Question

BAN - Best alignment normalisation error

0

Entering edit mode

6.3 years ago

pinn ▴ 210

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

software error snp nextgen alignment • 2.2k views

ADD COMMENT • link updated 6.3 years ago by Biostar 20 • written 6.3 years ago by pinn ▴ 210

1

Entering edit mode

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 REPLY • link 6.0 years ago by Ram 43k

score 1 · Answer 1 · 2018-01-22

1

Entering edit mode

6.3 years ago

h.mon 35k

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 COMMENT • link 6.3 years ago by h.mon 35k

0

Entering edit mode

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

Thanks!

ADD REPLY • link 6.3 years ago by Ramana • 0

0

Entering edit mode

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

ADD REPLY • link 6.0 years ago by pinn ▴ 210

0

Entering edit mode

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 REPLY • link 6.0 years ago by Ram 43k