Question: Abyss-pe de-novo assembler error
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gravatar for bruseq
2.7 years ago by
bruseq40
bruseq40 wrote:

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

de-novo assembly • 1.3k views
ADD COMMENTlink modified 2.7 years ago by WouterDeCoster40k • written 2.7 years ago by bruseq40

Hello divya.srivastava33!

It appears that your post has been cross-posted to another site: http://seqanswers.com/forums/showthread.php?p=202943#post202943

This is typically not recommended as it runs the risk of annoying people in both communities.

ADD REPLYlink written 2.7 years ago by WouterDeCoster40k
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