error in running of abyss-1.3.3

[gopal misra]

Hi Shaun,
               I have successfully installed the ABySS-1.3.3 . But after running on my paired-end data, i have got some error.Below , i have given that error . kindly help me .
              Error:
                 error: the histogram `pe1-3.hist' is empty
                 make: *** [pe1-3.dist] Error 1
                 make: *** Deleting file `pe1-3.dist'

--
“It is not the strongest of the species that survives, nor the most intelligent, but the one most responsive to change”
― Charles Darwin



Gopal Misra,
Senior Research Fellow,
National Institute of Plant Genome Research,
New Delhi,
India

[Shaun Jackman]

Hi Gopal,

Please report the exact command line that you used and the complete log.

Cheers,
Shaun

[Yifang Tan]

Not sure my message went thru? Apology if I repeated.
Hi, Shaun!

I met exactly the same problem as Gopal. Here is my command line and
the messages on the screen.
================================================================
yifang@grape3:/disks$ abyss-pe k=60 n=10 in='S00092C_CGATGT_L006_R1.fq
S00092C_CGATGT_L006_R2.fq S00092D_CTTGTA_L006_R1.fq
S00092D_CTTGTA_L006_R2.fq' name=bacpool
ABYSS -k60 -q3 --coverage-hist=coverage.hist -s bacpool-bubbles.fa -
o bacpool-1.fa S00092C_CGATGT_L006_R1.fq S00092C_CGATGT_L006_R2.fq
S00092D_CTTGTA_L006_R1.fq S00092D_CTTGTA_L006_R2.fq
ABySS 1.3.3
ABYSS -k60 -q3 --coverage-hist=coverage.hist -s bacpool-bubbles.fa -o
bacpool-1.fa S00092C_CGATGT_L006_R1.fq S00092C_CGATGT_L006_R2.fq
S00092D_CTTGTA_L006_R1.fq S00092D_CTTGTA_L006_R2.fq
Reading `S00092C_CGATGT_L006_R1.fq'...
`S00092C_CGATGT_L006_R1.fq': discarded 79329 reads shorter than 60
bases
`S00092C_CGATGT_L006_R1.fq': discarded 10476containing non-ACGT
characters
Reading `S00092C_CGATGT_L006_R2.fq'...
`S00092C_CGATGT_L006_R2.fq': discarded 263661 reads shorter than 60
bases
`S00092C_CGATGT_L006_R2.fq': discarded 2080containing non-ACGT
characters
Reading `S00092D_CTTGTA_L006_R1.fq'...
`S00092D_CTTGTA_L006_R1.fq': discarded 110127 reads shorter than 60
bases
`S00092D_CTTGTA_L006_R1.fq': discarded 13489containing non-ACGT
characters
Reading `S00092D_CTTGTA_L006_R2.fq'...
`S00092D_CTTGTA_L006_R2.fq': discarded 326281 reads shorter than 60
bases
`S00092D_CTTGTA_L006_R2.fq': discarded 2275containing non-ACGT
characters
Loaded 185484495 k-mer
Minimum k-mer coverage is 249
Using a coverage threshold of 4...
The median k-mer coverage is 16
The reconstruction is 50262077
The k-mer coverage threshold is 4
Setting parameter e (erode) to 4
Setting parameter E (erodeStrand) to 1
Setting parameter c (coverage) to 4
Generating adjacency
Added 370619063 edges.
Eroding tips
Eroded 129492755 tips.
Eroded 0 tips.
Pruning tips shorter than 1 bp...
Pruned 1006 k-mer in 1006 tips.
Pruning tips shorter than 2 bp...
Pruned 1201 k-mer in 836 tips.
Pruning tips shorter than 4 bp...
Pruned 3836 k-mer in 1571 tips.
Pruning tips shorter than 8 bp...
Pruned 12768 k-mer in 2798 tips.
Pruning tips shorter than 16 bp...
Pruned 42258 k-mer in 4810 tips.
Pruning tips shorter than 32 bp...
Pruned 130710 k-mer in 7970 tips.
Pruning tips shorter than 60 bp...
Pruned 291556 k-mer in 9825 tips.
Pruning tips shorter than 60 bp...
Pruned 1081 k-mer in 46 tips.
Pruning tips shorter than 60 bp...
Pruned 28862 tips in 8 rounds.
Marked 1828737 edges of 847144 ambiguous vertices.
Removing low-coverage contigs (mean k-mer coverage < 4)
Found 55506950 k-mer in 1054497 contigs before removing low-coverage
contigs.
Removed 5035482 k-mer in 153427 low-coverage contigs.
Split 293932 ambigiuous branches.
Eroding tips
Eroded 65466 tips.
Eroded 0 tips.
Pruning tips shorter than 1 bp...
Pruned 758 k-mer in 758 tips.
Pruning tips shorter than 2 bp...
Pruned 852 k-mer in 679 tips.
Pruning tips shorter than 4 bp...
Pruned 2640 k-mer in 1145 tips.
Pruning tips shorter than 8 bp...
Pruned 6896 k-mer in 1625 tips.
Pruning tips shorter than 16 bp...
Pruned 18049 k-mer in 1838 tips.
Pruning tips shorter than 32 bp...
Pruned 24676 k-mer in 1254 tips.
Pruning tips shorter than 60 bp...
Pruned 42331 k-mer in 1060 tips.
Pruning tips shorter than 60 bp...
Pruned 59 k-mer in 2 tips.
Pruning tips shorter than 60 bp...
Pruned 8361 tips in 8 rounds.
Popping bubbles
Removed 2920 bubbles.
Removed 2920 bubbles
Marked 1188462 edges of 562763 ambiguous vertices.
Left 37221 unassembled k-mer in circular contigs.
Assembled 50057048 k-mer in 701182 contigs.
Removed 135174380 k-mer.
The signal-to-noise ratio (SNR) is -4.29239 dB.
AdjList -k60 -m30 bacpool-1.fa >bacpool-1.adj
abyss-filtergraph -k60 -g bacpool-2.adj bacpool-1.adj >bacpool-1.path
PopBubbles -j2 -k60 -p0.9 -g bacpool-3.adj bacpool-1.fa
bacpool-2.adj >bacpool-2.path
MergeContigs -k60 -o bacpool-3.fa bacpool-1.fa bacpool-2.adj
bacpool-2.path
The minimum coverage of single-end contigs is 3.25.
The minimum coverage of merged contigs is 4.
Consider increasing the coverage threshold parameter, c, to 4.
awk '!/^>/ {x[">" $1]=1; next} {getline s} $1 in x {print $0 "\n" s}'
\
bacpool-2.path bacpool-1.fa >bacpool-indel.fa
ln -sf bacpool-3.fa bacpool-unitigs.fa
abyss-map -j2 -l60 S00092C_CGATGT_L006_R1.fq
S00092C_CGATGT_L006_R2.fq S00092D_CTTGTA_L006_R1.fq
S00092D_CTTGTA_L006_R2.fq bacpool-3.fa \
|abyss-fixmate -h bacpool-3.hist \
|sort -snk3 -k4 \
|DistanceEst -j2 -k60 -l60 -s200 -n10 -o bacpool-3.dist
bacpool-3.hist
error: abyss has been compiled to use the POPCNT
instruction, which this machine lacks. Recompile using
configure --disable-popcnt to disable this feature.
Mateless 0
Unaligned 0
Singleton 0
FR 0
RF 0
FF 0
Different 0
Total 0
error: the histogram `bacpool-3.hist' is empty
make: *** [bacpool-3.dist] Error 1
make: *** Deleting file `bacpool-3.dist'
yifang@grape3:disks/$
============================================================
How to fix it? Or, is the error just a warning? I am nervous if
everything is going well. Thanks a lot!

Yifang

[Shaun Jackman]

Hi Yifang,

The error message states:

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

Cheers,
Shaun

[Tony Raymond]

Hi,

If your goal is to test the installation, it is sufficient to run the command under "Assemble a small synthetic data set" from the README.md file. i.e.:

abyss-pe k=25 name=test \
se=https://raw.github.com/dzerbino/velvet/master/data/test_reads.fa

For details on how to run ABySS with paired end libraries, see the section "Assembling a paired-end library". 

Cheers,

Tony

On 2012-10-10, at 7:32 AM, Guang wrote:

Hi ，Please give me a standard paired-end file,i have installed Abyss,but i do not know how to use it,i need use it to deal paired-end,my email is 4171...@qq.com.Thanks~~~~~~~~~~~`

[Guang]

Hi,Tony:

     thank you .if i run ABySS with paired end libraries,i need input file,a PE file,se=https://raw.github.com/dzerbino/velvet/master/data/test_reads.fa is SE file.

    Guang

在 2012年10月11日星期四UTC+8上午8时08分19秒，tray...@bcgsc.ca写道：o

[Tony Raymond]

That is correct.

Tony