run error

[fengdong110]

Hi，

I use the control_freec(v9.6) Analysis my Target sequencing data,
but I get the follows error:

..............
..using GC-content to normalize copy number profiles
terminate called after throwing an instance of 'std::out_of_range'
what(): basic_string::substr
已放弃 (core dumped)

some people say is "Memory read cross-border".
How to solve this error?
Thank you very much !!!

my config as follow:
[general]
4
5 chrLenFile = /share/f/03.soft/FREEC/test/hg19.fa.fai
6 window = 0
7 ploidy = 2
8 outputDir = /share/f/03.soft/FREEC/test/out/
9 #sex=XY
10 breakPointType=4
11 chrFiles = /share/f/03.soft/FREEC/test/chromosomes/
12 maxThreads=6
13 breakPointThreshold=0.8
14 noisyData=TRUE
15 printNA=FALSE
16 readCountThreshold=50
17
18 [sample]
19
20 mateFile = /share/f/03.soft/FREEC/test/cancer.mpileup.txt
21 inputFormat = pileup
22 mateOrientation = FR
23
24 [control]
25
26 mateFile = /share/f/03.soft/FREEC/test/normal.mpileup.txt
27 inputFormat = pileup
28 mateOrientation = FR
29
30 [BAF]
31
32 #SNPfile = /bioinfo/users/vboeva/Desktop/annotations/hg19_snp131.SingleDiNucl.1based.txt
33 #minimalCoveragePerPosition = 5
34
35 [target]
36
37 captureRegions = /share/f/03.soft/FREEC/test/sorted.bed

[valeu]

Dear Feng Dong,
In case of troubles like this you should send me a complete output into the command line. Otherwise, it is impossible to say what went wrong. Also, I would like to see the first lines of your pileup files.

[valeu]

Was your issue solved by using v9.9?

[valeu]

I believed that the fix in v10.2 should solve this issue.

[SunYong0821]

I use 10.4, it`s still the same error

[valeu]

I would be happy to debug. Can you share the input files and the config, please?

[michelled3]

Hello, I have the same problem and I am using v10.2. How could I share the files with you to debug for this error? Thank you!

[valeu]

Dear Michelle, can you use an FTP server, dropbox, or something similar? Unfortunately, we do not have have an FTP ourselves.