Question: BAN - Best alignment normalisation error
0
gravatar for pinninti1991reddy
15 months ago by
pinninti1991reddy30 wrote:

Hi While performing vcf normalisation I go this error using BAN software. Is it mummer showing the error ?

Is their any better vcf normalisation softwares better than BAN ?

Check the execution process. Kindly suggest me, thanks.

CMD:

$ ban.sh dip /home/likithreddy/Downloads/BANv1/inoutput/hg38.fa /home/likithreddy/Downloads/BANv1/inoutput/SRR098401phased.vcf 


======================================
Best Alignment Normalization (BAN)
======================================
Command:               dip
Input fasta file name: /home/likithreddy/Downloads/BANv1/inoutput/hg38
Input VCF file name:   /home/likithreddy/Downloads/BANv1/inoutput/SRR098401phased
Normalization with available phasing (Input VCF must be phased)
======================================


 *BAN* Breaking down multiallelic variants into simple hetrozygous variants ... 
 *BAN* Done. 
 *BAN* Dividing diploid VCF into 2 haploid VCF (Phasing from VCF files) ... 
 *BAN* Done. 
 *BAN* Normalizing first haploid VCF ... 
 *BAN* Createing sequence from a haploid VCF ... 
INFO  19:06:21,281 HelpFormatter - --------------------------------------------------------------------------------- 
INFO  19:06:21,282 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12 
INFO  19:06:21,282 HelpFormatter - Copyright (c) 2010 The Broad Institute 
INFO  19:06:21,282 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk 
INFO  19:06:21,284 HelpFormatter - Program Args: -T FastaAlternateReferenceMaker -R /home/likithreddy/Downloads/BANv1/inoutput/hg38.fa -o /home/likithreddy/Downloads/BANv1/inoutput/SRR098401phased.A1.fasta -V /home/likithreddy/Downloads/BANv1/inoutput/SRR098401phased.A1.vcf 
INFO  19:06:21,286 HelpFormatter - Executing as likithreddy@Curium on Linux 4.13.0-26-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_151-8u151-b12-0ubuntu0.16.04.2-b12. 
INFO  19:06:21,286 HelpFormatter - Date/Time: 2018/01/20 19:06:21 
INFO  19:06:21,286 HelpFormatter - --------------------------------------------------------------------------------- 
INFO  19:06:21,286 HelpFormatter - --------------------------------------------------------------------------------- 
INFO  19:06:21,323 GenomeAnalysisEngine - Strictness is SILENT 
INFO  19:06:21,517 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 
INFO  19:06:23,223 RMDTrackBuilder - Writing Tribble index to disk for file /home/likithreddy/Downloads/BANv1/inoutput/SRR098401phased.A1.vcf.idx 
INFO  19:06:27,504 GenomeAnalysisEngine - Preparing for traversal 
INFO  19:06:27,515 GenomeAnalysisEngine - Done preparing for traversal 
INFO  19:06:27,515 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] 
INFO  19:06:27,516 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining 
INFO  19:06:27,516 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime 
INFO  19:06:57,572 ProgressMeter -  chr1:111479301     1.114E8    30.0 s       0.0 s        3.5%    14.4 m      13.9 m 
INFO  19:07:27,572 ProgressMeter -  chr1:225761701     2.257E8    60.0 s       0.0 s        7.0%    14.2 m      13.2 m 
INFO  19:07:57,573 ProgressMeter -  chr10:85436301   3.34356422E8    90.0 s       0.0 s       10.4%    14.4 m      12.9 m 
INFO  19:08:37,574 ProgressMeter -  chr11:93784001   4.76453844E8     2.2 m       0.0 s       14.8%    14.6 m      12.4 m 
INFO  19:09:17,574 ProgressMeter - chr12:102146801   6.20040782E8     2.8 m       0.0 s       19.3%    14.7 m      11.8 m 
INFO  19:09:47,575 ProgressMeter -  chr13:79427601   7.30616091E8     3.3 m       0.0 s       22.8%    14.6 m      11.3 m 
INFO  19:10:27,576 ProgressMeter -   chr15:8400101   8.82116757E8     4.0 m       0.0 s       27.5%    14.6 m      10.6 m 
INFO  19:11:07,576 ProgressMeter -  chr16:54926101   1.031056194E9     4.7 m       0.0 s       32.1%    14.5 m       9.9 m 
INFO  19:11:37,577 ProgressMeter -  chr17:75322001   1.143667298E9     5.2 m       0.0 s       35.6%    14.5 m       9.3 m 
INFO  19:12:17,578 ProgressMeter -    chr2:1316001   1.293237141E9     5.8 m       0.0 s       40.3%    14.5 m       8.6 m 
INFO  19:12:57,578 ProgressMeter -  chr2:151999901   1.443837141E9     6.5 m       0.0 s       45.0%    14.4 m       7.9 m 
INFO  19:13:27,579 ProgressMeter -  chr20:19460001   1.55353067E9     7.0 m       0.0 s       48.4%    14.5 m       7.5 m 
INFO  19:14:07,580 ProgressMeter -    chr3:7838601   1.705257606E9     7.7 m       0.0 s       53.1%    14.4 m       6.8 m 
INFO  19:14:37,580 ProgressMeter -  chr3:119177901   1.816557606E9     8.2 m       0.0 s       56.6%    14.4 m       6.3 m 
INFO  19:15:07,581 ProgressMeter -   chr4:31758701   1.927608562E9     8.7 m       0.0 s       60.1%    14.4 m       5.8 m 
INFO  19:15:47,582 ProgressMeter -  chr4:179237901   2.075108562E9     9.3 m       0.0 s       64.7%    14.4 m       5.1 m 
INFO  19:16:27,582 ProgressMeter -  chr5:138243201   2.224532826E9    10.0 m       0.0 s       69.3%    14.4 m       4.4 m 
INFO  19:16:57,583 ProgressMeter -   chr6:68162601   2.336063774E9    10.5 m       0.0 s       72.8%    14.4 m       3.9 m 
INFO  19:17:37,584 ProgressMeter -   chr7:47172301   2.485869753E9    11.2 m       0.0 s       77.5%    14.4 m       3.2 m 
INFO  19:18:07,585 ProgressMeter -  chr7:157826101   2.596569753E9    11.7 m       0.0 s       80.9%    14.4 m       2.8 m 
INFO  19:18:47,586 ProgressMeter -    chr9:2084101   2.745254362E9    12.3 m       0.0 s       85.5%    14.4 m       2.1 m 
INFO  19:19:27,586 ProgressMeter - chr6_GL000250v2_alt:3866801   2.897733021E9    13.0 m       0.0 s       90.3%    14.4 m      83.0 s 
INFO  19:19:57,587 ProgressMeter -   chrX:19353501   3.015280555E9    13.5 m       0.0 s       94.0%    14.4 m      52.0 s 
INFO  19:20:27,588 ProgressMeter -  chrX:131819001   3.127780555E9    14.0 m       0.0 s       97.5%    14.4 m      21.0 s 
INFO  19:20:47,825 ProgressMeter -            done   3.209286105E9    14.3 m       0.0 s      100.0%    14.3 m       0.0 s 
INFO  19:20:47,825 ProgressMeter - Total runtime 860.31 secs, 14.34 min, 0.24 hours 
INFO  19:20:49,708 GATKRunReport - Uploaded run statistics report to AWS S3 
 *BAN* Done. 
 *BAN* Aligning sequence to the reference ... 
1: PREPARING DATA
2,3: RUNNING mummer AND CREATING CLUSTERS
# reading input file "/home/likithreddy/Downloads/BANv1/inoutput/SRR098401phased.A1.ntref" of length 3209286560
# construct suffix tree for sequence of length 3209286560
# (maximum reference length is 536870908)
# (maximum query length is 4294967295)
# process 32092865 characters per dot
/home/likithreddy/Downloads/BANv1/BIN/MUMmer/mummer: suffix tree construction failed: textlen=3209286560 larger than maximal textlen=536870908
ERROR: mummer and/or mgaps returned non-zero
ERROR: Could not parse delta file, /home/likithreddy/Downloads/BANv1/inoutput/SRR098401phased.A1.delta
error no: 400
 *BAN* Done. 
 *BAN* Converting alignment to VCF format ... 
ERROR: Could not parse delta file, /home/likithreddy/Downloads/BANv1/inoutput/SRR098401phased.A1.filter
error no: 402
ADD COMMENTlink modified 15 months ago by Biostar ♦♦ 20 • written 15 months ago by pinninti1991reddy30
1

Hello pinninti1991reddy!

Please follow up on your questions. See C: Readgroups for a bam file ?

For this reason we have closed your question.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

ADD REPLYlink modified 12 months ago • written 12 months ago by RamRS21k
1
gravatar for h.mon
15 months ago by
h.mon24k
Brazil
h.mon24k wrote:

Yes, it was MUMmer that failed, due to:

/home/likithreddy/Downloads/BANv1/BIN/MUMmer/mummer: suffix tree construction failed: textlen=3209286560 larger than maximal textlen=536870908

You can try SMaSH or vt for normalization.

edit: by the way, the (still beta) MUMmer 4 may work as a replacement for use in BAN, if the command-line did not change:

The major changes in MUMmer4 primarily affect nucmer, which can now handle genomes of unlimited size and now runs multi-threaded. A paper is in preparation; stay tuned.

ADD COMMENTlink modified 15 months ago • written 15 months ago by h.mon24k

Hi, Is it normalization should be performed for a raw vcf file isn't ?

Thanks!

ADD REPLYlink written 15 months ago by Ramana0

yes, BAN works with latest version of mummer4. Thanks for your comments.

ADD REPLYlink written 11 months ago by pinninti1991reddy30

Thank you for your feedback on this post. I've moved h.mon's comment to an answer. Please accept it if the answer worked for you.

ADD REPLYlink written 11 months ago by RamRS21k
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