vpc-ccg / svict Goto Github PK

Is it possible for us to get the total number of reads at the variant position?

##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
This will help us in the allele fraction calculations.
Kindly revert back if possible guys.
thanks,
Venki
Venkatesh Chellappa

bam file sorted and index existed.
but this error recured

Hi
I am trying to use svict for prostate cancer cfdna data and I have trouble understanding the format of the vcf

#CHROM  POS ID  REF ALT QUAL  FILTER  INFO
1	26608813	.	<DEL>	C	.	PASS	SVTYPE=DEL;END=26608889;CLUSTER=2;CONTIG=2;SUPPORT=17;

Why is the REF column showing a DEL tag? and could you please explain what this particular variant means?

Thanks,
Venki
Venkatesh Chellappa

Hello,

When I run GRIDSS for a certain patient an error occurs when assembling the contigs.

chrM
chr1
chr2
chr3
chr4
chr5
chr6
chr7
chr8
chr9
chr10
chr11
chr12
chr13
chr14
chr15
chr16
chr17
chr18
chr19
chr20
chr21
chr22
chrX
chrY
chr1_gl000191_random
chr1_gl000192_random
chr4_ctg9_hap1
chr4_gl000193_random
chr4_gl000194_random
chr6_apd_hap1
chr6_cox_hap2
chr6_dbb_hap3
chr6_mann_hap4
chr6_mcf_hap5
chr6_qbl_hap6
chr6_ssto_hap7
chr7_gl000195_random
chr8_gl000196_random
chr8_gl000197_random
chr9_gl000198_random
chr9_gl000199_random
chr9_gl000200_random
chr9_gl000201_random
chr11_gl000202_random
chr17_ctg5_hap1
chr17_gl000203_random
chr17_gl000204_random
chr17_gl000205_random
chr17_gl000206_random
chr18_gl000207_random
chr19_gl000208_random
chr19_gl000209_random
chr21_gl000210_random
chrUn_gl000211
chrUn_gl000212
chrUn_gl000213
chrUn_gl000214
chrUn_gl000215
chrUn_gl000216
chrUn_gl000217
chrUn_gl000218
chrUn_gl000219
chrUn_gl000220
chrUn_gl000221
chrUn_gl000222
chrUn_gl000223
chrUn_gl000224
chrUn_gl000225
chrUn_gl000226
chrUn_gl000227
chrUn_gl000228
chrUn_gl000229
chrUn_gl000230
chrUn_gl000231
chrUn_gl000232
chrUn_gl000233
chrUn_gl000234
chrUn_gl000235
chrUn_gl000236
chrUn_gl000237
chrUn_gl000238
chrUn_gl000239
chrUn_gl000240
chrUn_gl000241
chrUn_gl000242
chrUn_gl000243
chrUn_gl000244
chrUn_gl000245
chrUn_gl000246
chrUn_gl000247
chrUn_gl000248
chrUn_gl000249
Assembling contigs...
chrchrM done
chrchr1 done
chrchr2 done
chrchr3 done
chrchr4 done
chrchr5 done
chrchr6 done
chrchr7 done
chrchr8 done
chrchr9 done
chrchr10 done
chrchr11 done
chrchr12 done
chrchr13 done
chrchr14 done
chrchr15 done
chrchr16 done
chrchr17 done
chrchr18 done
chrchr19 done
chrchr20 done
chrchr21 done
chrchr22 done
chrchrX done
chrchrY done
chrchr1_gl000191_random done
chrchr1_gl000192_random done
chrchr4_ctg9_hap1 done
chrchr4_gl000193_random done
chrchr4_gl000194_random done
chrchr6_apd_hap1 done
chrchr6_cox_hap2 done
chrchr6_dbb_hap3 done
chrchr6_mann_hap4 done
chrchr6_mcf_hap5 done
chrchr6_qbl_hap6 done
chrchr6_ssto_hap7 done
chrchr7_gl000195_random done
chrchr9_gl000198_random done
chrchr9_gl000199_random done
chrchr9_gl000200_random done
chrchr11_gl000202_random done
chrchr17_ctg5_hap1 done
chrchr17_gl000203_random done
chrchr17_gl000204_random done
chrchr17_gl000205_random done
chrchr19_gl000208_random done
chrchr19_gl000209_random done
chrchrUn_gl000211 done
chrchrUn_gl000212 done
chrchrUn_gl000213 done
chrchrUn_gl000214 done
chrchrUn_gl000215 done
chrchrUn_gl000216 done
chrchrUn_gl000217 done
chrchrUn_gl000218 done
chrchrUn_gl000219 done
chrchrUn_gl000220 done
chrchrUn_gl000221 done
chrchrUn_gl000222 done
chrchrUn_gl000223 done
chrchrUn_gl000224 done
chrchrUn_gl000225 done
chrchrUn_gl000226 done
chrchrUn_gl000227 done
chrchrUn_gl000228 done
chrchrUn_gl000229 done
chrchrUn_gl000230 done
chrchrUn_gl000231 done
chrchrUn_gl000232 done
chrchrUn_gl000233 done
chrchrUn_gl000234 done
chrchrUn_gl000235 done
chrchrUn_gl000237 done
chrchrUn_gl000239 done
chrchrUn_gl000240 done
chrchrUn_gl000241 done
chrchrUn_gl000242 done
chrchrUn_gl000244 done
chrchrUn_gl000246 done
chrchrUn_gl000247 done
chrchrUn_gl000248 done
Segmentation fault

Thank you for the time you can give me.

BoudSTER.

We need to evaluate the partition file generated by commit 43cdb49 and 30639c0 with -z. The differ in dealing with locating mappings with extremely long template length. 303639c0 would assign the read with larger anchor position while 43cbd40 assigns the read with smaller anchor position whenever possible.

Dear authors, I am trying to run svict with a gtf file to annotate variants.
I downloaded the gtf from igenomes and I get an error message of wrong file format.
I also tried to add an header to the gtf but this did not fix the issue.
Could you please help? code below

aws s3 --no-sign-request --region eu-west-1 sync s3://ngi-igenomes/igenomes/Homo_sapiens/UCSC/hg19/Annotation/Genes/ ./references/Homo_sapiens/UCSC/hg19/Annotation/Genes/ --exclude "*" --include "genes.gtf"

svict -P -i myfile.bam -r ./ucsc.hg19.fasta -g ./references/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf
-o myfile.annot
Error: Specified GTF file (references/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf) does not appear to be correctly formatted, or is missing a header.

Hi,

I'm trying to run this on a regular bwa mem bam file. I noticed 2 issues:

1. svict expects "SO:coordinate" as the third column but in the bam that I'm providing it is the fourth. Could you make this more generic?
2. svict then failed on the second to last decoy contigs, after going through most of the other supercontigs; right on or after NC_007605 and the last one is hs37d5. I didn't get any error messages. Is this a known issue?

Thanks,
Minita

Hi authors,
svict is a really fast tool of calling SVs，but I am a little confused about the format of the output vcf .
Here is an example, I do not understand what the MATE fusion means. In most cases, the 5th column of a BND mutation in a vcf file indicates its strand information, but in this vcf, there is an N. or .N in the line of the first MATE, and I do not know the orientation of the first MATE.

chr4    25665006        bnd_44_1        N       N.      .       TWO_BP  SVTYPE=BND;MATEID=bnd_44_2;CLUSTER=1;CONTIG=1;SUPPORT=7;
chr4    25665007        bnd_44_2        C       ]chr6:117337161]C       .       TWO_BP  SVTYPE=BND;MATEID=bnd_44_1;CLUSTER=1;CONTIG=1;SUPPORT=7;

In lumpy, there are also two continuous lines represents the same fusion, they are actually synonyms, because they are representing the same DNA fragment. But in svict cases, I do not know whether the two lines are synonyms (as in lumpy), or two DNA fragments generated by a reciprocal translocation?
Hope that I am clear when clarifying this question :)

logging file ：
Assembling contigs...
chrchr1 done
chrchr2 done
chrchr3 done
chrchr4 done
chrchr5 done
chrchr6 done
chrchr7 done
chrchr8 done
chrchr9 done
chrchr10 done
chrchr11 done
chrchr12 done
chrchr13 done
chrchr14 done
chrchr15 done
chrchr16 done
chrchr17 done
chrchr18 done
chrchr19 done
chrchr20 done
chrchr21 done
chrchr22 done
chrchrX done
chrchrY done
Supplemental mappings (null) are missing in SAM/BAM, file might be invalid

Supplemental mappings (null) are missing in SAM/BAM, file might be invalid

Segmentation fault (core dumped)

============================================

I wanna figure out why this problem raise?

Todo: make sure the results are consistency at least within the same version of gcc after modifying the operator for gcc 4.8.2.

Some FNs locate in messy region which consists of more than 10k anchors, and incorrect splitting cause problems for building correct contig. We need to check if there is a way to split a cluster whenever we detect dramatic distance variance, especially in a cluster where anchors distribute in a un-balanced way.

annotation.cc:43

uint32_t overlap_l( const uint32_t &s1, const uint32_t &e1, const uint32_t &s2, const uint32_t &e2)
{
	uint32_t l = 0;
	if ( s1 <= s2 && e2 <= e2 ) // <<<--- this sentence
	{ l = e2 - s2 + 1;	}
	else if ( s2 <= s1 && e1 <= e2 )
	{	l = e1 - s1 + 1;	}
	else if ( s1 <= s2 && s2 <= e1)
	{	l = e1 - s2 + 1;	}
	else if ( s2 <= s1 && s1 <= e2)
	{	l =	e2 - s1 + 1;	}
	return l;
}

The first if condition seems equal to just s1 <= s2 because e2 <= e2 is always true.

Test the accuracy between adding the less-mapped part and both-mate in the partition file.

Hi,

I tried svict on my cfDNA sample. while trying to use svict output vcf file for downstream analysis(IGV), I got this error as Your input file has a malformed header: there are not enough columns present in the header line: #CHROM POS ID REF ALT QUAL FILTER INFO,

The header line is separated by spaces instead of tab.

Thanks,

We need to add a two-pass mode in scanning sam/bam file and store all mapping records with supple mapping in memory to supply the information for hard-clipping reads in the second round which makes actual partition information.

Hi, I have read paper of SViCT and tried to use this tool for my analysis.

The compilation was successful and ran this tool using cfDNA sample and the core dump has raised.

Command line I have used is shown below.

svict -i /path/to/my/sample.bam -r hg19.fa -o /path/to/my/sample

The error is shown below.

chrM
chr1
chr2
chr3
chr4
chr5
chr6
chr7
chr8
chr9
chr10
chr11
chr12
chr13
chr14
chr15
chr16
chr17
chr18
chr19
chr20
chr21
chr22
chrX
chrY
Assembling contigs...
chrchrM done
chrchr1 done
chrchr2 done
chrchr3 done
chrchr4 done
chrchr5 done
chrchr6 done
chrchr7 done
chrchr8 done
chrchr9 done
chrchr10 done
chrchr11 done
chrchr12 done
chrchr13 done
chrchr14 done
chrchr15 done
chrchr16 done
chrchr17 done
chrchr18 done
chrchr19 done
chrchr20 done
chrchr21 done
chrchr22 done
chrchrX done
chrchrY done
Processing 1 supplementary clusters...
Indexing contigs...
Generating intervals...
chrchrM done
chrchr1 done
chrchr2 done
chrchr3 done
chrchr4 done
chrchr5 done
chrchr6 done
chrchr7 done
chrchr8 done
chrchr9 done
chrchr10 done
chrchr11 done
chrchr12 done
chrchr13 done
chrchr14 done
chrchr15 done
*** Error in `/usr/bin/svict': double free or corruption (!prev): 0x000000005d109200 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x81489)[0x7f437cc2a489]
/usr/bin/svict[0x42bd89]
/usr/bin/svict[0x433a18]
/usr/bin/svict[0x408b35]
/usr/bin/svict[0x4049f3]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x7f437cbcb3d5]
/usr/bin/svict[0x40505f]
======= Memory map: ========
00400000-0047c000 r-xp 00000000 fd:02 310083803 /usr/bin/svict
0067b000-0067c000 r--p 0007b000 fd:02 310083803 /usr/bin/svict
0067c000-0067d000 rw-p 0007c000 fd:02 310083803 /usr/bin/svict
0067d000-0067e000 rw-p 00000000 00:00 0
00a3c000-71c92000 rw-p 00000000 00:00 0 [heap]
7f4318000000-7f4318021000 rw-p 00000000 00:00 0
7f4318021000-7f431c000000 ---p 00000000 00:00 0
7f431dd97000-7f43233c3000 rw-p 00000000 00:00 0
7f432958c000-7f437cba9000 rw-p 00000000 00:00 0
7f437cba9000-7f437cd6b000 r-xp 00000000 fd:00 1574534 /usr/lib64/libc-2.17.so
7f437cd6b000-7f437cf6b000 ---p 001c2000 fd:00 1574534 /usr/lib64/libc-2.17.so
7f437cf6b000-7f437cf6f000 r--p 001c2000 fd:00 1574534 /usr/lib64/libc-2.17.so
7f437cf6f000-7f437cf71000 rw-p 001c6000 fd:00 1574534 /usr/lib64/libc-2.17.so
7f437cf71000-7f437cf76000 rw-p 00000000 00:00 0
7f437cf76000-7f437cf8b000 r-xp 00000000 fd:00 1616415 /usr/lib64/libgcc_s-4.8.5-20150702.so.1
7f437cf8b000-7f437d18a000 ---p 00015000 fd:00 1616415 /usr/lib64/libgcc_s-4.8.5-20150702.so.1
7f437d18a000-7f437d18b000 r--p 00014000 fd:00 1616415 /usr/lib64/libgcc_s-4.8.5-20150702.so.1
7f437d18b000-7f437d18c000 rw-p 00015000 fd:00 1616415 /usr/lib64/libgcc_s-4.8.5-20150702.so.1
7f437d18c000-7f437d28d000 r-xp 00000000 fd:00 1574542 /usr/lib64/libm-2.17.so
7f437d28d000-7f437d48c000 ---p 00101000 fd:00 1574542 /usr/lib64/libm-2.17.so
7f437d48c000-7f437d48d000 r--p 00100000 fd:00 1574542 /usr/lib64/libm-2.17.so
7f437d48d000-7f437d48e000 rw-p 00101000 fd:00 1574542 /usr/lib64/libm-2.17.so
7f437d48e000-7f437d577000 r-xp 00000000 fd:00 1574826 /usr/lib64/libstdc++.so.6.0.19
7f437d577000-7f437d776000 ---p 000e9000 fd:00 1574826 /usr/lib64/libstdc++.so.6.0.19
7f437d776000-7f437d77e000 r--p 000e8000 fd:00 1574826 /usr/lib64/libstdc++.so.6.0.19
7f437d77e000-7f437d780000 rw-p 000f0000 fd:00 1574826 /usr/lib64/libstdc++.so.6.0.19
7f437d780000-7f437d795000 rw-p 00000000 00:00 0
7f437d795000-7f437d7ac000 r-xp 00000000 fd:00 1574560 /usr/lib64/libpthread-2.17.so
7f437d7ac000-7f437d9ab000 ---p 00017000 fd:00 1574560 /usr/lib64/libpthread-2.17.so
7f437d9ab000-7f437d9ac000 r--p 00016000 fd:00 1574560 /usr/lib64/libpthread-2.17.so
7f437d9ac000-7f437d9ad000 rw-p 00017000 fd:00 1574560 /usr/lib64/libpthread-2.17.so
7f437d9ad000-7f437d9b1000 rw-p 00000000 00:00 0
7f437d9b1000-7f437d9c6000 r-xp 00000000 fd:00 1574985 /usr/lib64/libz.so.1.2.7
7f437d9c6000-7f437dbc5000 ---p 00015000 fd:00 1574985 /usr/lib64/libz.so.1.2.7
7f437dbc5000-7f437dbc6000 r--p 00014000 fd:00 1574985 /usr/lib64/libz.so.1.2.7
7f437dbc6000-7f437dbc7000 rw-p 00015000 fd:00 1574985 /usr/lib64/libz.so.1.2.7
7f437dbc7000-7f437dbe9000 r-xp 00000000 fd:00 1616418 /usr/lib64/ld-2.17.so
7f437ddc7000-7f437ddcd000 rw-p 00000000 00:00 0
7f437dde5000-7f437dde8000 rw-p 00000000 00:00 0
7f437dde8000-7f437dde9000 r--p 00021000 fd:00 1616418 /usr/lib64/ld-2.17.so
7f437dde9000-7f437ddea000 rw-p 00022000 fd:00 1616418 /usr/lib64/ld-2.17.so
7f437ddea000-7f437ddeb000 rw-p 00000000 00:00 0
7fffb071b000-7fffb073c000 rw-p 00000000 00:00 0 [stack]
7fffb07ed000-7fffb07ef000 r-xp 00000000 00:00 0 [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]
Aborted (core dumped)

Thanks

Add a function to do one-pass set cover if integration into streaming takes time to finish,

Hi, I have read paper of SViCT and tried to use this tool for my analysis

The compilation was successful and ran this tool using cfDNA sample and the core dump has raised.

Command line I have used is shown below

$SVICT/svict -i sample.bam -r hg38.fa -o outfile
The GDB's strack trace using core file generated shown below
#0 0x000000000042eddc in svict_caller::generate_intervals(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bool) () (gdb) bt #0 0x000000000042eddc in svict_caller::generate_intervals(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bool) () #1 0x0000000000436b60 in svict_caller::run(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int, int, int, int, int, int, bool, int, int, int, double, bool, bool) () #2 0x0000000000409d3b in predict(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bool, bool, int, int, int, int, int, int, int, int, int, bool, int, int, int, double, bool, bool, bool) () #3 0x0000000000404a4c in main ()

The computer is equipped with Ubuntu 16,04 LTS and 32 cores of Xeon Phi system.
Our compiler is gcc 5.4.0
The reference sequence I have used is GRCh38 version

Thanks ins advance

log file :

chrM
chr1
chr2
chr3
chr4
chr5
chr6
chr7
chr8
chr9
chr10
chr11
chr12
chr13
chr14
chr15
chr16
chr17
chr18
chr19
chr20
chr21
chr22
chrX
chrY
Assembling contigs...
chrchrM done
chrchr1 done
chrchr2 done
chrchr3 done
chrchr4 done
chrchr5 done
chrchr6 done
chrchr7 done
chrchr8 done
chrchr9 done
chrchr10 done
chrchr11 done
chrchr12 done
chrchr13 done
chrchr14 done
chrchr15 done
chrchr16 done
chrchr17 done
chrchr18 done
chrchr19 done
chrchr20 done
chrchr21 done
chrchr22 done
chrchrX done
chrchrY done
Processing 26183 supplementary clusters...
Discordant (INV): 2648
Discordant (DUP): 3618
Discordant (INS): 84500
OEA: 31962
Read Count: 2008199
Partition Count: 209992
Total Contigs: 1.77093e+06
Contigs: 0 44462
Average Num Contigs Pre-Filter: 8.43332
Average Num Contigs Post-Filter: 0.211732
Average Contig Support: 2.98799
Rate Parameter Estimate: 0.0756226
ASSEMBLY TIME: 583.9

Filtered 0 contigs.
PROBABILISTIC FILTER TIME: 0

Indexing contigs...
Number of unique kmers: 941427
Max hits: 0
INDEX TIME: 2.37

Generating intervals...
chrchrM done
chrchr1 done
chrchr2 done
*** Error in `/tools/svict/svict': free(): invalid next size (normal): 0x000000002a6c43c0 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x81299)[0x7f829195c299]
/tools/svict/svict[0x42bd89]
/tools/svict/svict[0x433a18]
/tools/svict/svict[0x408b35]
/tools/svict/svict[0x4049f3]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x7f82918fd555]
/tools/svict/svict[0x40505f]
======= Memory map: ========
00400000-0047c000 r-xp 00000000 00:2b 55864127279 /tools/svict/svict
0067b000-0067c000 r--p 0007b000 00:2b 55864127279 /tools/svict/svict
0067c000-0067d000 rw-p 0007c000 00:2b 55864127279 /tools/svict/svict
0067d000-0067e000 rw-p 00000000 00:00 0
019b6000-89db9000 rw-p 00000000 00:00 0 [heap]
7f822c000000-7f822c021000 rw-p 00000000 00:00 0
7f822c021000-7f8230000000 ---p 00000000 00:00 0
7f82319e3000-7f823eebe000 rw-p 00000000 00:00 0
7f823fabf000-7f82918db000 rw-p 00000000 00:00 0
7f82918db000-7f8291a9f000 r-xp 00000000 fd:00 404043695 /usr/lib64/libc-2.17.so
7f8291a9f000-7f8291c9e000 ---p 001c4000 fd:00 404043695 /usr/lib64/libc-2.17.so
7f8291c9e000-7f8291ca2000 r--p 001c3000 fd:00 404043695 /usr/lib64/libc-2.17.so
7f8291ca2000-7f8291ca4000 rw-p 001c7000 fd:00 404043695 /usr/lib64/libc-2.17.so
7f8291ca4000-7f8291ca9000 rw-p 00000000 00:00 0
7f8291ca9000-7f8291cbe000 r-xp 00000000 fd:00 402653315 /usr/lib64/libgcc_s-4.8.5-20150702.so.1
7f8291cbe000-7f8291ebd000 ---p 00015000 fd:00 402653315 /usr/lib64/libgcc_s-4.8.5-20150702.so.1
7f8291ebd000-7f8291ebe000 r--p 00014000 fd:00 402653315 /usr/lib64/libgcc_s-4.8.5-20150702.so.1
7f8291ebe000-7f8291ebf000 rw-p 00015000 fd:00 402653315 /usr/lib64/libgcc_s-4.8.5-20150702.so.1
7f8291ebf000-7f8291fc0000 r-xp 00000000 fd:00 404043704 /usr/lib64/libm-2.17.so
7f8291fc0000-7f82921bf000 ---p 00101000 fd:00 404043704 /usr/lib64/libm-2.17.so
7f82921bf000-7f82921c0000 r--p 00100000 fd:00 404043704 /usr/lib64/libm-2.17.so
7f82921c0000-7f82921c1000 rw-p 00101000 fd:00 404043704 /usr/lib64/libm-2.17.so
7f82921c1000-7f82921d8000 r-xp 00000000 fd:00 404043708 /usr/lib64/libpthread-2.17.so
7f82921d8000-7f82923d7000 ---p 00017000 fd:00 404043708 /usr/lib64/libpthread-2.17.so
7f82923d7000-7f82923d8000 r--p 00016000 fd:00 404043708 /usr/lib64/libpthread-2.17.so
7f82923d8000-7f82923d9000 rw-p 00017000 fd:00 404043708 /usr/lib64/libpthread-2.17.so
7f82923d9000-7f82923dd000 rw-p 00000000 00:00 0
7f82923dd000-7f82923ff000 r-xp 00000000 fd:00 402706987 /usr/lib64/ld-2.17.so
7f829244c000-7f8292451000 rw-p 00000000 00:00 0
7f8292451000-7f82924f3000 r--p 00000000 fd:00 404043686 /usr/lib64/libstdc++.so.6.0.26
7f82924f3000-7f8292572000 r-xp 000a2000 fd:00 404043686 /usr/lib64/libstdc++.so.6.0.26
7f8292572000-7f82925b3000 r--p 00121000 fd:00 404043686 /usr/lib64/libstdc++.so.6.0.26
7f82925b3000-7f82925be000 r--p 00161000 fd:00 404043686 /usr/lib64/libstdc++.so.6.0.26
7f82925be000-7f82925c2000 rw-p 0016c000 fd:00 404043686 /usr/lib64/libstdc++.so.6.0.26
7f82925c2000-7f82925c6000 rw-p 00000000 00:00 0
7f82925c6000-7f82925c9000 r--p 00000000 fd:00 404256474 /usr/lib64/libz.so.1.2.11
7f82925c9000-7f82925dd000 r-xp 00003000 fd:00 404256474 /usr/lib64/libz.so.1.2.11
7f82925dd000-7f82925e4000 r--p 00017000 fd:00 404256474 /usr/lib64/libz.so.1.2.11
7f82925e4000-7f82925e5000 r--p 0001d000 fd:00 404256474 /usr/lib64/libz.so.1.2.11
7f82925e5000-7f82925e6000 rw-p 0001e000 fd:00 404256474 /usr/lib64/libz.so.1.2.11
7f82925fa000-7f82925fe000 rw-p 00000000 00:00 0
7f82925fe000-7f82925ff000 r--p 00021000 fd:00 402706987 /usr/lib64/ld-2.17.so
7f82925ff000-7f8292600000 rw-p 00022000 fd:00 402706987 /usr/lib64/ld-2.17.so
7f8292600000-7f8292601000 rw-p 00000000 00:00 0
7ffeb6667000-7ffeb6688000 rw-p 00000000 00:00 0 [stack]
7ffeb66de000-7ffeb66e0000 r-xp 00000000 00:00 0 [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]

Which one do we need to put in the test dataset: chr1 or whole genome sequence?