SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
ABYSS pe error BabyFaruda Illumina/Solexa 1 09-28-2015 01:21 PM
ABySS error JManuelMonroyKuhn Bioinformatics 1 11-29-2014 04:17 AM
abyss error zjrouc Bioinformatics 8 07-09-2013 02:35 PM
abyss-pe error jjjscuedu Bioinformatics 2 06-02-2012 08:02 AM
Abyss-PE error joa_ds Bioinformatics 1 11-30-2010 09:32 PM

Reply
 
Thread Tools
Old 01-12-2017, 05:01 AM   #1
divya
Junior Member
 
Location: india

Join Date: Nov 2016
Posts: 5
Default Abyss-PE error

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.

[email protected]:~/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
divya is offline   Reply With Quote
Old 01-12-2017, 05:05 AM   #2
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 6,585
Default

@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 is offline   Reply With Quote
Old 01-12-2017, 07:18 AM   #3
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 6,585
Default

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

Code:
$ grep "NS500278:15:H2LTCAFXX:1:11101:12362:1019/1" D2_R1_split_filter.fastq
GenoMax is offline   Reply With Quote
Old 01-12-2017, 08:50 PM   #4
divya
Junior Member
 
Location: india

Join Date: Nov 2016
Posts: 5
Default

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

Last edited by divya; 01-12-2017 at 08:59 PM.
divya is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 01:21 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2017, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO