abyss-pe - no LIB-contigs.fa !!!

[savkart]

Hi all,

I'm new at using ABySS and when I ran the following command on ABySS v 1.2.7:

abyss-pe k=25 n=10 in=' /path/to/reads/file/1 /path/to/read/files/2' name=LIB

the following files got created in the output directory:
coverage.hist LIB-1.adj LIB-1.fa LIB-1.path LIB-3.adj LIB-3.fa LIB-3.sam.gz LIB-bubbles.fa LIB-indel.fa

Now, obviously I'm missing something because the main assembly file, LIB-contigs.fa is missing! Any ideas what I'm doing wrong?

Any help much appreciated! Thanks in advance!

[crazee]

Did you check if it completed? if yes, what was the error?

[kweitemier]

I'm a new ABySS user, too. What is the best way to tell if the whole abyss-pe program has completed? If there is no error message can I assume all of the separate pieces ran properly? What is the last file that gets made from an abyss-pe run?

[crazee]

I'm a new ABySS user, too. What is the best way to tell if the whole abyss-pe program has completed? If there is no error message can I assume all of the separate pieces ran properly? What is the last file that gets made from an abyss-pe run?

prefix.contigs.fa

[gpcr]

i have similar problem with abyss-pe

contig.fa file not created?

KAligner: Aligner.cpp:201: void Aligner<SeqPosHashMap>::coalesceAlignments(const std::string&, const std::string&, const std::map<unsigned int, std::vector<Alignment, std::allocator<Alignment> >, std::less<unsigned int>, std::allocator<std:air<const unsigned int, std::vector<Alignment, std::allocator<Alignment> > > > >&, oiterator&) [with oiterator = affix_ostream_iterator<Alignment, char, std::char_traits<char> >, SeqPosHashMap = google::sparse_hash_map<Kmer, Position, hashKmer, std::equal_to<Kmer>, google::libc_allocator_with_realloc<std:air<const Kmer, Position> > >]: Assertion `qstep >= 0 && qstep <= m_hashSize' failed.


any suggestions?

[crazee]

contig.fa file not created?

KAligner: Aligner.cpp:201: void Aligner<SeqPosHashMap>::coalesceAlignments(const std::string&, const std::string&, const std::map<unsigned int, std::vector<Alignment, std::allocator<Alignment> >, std::less<unsigned int>, std::allocator<std:air<const unsigned int, std::vector<Alignment, std::allocator<Alignment> > > > >&, oiterator&) [with oiterator = affix_ostream_iterator<Alignment, char, std::char_traits<char> >, SeqPosHashMap = google::sparse_hash_map<Kmer, Position, hashKmer, std::equal_to<Kmer>, google::libc_allocator_with_realloc<std:air<const Kmer, Position> > >]: Assertion `qstep >= 0 && qstep <= m_hashSize' failed.


any suggestions?

1) Check and make sure your FASTA/Q is properly formatted.
2) What OS and version of ABySS are you running?

[gpcr]

abyss 1.3.0

working on linux 64bit with
using fastq files as input:

abyss-pe k=25 n=5 in='read_1.fq read_2.fq' name=test_assembly

[gpcr]

abyss-pe log file

abyss-pe k=25 n=5 in='read_1.fq read_2.fq' name=l3.assemb
ABYSS -k25 -q3 --coverage-hist=coverage.hist -s l3.assemb-bubbles.fa -o l3.assemb-1.fa read_1.fq read_2.fq
ABySS 1.3.0
ABYSS -k25 -q3 --coverage-hist=coverage.hist -s l3.assemb-bubbles.fa -o l3.assemb-1.fa read_1.fq read_2.fq
Reading `read_1.fq'
warning: discarded 182472 reads shorter than 25 bases
warning: discarded 1432 reads containing non-ACGT characters
Reading `read_2.fq'
warning: discarded 238597 reads shorter than 25 bases
warning: discarded 2700 reads containing non-ACGT characters
Loaded 146346864 k-mer
Minimum k-mer coverage is 109
Using a coverage threshold of 1...
The median k-mer coverage is 1
The reconstruction is 146346864
The k-mer coverage threshold is 1
Setting parameter e (erode) to 2
Setting parameter E (erodeStrand) to 0
Setting parameter c (coverage) to 2
Generating adjacency
Generated 296878979 edges
Eroding tips
Eroded 90751073 tips
Eroded 0 tips
Trimming short branches: 1
Trimmed 27669 k-mer in 27669 branches
Trimming short branches: 2
Trimmed 49179 k-mer in 36794 branches
Trimming short branches: 4
Trimmed 111726 k-mer in 49654 branches
Trimming short branches: 8
Trimmed 364902 k-mer in 92156 branches
Trimming short branches: 16
Trimmed 1014622 k-mer in 137128 branches
Trimming short branches: 25
Trimmed 1461718 k-mer in 118076 branches
Trimming short branches: 25
Trimmed 2656 k-mer in 368 branches
Trimming short branches: 25
Trimmed 28 k-mer in 2 branches
Trimming short branches: 25
Trimmed 461847 branches in 8 rounds
Marked 10864648 edges of 4561491 ambiguous vertices.
Removing low-coverage contigs (mean k-mer coverage < 2)
Found 52488076 k-mer in 4455293 contigs before removing low-coverage contigs
Removed 18572627 k-mer in 1116544 low-coverage contigs
Split 2149168 ambiguous branches
Eroding tips
Eroded 23353 tips
Eroded 0 tips
Trimming short branches: 1
Trimmed 48815 k-mer in 48815 branches
Trimming short branches: 2
Trimmed 56035 k-mer in 37425 branches
Trimming short branches: 4
Trimmed 116454 k-mer in 46787 branches
Trimming short branches: 8
Trimmed 198753 k-mer in 44809 branches
Trimming short branches: 16
Trimmed 305805 k-mer in 36891 branches
Trimming short branches: 25
Trimmed 275715 k-mer in 19293 branches
Trimming short branches: 25
Trimmed 836 k-mer in 97 branches
Trimming short branches: 25
Trimmed 14 k-mer in 1 branches
Trimming short branches: 25
Trimmed 234118 branches in 8 rounds
Popping bubbles
Removed 6309 bubbles
Removed 6309 bubbles
Marked 5519489 edges of 2275426 ambiguous vertices.
108618 unassembled k-mer in circular contigs
Assembled 32672488 k-mer in 2249263 contigs
Removed 113381980 k-mer.
The signal-to-noise ratio (SNR) is -5.36492 dB.
AdjList -k25 -m30 l3.assemb-1.fa >l3.assemb-1.adj
PopBubbles -j2 -k25 -p0.9 -g l3.assemb-3.adj l3.assemb-1.fa l3.assemb-1.adj >l3.assemb-1.path
MergeContigs -k25 -o l3.assemb-3.fa l3.assemb-1.fa l3.assemb-1.adj l3.assemb-1.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}' \
l3.assemb-1.path l3.assemb-1.fa >l3.assemb-indel.fa
KAligner -j2 -k25 read_1.fq read_2.fq l3.assemb-3.fa \
|ParseAligns -k25 -h l3.assemb-3.hist \
|sort -snk3 -k4 \
|gzip >l3.assemb-3.sam.gz
KAligner: Aligner.cpp:201: void Aligner<SeqPosHashMap>::coalesceAlignments(const std::string&, const std::string&, const std::map<unsigned int, std::vector<Alignment, std::allocator<Alignment> >, std::less<unsigned int>, std::allocator<std:air<const unsigned int, std::vector<Alignment, std::allocator<Alignment> > > > >&, oiterator&) [with oiterator = affix_ostream_iterator<Alignment, char, std::char_traits<char> >, SeqPosHashMap = google::sparse_hash_map<Kmer, Position, hashKmer, std::equal_to<Kmer>, google::libc_allocator_with_realloc<std:air<const Kmer, Position> > >]: Assertion `qstep >= 0 && qstep <= m_hashSize' failed.
Mateless 0
Unaligned 1 2.86%
Singleton 3 8.57%
FR 5 14.3%
RF 0
FF 0
Different 2 5.71%
Multimap 0
Split 24 68.6%
Total 35
/bin/bash: line 3: 19667 Aborted KAligner -j2 -k25 read_1.fq read_2.fq l3.assemb-3.fa
19668 Done | ParseAligns -k25 -h l3.assemb-3.hist
19669 Done | sort -snk3 -k4
19670 Done | gzip > l3.assemb-3.sam.gz
make: *** [l3.assemb-3.hist] Error 134
make: *** Deleting file `l3.assemb-3.hist'


Any suggestions?

[crazee]

This the command i use: nohup /usr/local/bin/abyss/bin/abyss-pe k=25 j=8 n=10 in='s_4_1_sequence.txt s_4_2_sequence.txt' name=QC_10

Ubuntu 10.04 64 bit, abyss 1.2.5

...at this point try switching to 1.2.5

[jelhai]

I did essentially the same thing as gpcr, also using abyss 1.3.0, and got the same error message (at the KAligner step). I preceded abyss-pe with nohup, but the result was the same.

I tried using an earlier version (1.2.7 happened to be available). With that, I got an error message at the PopBubbles step (just before KAligner):

/usr/global/bioscope/bioscope/lib/local/libgomp.so.1: version `GOMP_2.0' not found (required by PopBubbles)

Perhaps installing Abyss 1.3.0 updated bioscope so that 1.2.7 would no longer work?

Uninstalling 1.3.0 is not a practical option.

Thanks.

[sagarutturkar]

I want to use abyss for paired reads assembly. But I have paired reads (Forward and reverse) in single file. This is the file generated after quality trimming.
The file structure is
>001_forward
ATGC.......
>001_reverse
ATGC....
>002_forward
ATGC....
>002_reverse
ATGC....

How do I run Abyss for such file? I need command for this. Any suggestions?