I am trying to use abyss, but even if I get the results and any error, the final file just have a few lines.

sample41-contigs.fa

>86 92 510 0+,13+
TGAGTCTCGTGTACCCATTCATTCATTTATTCATTCAGGTTAAGTTCCTATTTGAGGGCAGACCTTTGAGTCCAAGGAACTTGCCTTTTCCG
>87 100 510 1+,19+
TGACATGCTAGAAATGATATGAGTTGCTTCAACCTAGTTAAAGTGAAAATTTTAGTAGGAAATGAGGAAGGTGGCCTAGCCCATGACAGCATCAGGAACT
>88 94 510 16+,31+
TAGATGCTGGAATAAAACATAAAAACAAAACAAAGACCTTGGTGTAATGTACTATACAGGGAAGGGAATCAGATATTAAATACATATGTAGTAA
>89 97 510 20+,35+
CTGATTCTACATTATGATGAGTTGTATAATTATTTCATTATGAATTACAATGTAATAATAATAGAAATAAACTGCACAACAAATGTAATGCACTTGA
>90 100 510 33+,60+
AATAAAGACACATACTTCATGTAGTCAGAAGAGTGGTCTGAAGCAAAATATTCAAAGCCTATTGAAGAAATCATTTTAGAATTTTTCTACAAGTTTTTTC
>91 100 510 37+,59+
TTCTGTATTGCATTTCCGAACACTGGTGAGGAGTGCTTGGACCTGTGCCCTTTGCTGTCCAGGCTGCAATTTTCTCGTTGAGTATCACGTGAATATTTAT
>92 100 510 61+,85+
TAGGTGGGAGAATGCTTGAACCCAGGAGTTCAAGTCAAGCCAGGCAACACAGTGAAACCCTGTCTCTAAAACATAAATAAATAAAATAAAAATGGGACTT
>93 99 510 62+,84+
GTTTAAAATGTATATTTTACATACTTATTCTTCATTAGTGTTATGTAATATTAATGTCCTAAAGTCAGTTAACTGTAGCAACAACTTATGAGTTTTTCA

The samples looks like this:

@SRR062641.1 HWI-EAS110_103327062:5:1:1091:7885/1
GAAAGAAAGAAAGTCAACTGTATGCTTAAAAATCCAAGTTGTGGGTGGGAAGCTGATTGAATTTTTTACTACGGTTCATAAAAAAACACAAGACTCACAT
+
@7:6+)=0577''3=?->>;:A>A############################################################################
@SRR062641.2 HWI-EAS110_103327062:5:1:1092:19656/1
AGACTTTATCAAATTATAACTGGGATTAGATAGACAGTCCAGAATAATTTTAATAATTCATGTACATGCTTCATGTATTTTCCTTGCTTACACTTGCCTA
+
=@>@6?>A;AA?5?DDB5DD=DAD5-=?6@::A-ADDCD?C55,CB:AD?BD:5DD?BD=:5C@5C##################################
@SRR062641.3 HWI-EAS110_103327062:5:1:1092:17219/1
TTGAAGGATACAAAGTATTGATCCTGGGTGTGTCTGTGTGGGTGTTGCCAAAGGAGACTAACAGTGGAGTCAGGGGGCGGGGAAAGGCAGACCACCTGCT

and the 2 file

@SRR062641.1 HWI-EAS110_103327062:5:1:1091:7885/2
TCAATGAATGCACTTTAATTTTTTAAAATNNNNNNANATNATGATNTANTTTANNNNTNCAANAGAAGTGTTGGGTTTTTTTATGAACCGTTTTATCAAA
+
5DD=-B#######################!!!!!!#!##!#####!##!####!!!!#!###!#####################################
@SRR062641.2 HWI-EAS110_103327062:5:1:1092:19656/2
TCAATAACTTTATGGATAGTGTATCATCTNNNNNNCNAGNGAAATNTTNATACNNNNGNAACNACTGAAAATCTAGTTCATTGTTAGGCAAGATTCACCA
+
5DB-D-BDDD=D=D:--<9:-??6@3738!!!!!!6!15!;0?A9!;5!,782!!!!;!16*!25?25+=?<+@<CC=-:A?><A)4;->A:55:+=466
@SRR062641.3 HWI-EAS110_103327062:5:1:1092:17219/2
TGGGAGGCAAGGCCAGACTCACGTTCTTANNNNNNANTANCGGCTNTCNTCCGNNNNGNCGGNCAGCTGGGTAGGGTGTGTCCTCCCCCCTCAGGGGTGG

I run abyss like this:

abyss-pe k=88 name=sample41 B=50 in='SRR062641_1.fastq.gz SRR062641_2.fastq.gz'

The final report of abyss is this:

Best scaffold N50 is 100 at n=15 s=100. 



n       n:100   L50     min     N75     N50     N25     E-size  max     sum     name 

8       4       4       100     100     100     100     100     100     400     n=15 s=100 

abyss-stack-size 65536 PathConsensus  --dot -k88  -p0.9  -s sample41-7.fa -g sample41-7.dot -o sample41-7.path sample41-6.fa sample41-6.dot sample41-6.path 

Running with max stack size of 65536 KB: PathConsensus --dot -k88 -p0.9 -s sample41-7.fa -g sample41-7.dot -o sample41-7.path sample41-6.fa sample41-6.dot sample41-6.path 

Ambiguous paths: 0 

Merged:          0 

No paths:        0 

Too many paths:  0 

Too complex:     0 

Dissimilar:      0 

cat sample41-6.fa sample41-7.fa \ 

        | MergeContigs   -k88 -o sample41-8.fa - sample41-7.dot sample41-7.path 

ln -sf sample41-8.fa sample41-scaffolds.fa 

PathOverlap --overlap   -k88 --dot sample41-7.dot sample41-7.path >sample41-8.dot 

ln -sf sample41-8.dot sample41-scaffolds.dot 

abyss-fac   sample41-unitigs.fa sample41-contigs.fa sample41-scaffolds.fa |tee sample41-stats.tab 

n       n:500   L50     min     N75     N50     N25     E-size  max     sum     name 

8       0       0       0       0       0       0       0       0       0       sample41-unitigs.fa 

8       0       0       0       0       0       0       0       0       0       sample41-contigs.fa 

8       0       0       0       0       0       0       0       0       0       sample41-scaffolds.fa 

ln -sf sample41-stats.tab sample41-stats 

tr '\t' , <sample41-stats.tab >sample41-stats.csv 

abyss-tabtomd sample41-stats.tab >sample41-stats.md 

I dont understand the problem