free() : invalid size, Aborted or segmentation faults #32
Description
Hello ! I used your tool on a dataset recently and everything went fine, but with the new alignments, I have either no error output, a Segmentation fault, or a memory problem (I guess).
The command:
for i in CarpeDeam/alignments/*.bam ; do name=$(basename "${i//\.sorted_by_name\.bam/}") ; ../../tools/metaDMG-cpp/metaDMG-cpp getdamage -n 30 -o CarpeDeam/metaDMG/"$name" "$i" ; done
Errors:
-> metaDMG version: v0.4-123-g2cf6a01 (htslib: 1.17-28-ge13611a9) build(May 7 2025 09:54:35)
-> ../../tools/metaDMG-cpp/metaDMG-cpp getdamage -n 30 -o 3413MW_S8_L001 CarpeDeam/alignments/3413MW_S8_L001.sorted_by_name.bam
-> ./metaDMG-cpp refName: (null) min_length: 35 print_length: 5 run_mode: 0 out_prefix: 3413MW_S8_L001 nthreads: 30 ignore_errors: 0
skipping: M03353:64:000000000-CRD57:1:1101:2033:16821 unmapped, this msg is printed: 2 times more
skipping: M03353:64:000000000-CRD57:1:1101:2152:13774 unmapped, this msg is printed: 1 times more
skipping: M03353:64:000000000-CRD57:1:1101:2155:15461 unmapped, this msg is printed: 0 times more
pos A>C A>G A>T C>A C>G C>T G>A G>C G>T T>A T>C T>G
0 0.00986 0.03237 0.00270 0.00332 0.02025 0.00249 0.00978 0.00712 0.00234 0.01246 0.05421 0.01792
1 0.00917 0.00982 0.01068 0.00277 0.01442 0.03055 0.01791 0.00975 0.01031 0.00373 0.00986 0.00228
2 0.00307 0.01399 0.00853 0.00775 0.00894 0.01740 0.03409 0.01240 0.00562 0.00367 0.01994 0.00262
3 0.01047 0.01404 0.00666 0.00299 0.00448 0.02937 0.02213 0.02484 0.01820 0.00068 0.01236 0.00491
4 0.00304 0.00912 0.00756 0.00414 0.01280 0.04282 0.03837 0.01456 0.01241 0.00452 0.00904 0.00286
pos A>C A>G A>T C>A C>G C>T G>A G>C G>T T>A T>C T>G
0 0.03883 0.05002 0.01360 0.00172 0.00840 0.00826 0.00491 0.01837 0.00878 0.00168 0.04843 0.00567
1 0.00391 0.01345 0.00064 0.01816 0.01224 0.02458 0.03114 0.01471 0.00436 0.00593 0.01886 0.01112
2 0.00191 0.01449 0.00537 0.01329 0.01909 0.02433 0.01491 0.00722 0.00222 0.00583 0.01480 0.00861
3 0.00187 0.01170 0.00301 0.01959 0.01330 0.02125 0.02460 0.00655 0.00393 0.00670 0.01175 0.00705
4 0.00211 0.00818 0.00165 0.01679 0.02321 0.03464 0.03578 0.01592 0.00842 0.00405 0.01163 0.00503
-> Will dump: '3413MW_S8_L001.res.gz' this contains damage patterns for: 1 items
-> Setting threads to: 30
-> Will dump: '3413MW_S8_L001.bdamage.gz' this contains damage patterns for: 1 items
-> Setting threads to: 30
-> Will dump: '3413MW_S8_L001.rlens.gz' this contains read length distributions for: 1 items
-> Setting threads to: 30
-> Outputting overall statistic in file: "3413MW_S8_L001.stat"
free(): invalid size
Aborted
-> metaDMG version: v0.4-123-g2cf6a01 (htslib: 1.17-28-ge13611a9) build(May 7 2025 09:54:35)
-> ../../tools/metaDMG-cpp/metaDMG-cpp getdamage -n 30 -o 34130-02_S15_L001 CarpeDeam/alignments/34130-02_S15_L001.sorted_by_name.bam
-> ./metaDMG-cpp refName: (null) min_length: 35 print_length: 5 run_mode: 0 out_prefix: 34130-02_S15_L001 nthreads: 30 ignore_errors: 0
skipping: M03353:64:000000000-CRD57:1:1101:2277:12257 unmapped, this msg is printed: 2 times more
skipping: M03353:64:000000000-CRD57:1:1101:2326:12694 unmapped, this msg is printed: 1 times more
skipping: M03353:64:000000000-CRD57:1:1101:2345:17730 unmapped, this msg is printed: 0 times more
pos A>C A>G A>T C>A C>G C>T G>A G>C G>T T>A T>C T>G
0 0.00506 0.01925 0.00237 0.00214 0.00589 0.00472 0.00429 0.00215 0.00198 0.00209 0.02149 0.00970
1 0.00507 0.00910 0.00485 0.00199 0.00221 0.01312 0.00811 0.00493 0.00502 0.00108 0.00789 0.00218
2 0.00431 0.00994 0.00328 0.00211 0.00286 0.00740 0.00972 0.00533 0.00478 0.00120 0.00938 0.00191
3 0.00576 0.00899 0.00468 0.00104 0.00191 0.00893 0.00902 0.00715 0.00840 0.00102 0.00840 0.00218
4 0.00255 0.00637 0.00238 0.00335 0.00352 0.02178 0.01540 0.00451 0.01015 0.00183 0.00559 0.00271
pos A>C A>G A>T C>A C>G C>T G>A G>C G>T T>A T>C T>G
0 0.00937 0.02002 0.00285 0.00235 0.00263 0.00383 0.00518 0.00522 0.00233 0.00167 0.02063 0.00432
1 0.00136 0.00750 0.00151 0.00589 0.00546 0.00843 0.01280 0.00328 0.00240 0.00452 0.00984 0.00457
2 0.00169 0.01020 0.00128 0.00378 0.00557 0.00998 0.00777 0.00318 0.00252 0.00230 0.00947 0.00439
3 0.00126 0.00983 0.00122 0.00801 0.00859 0.00903 0.00996 0.00176 0.00159 0.00359 0.00913 0.00470
4 0.00200 0.00445 0.00190 0.01047 0.00390 0.01594 0.02265 0.00400 0.00375 0.00240 0.00480 0.00153
-> Will dump: '34130-02_S15_L001.res.gz' this contains damage patterns for: 1 items
-> Setting threads to: 30
-> Will dump: '34130-02_S15_L001.bdamage.gz' this contains damage patterns for: 1 items
-> Setting threads to: 30
-> Will dump: '34130-02_S15_L001.rlens.gz' this contains read length distributions for: 1 items
-> Setting threads to: 30
-> Outputting overall statistic in file: "34130-02_S15_L001.stat"
-> metaDMG version: v0.4-123-g2cf6a01 (htslib: 1.17-28-ge13611a9) build(May 7 2025 09:54:35)
-> ../../tools/metaDMG-cpp/metaDMG-cpp getdamage -n 30 -o 34130-1_S14_L001 CarpeDeam/alignments/34130-1_S14_L001.sorted_by_name.bam
-> ./metaDMG-cpp refName: (null) min_length: 35 print_length: 5 run_mode: 0 out_prefix: 34130-1_S14_L001 nthreads: 30 ignore_errors: 0
skipping: M03353:64:000000000-CRD57:1:1101:1797:14979 unmapped, this msg is printed: 2 times more
skipping: M03353:64:000000000-CRD57:1:1101:1931:16493 unmapped, this msg is printed: 1 times more
skipping: M03353:64:000000000-CRD57:1:1101:2039:15978 unmapped, this msg is printed: 0 times more
pos A>C A>G A>T C>A C>G C>T G>A G>C G>T T>A T>C T>G
0 0.01128 0.02268 0.00025 0.00491 0.00974 0.00237 0.00585 0.00250 0.00160 0.01029 0.02407 0.00535
1 0.00819 0.01151 0.00627 0.00118 0.00377 0.01344 0.00714 0.01010 0.00448 0.00074 0.00717 0.00244
2 0.00509 0.01822 0.00522 0.00444 0.00384 0.00841 0.01058 0.00529 0.00682 0.00046 0.01475 0.00083
3 0.00093 0.01388 0.00756 0.00019 0.00155 0.01455 0.01580 0.00651 0.00733 0.00089 0.01584 0.00130
4 0.00396 0.00808 0.00275 0.00636 0.00707 0.02645 0.01162 0.00449 0.00948 0.00153 0.00670 0.00048
pos A>C A>G A>T C>A C>G C>T G>A G>C G>T T>A T>C T>G
0 0.01745 0.02869 0.00120 0.00152 0.00657 0.00387 0.00627 0.00802 0.00384 0.00055 0.02315 0.00582
1 0.00204 0.01154 0.00241 0.01128 0.00874 0.00915 0.01378 0.00183 0.00487 0.00797 0.01303 0.00911
2 0.00488 0.00976 0.00045 0.00156 0.00690 0.01526 0.00881 0.00133 0.00358 0.00136 0.01442 0.00407
3 0.00357 0.00967 0.00157 0.00841 0.00357 0.00933 0.00797 0.00319 0.00353 0.00616 0.00220 0.01188
4 0.00095 0.00467 0.00633 0.00603 0.00571 0.01586 0.01844 0.00771 0.00667 0.00226 0.00257 0.00140
-> Will dump: '34130-1_S14_L001.res.gz' this contains damage patterns for: 1 items
-> Setting threads to: 30
-> Will dump: '34130-1_S14_L001.bdamage.gz' this contains damage patterns for: 1 items
-> Setting threads to: 30
-> Will dump: '34130-1_S14_L001.rlens.gz' this contains read length distributions for: 1 items
-> Setting threads to: 30
-> Outputting overall statistic in file: "34130-1_S14_L001.stat"
Segmentation fault
The files are not readable:
-rwx------ 1 guelou01 nogroup 498 May 21 15:16 R142A_S10_L001.bdamage.gz
-rwx------ 1 guelou01 nogroup 383 May 21 15:16 R142A_S10_L001.res.gz
-rwx------ 1 guelou01 nogroup 1.8K May 21 15:16 R142A_S10_L001.rlens.gz
-rwx------ 1 guelou01 nogroup 123 May 21 15:16 R142A_S10_L001.stat
Link to the Bam files that I cannot upload to github.
I recompiled before trying again and the errors still show up. Linux version:
PRETTY_NAME="Debian GNU/Linux 12 (bookworm)"
NAME="Debian GNU/Linux"
VERSION_ID="12"
VERSION="12 (bookworm)"
VERSION_CODENAME=bookworm
ID=debian
HOME_URL="https://www.debian.org/"
SUPPORT_URL="https://www.debian.org/support"
BUG_REPORT_URL="https://bugs.debian.org/"
Make version:
GNU Make 4.3
Built for x86_64-pc-linux-gnu
Copyright (C) 1988-2020 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.
I hope I included the relevant informations.