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ogotoh / spaln

Genome mapping and spliced alignment of cDNA or amino acid sequences
GNU General Public License v2.0
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spaln crashes with FORTIFY_SOURCE=3 #71

Open LocutusOfBorg opened 1 month ago

LocutusOfBorg commented 1 month ago

Hello, I found spaln crashing on this command, when -D_FORTIFY_SOURCE=3 is used during build

345s autopkgtest [20:14:46]: test run-unit-test: [----------------------- 346s Gd:187913 No:71174 My:3057 MS:157 Mb:188 Tw:2331733 Tl:33850852 71.68 1.17 27.15 347s #Segs 6630, TabSize 262144, Words: 2331733, GenomeSize 33928503, GIDs 6 354s Gd:4336377 No:59650673 My:12950 MS:365 Mb:69 Tw:6664558 Tl:44608849 6.78 0.02 93.20 356s #Segs 6630, TabSize 64000000, Words: 6664558, GenomeSize 33928503, GIDs 6 358s buffer overflow detected : terminated 372s /tmp/autopkgtest.xYGgJE/build.dZa/src/debian/tests/run-unit-test: line 23: 2420 Aborted (core dumped) spaln -Q7 -d dictdisc_g -T dictdisc dictdisc.faa.gz > /dev/null 372s autopkgtest [20:15:13]: test run-unit-test: -----------------------] 379s run-unit-test FAIL non-zero exit status 134

this is the testsuite content

#!/bin/bash
set -e

pkg=spaln

export LC_ALL=C.UTF-8
if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
  AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
  trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
fi

cp -a /usr/share/${pkg}/seqdb/* "${AUTOPKGTEST_TMP}"

cd "${AUTOPKGTEST_TMP}"

#export ALN_DBS="${AUTOPKGTEST_TMP}"
NCPUS=`grep '^cpu cores' /proc/cpuinfo | head -n 1 | sed 's/cpu cores[[:space:]:]\+//'`

# Avoid using makeidx.pl (see https://github.com/ogotoh/spaln/issues/46#issuecomment-1025331901)
#perl makeidx.pl -v -inp dictdisc_g.gf.gz
spaln -W -KD -t${NCPUS} dictdisc_g.gf.gz >/dev/null
spaln -W -KP -t${NCPUS} dictdisc_g.gf.gz > /dev/null
spaln -Q7 -d dictdisc_g -T dictdisc dictdisc.faa.gz > /dev/null
spaln -Q7 -d dictdisc_g -yS -T dictdisc -O12 -g dictdisc.cf.gz > /dev/null
sortgrcd -O15 -F2 dictdisc.cf.grd.gz > /dev/null

and this is how the package is built (Ubuntu enforces FORTIFY_SOURCE=3 by default) https://launchpadlibrarian.net/748233307/buildlog_ubuntu-oracular-amd64.spaln_3.0.2+dfsg-2build2_BUILDING.txt.gz

x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/spaln-3.0.2+dfsg-2build2 -pedantic -Wdate-time -D_FORTIFY_SOURCE=3 -DM_THREAD=1 -c blksrc.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/spaln-3.0.2+dfsg-2build2 -pedantic -Wdate-time -D_FORTIFY_SOURCE=3 -DM_THREAD=1 -c aln2.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/spaln-3.0.2+dfsg-2build2 -pedantic -Wdate-time -D_FORTIFY_SOURCE=3 -DM_THREAD=1 -c dbs.cc x86_64-linux-gnu-g++ -g -O2 -Werror=implicit-function-declaration -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/spaln-3.0.2+dfsg-2build2 -pedantic -Wdate-time -D_FORTIFY_SOURCE=3 -DM_THREAD=1 -c gaps.cc

LocutusOfBorg commented 1 month ago 
(gdb) bt full
#0  0x00007ffff78a3f1c in pthread_kill () from /lib/x86_64-linux-gnu/libc.so.6
No symbol table info available.
#1  0x00007ffff784519e in raise () from /lib/x86_64-linux-gnu/libc.so.6
No symbol table info available.
#2  0x00007ffff7828902 in abort () from /lib/x86_64-linux-gnu/libc.so.6
No symbol table info available.
#3  0x00007ffff782976c in ?? () from /lib/x86_64-linux-gnu/libc.so.6
No symbol table info available.
#4  0x00007ffff7941049 in __fortify_fail () from /lib/x86_64-linux-gnu/libc.so.6
No symbol table info available.
#5  0x00007ffff79409e4 in __chk_fail () from /lib/x86_64-linux-gnu/libc.so.6
No symbol table info available.
#6  0x00005555555bb50c in memset (__dest=<optimized out>, __ch=0, __len=<optimized out>) at /usr/include/x86_64-linux-gnu/bits/string_fortified.h:59
No locals.
#7  vclear<unsigned int> (ary=<optimized out>, n=<optimized out>) at /usr/src/spaln-3.0.2+dfsg-2/src/clib.h:105
No locals.
#8  ExinPot::calcScr_3(Seq const*, float*) const [clone .constprop.0] (this=this@entry=0x5555555f5370, sd=sd@entry=0x5555555f5ff0, scr=0x0) at /usr/src/spaln-3.0.2+dfsg-2/src/utilseq.cc:1458
        redctab = 0x5555555ddd30 <tnredctab> "\004\004\004\001\002"
        len = <optimized out>
        ss = <optimized out>
        tt = <optimized out>
        cdp = 0x555555609d00
        result = 0x555555678370
        rest = <optimized out>
        kk = 6
        x = <optimized out>
        buf = {8838, 6696, 2208}
        w = <optimized out>
        acc = 0
#9  0x0000555555575618 in ExinPot::calcScr (scr=0x0, this=0x5555555f5370, sd=<optimized out>) at /usr/src/spaln-3.0.2+dfsg-2/src/utilseq.h:161
No locals.
#10 Exinon::intron53_p (this=0x55555564c240, dvsp=true) at /usr/src/spaln-3.0.2+dfsg-2/src/codepot.cc:543
        th5 = <optimized out>
        posB = <optimized out>
        last = <optimized out>
        prefS = <optimized out>
        prfS = <optimized out>
        fs = <optimized out>
        fT = <optimized out>
        fB = 0
        prefT = 0x555555673360
        prefB = 0x0
        prfT = <optimized out>
        prfB = <optimized out>
        fI = <optimized out>
        fO = -300
        thB = <optimized out>
        pref3 = 0x555555669340
        prefI = <optimized out>
        prf3 = <optimized out>
        prfI = <optimized out>
        th3 = <optimized out>
        ss = <optimized out>
        wk53 = <optimized out>
        fE = <optimized out>
        pref5 = 0x555555664330
        prefE = <optimized out>
        prf5 = <optimized out>
        prfE = <optimized out>
        sigB = <optimized out>
        fE = <optimized out>
        fI = <optimized out>
        fT = <optimized out>
        fB = <optimized out>
        fO = <optimized out>
        th3 = <optimized out>
        th5 = <optimized out>
        thB = <optimized out>
        pref5 = <optimized out>
        pref3 = <optimized out>
        prefS = <optimized out>
        prefT = <optimized out>
        prefB = <optimized out>
        prefE = <optimized out>
        prefI = <optimized out>
        prf5 = <optimized out>
        prf3 = <optimized out>
        prfS = <optimized out>
        prfT = <optimized out>
        prfB = <optimized out>
        prfE = <optimized out>
        prfI = <optimized out>
        ss = <optimized out>
        sigB = <optimized out>
        posB = <optimized out>
        last = <optimized out>
        wk53 = <optimized out>
        fs = <optimized out>
        wkb = <optimized out>
        sig5 = <optimized out>
        sig3 = <optimized out>
        sigE = <optimized out>
        sigb = <optimized out>
#11 Exinon::Exinon (this=<optimized out>, sd_=<optimized out>, pwd_=<optimized out>, bo=<optimized out>, this=<optimized out>, sd_=<optimized out>, pwd_=<optimized out>, bo=<optimized out>)
    at /usr/src/spaln-3.0.2+dfsg-2/src/codepot.cc:396
        zero53 = {dinc5 = 0, dinc3 = 0, cano5 = 0, cano3 = 0}
        zero53 = <optimized out>
        prefE = <optimized out>
        prfE = <optimized out>
        fE = <optimized out>
        wkb = <optimized out>
#12 0x000055555555fb74 in genomicseq (sqs=sqs@entry=0x5555555f5998, pwd=pwd@entry=0x5555555f52b0, ori=ori@entry=1) at /usr/src/spaln-3.0.2+dfsg-2/src/spaln.cc:1120
No locals.
#13 0x0000555555563809 in spalign2 (sqs=0x5555555f5990, pwd=0x5555555f52b0, GsI=0x555555609058, ori=1) at /usr/src/spaln-3.0.2+dfsg-2/src/spaln.cc:664
No locals.
#14 0x00005555555c5b7c in blkaln(Seq**, SrchBlk*, RANGE*, ThQueue*) [clone .isra.0] (sqs=<optimized out>, bks=<optimized out>, q=<optimized out>, rng=<optimized out>)
    at /usr/src/spaln-3.0.2+dfsg-2/src/spaln.cc:891
        dir = <optimized out>
        sigb = <optimized out>
#11 Exinon::Exinon (this=<optimized out>, sd_=<optimized out>, pwd_=<optimized out>, bo=<optimized out>, this=<optimized out>, sd_=<optimized out>, pwd_=<optimized out>, bo=<optimized out>)
    at /usr/src/spaln-3.0.2+dfsg-2/src/codepot.cc:396
        zero53 = {dinc5 = 0, dinc3 = 0, cano5 = 0, cano3 = 0}
        zero53 = <optimized out>
        prefE = <optimized out>
        prfE = <optimized out>
        fE = <optimized out>
        wkb = <optimized out>
#12 0x000055555555fb74 in genomicseq (sqs=sqs@entry=0x5555555f5998, pwd=pwd@entry=0x5555555f52b0, ori=ori@entry=1) at /usr/src/spaln-3.0.2+dfsg-2/src/spaln.cc:1120
No locals.
#13 0x0000555555563809 in spalign2 (sqs=0x5555555f5990, pwd=0x5555555f52b0, GsI=0x555555609058, ori=1) at /usr/src/spaln-3.0.2+dfsg-2/src/spaln.cc:664
No locals.
#14 0x00005555555c5b7c in blkaln(Seq**, SrchBlk*, RANGE*, ThQueue*) [clone .isra.0] (sqs=<optimized out>, bks=<optimized out>, q=<optimized out>, rng=<optimized out>)
    at /usr/src/spaln-3.0.2+dfsg-2/src/spaln.cc:891
        dir = <optimized out>
--Type <RET> for more, q to quit, c to continue without paging--
        n = <optimized out>
        nparalog = <optimized out>
        grng = <optimized out>
        wrng = <optimized out>
        frng = <optimized out>
        a = <optimized out>
        b = <optimized out>
        b_intr = <optimized out>
        hfg = {left = 0, right = 2147483647, segno = 0, sname = 0x0}
        GsI = 0x555555609058
        gsinf = <optimized out>
        n_out = <optimized out>
        gener = <optimized out>
        basis = <optimized out>
        odr = <optimized out>
#15 0x00005555555c3a03 in quick4(Seq**, SrchBlk*, ThQueue*) [clone .isra.0] (sqs=0x5555555f5990, bks=0x5555555f5100, q=0x0) at /usr/src/spaln-3.0.2+dfsg-2/src/spaln.cc:1095
        a = @0x5555555f5990: 0x5555555f59e0
        orgrng = <optimized out>
        covrng = <optimized out>
        rbdry = <optimized out>
#16 0x0000555555567065 in all_in_func (sqs=0x5555555f5990, svr=0x7fffffffddf0, prm=0x5555555f5100) at /usr/src/spaln-3.0.2+dfsg-2/src/spaln.cc:1167
        nf = 0
        sbk = <optimized out>
#17 0x000055555555d9a4 in main (argc=1, argv=0x7fffffffe788) at /usr/src/spaln-3.0.2+dfsg-2/src/spaln.cc:1562
        bprm = 0x5555555f5100
        messg = 0x0
        insuf = 0x5555555c91c0 "No input seq file !\n"
        n = <optimized out>
        nseqs = 8
        seqs = 0x5555555f5990
        a = @0x5555555f5990: 0x5555555f59e0
        b = @0x5555555f5998: 0x5555555f5ff0
        mb = <optimized out>
        dbs = <optimized out>
        svr = {argc = 0, argc0 = 1, argv = 0x7fffffffe790, argv0 = 0x7fffffffe788, fd = {0x0, 0x0}, gzfd = {0x5555555f56b0, 0x0}, fc = 0x0, nfrom = {0, 0}, nto = {2147483647, 2147483647}, cfrom = {0x0, 0x0}, 
          cto = {0x0, 0x0}, counter = {1, 0}, sw = {true, false}, molc = {1, 0}, attr = {0x5555555f49a0 " SP", 0x0}, atsz = {8, 0}, input_form = IM_SNGL, input_ns = 1, target_dbf = 0x5555555f12b0, 
          query_dbf = 0x0}
LocutusOfBorg commented 1 month ago

the failure is in vclear function vclear (ary=0x55555567d364, n=5) at /usr/src/spaln-3.0.2+dfsg-2/src/clib.h:105 warning: 105 /usr/src/spaln-3.0.2+dfsg-2/src/clib.h: No such file or directory (gdb) p ary $363 = (unsigned int ) 0x55555567d364 (gdb) p n $364 = 5 (gdb) p n sizeof(ary) $366 = 40

LocutusOfBorg commented 1 month ago

Since I don't fully understand your code, I asked chatGPT to analyze it:

To fix the function ExinPot::calcScr_3 to correctly calculate the coding potential from a DNA sequence based on a 5th-order Markov model, we need to address several issues in the code:

Key Fixes Needed: Memory Alignment: Align pointers correctly to avoid accessing out-of-bounds memory. Buffer Management: Ensure that the buffer accesses are within bounds. Initialization: Properly initialize variables to avoid undefined behavior. Correct Markov Calculation: Make sure the logic for computing values based on the 5th-order Markov model is correct. Correct Length Calculation for vclear: Ensure the vclear function call correctly clears the necessary range of data. Here's a corrected and more robust implementation of the function:

and this is the patch

--- spaln-3.0.2+dfsg.orig/src/utilseq.cc
+++ spaln-3.0.2+dfsg/src/utilseq.cc
@@ -1429,7 +1429,7 @@ const     CHAR*   tt = sd->at(sd->right);

 const  float*  cdp = begin();
        float*  result = new float[len];
-       float*  rest = result - 5;
+       float*  rest = result;
 const  int     kk = morder + 1;
        int     x = kk;
        int     buf[3] = {0, 0, 0};
@@ -1438,19 +1438,19 @@ double  acc = 0.;
        for (int p = 1; ss < tt; p = next_p[p], ++rest) {
            int c = redctab[*ss++];
            if (c < 4) {
-               buf[p] = 3 * (w = (4 * w + c) % ndata);
-               if (x) --x;
+               buf[p % 3] = 3 * (w = (4 * w + c) % ndata);
+               if (x > 0) --x;
            } else {
                w = 0;
                x = kk;
            }
            float       val = 0;
-           if (!x) {
-               val += cdp[buf[next_p[p]] + 2]; // -1
-               val += cdp[buf[prev_p[p]]];     // 0
-               val += cdp[buf[p] + 1];         // +1
+           if (x == 0) {
+               val += cdp[buf[next_p[p % 3]] + 2];     // -1
+               val += cdp[buf[prev_p[p % 3]]]; // 0
+               val += cdp[buf[p % 3] + 1];             // +1
            }
-           if (rest >= result) {
+           if (rest < result + len) {
                *rest = val;
                if (scr && p == 1) acc += val;
            }

that made tests pass and no segfault happen Key Changes Made: Pointer Alignment: rest is initialized as result to avoid out-of-bounds memory access. Buffer Indexing: The buffer index p is wrapped with modulo operation to prevent out-of-bounds access. Initialization: All necessary variables are initialized correctly to avoid undefined behaviors. Correct Length in vclear: The range passed to vclear is corrected to ensure proper clearing of the result array. Error Checking and Safety: Additional checks ensure that the pointers remain within bounds during processing. This version of the function should properly calculate the coding potential of a DNA sequence using a 5th-order Markov model, while adhering to proper C++ practices to avoid memory errors.

ogotoh commented 1 month ago

Dear Gianfranco,

Thank you for your comments.

The crash is likely to be caused by a simple bug at reading gzipped query sequences. I have uploaded a fixed version today. Please try the new version whether it is still problematic in your system.

As for coding potential, I will look at the code again according to your suggestions.

Osamu,

LocutusOfBorg commented 1 month ago

Hello, unfortunately your commit 6ffcd906466a2f75bbde5ba6731d3a3a60c90111 looks not enough to fix the issue

#0  0x00007ffff78a3f1c in pthread_kill () from /lib/x86_64-linux-gnu/libc.so.6
No symbol table info available.
#1  0x00007ffff784519e in raise () from /lib/x86_64-linux-gnu/libc.so.6
No symbol table info available.
#2  0x00007ffff7828902 in abort () from /lib/x86_64-linux-gnu/libc.so.6
No symbol table info available.
#3  0x00007ffff782976c in ?? () from /lib/x86_64-linux-gnu/libc.so.6
No symbol table info available.
#4  0x00007ffff7941049 in __fortify_fail () from /lib/x86_64-linux-gnu/libc.so.6
No symbol table info available.
#5  0x00007ffff79409e4 in __chk_fail () from /lib/x86_64-linux-gnu/libc.so.6
No symbol table info available.
#6  0x00005555555bb50c in memset (__dest=<optimized out>, __ch=0, __len=<optimized out>) at /usr/include/x86_64-linux-gnu/bits/string_fortified.h:59
No locals.
#7  vclear<unsigned int> (ary=<optimized out>, n=<optimized out>) at /usr/src/spaln-3.0.2+dfsg-2ubuntu3/src/clib.h:105
No locals.
#8  ExinPot::calcScr_3(Seq const*, float*) const [clone .constprop.0] (this=this@entry=0x5555555f5480, sd=sd@entry=0x5555555f5ff0, scr=0x0) at /usr/src/spaln-3.0.2+dfsg-2ubuntu3/src/utilseq.cc:1458
        redctab = 0x5555555ddd30 <tnredctab> "\004\004\004\001\002"
        len = <optimized out>
        ss = <optimized out>
        tt = <optimized out>
        cdp = 0x555555609d00
        result = 0x555555678470
        rest = <optimized out>
        kk = 6
        x = <optimized out>
        buf = {8838, 6696, 2208}
        w = <optimized out>
        acc = 0
#9  0x0000555555575618 in ExinPot::calcScr (scr=0x0, this=0x5555555f5480, sd=<optimized out>) at /usr/src/spaln-3.0.2+dfsg-2ubuntu3/src/utilseq.h:161
No locals.
#10 Exinon::intron53_p (this=0x55555564c340, dvsp=true) at /usr/src/spaln-3.0.2+dfsg-2ubuntu3/src/codepot.cc:543
        th5 = <optimized out>
        posB = <optimized out>
        last = <optimized out>
        prefS = <optimized out>
        prfS = <optimized out>
        fs = <optimized out>
        fT = <optimized out>
        fB = 0
        prefT = 0x555555673460
        prefB = 0x0
        prfT = <optimized out>
        prfB = <optimized out>
        fI = <optimized out>
        fO = -300
        thB = <optimized out>
        pref3 = 0x555555669440
        prefI = <optimized out>
        prf3 = <optimized out>
        prfI = <optimized out>
        th3 = <optimized out>
        ss = <optimized out>
        wk53 = <optimized out>
        fE = <optimized out>
        pref5 = 0x555555664430
        prefE = <optimized out>
        prf5 = <optimized out>
        prfE = <optimized out>
        sigB = <optimized out>
        fE = <optimized out>
        fI = <optimized out>
        fT = <optimized out>
        fB = <optimized out>
        fO = <optimized out>
        th3 = <optimized out>
        th5 = <optimized out>
        thB = <optimized out>
        pref5 = <optimized out>
        pref3 = <optimized out>
        prefS = <optimized out>
        prefT = <optimized out>
        prefB = <optimized out>
        prefE = <optimized out>
        prefI = <optimized out>
        prf5 = <optimized out>
        prf3 = <optimized out>
        prfS = <optimized out>
        prfT = <optimized out>
        prfB = <optimized out>
        prfE = <optimized out>
        prfI = <optimized out>
        ss = <optimized out>
        sigB = <optimized out>
        posB = <optimized out>
        last = <optimized out>
        wk53 = <optimized out>
        fs = <optimized out>
        wkb = <optimized out>
        sig5 = <optimized out>
        sig3 = <optimized out>
        sigE = <optimized out>
        sigb = <optimized out>
#11 Exinon::Exinon (this=<optimized out>, sd_=<optimized out>, pwd_=<optimized out>, bo=<optimized out>, this=<optimized out>, sd_=<optimized out>, pwd_=<optimized out>, bo=<optimized out>)
    at /usr/src/spaln-3.0.2+dfsg-2ubuntu3/src/codepot.cc:396
        zero53 = {dinc5 = 0, dinc3 = 0, cano5 = 0, cano3 = 0}
        zero53 = <optimized out>
        prefE = <optimized out>
        prfE = <optimized out>
        fE = <optimized out>
        wkb = <optimized out>
#12 0x000055555555fb74 in genomicseq (sqs=sqs@entry=0x5555555f5998, pwd=pwd@entry=0x5555555f53c0, ori=ori@entry=1) at /usr/src/spaln-3.0.2+dfsg-2ubuntu3/src/spaln.cc:1120
No locals.
#13 0x0000555555563809 in spalign2 (sqs=0x5555555f5990, pwd=0x5555555f53c0, GsI=0x555555617348, ori=1) at /usr/src/spaln-3.0.2+dfsg-2ubuntu3/src/spaln.cc:664
No locals.
#14 0x00005555555c5b7c in blkaln(Seq**, SrchBlk*, RANGE*, ThQueue*) [clone .isra.0] (sqs=<optimized out>, bks=<optimized out>, q=<optimized out>, rng=<optimized out>)
    at /usr/src/spaln-3.0.2+dfsg-2ubuntu3/src/spaln.cc:891
        dir = <optimized out>
        n = <optimized out>
        nparalog = <optimized out>
        grng = <optimized out>
        wrng = <optimized out>
        frng = <optimized out>
        a = <optimized out>
        b = <optimized out>
        b_intr = <optimized out>
        hfg = {left = 0, right = 2147483647, segno = 0, sname = 0x0}
        GsI = 0x555555617348
        gsinf = <optimized out>
        n_out = <optimized out>
        gener = <optimized out>
        basis = <optimized out>
        odr = <optimized out>
#15 0x00005555555c3a03 in quick4(Seq**, SrchBlk*, ThQueue*) [clone .isra.0] (sqs=0x5555555f5990, bks=0x5555555f5210, q=0x0) at /usr/src/spaln-3.0.2+dfsg-2ubuntu3/src/spaln.cc:1095
        a = @0x5555555f5990: 0x5555555f59e0
        orgrng = <optimized out>
        covrng = <optimized out>
        rbdry = <optimized out>
#16 0x0000555555567065 in all_in_func (sqs=0x5555555f5990, svr=0x7fffffffddf0, prm=0x5555555f5210) at /usr/src/spaln-3.0.2+dfsg-2ubuntu3/src/spaln.cc:1167
        nf = 0
        sbk = <optimized out>
#17 0x000055555555d9a4 in main (argc=1, argv=0x7fffffffe788) at /usr/src/spaln-3.0.2+dfsg-2ubuntu3/src/spaln.cc:1562
        bprm = 0x5555555f5210
        messg = 0x0
        insuf = 0x5555555c91c0 "No input seq file !\n"
        n = <optimized out>
        nseqs = 8
        seqs = 0x5555555f5990
        a = @0x5555555f5990: 0x5555555f59e0
        b = @0x5555555f5998: 0x5555555f5ff0
        mb = <optimized out>
        dbs = <optimized out>
        svr = {argc = 0, argc0 = 1, argv = 0x7fffffffe790, argv0 = 0x7fffffffe788, fd = {0x0, 0x0}, gzfd = {0x5555555f56b0, 0x0}, fc = 0x0, nfrom = {0, 0}, nto = {2147483647, 2147483647}, cfrom = {0x0, 
            0x0}, cto = {0x0, 0x0}, counter = {1, 0}, sw = {true, false}, molc = {1, 0}, attr = {0x5555555f49a0 " SP", 0x0}, atsz = {8, 0}, input_form = IM_SNGL, input_ns = 1, 
          target_dbf = 0x5555555f12b0, query_dbf = 0x0}