Source: kallisto
Followup-For: Bug #1118526
X-Debbugs-Cc: [email protected]
Additional information after using gdb in the sbuild container when it
fails. Unfortunately it is proving difficult/impossible to add a
breakpoint just after the last successful opt.verbose message since it
is in the template, even though a breakpoint on the function entry point
does work.
root@sbuild:/build/reproducible-path/kallisto-0.51.1+dfsg/obj-x86_64-linux-gnu#
gdb --args ./src/kallisto index -i ./func_tests/basic7.idx -k 7
./func_tests/simple.fasta
...
CompactedDBG::construct(): Joined 0 unitigs
18:41:42 [45/4583]
corrupted size vs. prev_size
Thread 1 "kallisto" received signal SIGABRT, Aborted.
[Switching to Thread 0x7ffff787bbc0 (LWP 5545)]
0x00007ffff79a695c in ?? () from /lib/x86_64-linux-gnu/libc.so.6
(gdb) bt full
#0 0x00007ffff79a695c in ?? () from /lib/x86_64-linux-gnu/libc.so.6
No symbol table info available.
#1 0x00007ffff7951cc2 in raise () from /lib/x86_64-linux-gnu/libc.so.6
No symbol table info available.
#2 0x00007ffff793a4ac in abort () from /lib/x86_64-linux-gnu/libc.so.6
No symbol table info available.
#3 0x00007ffff793b291 in ?? () from /lib/x86_64-linux-gnu/libc.so.6
No symbol table info available.
#4 0x00007ffff79b0465 in ?? () from /lib/x86_64-linux-gnu/libc.so.6
No symbol table info available.
#5 0x00007ffff79b0e7e in ?? () from /lib/x86_64-linux-gnu/libc.so.6
No symbol table info available.
#6 0x00007ffff79b3e3a in ?? () from /lib/x86_64-linux-gnu/libc.so.6
No symbol table info available.
#7 0x00007ffff79b4c4e in malloc () from /lib/x86_64-linux-gnu/libc.so.6
No symbol table info available.
#8 0x00007ffff7ce093c in operator new(unsigned long) () from
/lib/x86_64-linux-gnu/libstdc++.so.6
No symbol table info available.
#9 0x00005555555b4b07 in KmerHashTable<CompressedCoverage_t<Node>
>::init_tables (this=<optimized out>, sz=<optimized out>) at
./ext/bifrost/src/KmerHashTable.hpp:218
No locals.
#10 KmerHashTable<CompressedCoverage_t<Node> >::KmerHashTable (this=<optimized
out>, sz=<optimized out>) at ./ext/bifrost/src/KmerHashTable.hpp:98
sz_with_empty = <optimized out>
rdnup_sz = <optimized out>
#11 CompactedDBG<Node, void>::toDataGraph (this=this@entry=0x7fffffffdc40,
o=..., nb_threads=<optimized out>) at ./ext/bifrost/src/CompactedDBG.tcc:141
moveUnitigs = {__this = 0x7fffffffdc40, __o = @0x7fffffff9140}
it_s = {<std::iterator<std::forward_iterator_tag,
CompressedCoverage_t<void>, long, CompressedCoverage_t<void>*,
CompressedCoverage_t<void>&>> = {<No data fields>}, ht = <optimized out>, h = 0}
it_e = <optimized out>
#12 0x00005555555c08ba in CompactedDBG<Node, void>::build (this=0x7fffffffdc40,
opt=...) at ./ext/bifrost/src/CompactedDBG.tcc:648
graph = {_vptr.CompactedDBG = 0x5555556db120 <vtable for
CompactedDBG<void, void>+16>, k_ = 7, g_ = 5, invalid = false, static
min_abundance_lim = 15, static max_abundance_lim = 15, v_unitigs = std::vector
of length 0, capacity 0, km_unitigs = {static block_sz = 1024, static cov_full
= 1, shift_div = 10,
mask_mod = 1023, sz = 0, v_blocks = std::vector of length 0,
capacity 1}, h_kmers_ccov = {size_ = 1024, pop = 26, num_empty = 998,
table_keys = 0x555555785d70, table_values = 0x555555787d88}, hmap_min_unitigs =
{is_static = false, size_ = 0, pop = 0, num_empty = 0, table_keys = 0x0,
table_tinyv = 0x0,
table_tinyv_sz = 0x0, mphf = 0x0, lck_min = std::vector of length
0, capacity 0, lck_edit_table = {_bits = std::atomic<unsigned int> = { 0 },
padding = {0 <repeats 15 times>}}, pop_p = std::atomic<unsigned long> = {
93824994399712 }, num_empty_p = std::atomic<unsigned long> = { 140737488327776
}},
data = {<No data fields>}}
max_threads = <optimized out>
construct_finished = <optimized out>
k_cpy = 7
g_cpy = 5
invalid_cpy = false
reference_mode = <optimized out>
nb_unique_kmers = <optimized out>
nb_unique_minimizers = <optimized out>
nb_non_unique_kmers = <optimized out>
nb_non_unique_minimizers = <optimized out>
bf = <optimized out>
r = <optimized out>
v_files = <optimized out>
kms_opt = <optimized out>
kms = <optimized out>
s = <optimized out>
__for_range = <optimized out>
__for_begin = <optimized out>
__for_end = <optimized out>
filter_out = <optimized out>
#13 KmerIndex::BuildDeBruijnGraph (this=this@entry=0x7fffffffdc30, opt=...,
tmp_file="tmp/kallisto.4g0ULG4xKK4oaaSv2Mpvj8S", out=...) at
./src/KmerIndex.cpp:595
c_opt = {verbose = true, nb_threads = 1, min_count_km = 1,
nb_bits_kmers_bf = 14, inFilenameBBF = "", outFilenameBBF = "", filename_seq_in
= std::vector of length 0, capacity 0, filename_ref_in = std::vector of length
1, capacity 1 = {"tmp/kallisto.4g0ULG4xKK4oaaSv2Mpvj8S"}, k = 7, g = 5, build =
true,
update = false, query = false, clipTips = false, deleteIsolated =
false, useMercyKmers = false, outputGFA = true, outputFASTA = false, outputBFG
= false, compressOutput = true, inexact_search = false, writeIndexFile = true,
ratio_kmers = 0.80000000000000004, prefixFilenameOut = "", filename_graph_in =
"",
filename_index_in = "", filename_query_in = std::vector of length 0,
capacity 0}
dfks = {<ankerl::unordered_dense::v3_1_1::detail::base_table_type_set>
= {<No data fields>}, m_values = std::vector of length 0, capacity 0, m_buckets
= 0x0, m_num_buckets = 0, m_max_bucket_capacity = 0, m_max_load_factor = 0,
m_hash = {<No data fields>},
m_equal = {<std::binary_function<Kmer, Kmer, bool>> = {<No data
fields>}, <No data fields>}, m_shifts = 0 '\000'}
pos1 = <optimized out>
tmp_size = 0
res = <optimized out>
pos2 = <optimized out>
minz = std::vector of length 0, capacity 0
mphf = <optimized out>
dfks_size = 0
dlist_overhang = 0
infile = <incomplete type>
in = <incomplete type>
running_id = <optimized out>
#14 0x00005555555c3afe in KmerIndex::BuildTranscripts (this=<optimized out>,
opt=..., out=...) at ./src/KmerIndex.cpp:407
unique_names =
{<ankerl::unordered_dense::v3_1_1::detail::base_table_type_set> = {<No data
fields>}, m_values = std::vector of length 5, capacity 8 = {"t1", "t2", "t3",
"t4", "t5"}, m_buckets = 0x5555557654d0, m_num_buckets = 16,
m_max_bucket_capacity = 12, m_max_load_factor = 0.800000012,
--Type <RET> for more, q to quit, c to continue without paging--
m_hash = {<No data fields>}, m_equal =
{<std::binary_function<std::__cxx11::basic_string<char, std::char_traits<char>,
std::allocator<char> >, std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> >, bool>> = {<No data fields>},
<No data fields>}, m_shifts = 60 '<'}
tmp_file = "tmp/kallisto.4g0ULG4xKK4oaaSv2Mpvj8S"
of = <incomplete type>
fp = 0x0
seq = <optimized out>
l = <optimized out>
gen = {static state_size = 624, _M_x = {42, 3107752595, 1895908407,
3900362577, 3030691166, 4081230161, 2732361568, 1361238961, 3961642104,
867618704, 2837705690, 3281374275, 3928479052, 3691474744, 3088217429,
1769265762, 3769508895, 2731227933, 2930436685, 486258750, 1452990090,
3321835500, 3520974945,
2343938241, 928051207, 2811458012, 3391994544, 3688461242,
1372039449, 3706424981, 1717012300, 1728812672, 1688496645, 1203107765,
1648758310, 440890502, 1396092674, 626042708, 3853121610, 669844980,
2992565612, 310741647, 3820958101, 3474052697, 305511342, 2053450195,
705225224, 3836704087, 3293527636,
1140926340, 2738734251, 574359520, 1493564308, 269614846,
427919468, 2903547603, 2957214125, 181522756, 4137743374, 2557886044,
3399018834, 1348953650, 1575066973, 3837612427, 705360616, 4138204617,
1604205300, 1605197804, 590851525, 2371419134, 2530821810, 4183626679,
2872056396, 3895467791, 1156426758,
184917518, 2502875602, 2730245981, 3251099593, 2228829441,
2591075711, 3048691618, 3030004338, 1726207619, 993866654, 823585707,
936803789, 3180156728, 1191670842, 348221088, 988038522, 3281236861,
1153842962, 4152167900, 98291801, 816305276, 575746380, 1719541597, 2584648622,
1791391551, 3234806234,
413529090, 219961136, 4180088407, 1135264652, 3923811338,
2304598263, 762142228, 1980420688, 1225347938, 3657621885, 3762382117,
1157119598, 2556627260, 2276905960, 3857700293, 1903185298, 4258743924,
2078637161, 4160077183, 3569294948, 2138906140, 1346725611, 1473959117,
2798330104, 3785346335,
4103334026, 3448442764, 1142532843, 4278036691, 3071994514,
3474299731, 1121195796, 1536841934, 2132070705, 1064908919, 2840327803,
992870214, 2041326888, 2906112696, 4182466030, 1031463950, 703166484,
854266995, 4157971695, 4071962029, 2600094776, 2770410869, 3776335751,
2599879593, 2451043853,
2223709058, 2098813464, 4008111478, 2959232195, 3072496064,
2498909222, 4020139729, 785990520, 958060279, 4183949075, 2392404465,
533774465, 4092066952, 3967420027, 1726137853, 2907699474, 3158758391,
1460845905, 1323598137, 2446717890, 3004885867, 3447263769, 1378488047,
3172418196, 652839901,
1695052769, 226007057, 778836071, 1216725078, 655651335,
1850195064, 427367795, 800074262, 2241880422, 1713434925, 339981078,
1730571881, 672610244, 1952245009, 2729177102, 3516932475, 4032720152,
3177283432, 411893652, 2440235559, 3587427933, 43170267, 39225133,
3904203400...}, _M_p = 624}
countNonNucl = <optimized out>
countUNuc = <optimized out>
polyAcount = <optimized out>
#15 0x0000555555572675 in main (argc=<optimized out>, argv=0x7fffffffeb18) at
./src/main.cpp:2317
index = {k = 7, num_trans = 5, skip = 1, dbg = {_vptr.CompactedDBG =
0x5555556db0b0 <vtable for CompactedDBG<Node, void>+16>, k_ = 7, g_ = 5,
invalid = false, v_unitigs = std::vector of length 0, capacity 0, km_unitigs =
{static block_sz = 1024, shift_div = 10, mask_mod = 1023, sz = 0,
v_blocks = std::vector of length 0, capacity 0}, h_kmers_ccov =
{size_ = 1024, pop = 0, num_empty = 1024, table_keys = 0x555555757560,
table_values = 0x555555765928}, hmap_min_unitigs = {is_static = false, size_ =
64, pop = 2, num_empty = 62, table_keys = 0x555555754e50, table_tinyv =
0x55555578baa0,
table_tinyv_sz = 0x555555757330 "", mphf = 0x0, lck_min =
std::vector of length 0, capacity 0, lck_edit_table = {_bits =
std::atomic<unsigned int> = { 0 }, padding = {0 <repeats 15 times>}}, pop_p =
std::atomic<unsigned long> = { 4096 }, num_empty_p = std::atomic<unsigned long>
= { 25769803778 }},
data = {<No data fields>}}, ecmapinv =
{<ankerl::unordered_dense::v3_1_1::detail::base_table_type_map<int>> = {<No
data fields>}, m_values = std::vector of length 0, capacity 0, m_buckets = 0x0,
m_num_buckets = 0, m_max_bucket_capacity = 0, m_max_load_factor = 0.800000012,
m_hash = {<No data fields>},
m_equal = {<std::binary_function<Roaring, Roaring, bool>> = {<No
data fields>}, <No data fields>}, m_shifts = 61 '='}, INDEX_VERSION = 13,
target_lens_ = std::vector of length 5, capacity 8 = {19, 23, 17, 10, 10},
target_names_ = std::vector of length 5, capacity 8 = {"t1", "t2", "t3", "t4",
"t5"},
target_seqs_ = std::vector of length 0, capacity 0, dfk_onlist =
false, do_union = false, no_jump = false, target_seqs_loaded = false,
load_positional_info = true, onlist_sequences = {roaring = {high_low_container
= {size = 0, allocation_size = 4, containers = 0x555555724d80, keys =
0x555555724da0,
typecodes = 0x555555724da8 ""}, copy_on_write = false}}, d_list
= {<ankerl::unordered_dense::v3_1_1::detail::base_table_type_set> = {<No data
fields>}, m_values = std::vector of length 0, capacity 0, m_buckets = 0x0,
m_num_buckets = 0, m_max_bucket_capacity = 0, m_max_load_factor = 0.800000012,
m_hash = {<No data fields>}, m_equal = {<std::binary_function<Kmer,
Kmer, bool>> = {<No data fields>}, <No data fields>}, m_shifts = 61 '='},
dummy_dfk = {static MAX_K = 32, {bytes = "0\004\000\000\000\000\000", longs =
{1072}}}, um_dummy = {<UnitigMapBase> = {dist = 0, len = 1, size = 0, strand =
true,
isEmpty = true}, pos_unitig = 0, isShort = false, isAbundant =
false, cdbg = 0x0}, shadeToColorTranscriptMap = std::unordered_map with 0
elements, shade_sequences = {roaring = {high_low_container = {size = 0,
allocation_size = 4, containers = 0x555555755260, keys = 0x555555755280,
typecodes = 0x555555755288 ""}, copy_on_write = false}},
use_shade = false}
out = <incomplete type>
start_time = "Tue Oct 21 18:40:00 2025"
opt = {verbose = false, aa = false, distinguish = false, threads = 1,
index = "./func_tests/basic7.idx", k = 7, g = 0, max_ec_size = -1, iterations =
500, output = "", skip = 1, seed = 42, error_rate = 0, threshold =
0.80000000000000004, fld = 0, sd = 0, min_range = 1, bootstrap = 0,
max_num_reads = 0,
transfasta = std::vector of length 1, capacity 1 =
{"./func_tests/simple.fasta"}, batch_mode = false, bus_mode = false, busOptions
= {nfiles = 0, keep_fastq_comments = false, umi = std::vector of length 0,
capacity 0, bc = std::vector of length 0, capacity 0, seq = std::vector of
length 0, capacity 0,
paired = false, long_read = false, unmapped = false, error_rate =
0, threshold = 0, aa = false}, bam = false, num = false, batch_file_name = "",
batch_files = std::vector of length 0, capacity 0, batch_ids = std::vector of
length 0, capacity 0, files = std::vector of length 0, capacity 0,
d_list = std::vector of length 0, capacity 0, d_list_overhang = 1,
plaintext = false, write_index = false, single_end = false, long_read = false,
unmapped = false, strand_specific = false, peek = false, bias = false,
pseudobam = false, genomebam = false, make_unique = false, fusion = false,
dfk_onlist = false, do_union = false, no_jump = false, strand =
ProgramOptions::StrandType::None, gfa = "", inspect_thorough = false,
single_overhang = false, record_batch_bus_barcode = false, matrix_to_files =
false, matrix_to_directories = false, input_interleaved_nfiles = 0, gtfFile =
"", chromFile = "",
bedFile = "", technology = "", platform = "", tagsequence = "",
tccFile = "", ecFile = "", fldFile = "", transcriptsFile = "", genemap = "",
priors = "", tmp_dir = "tmp"}
cmd = "index"
