Window size flag and testing

[s-boardman]

Pass CNVnator window size as a flagged option. Test if window size passed without read depth flag and return usage and informative error message.

[s-boardman]

Hi Colby, I've just started doing some testing suing the latest set of commits. Running speedseq sv using the -d flag without -w works fine and defaults to 100bp windows. Using the -w flag errors out stating the program has crashed.

I was wondering whether this is to do with the SpeedSeq implementation of CNVnator-multi? Is it limited to a max window size in some way? I was able to use windows of 5k and 10k with the original version of CNVnator without seeing error messages.

Command used

qsub -V -b Y -e win_e -o win_o -cwd -N speedseq_test_windowed ~/speedseq/gcc-4.4.6+root-5.34.30+samtools-0.1.19+python-2.7.3/bin/speedseq sv -B ./bam/NA12877.bam -S ./bam/NA12877.splitters.bam -D ./bam/NA12877.discordants.bam -R /mnt/lustre/references/speedseq/GRCh37/grch37.fasta -o NA12877_5k -d -w 5000

Output log

Sourcing executables from /opt/gridware/pkg/apps/speedseq/0.0.3a/gcc-4.4.6+root-5.34.30+samtools-0.1.19+python-2.7.3/etc/speedseq.config ...

Checking for required python modules (/opt/gridware/pkg/apps/python/2.7.3/gcc-4.4.6/bin/python2.7)...

Running LUMPY express
Sourcing executables from /opt/gridware/pkg/apps/speedseq/0.0.3a/gcc-4.4.6+root-5.34.30+samtools-0.1.19+python-2.7.3/etc/speedseq.config ...

Checking for required python modules (/opt/gridware/pkg/apps/python/2.7.3/gcc-4.4.6/bin/python2.7)...

    create temporary directory
Calculating insert distributions... 
Library read groups: NA12877
Library read length: 101
done
0
Running LUMPY... 

/opt/gridware/pkg/apps/speedseq/0.0.3a/gcc-4.4.6+root-5.34.30+samtools-0.1.19+python-2.7.3/bin/lumpy  \
    -t NA12877_5k.2cmD8Xy5HJbj/temp_lumpyexpress/NA12877_5k.sv.vcf \
    -msw 4 \
    -tt 0 \
     \
     -pe bam_file:./bam/NA12877.discordants.bam,histo_file:NA12877_5k.2cmD8Xy5HJbj/temp_lumpyexpress/NA12877_5k.sv.vcf.sample1.lib1.x4.histo,mean:318.400715811,stdev:70.1978183563,read_length:101,min_non_overlap:101,discordant_z:5,back_distance:10,weight:1,id:NA12877,min_mapping_threshold:20,read_group:NA12877 \
     -sr bam_file:./bam/NA12877.splitters.bam,back_distance:10,min_mapping_threshold:20,weight:1,id:NA12877,min_clip:20 \
    > NA12877_5k.2cmD8Xy5HJbj/NA12877_5k.sv.vcf
LUMPY Express done
Calculating read depth
67052 alignments were processed corresponding to chrom M
4323468 alignments were processed corresponding to chrom 2
458430 alignments were processed corresponding to chrom Y
593192 alignments were processed corresponding to chrom 22
708685 alignments were processed corresponding to chrom 21
961822 alignments were processed corresponding to chrom 19
1010602 alignments were processed corresponding to chrom 20
4031418 alignments were processed corresponding to chrom 1
1351433 alignments were processed corresponding to chrom 17
1396298 alignments were processed corresponding to chrom 18
1400284 alignments were processed corresponding to chrom 15
1363831 alignments were processed corresponding to chrom X
1508170 alignments were processed corresponding to chrom 14
1508927 alignments were processed corresponding to chrom 16
1622446 alignments were processed corresponding to chrom 13
3332245 alignments were processed corresponding to chrom 3
2159325 alignments were processed corresponding to chrom 9
2225977 alignments were processed corresponding to chrom 12
2274517 alignments were processed corresponding to chrom 11
2529124 alignments were processed corresponding to chrom 10
2593580 alignments were processed corresponding to chrom 8
2707066 alignments were processed corresponding to chrom 7
2898731 alignments were processed corresponding to chrom 6
3058828 alignments were processed corresponding to chrom 5
3461969 alignments were processed corresponding to chrom 4 Filling and saving tree for '1' ...
Filling and saving tree for '2' ...
Filling and saving tree for '3' ...
Filling and saving tree for '4' ...
Filling and saving tree for '5' ...
Filling and saving tree for '6' ...
Filling and saving tree for '7' ...
Filling and saving tree for '8' ...
Filling and saving tree for '9' ...
Filling and saving tree for '10' ...
Filling and saving tree for '11' ...
Filling and saving tree for '12' ...
Filling and saving tree for '13' ...
Filling and saving tree for '14' ...
Filling and saving tree for '15' ...
Filling and saving tree for '16' ...
Filling and saving tree for '17' ...
Filling and saving tree for '18' ...
Filling and saving tree for '19' ...
Filling and saving tree for '20' ...
Filling and saving tree for '21' ...
Filling and saving tree for '22' ...
Filling and saving tree for 'X' ...
Filling and saving tree for 'Y' ...
Filling and saving tree for 'M' ...
A total of 49547420 aligned reads have been processed.
Writing histograms ... 
Allocating memory ...
Done.
Calculating histograms with bin size of 5000 for '1' ...
Making directory bin_5000 ...
Making GC histogram for '1' ...
Processing data from the following chromosomes: ['1', '2', '3', '4', '5', '6', '7', '8', '9', '10', '11', '12', '13', '14', '15', '16', '17', '18', '19', '20', '21', '22', 'X', 'Y', 'M'] ===== Running tree on input data ===== Running histograms on input data for input bin size Error computing histograms (input bin size).

Error log

Removed 127 outliers with isize >= 766
1   1000000
2   1000000
3   1000000
4   1000000
5   1000000
6   1000000
7   1000000
8   1000000
9   1000000
10  1000000
11  1000000
12  1000000
13  1000000
13  2000000
13  4000000
13  8000000
13  16000000
13  32000000
14  1000000
14  2000000
14  4000000
14  8000000
14  16000000
14  32000000
15  1000000
15  2000000
15  4000000
15  8000000
15  16000000
15  32000000
16  1000000
17  1000000
18  1000000
19  1000000
20  1000000
21  1000000
21  2000000
21  4000000
21  8000000
21  16000000
22  1000000
22  2000000
22  4000000
22  8000000
22  16000000
22  32000000
X   1000000
Y   1000000
Y   2000000
Y   4000000
M   1000000

 *** Break *** segmentation violation



===========================================================
There was a crash.
This is the entire stack trace of all threads:
===========================================================
#0  0x00000031848ac61e in waitpid () from /lib64/libc.so.6
#1  0x000000318483e609 in do_system () from /lib64/libc.so.6
#2  0x00002b8fd36fd628 in TUnixSystem::StackTrace() () from /opt/gridware/pkg/libs/root/5.34.30/gcc-4.4.6/lib/libCore.so.5.34
#3  0x00002b8fd36fcab3 in TUnixSystem::DispatchSignals(ESignals) () from /opt/gridware/pkg/libs/root/5.34.30/gcc-4.4.6/lib/libCore.so.5.34
#4  <signal handler called>
#5  0x0000000000420b9b in HisMaker::produceHistograms(std::basic_string<char, std::char_traits<char>, std::allocator<char> >*, int, std::basic_string<char, std::char_traits<char>, std::allocator<char> >*, int, bool) ()
#6  0x000000000040853b in main ()
===========================================================


The lines below might hint at the cause of the crash.
If they do not help you then please submit a bug report at http://root.cern.ch/bugs. Please post the ENTIRE stack trace from above as an attachment in addition to anything else that might help us fixing this issue.
===========================================================
#5  0x0000000000420b9b in HisMaker::produceHistograms(std::basic_string<char, std::char_traits<char>, std::allocator<char> >*, int, std::basic_string<char, std::char_traits<char>, std::allocator<char> >*, int, bool) ()
#6  0x000000000040853b in main ()
===========================================================