c00ce9c.smooth.final.og
75460.47s user 1748.54s system 4510% cpu 1711.82s total 36418000Kb max memory
odgi view -i chr01-10/chr01-10.fa.gz.3907ad6.417fcdf.c00ce9c.smooth.final.og -g
161.22s user 85.18s system 98% cpu 251.08s total 15773864Kb max memory
Warning [vg deconstruct]: -H is deprecated, and will be ignored

libgomp:
libgomp: Thread creation failed: Resource temporarily unavailable

libgomp:
libgomp: Thread creation failed: Resource temporarily unavailable
Thread creation failed: Resource temporarily unavailable
Thread creation failed: Resource temporarily unavailable

libgomp: Thread creation failed: Resource temporarily unavailable

libgomp:
libgomp: Thread creation failed: Resource temporarily unavailable
Thread creation failed: Resource temporarily unavailable

libgomp: Thread creation failed: Resource temporarily unavailable

libgomp:
libgomp:
libgomp:
libgomp:
libgomp: Thread creation failed: Resource temporarily unavailable

libgomp:
libgomp: Thread creation failed: Resource temporarily unavailableThread creation failed: Resource temporarily unavailable

libgomp:
libgomp:
libgomp: Thread creation failed: Resource temporarily unavailable

This time the command was:

pggb -i ../Genomes/community/chr01-10.fa.gz \
     -o chr01-10 \
     -D chr01-10_tmp \
     --keep-temp-files \
     -n 11 \ #it should be 10 mistakenly running with 11
     -t ${NSLOTS} \
     -p 90 \
     -s 5k \
     -V 'Genome1:1000' \ #Genome1 as reference
    --multiqc -S -r

[arslan9732]

I am able to solve the issue. It was stuck at vg deconstruct step and gave thread creation failed error. I separately ran the vg deconstruct step and again got the same error. Actually it was a memory error. So I increased the memory and it ran successfully.