segfault in the diff step

[rchikhi]

$ \time ~/tools/kmdiff/kmdiff-v1.1.0-bin-Linux/bin/kmdiff diff --km-run kmdiff_run  --output-dir kmdiff_out -s 0.01 -1 12 -2 17
[2025-02-22 13:23:11.777] [info] Process partitions
[2025-02-22 13:23:12.581] [error] Killed after receive Segmentation fault:SIGSEGV(11) signal. Demangled backtrace dumped at ./kmdiff_backtrace.log. If the problem persists, please open an issue with the return of 'kmdiff infos' and the content of ./kmdiff_backtrace.log
Command exited with non-zero status 11
0.33user 0.07system 0:00.84elapsed 47%CPU (0avgtext+0avgdata 34396maxresident)k
0inputs+0outputs (0major+7097minor)pagefaults 0swaps

$ cat kmdiff_backtrace.log 

Backtrace:
1 0x50bff0

(no more output)

version: latest release

$ cat fof.txt
control0: reads/ERR12506745_1.fastq ; reads/ERR12506745_2.fastq
control1: reads/ERR12506766_1.fastq ; reads/ERR12506766_2.fastq
control2: reads/ERR12506768_1.fastq ; reads/ERR12506768_2.fastq
control3: reads/ERR12506755_1.fastq ; reads/ERR12506755_2.fastq
control4: reads/ERR12506765_1.fastq ; reads/ERR12506765_2.fastq
control5: reads/ERR12506761_1.fastq ; reads/ERR12506761_2.fastq
control6: reads/ERR12506769_1.fastq ; reads/ERR12506769_2.fastq
control7: reads/ERR12506760_1.fastq ; reads/ERR12506760_2.fastq
control8: reads/ERR12506767_1.fastq ; reads/ERR12506767_2.fastq
control9: reads/ERR12506764_1.fastq ; reads/ERR12506764_2.fastq
control10: reads/ERR12506773_1.fastq ; reads/ERR12506773_2.fastq
control11: reads/ERR12506779_1.fastq ; reads/ERR12506779_2.fastq
case0: reads/ERR12506741_1.fastq ; reads/ERR12506741_2.fastq
case1: reads/ERR12506750_1.fastq ; reads/ERR12506750_2.fastq
case3: reads/ERR12506753_1.fastq ; reads/ERR12506753_2.fastq
case4: reads/ERR12506748_1.fastq ; reads/ERR12506748_2.fastq
case5: reads/ERR12506746_1.fastq ; reads/ERR12506746_2.fastq
case6: reads/ERR12506751_1.fastq ; reads/ERR12506751_2.fastq
case7: reads/ERR12506758_1.fastq ; reads/ERR12506758_2.fastq
case8: reads/ERR12506759_1.fastq ; reads/ERR12506759_2.fastq
case9: reads/ERR12506740_1.fastq ; reads/ERR12506740_2.fastq
case10: reads/ERR12506743_1.fastq ; reads/ERR12506743_2.fastq
case11: reads/ERR12506775_1.fastq ; reads/ERR12506775_2.fastq
case12: reads/ERR12506762_1.fastq ; reads/ERR12506762_2.fastq
case13: reads/ERR12506752_1.fastq ; reads/ERR12506752_2.fastq
case14: reads/ERR12506747_1.fastq ; reads/ERR12506747_2.fastq
case15: reads/ERR12506776_1.fastq ; reads/ERR12506776_2.fastq
case16: reads/ERR12506757_1.fastq ; reads/ERR12506757_2.fastq
case17: reads/ERR12506756_1.fastq ; reads/ERR12506756_2.fastq

$ du -hsc kmdiff_run/
137G    kmdiff_run/
137G    total
$ ll kmdiff_run/
total 24
-rw-r--r-- 1 rchikhi seqbio  631 Feb 21 15:14 build_infos.txt
drwxr-xr-x 1 rchikhi seqbio    0 Feb 21 15:14 config_gatb
drwxr-xr-x 1 rchikhi seqbio    0 Feb 21 15:14 counts
drwxr-xr-x 1 rchikhi seqbio    0 Feb 21 15:14 filters
drwxr-xr-x 1 rchikhi seqbio    0 Feb 21 15:14 fpr
-rw-r--r-- 1 rchikhi seqbio   36 Feb 21 15:14 hash.info
drwxr-xr-x 1 rchikhi seqbio    0 Feb 21 17:46 histograms
drwxr-xr-x 1 rchikhi seqbio    0 Feb 21 15:14 howde_index
-rw-r--r-- 1 rchikhi seqbio  192 Feb 21 17:46 kmdiff-count.opt
-rw-r--r-- 1 rchikhi seqbio 1815 Feb 21 15:14 kmtricks.fof
drwxr-xr-x 1 rchikhi seqbio    0 Feb 21 15:14 matrices
drwxr-xr-x 1 rchikhi seqbio    0 Feb 21 15:14 merge_infos
drwxr-xr-x 1 rchikhi seqbio    0 Feb 21 15:14 minimizers
-rw-r--r-- 1 rchikhi seqbio  406 Feb 21 15:14 options.txt
drwxr-xr-x 1 rchikhi seqbio    0 Feb 21 17:43 partition_infos
drwxr-xr-x 1 rchikhi seqbio    0 Feb 21 15:14 repartition_gatb
-rw-r--r-- 1 rchikhi seqbio   41 Feb 21 17:46 run_infos.txt
drwxr-xr-x 1 rchikhi seqbio    0 Feb 21 17:22 superkmers

About 2 TB of input fastq, 135 GB of count output. (non-consecutive fof numbers btw) Count ran ok.