Abyss-PE error

[divya]

Hello
I am newer for abyss-pe assembler tool, the following mention below error is occur, but in my data there is no any duplicate ID present and i also run on different k-mer values are 32, 64,76.
The command I used is: abyss-pe name=de_novo_assemble k=76 in='D2_R1_split_filter.fastq D2_R2_split_filter.fastq'

Please guide me to solve this error.

genomics2@genomics2-Precision-Tower-7810:~/tools/imrdenom-0.4.1/abyss$ abyss-pe name=de_novo_assemble k=76 in='D2_R1_split_filter.fastq D2_R2_split_filter.fastq'
ABYSS -k76 -q3 --coverage-hist=coverage.hist -s de_novo_assemble-bubbles.fa -o de_novo_assemble-1.fa D2_R1_split_filter.fastq D2_R2_split_filter.fastq
ABySS 2.0.2
ABYSS -k76 -q3 --coverage-hist=coverage.hist -s de_novo_assemble-bubbles.fa -o de_novo_assemble-1.fa D2_R1_split_filter.fastq D2_R2_split_filter.fastq
Reading `D2_R1_split_filter.fastq'...
`D2_R1_split_filter.fastq': discarded 36 reads containing non-ACGT characters
Reading `D2_R2_split_filter.fastq'...
`D2_R2_split_filter.fastq': discarded 308 reads containing non-ACGT characters
Loaded 499505416 k-mer
Minimum k-mer coverage is 85
Using a coverage threshold of 3...
The median k-mer coverage is 7
The reconstruction is 128007680
The k-mer coverage threshold is 2.64575
Setting parameter e (erode) to 3
Setting parameter E (erodeStrand) to 1
Setting parameter c (coverage) to 2.64575
Generating adjacency
Added 1000899508 edges.
Eroding tips
Eroded 346910042 tips.
Eroded 0 tips.
Pruning tips shorter than 1 bp...
Pruned 12919 k-mer in 12919 tips.
Pruning tips shorter than 2 bp...
Pruned 7306 k-mer in 4035 tips.
Pruning tips shorter than 4 bp...
Pruned 12877 k-mer in 4525 tips.
Pruning tips shorter than 8 bp...
Pruned 34042 k-mer in 6708 tips.
Pruning tips shorter than 16 bp...
Pruned 122994 k-mer in 12951 tips.
Pruning tips shorter than 32 bp...
Pruned 406365 k-mer in 23260 tips.
Pruning tips shorter than 64 bp...
Pruned 1190519 k-mer in 37110 tips.
Pruning tips shorter than 76 bp...
Pruned 511513 k-mer in 11648 tips.
Pruning tips shorter than 76 bp...
Pruned 1247 k-mer in 29 tips.
Pruning tips shorter than 76 bp...
Pruned 113185 tips in 9 rounds.
Marked 3654131 edges of 1653207 ambiguous vertices.
Removing low-coverage contigs (mean k-mer coverage < 2.64575)
Found 150295213 k-mer in 2085178 contigs before removing low-coverage contigs.
Removed 25438641 k-mer in 702810 low-coverage contigs.
Split 1403295 ambigiuous branches.
Eroding tips
Eroded 2885197 tips.
Eroded 0 tips.
Pruning tips shorter than 1 bp...
Pruned 8520 k-mer in 8520 tips.
Pruning tips shorter than 2 bp...
Pruned 4180 k-mer in 2248 tips.
Pruning tips shorter than 4 bp...
Pruned 5448 k-mer in 1879 tips.
Pruning tips shorter than 8 bp...
Pruned 9936 k-mer in 2001 tips.
Pruning tips shorter than 16 bp...
Pruned 25514 k-mer in 2518 tips.
Pruning tips shorter than 32 bp...
Pruned 64040 k-mer in 3164 tips.
Pruning tips shorter than 64 bp...
Pruned 163941 k-mer in 3939 tips.
Pruning tips shorter than 76 bp...
Pruned 75415 k-mer in 1181 tips.
Pruning tips shorter than 76 bp...
Pruned 104 k-mer in 8 tips.
Pruning tips shorter than 76 bp...
Pruned 25458 tips in 9 rounds.
Popping bubbles
Removed 9468 bubbles.
Removed 9468 bubbles
Marked 911690 edges of 418182 ambiguous vertices.
Left 4725 unassembled k-mer in circular contigs.
Assembled 120784058 k-mer in 552479 contigs.
Removed 377890760 k-mer.
The signal-to-noise ratio (SNR) is -4.9238 dB.
AdjList -k76 -m50 --dot de_novo_assemble-1.fa >de_novo_assemble-1.dot
abyss-filtergraph --dot -k76 -g de_novo_assemble-2.dot1 de_novo_assemble-1.dot de_novo_assemble-1.fa >de_novo_assemble-1.path
MergeContigs -k76 -g de_novo_assemble-2.dot -o de_novo_assemble-2.fa de_novo_assemble-1.fa de_novo_assemble-2.dot1 de_novo_assemble-1.path
PopBubbles --dot -j2 -k76 -p0.9 -g de_novo_assemble-3.dot de_novo_assemble-2.fa de_novo_assemble-2.dot >de_novo_assemble-2.path
MergeContigs -k76 -o de_novo_assemble-3.fa de_novo_assemble-2.fa de_novo_assemble-2.dot de_novo_assemble-2.path
The minimum coverage of single-end contigs is 2.5625.
The minimum coverage of merged contigs is 2.64706.
Consider increasing the coverage threshold parameter, c, to 2.64706.
awk '!/^>/ {x[">" $1]=1; next} {getline s} $1 in x {print $0 "\n" s}' \
de_novo_assemble-2.path de_novo_assemble-1.fa >de_novo_assemble-indel.fa
ln -sf de_novo_assemble-3.fa de_novo_assemble-unitigs.fa
abyss-map -j2 -l40 D2_R1_split_filter.fastq D2_R2_split_filter.fastq de_novo_assemble-3.fa \
|abyss-fixmate -l40 -h de_novo_assemble-3.hist \
|sort -snk3 -k4 \
|DistanceEst -j2 -k76 -l40 -s1000 -n10 -o de_novo_assemble-3.dist de_novo_assemble-3.hist
Building the suffix array...
Building the Burrows-Wheeler transform...
Building the character occurrence table...
error: duplicate read ID `NS500278:15:H2LTCAFXX:1:11101:12362:1019/1'
error: `de_novo_assemble-3.hist': No such file or directory
/usr/local/bin/abyss-pe:559: recipe for target 'de_novo_assemble-3.dist' failed
make: *** [de_novo_assemble-3.dist] Error 1
make: *** Deleting file 'de_novo_assemble-3.dist'



Thank you,
Divya

[GenoMax]

@divya: Please don't post new questions in unrelated threads. You are not likely to get answers if you do that. I moved your post to a new question.

For future reference to create a new thread do this: From seqanswers.com --> Forum (link at top left of page) --> Select forum you want to post in --> Click on "New Thread" button at top left of next page.

[GenoMax]

Have you checked your file with grep to see if you indeed have two records?

$ grep "NS500278:15:H2LTCAFXX:1:11101:12362:1019/1" D2_R1_split_filter.fastq

[divya]

sir,
I have already checked with this grep command , there are no duplicates reads both in R1 and R2 files.