Question: Breakdancer Max Kahan Error:0
1
gravatar for Jack
3.6 years ago by
Jack60
Jack60 wrote:

I'm using breakdancer-max 1.4.4-unstable-7-6213d5a on exome sequencing data from tumor-normal pairs (all from Illumina HiSeq 2500, 200x coverage, whole exome using NimbleGen Exome v3.0). BAM files are ~40Gb in size, all quality-trimmed using fastqc, aligned using BWA-sampe, processed using GATK pipeline (remove duplicates, do indel realignment, relirecalibrate base quality score).

I first generate the config file using

bam2cfg.pl -g -h tumor.bam normal.bam >  t.cfg

The output is

readgroup:CGATGT.L002    platform:ILLUMINA    map:t.bam    readlen:101.00    lib:310.T1.CGATGT    num:9984    lower:0.00    upper:760.11    mean:245.43    std:101.07    SWnormality:-59.31    flag:0(13.62%)18(85.59%)2(0.13%)32(0.43%)4(0.23%)10771    exe:samtools view
    readgroup:CGATGT.L001    platform:ILLUMINA    map:t.bam    readlen:101.00    lib:310.T1.CGATGT    num:9984    lower:0.00    upper:760.11    mean:245.43    std:101.07    SWnormality:-59.31    flag:0(11.15%)18(88.06%)2(0.12%)32(0.53%)4(0.13%)8(0.02%)12148    exe:samtools view
    readgroup:ATCACG.L002    platform:ILLUMINA    map:n.bam    readlen:101.00    lib:310.N.ATCACG    num:9994    lower:0.00    upper:737.03    mean:241.92    std:99.54    SWnormality:-57.95    flag:0(14.29%)18(84.85%)2(0.11%)32(0.47%)4(0.27%)9586    exe:samtools view
    readgroup:ATCACG.L001    platform:ILLUMINA    map:n.bam    readlen:101.00    lib:310.N.ATCACG    num:9994    lower:0.00    upper:737.03    mean:241.92    std:99.54    SWnormality:-57.95    flag:0(12.77%)18(86.36%)2(0.11%)32(0.55%)4(0.21%)10618    exe:samtools view

I run breakdancer as shown below

breakdancer-max -q 10 -d t t.cfg > t.ctx

The run takes about 90 min, and it terminates with a "Max Kahan error:0." However, it also produces a 16Mb .ctx file. The file contains calls from all chromosomes, so it seems like breakdancer-max ran fine, except the error message. First couple lines from the output is below.

#Software: 1.4.4-unstable-7-6213d5a (commit 6213d5a)
#Command: breakdancer-max -q 10 -d t t.cfg 
#Library Statistics:
#n.bam    mean:241.92    std:99.54    uppercutoff:737.03    lowercutoff:0    readlen:101    library:310.N.ATCACG    reflen:3052047611    seqcov:6.83207    phycov:8.18225    1:14714    2:393238    4:426044    8:16096    32:569558
#t.bam    mean:245.43    std:101.07    uppercutoff:760.11    lowercutoff:0    readlen:101    library:310.T1.CGATGT    reflen:3052047611    seqcov:6.77381    phycov:8.23018    1:15354    2:549576    4:367739    8:16740    32:635131
#Chr1    Pos1    Orientation1    Chr2    Pos2    Orientation2    Type    Size    Score    num_Reads    num_Reads_lib    310.bam    310t.bam
chrM    4    6+17-    chrM    16564    17+3-    ITX    16001    99    14    n.bam|8:t.bam|6    129.24    111.03
chrM    509    100+26-    chrM    743    100+26-    ITX    -144    99    12    n.bam|8:t.bam|4    NA    NA
chrM    839    100+26-    chrM    1201    2+4-    DEL    535    46    2    t.bam|2    124.40    100.40
chrM    828    3+11-    chrM    3198    151+249-    ITX    -144    99    58    .bam|32:t.bam|26    6.05    5.05
chrM    3102    151+249-    chrM    3160    1+11-    DEL    584    98    8    .bam|4:t.bam|4    47.92    45.76

I saw older unresolved posts on Biostar about the same issue. (Error Running Breakdancer-Max: Max Kahan Error: 0) I was wondering if anyone came up with a solution since then.

Thanks.

breakdancer error • 1.2k views
ADD COMMENTlink modified 3.6 years ago by ernfrid380 • written 3.6 years ago by Jack60
3
gravatar for ernfrid
3.6 years ago by
ernfrid380
Saint Louis
ernfrid380 wrote:

That is a status message. It is shown every time that BreakDancer runs and does not indicate that BreakDancer had a problem while it was running. Your results are valid.

We will consider changing the wording of that message or removing it all together.

ADD COMMENTlink written 3.6 years ago by ernfrid380
2

I got intrigued, who is Max Kahan, whose Error of Zero should be taken as a good sign.

Then I realized! It must be the maximal Kahan summation error that we're happy to see at being zero.

ADD REPLYlink modified 3.6 years ago • written 3.6 years ago by Istvan Albert ♦♦ 74k
1

That's hilarious! I've been thinking it was an inside joke, a reference to a TV show I've never seen or something similar. Google gave me this, which kind of puzzled me... http://www.crainsnewyork.com/article/20131117/FINANCE/311179997/max-kahan-sets-the-gold-standard#

ADD REPLYlink modified 3.6 years ago • written 3.6 years ago by Danielk530
1

...that's quite possibly the worst status message ever... Nice tool, though. :)

ADD REPLYlink written 3.6 years ago by Danielk530
1

Agreed lol. I added that a long time ago when I was worried about numerical precision in the scoring code, and never got around to taking it out... until now. It's gone in master on github :)

ADD REPLYlink written 3.6 years ago by tgi.tabbott220
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