Segmentation fault

[BoudSTER]

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.

[BoudSTER]

Do you have an idea? :)
I tried several different settings of BWA thinking that the problem could be from the alignment but the problem persists.

Boudster

[SophieS9]

Hi @BoudSTER did you find a solution to this problem? I'm also seeing the same thing - was it a memory issue or an issue with the alignment?

[BoudSTER]

Hi @SophieS9, no solution to solve this error unfortunately... What did you want to use svict for?

[SophieS9]

@BoudSTER I'm looking to carry out fusion calling with ctDNA data, so this tool sounds perfect! I have figured out that it is an issue with the BAM file, but I don't know what that issue is yet - I'll keep you updated if I work it out.

[BoudSTER]

Hi @SophieS9, Have you found a solution? :)

[SophieS9]

Sorry @BoudSTER, couldn't work it out. I tried a few different things (increasing memory, different aligners, different reference genome) but SViCT would crash on some (but not all) of my samples. I'm looking at alternative software instead now.

[BoudSTER]

Hi @SophieS9, thank you for your answer, same things for me ! I tried Aperture and I highly recommand it :).
Have a nice day !