the histogram `human-3.hist' is empty

[Mie]

Hi

I have a problem here when I used ABySS to assemble paired-end fastq data, the error as below and my command is here ( abyss-pe name=human k=64 in='SRR201165_1.fastq SRR201165_2.fastq' )
 
Please advice, thank you.


Marked 1341547 edges of 511681 ambiguous vertices.
Left 669 unassembled k-mer in circular contigs.
Assembled 17518402 k-mer in 465587 contigs.
Removed 113411781 k-mer.
The signal-to-noise ratio (SNR) is -8.08002 dB.
AdjList  -k64 -m50 human-1.fa >human-1.adj
abyss-filtergraph  -k64 -g human-2.adj human-1.adj >human-1.path
PopBubbles  -j2 -k64 -p0.9  -g human-3.adj human-1.fa human-2.adj >human-2.path
MergeContigs  -k64 -o human-3.fa human-1.fa human-2.adj human-2.path
The minimum coverage of single-end contigs is 2.
The minimum coverage of merged contigs is 2.
awk '!/^>/ {x[">" $1]=1; next} {getline s} $1 in x {print $0 "\n" s}' \
                human-2.path human-1.fa >human-indel.fa
ln -sf human-3.fa human-unitigs.fa
abyss-map  -j2 -l64   SRR201165_1.fastq SRR201165_2.fastq human-3.fa \
                |abyss-fixmate   -h human-3.hist \
                |sort -snk3 -k4 \
                |DistanceEst  -j2 -k64 -l64 -s200 -n10   -o human-3.dist human-3.hist
error: abyss has been compiled to use the POPCNT
instruction, which this machine lacks. Recompile using
configure --disable-popcnt to disable this feature.
Mateless   0
Unaligned  0
Singleton  0
FR         0
RF         0
FF         0
Different  0
Total      0
error: the histogram `human-3.hist' is empty
make: *** [human-3.dist] Error 1
make: *** Deleting file `human-3.dist'

[Wan Fahmi]

This is the output data that I generated.

-rw-------  1 v1wwanm users      94347 Oct 23 11:11 coverage.hist
-rw-------  1 v1wwanm users   19027847 Oct 23 11:41 human-1.adj
-rw-------  1 v1wwanm users   54018269 Oct 23 11:41 human-1.fa
-rw-------  1 v1wwanm users      61809 Oct 23 11:42 human-1.path
-rw-------  1 v1wwanm users   19042994 Oct 23 11:42 human-2.adj
-rw-------  1 v1wwanm users     199957 Oct 23 11:42 human-2.path
-rw-------  1 v1wwanm users   18494460 Oct 23 11:42 human-3.adj
-rw-------  1 v1wwanm users   52449900 Oct 23 11:42 human-3.fa
-rw-------  1 v1wwanm users          0 Oct 23 11:42 human-3.hist
-rw-------  1 v1wwanm users     559097 Oct 23 11:40 human-bubbles.fa
-rw-------  1 v1wwanm users     118730 Oct 23 11:42 human-indel.fa
lrwxrwxrwx  1 v1wwanm users         10 Oct 23 11:42 human-unitigs.fa -> human-3.fa
-rw-------  1 v1wwanm users        150 Oct 23 10:08 optimize
-rw-------  1 v1wwanm users 8367797141 Oct 18 12:35 SRR201165_1.fastq
-rw-------  1 v1wwanm users 8367797141 Oct 18 12:33 SRR201165_2.fastq


Thanks

[Tony Raymond]

Hi,

The important error here is this:

error: abyss has been compiled to use the POPCNT
instruction, which this machine lacks. Recompile using
configure --disable-popcnt to disable this feature.

Recompiling using the configure option --disable-popcnt will fix the problem.

Cheers,

Tony

[Wan Fahmi]

Its works!

Thanks Tony