stack smashing detected

[edeuse]

When running Control-FREEC analysis on patients with segmental isodisomy, we encounter "stack smashing detected" errors. How can we resolve this issue?

[valeu]

Dear Edeuse, what happens when you run the last command manually? (samtools view ...)

[kennethgeerts]

Just as a bump, I'm running into the same problem:

Output:

$ freec/freec -conf /data/freec.conf                                             
Control-FREEC v11.6 : a method for automatic detection of copy number alterations, subclones and for accurate estimation of contamination and main ploidy using deep-sequencing data
Non Multi-threading mode
..Breakpoint threshold for segmentation of copy number profiles is 0.8
..telocenromeric set to 50000
..FREEC is not going to output normalized copy number profiles into a BedGraph file (for example, for visualization in the UCSC GB). Use "[general] BedGraphOutput=TRUE" if you want a BedGraph file
..FREEC is not going to adjust profiles for a possible contamination by normal cells
..Window = 500000 was set
..Output directory:	./processing
..Directory with files containing chromosome sequences:	/data/hg38
..Sample file:	/opt/ngs/processing/AXZ293_skip_ae4b1885_7f0feaae.sorted.bam
..Sample input format:	bam
..will use this instance of samtools: 'samtools' to read BAM files
..minimal expected GC-content (general parameter "minExpectedGC") was set to 0.35
..maximal expected GC-content (general parameter "maxExpectedGC") was set to 0.55
..Polynomial degree for "ReadCount ~ GC-content" normalization is 3 or 4: will try both
..Minimal CNA length (in windows) is 1
..File with chromosome lengths:	/data/hg38.freec
..Using the default minimal mappability value of 0.85
..uniqueMatch = FALSE
..FREEC will try to guess the correct ploidy (for each ploidy specified in 'ploidy' parameter)
..It will try ploidies: 2
3
4
..break-point type set to 2
..noisyData set to 0
..Control-FREEC will not look for subclones
..File /data/hg38.freec was read
..[genomecopynumber] Starting reading /opt/ngs/processing/AXZ293_skip_ae4b1885_7f0feaae.sorted.bam
..samtools should be installed to be able to read BAM files; will use the following command for samtools: samtools view -@ 1 /opt/ngs/processing/AXZ293_skip_ae4b1885_7f0feaae.sorted.bam
*** stack smashing detected ***: terminated

The samtools view command seems to run fine:

$ samtools view -@ 1 /opt/ngs/processing/AXZ293_skip_ae4b1885_7f0feaae.sorted.bam | head -1
deccf511-7a00-4e61-879c-073574ba688f	272	chr1	10002	0	55S20M1I6M1I6M1I12M1D21M1I20M1I6M1I6M1I47M1D15M1D22M1D5M1D5M1D12M1D16M2D5M1D18M2D8M1I12M1I42M25134S	*	0	0	*	*	qs:f:14.887	du:f:49.4984	ns:i:247492	ts:i:322	mx:i:1	ch:i:46	st:Z:2025-05-05T14:19:25.236+00:00	rn:i:424	fn:Z:AXZ293_skip_ae4b1885_7f0feaae_1.pod5	sm:f:391.442	sd:f:102.224	sv:Z:pa	dx:i:0	RG:Z:7f0feaae88b61a9d2a69109140de300825d6fca7_dna_r10.4.1_e8.2_400bps_hac@v5.0.0	NM:i:32	ms:i:425	AS:i:424	nn:i:0	de:f:0.0928793	tp:A:S	cm:i:8	s1:i:64	MD:Z:5T5T5T19A6^C17C82^C15^T16T5^T5^T5^T12^A16^TA5^T5T5T2A3^TA5T23T32	rl:i:1998

[chuankeng-goh]

Hi
I am new to using this program and i have also encountered the same issues. Have either of you been able to resolve it?

samtools view ./bam/NB13.haplotagged.bam | head -1
7f0fc617-14fc-4418-a206-342d2236614e    256     chr1    10001   0       4372S12M1D60M1I6M1I29M1I2M1I40M1D27M1I38M1I6M1I6M1I13M1I40M1I4M7I6M1I6M1I14M1I25M1I16M1I7M1I6M1I25M5I7M2I22M3I20M1D21M1I3M473I17M4D83M3I4M1D119M1D116I42M2I80M1I65M1D138M2D129M1D252M2I30M2I123M1I7M1I2M1I9M6I289M1D740M2D33M1D29M1D2M1I3M5D2M1I97M1D364M2D23M1I3M1D265M1D33M1I180M1I165M2I6M1D345M2D48M1I105M1D130M5I33M3D10M1D15M1D40M1D39M1I111M1I6M1I105M1I74M1D317M1D41M2D6M1I156M1I108M2I106M1I61M1I5M2I7M1I198M1I133M1I854M1D52M1D3M3I197M1D77M1D172M1I1M1I3M4I1M1I14M1D51M1D7M1I18M1I236M4D73M1D405M2I110M1I1M2D89M1D249M1D108M1D63M1D240M2I124M1D37M1I153M1I24M2D4M2D279M2S    *       0       0       *       *       NM:i:857        ms:i:17919      AS:i:17261      nn:i:0  tp:A:S  cm:i:1389       s1:i:8214       de:f:0.0218     rl:i:3111  

my chrLenFile is the index file for my genome

cut -f1 ./genome/hg38/hg38.fa.fai
chr1
chr10
chr11

my GCcontentProfile is also has chromosomes labelled the same way, with the correct window.