ID h31
TITLE Malloc failure in hmmsearch
STATUS CLOSED
XREF 2005:1002-hmmer-bug-h31
REPORTED_BY Robert Petryszak [email protected]
OPENED_DATE SRE, Sun Oct 2 10:39:30 2005
CLOSED_DATE SRE, Sun Oct 16 13:37:50 2005
DESCRIPTION
hmmsearch fails w/ "realloc of X bytes failed: file core_algorithms.c line
157". Petryszak provides a "test case" consisting of a 1.9 GB FASTA
file and an HMM:
hmmsearch PF01121.10.fs UPI0000000001_UPI00005B0DDD

However, this runs fine on whelk01, wildebeest (Power5/Linux), and
an AIX Power 5 in Warren's lab. Petryszak's machine is an IBM p690
Regatta (8x Power4, AIX 5.2), hanni1 at HLRN
(http://www.hlrn.de/doc/basics.html). Tests on hanni1 reproduce
the failure.

The problem appears to be that IBM AIX inscrutably limits 32-bit
applications to one 256 MB data segment of memory by default. On
hanni, w/ 8 processors and a RAMLIMIT of 32 MB/proc, this limitation
is exposed. This memory limitation needs to be lifted. There are
three options:

1. Compile w/ xlc_r -q64 flag, to create a 64-bit executable.
   ar needs -X64 flag as well, to archive 64-bit object files.
   Manually modify AR command in Makefile.in in hmmer/ and squid/
   subdirs.

2. Compile w/ xlc_r -bmaxdata:0x80000000 flag, to make a 32-bit
   executable w/ "large memory model".

3. Don't run that many cpus; use --cpu flag.

ID h38
TITLE hmmscan failed to report some hits (rarely).
STATUS CLOSED in 3.0a2
XREF J4/70
REPORTED_BY me
OPENED_DATE 20 Jan 2009 [J4/61]
CLOSED_DATE 29 Jan 2009 [J4/70]
DESCRIPTION
compo was in 2nd part of pressed HMM db, but it needs to
be in first part for MSV.

ID h20
TITLE hmmpfam E-values dependent on # of threads.
STATUS CLOSED
XREF STL7 p.70
REPORTED_BY Robert A. Wilson [email protected]
CLOSED_DATE SRE, Fri Jun 6 18:56:43 2003
DESCRIPTION
Original report cited difference in E-values between
IBM 2.2g binaries and 2.3 binaries. Investigation shows
problem is really in both: # of threads is added to
nhmms, and counted as Z, so E-values end up depending
on thread #. (IBM 2.2g binaries weren't compiled w/ threads,
hence the difference seen by IBM.) In hmmpfam.c:worker_thread(),
we were bumping nhmm++ before successfully reading the HMM,
so on normal exit, each thread bumps nhmm one extra time after
the HMM file is emptied.

To reproduce: hmmpfam --cpu 0 vs.
hmmpfam --cpu
should give identical E-values.
Fixed; verified on Intel/Linux.
No test case built for bugs.sqc.

ID h24
TITLE Does not use CPPFLAGS, LDFLAGS in environment
STATUS CLOSED
XREF STL7 p.71
REPORTED_BY Ajay Khanna [email protected] 13 June 2003
CLOSED_DATE SRE, Fri Jun 13 14:59:13 2003
DESCRIPTION
./configure claims to use CPPFLAGS, LDFLAGS from environment,
but doesn't.

################################################################

HMMER3 / HMMER2 boundary

################################################################

ID h34
TITLE hmmbuild -o crashes if alignment has #=GR SS or #=GR SA lines
STATUS CLOSED in 2.3 branch
XREF ~/notebook/2008/0802-hmmer-bug-h34 [J3/87]
REPORTED_BY Bernd Brandt [email protected]
OPENED_DATE SRE, Sat Aug 2 11:49:40 2008
CLOSED_DATE SRE, Sat Aug 2 11:57:37 2008: SVN r2518
DESCRIPTION
hmmbuild -o foo segfaults when trying to re-save an alignment if
the alignment contains #=GR SS or SA annotation.
trace.c:P7Traces2Alignment() wasn't initializing these optional
fields correctly to NULL after allocating them.

ID 10
STATUS closed
DESCRIPTION Floating point exception in ExtremeValueP() on Digital 4.0b:
range error.
NOTED_DATE 7/2/99
NOTED_XREF
REPORTED_BY ju@harvard
REPRODUCE_WITH
REPRODUCE_ON Digital UNIX 4.0b
CLOSED_DATE 9/17/99
CLOSED_XREF
CLOSED_ACTION

ID h29
TITLE hmmsearch does not scale on SMP Xeons with hyperthreads
STATUS CLOSED
XREF notebook/0115-hmmer-bug-h29
REPORTED_BY Gordon Gremme [email protected]
OPENED_DATE SRE, Thu Jan 15 13:30:00 2004
CLOSED_DATE SRE, Thu Jan 15 15:43:25 2004
DESCRIPTION
See the notes [xref] for details.

This appears to be a Linux 2.4 SMP scheduler problem.
No action taken.

ID 16
STATUS untested
DESCRIPTION PVMConfirmSlaves() assumes nslaves=nhosts
NOTED_DATE 10/25/01
NOTED_XREF STL5 p. 66
REPORTED_BY John Blanchard ([email protected]), email 10/17/01
REPRODUCE_WITH
REPRODUCE_ON any PVM; only when DEBUGLEVEL>0
CLOSED_DATE
CLOSED_XREF STL5 p.66
CLOSED_ACTION pvm.c:PVMConfirmSlaves()... replace pvm_config() w/ pvm_tasks().

ID 11
STATUS OPEN
NOTED_DATE 11/15/99
NOTED_XREF
REPORTED_BY [email protected]
REPRODUCE_WITH
REPRODUCE_ON
CLOSED_DATE
CLOSED_XREF
CLOSED_ACTION
DESCRIPTION
hmmbuild, illegal B->E in traceback.
Appears to be exacerbated by fragment detection code;
a blank sequence in a multiple alignment will trigger it.

ID h28
TITLE P7Forward typo: bsc[M-1] should be bsc[M]
STATUS CLOSED
XREF STL7 p.123
REPORTED_BY Robel Kahsay [email protected]
CLOSED_DATE SRE, Fri Oct 3 12:48:50 2003
DESCRIPTION
Calculation of mmx[M] should touch bsc[M], not bsc[M-1].

ID 17
STATUS closed
DESCRIPTION threaded, unthreaded hmmsearch don't give same histogram
NOTED_DATE 2/27/02
NOTED_XREF STL6 p.1
REPORTED_BY Yang Yang
REPRODUCE_WITH bug17.sh
REPRODUCE_ON any
CLOSED_DATE 2/27/02
CLOSED_XREF STL6 p.1
CLOSED_ACTION modifications to hmmsearch.c; see notes.

ID 3
STATUS closed
DESCRIPTION hmmbuild segfaults on alignments labeled with #=ID
NOTED_DATE 1/15/99
NOTED_XREF
REPORTED_BY SRE
REPRODUCE_WITH
REPRODUCE_ON Solaris
CLOSED_DATE 1/19/99
CLOSED_XREF
CLOSED_ACTION

ID 5
STATUS closed
DESCRIPTION hmmbuild core dumps when building model from single
seqs FASTA file
NOTED_DATE 1/18/99
NOTED_XREF
REPORTED_BY agb
REPRODUCE_WITH
REPRODUCE_ON
CLOSED_DATE 1/19/99
CLOSED_XREF
CLOSED_ACTION

ID 9
STATUS OPEN
DESCRIPTION C->T transition doesn't seem to be parsed from save files
NOTED_DATE 6/29/99
NOTED_XREF
REPORTED_BY Bob Farrington
REPRODUCE_WITH
REPRODUCE_ON
CLOSED_DATE
CLOSED_XREF
CLOSED_ACTION

ID h39
TITLE hmmsearch faults when reading alignment file.
STATUS CLOSED in 3.0a2
XREF J4/84
REPORTED_BY me
OPENED_DATE 13 Feb 2009 [J4/81]
CLOSED_DATE 16 Feb 2009 [J4/94]
DESCRIPTION
hmmsearch faults when reading alignment file because it tries
to Position() it to 0 to rewind. Have esl_sqfile_Position(0)
close/reopen MSAs as a special case of a full rewind.

ID h19
TITLE floating point exception on Alpha/Linux
STATUS CLOSED
XREF none
REPORTED_BY "Yungok S. Ihm" [email protected]
CLOSED_DATE SRE, Fri May 9 15:31:23 2003
DESCRIPTION
hmmpfam crashes on extremely low scoring hits (<-1000),
on Alpha/Linux. Appears in both 2.2g and 2.3dev.
mathsupport.c:PValue() doesn't check for underflow before
calling sreEXP2() on the score; the Alpha crashes on this.
No test case built for bugs.sqc.

ID 14
STATUS closed
DESCRIPTION hmmconvert doesn't complain about appending binary to
ASCII HMMs, or vice versa
NOTED_DATE 12/24/00
NOTED_XREF STL3 p.133
REPORTED_BY [email protected], email 12/14/00
REPRODUCE_WITH bug13.pl
REPRODUCE_ON any
CLOSED_DATE SRE, Sun Dec 24 15:33:11 2000
CLOSED_XREF STL3 p. 133
CLOSED_ACTION hmmconvert.c now tests for this case

ID h27
TITLE Negative element in dsq; char vs. unsigned char.
STATUS CLOSED
XREF STL7 p.123
REPORTED_BY Kaivalya Dixit [email protected], Sept 2003.
OPENED_DATE SRE, Thu Oct 2 2003
CLOSED_DATE SRE, Thu Oct 2 11:25:57 2003
DESCRIPTION
Turned up in SPEC certification process. Alan L. MacKay
[email protected], of IBM AIX Compilers/Performance group, sends
an Insure++ report that shows a case where dsq[] was a negative
number. Kaivalya reports that they "fixed" this by forcing compilers
to use unsigned chars by default. A confusing discussion ensues;
MacKay thinks the problem is the use of char dsq[] as an array index,
whereas I think the code "guarantees" nonnegative dsq[] and that
there isn't a problem here; I think the crash IBM saw was coming
from memory corruption due to bug #h25.

Nonetheless, he has a point: if I'm going to use dsq[] as an array
index, it would be better coding practice to declare it as
unsigned char.

Changed dsq from char to unsigned char throughout (and some
instances of sym, symidx). Removed (int) casts whereever dsq[],
symidx were being used as array indices.

ID h35
TITLE jackhmmer crashed because code wasn't done.
STATUS CLOSED in 3.0a2
XREF J4/55
REPORTED_BY Rob Finn
OPENED_DATE 16 Jan 2009 [J4/55]
CLOSED_DATE 16 Jan 2009 [J4/55]
DESCRIPTION
jackhmmer code wasn't finished, but executable got built
for 3.0a1.

ID h42
TITLE Low information content models have poor sensitivity
STATUS OPEN
XREF J4/82
REPORTED_BY me
OPENED_DATE 13 Feb 2009 [J4/82]
CLOSED_DATE -
DESCRIPTION
Title was: PF00301 Rubredoxin fails to identify four seqs in its seed

This may be related to issues with low information content
models and glocal power. Rob did a comprehensive experiment
on H3 vs H2 [J5/13, 15 May 09].

ID 7
STATUS closed
DESCRIPTION Digital 4.0d binaries do not run on 4.0b;
pthread_setconcurrency() missing
NOTED_DATE 1/18/99
NOTED_XREF
REPORTED_BY Bill Pearson
REPRODUCE_WITH
REPRODUCE_ON Digital UNIX
CLOSED_DATE 1/19/99
CLOSED_XREF
CLOSED_ACTION

ID h22
TITLE hmmpfam crash related to resizing DP matrix
STATUS CLOSED
XREF STL7 p.70
REPORTED_BY James Cuff [email protected] 12 June 2003
CLOSED_DATE SRE, Fri Jun 13 14:56:42 2003
DESCRIPTION
hmmpfam crashes on Pfam_ls.
Problem is with reallocation in ResizePlan7Matrix(), when it
is called with N < maxN - it didn't reinitialize ptrs up to
maxN, it only did it up to N.

ID h37
TITLE hmmfetch failed on hmmpress'ed HMM files.
STATUS CLOSED in 3.0a2
XREF J4/61
REPORTED_BY me
OPENED_DATE 20 Jan 2009 [J4/61]
CLOSED_DATE 20 Jan 2009 [J4/61]
DESCRIPTION
.ssi is the SSI index of the flatfile; it is generated with
hmmfetch --index. .h3{mifp} are the press'ed indices for
binary db, generated by hmmpress. Wasn't keeping these
straight enough in hmm i/o.

STATUS closed
DESCRIPTION HMMs differ when built from mul vs. Stockholm format
NOTED_DATE 3/16/02
NOTED_XREF STL6 p.12
REPORTED_BY Sam Griffiths ([email protected])
REPRODUCE_WITH bug18.sh - was deleted from CVS.
REPRODUCE_ON Alpha (waterbug)
CLOSED_DATE 3/29/02
CLOSED_XREF STL6 p.12
CLOSED_ACTION Not a bug.

ID h33
TITLE ExtremeValueFitHistogram() crashes on uncensored fitting
STATUS CLOSED (in 2.4-stable branch)
XREF ~/notebook/2007/0531-hmmer-bug-h32
REPORTED_BY Yaniv Loewenstein ([email protected])
OPENED_DATE SRE, Thu May 31 13:49:27 2007
CLOSED_DATE SRE, Thu May 31 13:49:29 2007
DESCRIPTION
ExtremeValueFitHistogram() crashes with a bad malloc() if
asked to fit an uncensored histogram. z is uninitialized.
Fix is to initialize z=0. Made this change in 2.4stable branch.

ID 13
STATUS closed
DESCRIPTION hmmconvert happily converts a bogus HMM database w/
both DNA and protein
NOTED_DATE 12/24/00
NOTED_XREF STL3 p.133
REPORTED_BY [email protected], email 12/14/00
REPRODUCE_WITH bug13.pl
REPRODUCE_ON any
CLOSED_DATE SRE, Sun Dec 24 11:58:28 2000
CLOSED_XREF STL3 p.133
CLOSED_ACTION hmmio.c now checks for changes in Alphabet_type while reading HMMs.

ID h25
TITLE Memory-related hmmsearch crash on Swissprot.
STATUS CLOSED
XREF STL7 p.121
REPORTED_BY Niklaus Fankhauser [email protected] 26 Sept 2003;
Kaivalya Dixit [email protected], 24 Sept 2003.
OPENED_DATE SRE, Tue Sep 30 14:53:19 2003
CLOSED_DATE SRE, Wed Oct 1 08:07:18 2003
DESCRIPTION
hmmsearch crashes unpredictably on Swissprot searches (EMBL
format).

AMD contributes an Insure++ report showing three problems:

1. Alphabet[] is not a string but is being passed to strchr();
2. readEMBL is looking for a \0 in a growing seq, but a growing
   seq has no \0 until ReadSeq() polishes it off;
3. xmx[] is shown as a dangling/wild ptr in core_algorithms.c
   and fast_algorithms.c.
   AMD and/or Intel also indicate, via Kaivalya, that the problem
   is in sqio.c: they explicitly nul-terminate after every reallocation
   of the seq, and the problem disappears.
   Fixed problems 1 and 2. Can't find the problem that Insure++ is
   bitching about for 3; worrying. Bug goes away: it was clearly the result
   of problem 2. Bugs in #1 should only appear for databases with
   nonstandard residues.

Hi,

I've been using nhmm* executables to find probable matches to instances of Alu families in DNA sequences. For a classification problem, I found it useful to emit tabular output for matching sequences to one stream and sequences without sufficiently-scoring hits to a separate stream.

My fork can be compared to h3-develop with this link. However, it may break on protein fasta and would certainly do so for any other file types.

I feel that this solution, while effective for me, fails to match the flexibility of the rest of the code base. Is there a canonical way I might emit nhmmscan query records of any file format which have no passing hits?

ID h41
TITLE hmmbuild --enone reports duplicate lines in header
STATUS CLOSED in 3.0a2
XREF J4/82
REPORTED_BY me
OPENED_DATE 13 Feb 2009 [J4/82]
CLOSED_DATE 14 Feb 2009 [J4/83]
DESCRIPTION
Testing for ! esl_opt_IsDefault() doesn't work because option
might be ON by default and OFF by toggle-tying. To show it in
the header nondefault-options-that-are-on table, logic is different;
want to know what options are on that weren't on by default.
Wrote esl_opt_IsUsed() for this.

ID h36
TITLE hmmscan gave error message of (null).
STATUS CLOSED in 3.0a2
XREF J4/61,70
REPORTED_BY me
OPENED_DATE 20 Jan 2009 [J4/61]
CLOSED_DATE 29 Jan 2009 [J4/70]
DESCRIPTION
sqfp->linenumber is a uint64_t, and this MUST be formatted
as <%" PRId64 "> or cast to an int.

ID 12
STATUS closed
DESCRIPTION --domE, --domT don't work correctly in hmmpfam; E-value
is assumed to be monotonic w/ score.
NOTED_DATE 11/29/00
NOTED_XREF STL3 p.127
REPORTED_BY [email protected]
REPRODUCE_WITH bug12.pl
REPRODUCE_ON any
CLOSED_DATE SRE, Tue Dec 19 17:47:01 2000
CLOSED_XREF STL3 p.127
CLOSED_ACTION removed the break statements when looping over domain list.

Hi!

I have been using hmmer (mainly hmmsearch) for the past couple months and have been looking at its MPI performance. I was wondering if there was any specific reason for the value given to the MAX_BLOCK_SIZE constant (512x1024 = 0.5 Megabytes). If I am correct, this variable dictates how large a block of the sequence database is given at a time to an MPI worker. Did you arrive to this number empirically? If so, do you still have the results laying around? Would it be a good idea to vary this number depending on the size of the sequence database given and also the number of mpi workers available?

Also in the Accelerated profile HMM searches paper, you mention that the MPI parallelization scales poorly (2-4 cores), but I have actually seen it scale a bit better than that when given a large enough problem size. Has there been any significant modifications to the MPI parallelization?

When running hmmsearch I usually give it the Pfam-A.hmm database and .fasta files of varying sizes.

Thank you!
Best,
Felipe

ID h43
TITLE "non-aligned pointer being freed" on MacOS/X x86_64 icc
STATUS OPEN
XREF J4/110
REPORTED_BY Ryan Richt [email protected] 5 Mar 2009
OPENED_DATE SRE, Sun Mar 8 10:21:57 2009
CLOSED_DATE -
DESCRIPTION

Ryan's email:

Hey Sean!

I hope you are well. Just FYI, this could be somehow my fault, but at
the tail of every hmm* program of HMMER3 on MacOSX, x86_64, which I
recompiled from your source using icc as you suggested (which gave a
ton of "option -xk not supported" warnings"), I get the little error:

hmmstat(53966) malloc: *** error for object 0x7fff703c7b20: Non-
aligned pointer being freed (2)
*** set a breakpoint in malloc_error_break to debug
hmmstat(53966) malloc: *** error for object 0x7fff703c7c50: Non-
aligned pointer being freed (2)
*** set a breakpoint in malloc_error_break to debug

Have a nice day!

Ryan

Ryan Richt
CEO, Cofactor Genomics
[email protected]
+1 (314) 412-1537
+1 (888) 8-COFACTOR

ID h30
TITLE get_wee_midpt crashes out if given seq of L=1
STATUS CLOSED
XREF 2004:1119-hmmer-bug-h30
REPORTED_BY James Stroud [email protected]
OPENED_DATE SRE, Fri Nov 19 13:28:55 2004
CLOSED_DATE SRE, Fri Nov 19 13:58:08 2004
DESCRIPTION
hmmpfam crashes on Pfam_fs w/ "FATAL: you can't init get_wee_midpt
with a T", on a long HMM Arena_RNA_pol.

The problem is that P7WeeViterbi() is called w/ subseq of L=1. The
init of P7WeeViterbi sets begin,end points initially to STS, STT;
but when 1==L, assignment of tassign[L] to STT clobbers tassign[1].

Fixing this properly will require rethinking get_wee_midpt carefully.

Instead, hack around it. P7WeeViterbi() is only called once, from
within P7SmallViterbi(). Insert an extra test; if sqlen==1, do not
call P7WeeViterbi(), instead allocate a tiny L=1 matrix and use
P7Viterbi().

Document P7WeeViterbi(): it can't take L=1.

ID 8
STATUS closed
DESCRIPTION hmmpfam segfaults on GCG-reformatted Swissprot file
NOTED_DATE 1/19/99
NOTED_XREF
REPORTED_BY James Holzwarth
REPRODUCE_WITH
REPRODUCE_ON
CLOSED_DATE 1/19/99
CLOSED_XREF
CLOSED_ACTION

ID h23
TITLE Does not compile w/ --enable-pvm
STATUS CLOSED
XREF STL7 p.71
REPORTED_BY Goran Ceric [email protected] 12 June 2003
CLOSED_DATE SRE, Fri Jun 13 14:57:58 2003
DESCRIPTION
Didn't compile w/ PVM support, because of #define name changes
in 2.3.

ID 15
STATUS untested
DESCRIPTION hmmpfam slave process leak when nhmm < nslaves
NOTED_DATE 10/25/01
NOTED_XREF STL5 p. 66
REPORTED_BY John Blanchard ([email protected]), email 10/17/01
REPRODUCE_WITH
REPRODUCE_ON any PVM
CLOSED_DATE
CLOSED_XREF STL5 p.66
CLOSED_ACTION hmmpfam.c modified: kill slaves off in a separate loop

Using the Intel 2016 compiler on a RHEL 6.3 system, the random-utest regression test fails:

$ icc --version
icc (ICC) 16.0.0 20150815
Copyright (C) 1985-2015 Intel Corporation.  All rights reserved.

$ ./configure CC=icc
...
$ make check
...
    exercise   29 [         random-utest] ...     FAILED [command failed]

In the 2015-08-20 master branch commit (3ecde75), both random-utest and normal-utest fail.

ID h44
TITLE Compiler "option -xk not supported" warnings on MacOS/X
STATUS OPEN
XREF J4/110
REPORTED_BY Ryan Richt, 5 March 2009
OPENED_DATE 8 March 2009
CLOSED_DATE -
DESCRIPTION
These are harmless, but the autoconf macro for choosing optimized
options needs to be improved.

ID 2
STATUS closed
DESCRIPTION null2 consistency problem between per-seq and per-domain
NOTED_DATE 1/7/99
NOTED_XREF notebook STL1 p.117
REPORTED_BY David Kerk
REPRODUCE_WITH bug2.pl
REPRODUCE_ON ANY
CLOSED_DATE SRE, Tue Dec 19 17:45:46 2000
CLOSED_XREF STL3 notebook, p.127
CLOSED_ACTION created postprocess_hit() in hmmpfam.c

ID h26
TITLE Memory crash in hmmpfam.
STATUS CLOSED
XREF STL7 p.122.
REPORTED_BY Gary Montry [email protected], 15 Aug 2003.
OPENED_DATE SRE, Wed Oct 1 12:29:25 2003
CLOSED_DATE SRE, Thu Oct 2 11:20:00 2003
DESCRIPTION
hmmpfam search with 125,000aa sequence eventually crashes
because of lack of RAM, instead of successfully using small
memory routines.

Problem is that the code assumed that M,N can't both grow in
allocating a matrix, but that's not true in hmmpfam; after P7SmallViterbi(),
we may hand various sized bits of sequence off for subalignment,
with different sized models.

Wrote P7ViterbiSpaceOK(); used it instead of P7ViterbiSize() to switch
between normal and small variants; allow creation routine to grow in M
and N (padM and padN can both be positive); make initial allocs for
hmmpfam matrices to be 300x300, to avoid pathologically asymmetric
matrices.

ID 4
STATUS closed
DESCRIPTION sreformat core dumps when reformatting single seq to SELEX
NOTED_DATE 1/18/99
NOTED_XREF
REPORTED_BY sre
REPRODUCE_WITH
REPRODUCE_ON any
CLOSED_DATE 1/19/99
CLOSED_XREF
CLOSED_ACTION

ID 1
STATUS closed
DESCRIPTION BPA1_HUMAN crashes Pfam server
NOTED_DATE 1/16/98
NOTED_XREF
REPORTED_BY David Kerk
REPRODUCE_WITH
REPRODUCE_ON ANY
CLOSED_DATE 1/16/98
CLOSED_XREF
CLOSED_ACTION

ID h40
TITLE Different runs of hmmsearch give different answers.
STATUS CLOSED in 3.0a2
XREF J4/81
REPORTED_BY me
OPENED_DATE 13 Feb 2009 [J4/81]
CLOSED_DATE 24 Feb 2009 [J4/95,97,99]
DESCRIPTION
Random number generator needs to be seeded reproducibly by default.

hmmer 3.1b2 , openSUSE x86_64, gcc 6.2.1, warning as shown by rpmlint:

I: Program causes undefined operation
   (likely same variable used twiceand post/pre incremented in the same expression).
   e.g. x = x++; Split it in two operations.
W: hmmer sequence-point esl-ssdraw.c:858, 859, 860, 861

I: Statement might be overflowing a buffer in strncat. Common mistake:
   BAD: strncat(buffer,charptr,sizeof(buffer)) is wrong, it takes the left over size as 3rd argument
   GOOD: strncat(buffer,charptr,sizeof(buffer)-strlen(buffer)-1)
E: hmmer bufferoverflowstrncat hmmc2.c:364:7
E: hmmer bufferoverflowstrncat hmmdmstr.c:1405:5

Since the --enable-gprof option only uses -O, and since so many functions are inlined, compiling fwdfilter.c actually causes the compiler to run out of registers. I fixed this by removing the -O flag in the gprof compiler flag options, which may or may not be what we want. I ran into this problem on the NVIDIA board running all 64-bit (kernel and userspace) software. Since this might affect several branches I've refrained from making a pull request.

ID h21
TITLE "make install" doesn't create target directories
STATUS CLOSED
XREF STL7 p.70
REPORTED_BY Gisle S���lensminde [email protected] [10 Jun 2003]
CLOSED_DATE SRE, Thu Jun 12 12:37:54 2003
DESCRIPTION
"make install" doesn't create target directories if they
don't exist, and fails w/ poor error message. Added and documented
mkdir -p steps in Makefile.in

Hi Sean,

Just spotted a minor issue. We've used a multi-hmm to search a bunch of genomes with either nhmmer or hmmsearch. When we use "-A" we get some lovely Stockholm alignments, but it'd be handy to have a "#=GF ID" line containing the name of which hmm the alignment was generated from (each hmm has a corresponding unique e.g. "NAME GlmY". e.g.

STOCKHOLM 1.0

#=GF ID GlmY
#=GS CP007259/3866060-3867261 DE [subseq from] [subseq from] CP007259
...
//

We can map each alignment back to each hmm using "tblout" outputs, but it'd be much easier with ID lines. Then we can esl-afetch goodness too.

Some minimal illustration+versions below.

I hope all is well in Boston. I see the US is losing the Olympics. ;-)
http://www.medalspercapita.com/

Cheers,
@ppgardne & @biobeth

nhmmer :: search a DNA model or alignment against a DNA database

HMMER 3.1b2 (February 2015); http://hmmer.org/

nhmmer -A test.stk --tblout test.tblout sRNA.hmm test.fa > test.nhmmerout

Produces:

STOCKHOLM 1.0

#=GS CP007259/3866060-3867261 DE [subseq from] CP007259
...
CP007259/3866060-3867261 GAAT...
...
//

hmmsearch :: search profile(s) against a sequence database

HMMER 3.1b2 (February 2015); http://hmmer.org/

hmmsearch -A test.stk --tblout test.tblout sRNA.hmm test.fa > test.hmmsearchout

Produces:

STOCKHOLM 1.0

#=GS CP007259/3866060-3867261 DE [subseq from] [subseq from] CP007259
...
CP007259/3866060-3867261 GAATGC...
...
//

ID h32
TITLE hmmalign can't handle length 0 sequences
STATUS OPEN
XREF 2006/0316-hmmer-bug-h32
REPORTED_BY Allen Bryan [email protected]
OPENED_DATE SRE, Thu Mar 16 17:46:42 2006
CLOSED_DATE -
DESCRIPTION
hmmalign segfaults when a sequence is "empty" (length 0) in
an input fasta file.

ID 6
STATUS closed
DESCRIPTION getseq clashes with GCG program of same name
NOTED_DATE 1/18/99
NOTED_XREF
REPORTED_BY sre
REPRODUCE_WITH
REPRODUCE_ON n/a
CLOSED_DATE 1/19/99
CLOSED_XREF
CLOSED_ACTION renamed getseq to sfetch