Dear Maintainer, just tried to get some more information out of the crash. It was not showing up with t-coffee 12 compiled in testing. Just with switching to unstable and recompiling t-coffee the crash manifested when building libbio-tools-run-alignment-tcoffee-perl-1.7.4.
Unfortunately the signal is 'eaten' and therefore no core file is generated. With a modification adding a call to gdb I was able to get one. Below is the backtrace of the first failing pid. Some more information is in the attached file describing how the information was collected. It looks like the static array name_list is accessed beyond the initilialized memory. Kind regards, Bernhard $ gdb -q -ex 'set pagination off' -ex 'set width 0' -ex 'directory /home/benutzer/source/t-coffee/try2/t-coffee-12.00.7fb08c2/t_coffee_source' /usr/bin/t_coffee --core ./core.3995 Reading symbols from /usr/bin/t_coffee...Reading symbols from /usr/lib/debug/.build-id/26/7314cbd87aae405b78889c1e3af85806aea901.debug...done. done. [New LWP 3995] Core was generated by `/usr/bin/t_coffee'. #0 0x00007fe6b33eb7f7 in __GI___waitpid (pid=4065, stat_loc=stat_loc@entry=0x7ffe74a7b488, options=options@entry=0) at ../sysdeps/unix/sysv/linux/waitpid.c:30 30 ../sysdeps/unix/sysv/linux/waitpid.c: Datei oder Verzeichnis nicht gefunden. Source directories searched: /home/benutzer/source/t-coffee/try2/t-coffee-12.00.7fb08c2/t_coffee_source:$cdir:$cwd (gdb) bt #0 0x00007fe6b33eb7f7 in __GI___waitpid (pid=4065, stat_loc=stat_loc@entry=0x7ffe74a7b488, options=options@entry=0) at ../sysdeps/unix/sysv/linux/waitpid.c:30 #1 0x00007fe6b336980f in do_system (line=<optimized out>) at ../sysdeps/posix/system.c:149 #2 0x000055f262eef2b0 in error_exit (exit_code=11) at util_lib/util.c:10008 #3 <signal handler called> #4 0x000055f262ebb84d in decode_name (name=name@entry=0x55f26537f1f0 "TCTAG_53775_4", mode=mode@entry=2) at util_lib/reformat.c:14644 #5 0x000055f262ebbbdd in translate_name (name=0x55f26537f1f0 "TCTAG_53775_4") at util_lib/reformat.c:14575 #6 0x000055f262ebd1da in get_fasta_sequence (fname=<optimized out>, comment_out=0x0) at util_lib/reformat.c:5304 #7 0x000055f262ebe7b7 in main_read_aln (name=name@entry=0x55f265366250 "/var/tmp/tco/tcoifo4u0ng3972//11383988396", A=0x55f26538bf90, A@entry=0x0) at util_lib/reformat.c:1532 #8 0x000055f262f28db1 in aln_file2constraint_list (alname=alname@entry=0x55f265366250 "/var/tmp/tco/tcoifo4u0ng3972//11383988396", CL=CL@entry=0x55f2652de520, weight_mode=weight_mode@entry=0x55f265363858 "sim") at util_lib/util_constraints_list.c:4304 #9 0x000055f262f3decf in read_constraint_list (CL=0x55f2652de520, in_fname=<optimized out>, in_mode=in_mode@entry=0x55f262f582fc "aln", mem_mode=mem_mode@entry=0x55f262f6702f "disk", weight_mode=weight_mode@entry=0x55f265363858 "sim") at util_lib/util_constraints_list.c:2368 #10 0x000055f262f3dfaa in retrieve_lib_job (job=0x55f2635cb990) at util_lib/util_constraints_list.c:473 #11 0x000055f262f20bb5 in fork_subset_produce_list (CL=CL@entry=0x55f2652de520, method=method@entry=0x55f263617d71 "clustalw_pair", job=0x55f2635cb990, job@entry=0x55f263ab2f00, nproc=<optimized out>, local_stderr=0x55f2634f9bd0, mem_mode=0x55f2634f9bd0 "\204,\255", <incomplete sequence \373>, weight=<optimized out>, S=0x55f263617d71) at util_lib/util_constraints_list.c:177 #12 0x000055f262f3d1bf in produce_list (CL=CL@entry=0x55f2652de520, S=<optimized out>, method=method@entry=0x55f263617d71 "clustalw_pair", weight=weight@entry=0x55f2639d4020 "default", mem_mode=mem_mode@entry=0x55f2635cfbc0 "mem") at util_lib/util_constraints_list.c:94 #13 0x000055f262f3dc70 in read_constraint_list (CL=CL@entry=0x55f2652de520, in_fname=<optimized out>, in_mode=in_mode@entry=0x0, mem_mode=mem_mode@entry=0x55f2635cfbc0 "mem", weight_mode=weight_mode@entry=0x55f2639d4020 "default") at util_lib/util_constraints_list.c:2332 #14 0x000055f262f3e253 in fork_read_n_constraint_list (fname=0x55f2636139e0, n_list=<optimized out>, in_mode=0x0, mem_mode=0x55f2635cfbc0 "mem", weight_mode=0x55f2639d4020 "default", type=<optimized out>, local_stderr=0x55f2634f9bd0, CL=0x55f2652de520, seq_source=0x55f2639a9560 "ANY", nproc=8) at util_lib/util_constraints_list.c:2218 #15 0x000055f262f3e812 in read_n_constraint_list (fname=0x55f2636139e0, n_list=4, in_mode=0x0, mem_mode=0x55f2635cfbc0 "mem", weight_mode=0x55f2639d4020 "default", type=0x55f2635c74a0 "", local_stderr=0x55f2634f9bd0, CL=0x55f2652de520, seq_source=0x55f2639a9560 "ANY") at util_lib/util_constraints_list.c:2141 #16 0x000055f262e697f0 in batch_main (argc=<optimized out>, argv=<optimized out>) at t_coffee_lib/t_coffee.c:4942 #17 0x000055f262d905ad in main (argc=<optimized out>, argv=<optimized out>) at t_coffee_lib/t_coffee.c:179 #4 0x000055f262ebb84d in decode_name (name=name@entry=0x55f26537f1f0 "TCTAG_53775_4", mode=mode@entry=2) at util_lib/reformat.c:14644 14644 return name_list[i-1][0];
