icebert/pblat

parallelized blat with multi-threads support

pblat's Issues

shared memory

Hi, icebert:
Thanks for your very nice tool, it helps me a lot. I have multiple sample fasta, and want to use pblat in parallel. Can pblat share memory that multiple process use the same memory?

Thank you!

Bad file descriptor

Hi,

When I use pblat, I always get following errors (both github and biconda version):

Bad file descriptor
Write error to .psl

what's wrong?
here is my command line
pblat -t=dnax -q=prot -threads=6 -mask=lower -minIdentity=81 -minScore=15 -noHead Op-f.msksoft.fa merge.okay.aa.0001.fa merge.okay.aa.0001.psl

Best,
Kun

should update htslib version

the old version (1.3) give me a error when build it:
hts.c:92:1: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘{’ token { ^ hts.c:125:31: error: expected declaration specifiers or ‘...’ before ‘hFILE’ static size_t decompress_peek(hFILE *fp, unsigned char *dest, size_t destsize) ^~~~~ hts.c:158:1: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘{’ token { ^ hts.c:179:23: error: expected declaration specifiers or ‘...’ before ‘hFILE’ int hts_detect_format(hFILE *hfile, htsFormat *fmt)

Fixed after upgrade to version 1.11, but need to add -lbz2 -llzma -lcurl -lpthread to Makefile CFLAGS

push new tag

Could you please push a new tag.

To promote reproducible science, we require tagged releases when building scientific software. Pulling from the master is not reproducible.

thanks

multiple definition with GCC > 10

htmlRecover has multiple definitions. GCC 10 defaults to -fno-common, which means a linker error will now be reported.

gcc -O -Wall  -o pblat blat.o jkOwnLib.a jkweb.a htslib/libhts.a  -lm -lpthread -lz -lssl -lcrypto
/app/software/binutils/2.35-GCCcore-10.2.0/bin/ld.gold: error: jkweb.a(htmshell.o): multiple definition of 'htmlRecover'
/app/software/binutils/2.35-GCCcore-10.2.0/bin/ld.gold: jkweb.a(cheapcgi.o): previous definition here
/app/software/binutils/2.35-GCCcore-10.2.0/bin/ld.gold: error: jkweb.a(portimpl.o): multiple definition of 'htmlRecover'
/app/software/binutils/2.35-GCCcore-10.2.0/bin/ld.gold: jkweb.a(cheapcgi.o): previous definition here
collect2: error: ld returned 1 exit status
Makefile:41: recipe for target 'all' failed
make: *** [all] Error 1

Internal error jkOwnLib/trans3.c 71

Please note source files for this example available at: https://genome-test.gi.ucsc.edu/~hiram/pblat/

Tried command:
time ./pblat -threads=2 -noHead -q=rnax -t=dnax -mask=lower \ GCF_901000725.2_fTakRub1.2.2bit refSeqMrna.fa \ GCF_901000725.2_fTakRub1.2.xenoRefGene.psl

Failure:
`Loaded 384126662 letters in 128 sequences
Blatx 128 sequences in database, 237906 files in query
Internal error jkOwnLib/trans3.c 71

real 591m4.026s
user 1085m0.023s
sys 16m38.805s
`

See example files:
`-rw-rw-r-- 1 997165206 Aug 9 2019 refSeqMrna.fa

-rw-rw-r-- 1 109199773 Jan 15 07:10 GCF_901000725.2_fTakRub1.2.2bit

-rwxrwxr-x 1 1062472 May 1 15:28 pblat

-rw-rw-r-- 1 171 May 3 12:27 run.sh

-rw-rw-r-- 1 182 May 3 12:28 run.log
`

Running on system:

`file pblat

pblat: ELF 64-bit LSB executable, x86-64, version 1 (SYSV), dynamically linked (uses shared libs), for GNU/Linux 2.6.32, BuildID[sha1]=980da6786dfd0811359b238fa0e4c1d955ece3b1, not stripped
`

installation fatal error 'openssl/ssl.h' file not found

Hi,
When trying to compile with make, I see the following error:
gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o https.o lib/https.c
lib/https.c:6:10: fatal error: 'openssl/ssl.h' file not found
#include "openssl/ssl.h"
^~~~~~~~~~~~~~~
1 error generated.
make: *** [https.o] Error 1

I am following installation instructions from Nature Protocols volume 15, pages1098–1131(2020), (link: https://www.nature.com/articles/s41596-019-0279-7#Sec23), on a MacOS Version 10.13.6, if this information helps.
Any help or thoughts would be greatly appreciated! Maybe I need to adjust the paths for openssl? but i'm not sure how to do it properly. Thank you

[malloc] error with protein query and DNA database

I have just installed pblat v.2.3 through bioconda in Mac. When trying to replicate blat results with the command:

pblat -t=dnax -q=prot -noHead  -minIdentity=54 -minScore=15 assembly_dna.fasta ref_proteins.faa output.psl

The following error occurs:

pblat(4387,0x7fff8ea61380) malloc: *** error for object 0x7ff72fade900: pointer being freed was not allocated
*** set a breakpoint in malloc_error_break to debug
Loaded 26764612 letters in 39673 sequences
Blatx 39673 sequences in database, 4782 files in query
...done in 13 seconds

The .psl is produced but with roughly as half the hits as the ones that are obtained by blat
Am I missing something? Any help is appreciated

Edgardo

empty tmp files

Hi,

I am using pblat v2.1 to align two genomes (200 Mb, 6 chromosomes each). I gave it 28 threads and 200 Gb RAM, and all but one of the 28 .psl.tmp.x temp files are empty. The software seems to be running since CPU time is increasing faster than clock time but I don't see anything being written to the files.

Is this normal behavior?

Thanks,
Gui

Time usage is the same between normal blat and pblat

I use 24 threads. There are 24 tmp files when running, but all blank.
Finally, pblat get identical result with normal blat. But the time usage is the same. Both ~700s
Am I getting something wrong?

Segmentation fault core dumped on large genome

in one of the closed issue says the Seg fault issue is fixed on v2.5 but I am still getting it on a 14gb genome:
pblat -threads=6 -noHead -fastMap -tileSize=12 -ooc=4461.ooc -minScore=100 -minIdentity=98 source.fa chunk_08.fa chunk_08.fa.psl
Loaded 14547261565 letters in 22 sequences
Segmentation fault (core dumped)

Reading query from list

I noticed that pblat doesn't support reading query files from a file containing a list.
The strange thing is that I used a file containing query files and pblat used only the first query file and then stopped.

In order to avoid confusion, I think pblat should either:

• Read query files from a list like blat does. (Probably the best, even using databases from a list is supported)
• Not read any query files from a list and notify the user that the query is not valid.

The current behavior is confusing because the user can think that pblat used all query files from the list when it only used one.

pblat produces empty output file

I was able to run the pblat program on my local ubuntu 14.04 machine with parallelization and generate a nice output file. However, when I tried to recompile the program and run it on a single node in a cluster (CentOS based cluster), I could compile and run it but the output file generated after the run was surprisingly empty.

Does anyone have any idea why I might be getting an empty output file when running the program on a cluster?

Thanks!

update to blat v36x2?

Do you have plans to update pblat based off the latest version of the blat v36x2 source?
http://hgdownload.soe.ucsc.edu/admin/jksrc.v376.zip

installation issue (make: *** [all] Error 1)

Hello
I have been unable to successfully install pblat due to some ERROR.
I enter the source code directory in terminal and issue the "make" command, the following error message has appeared.

gcc -O -Wall -o pblat blat.o jkOwnLib.a jkweb.a htslib/libhts.a -lm -lpthread -lz -lssl -lcrypto
jkweb.a(https.o): In function openSslInit': https.c:(.text+0xb1): undefined reference to OPENSSL_init_ssl'
https.c:(.text+0xc0): undefined reference to OPENSSL_init_crypto' https.c:(.text+0xd4): undefined reference to OPENSSL_init_crypto'
jkweb.a(https.o): In function netConnectHttpsThread': https.c:(.text+0x136): undefined reference to TLS_client_method'
https.c:(.text+0xaea): undefined reference to `TLS_client_method'
collect2: error: ld returned 1 exit status
make: *** [all] Error 1

I checked my OpenSSL:

[yugy.life@login02 lib]$pwd
/usr/local/openssl/lib
[yugy.life@login02 lib]$nm -D libcrypto.so | grep OPENSSL_init
0000000000195ff0 T OPENSSL_init
0000000000185730 T OPENSSL_init_crypto
[yugy.life@login02 lib]$nm -D libssl.so | grep OPENSSL_init
U OPENSSL_init_crypto
00000000000361e0 T OPENSSL_init_ssl
[yugy.life@login02 lib]$nm -D libssl.so | grep TLS_slient_method
[yugy.life@login02 lib]$nm -D libssl.so | grep TLS_client_method
000000000001fdf0 T DTLS_client_method
000000000001fd10 T TLS_client_method
[yugy.life@login02 lib]$

segmentation fault

Hi

I'm running pblat for running AUGUSTUS gene prediction
however, segmentation fault error was occurred during running pblat

I used this command
pblat -threads=40 -t=dnax -q=prot -noHead -minIdentity=81 -minScore=15 genome.fa protein.fa output.out

The size of genome.fa is 2.4G and the size of protein.fa is 8.8M
please let me know how to solve the problem
Thanks

installation issue

I've tried both to install it in the cluster and locally and I get 2 different errors:

1. in the cluster: /usr/bin/ld: cannot find -lgcc_s (for this I'm trying to ask the admin of the cluster to add the path of the correct library using command ...not sure it will work).
2. locally it seems that the compiling works bot trying to run the program doesn't work and get this error: <pblat: command not found>

here follows the compiling output doing command in the program directory:
<make
gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o blat.o blatSrc/blat.c
blatSrc/blat.c: In function ‘performSearch’:
blatSrc/blat.c:342:21: warning: unused variable ‘i’ [-Wunused-variable]
int i;
^
blatSrc/blat.c: In function ‘performBigblat’:
blatSrc/blat.c:527:21: warning: unused variable ‘i’ [-Wunused-variable]
int i;
^
blatSrc/blat.c:513:23: warning: unused variable ‘queryFiles’ [-Wunused-variable]
char queryFiles=(char)(((void**)args)[2]);
^~~~~~~~~~
blatSrc/blat.c:511:21: warning: unused variable ‘id’ [-Wunused-variable]
int id=((int)(((void**)args)[0]));
^~
blatSrc/blat.c: In function ‘performSearch’:
blatSrc/blat.c:416:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
blatSrc/blat.c: In function ‘performBigblat’:
blatSrc/blat.c:568:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o bandExt.o jkOwnLib/bandExt.c
gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o crudeali.o jkOwnLib/crudeali.c
gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o ffAliHelp.o jkOwnLib/ffAliHelp.c
gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o ffSeedExtend.o jkOwnLib/ffSeedExtend.c
gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o fuzzyFind.o jkOwnLib/fuzzyFind.c
gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o genoFind.o jkOwnLib/genoFind.c
jkOwnLib/genoFind.c: In function ‘gfFindClumpsWithQmask’:
jkOwnLib/genoFind.c:1907:9: warning: variable ‘cmpQuerySize’ set but not used [-Wunused-but-set-variable]
int cmpQuerySize;
^~~~~~~~~~~~
gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o gfBlatLib.o jkOwnLib/gfBlatLib.c
gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o gfClientLib.o jkOwnLib/gfClientLib.c
gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o gfInternal.o jkOwnLib/gfInternal.c
gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o gfOut.o jkOwnLib/gfOut.c
gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o gfPcrLib.o jkOwnLib/gfPcrLib.c
gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o gfWebLib.o jkOwnLib/gfWebLib.c
gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o ooc.o jkOwnLib/ooc.c
gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o patSpace.o jkOwnLib/patSpace.c
gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o supStitch.o jkOwnLib/supStitch.c
gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o trans3.o jkOwnLib/trans3.c
ar rcus jkOwnLib.a bandExt.o crudeali.o ffAliHelp.o ffSeedExtend.o fuzzyFind.o genoFind.o gfBlatLib.o gfClientLib.o gfInternal.o gfOut.o gfPcrLib.o gfWebLib.o ooc.o patSpace.o supStitch.o trans3.o
ar: u' modifier ignored since D' is the default (see U') gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o aliType.o lib/aliType.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o apacheLog.o lib/apacheLog.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o asParse.o lib/asParse.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o axt.o lib/axt.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o axtAffine.o lib/axtAffine.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o base64.o lib/base64.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o bits.o lib/bits.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o binRange.o lib/binRange.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o blastOut.o lib/blastOut.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o blastParse.o lib/blastParse.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o boxClump.o lib/boxClump.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o boxLump.o lib/boxLump.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o bPlusTree.o lib/bPlusTree.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o cda.o lib/cda.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o chain.o lib/chain.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o chainBlock.o lib/chainBlock.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o chainConnect.o lib/chainConnect.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o chainToAxt.o lib/chainToAxt.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o chainToPsl.o lib/chainToPsl.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o cheapcgi.o lib/cheapcgi.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o codebias.o lib/codebias.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o colHash.o lib/colHash.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o common.o lib/common.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o correlate.o lib/correlate.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o dgRange.o lib/dgRange.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o diGraph.o lib/diGraph.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o dlist.o lib/dlist.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o dnaLoad.o lib/dnaLoad.c lib/dnaLoad.c: In function ‘dnaLoadNextFromStack’: lib/dnaLoad.c:194:66: warning: passing argument 4 of ‘faMixedSpeedReadNext’ from incompatible pointer type [-Wincompatible-pointer-types] if (faMixedSpeedReadNext(dls->textFile, &dna, &size, &name, &faFastBuf, &faFastBufSize)) ^ In file included from lib/dnaLoad.c:10:0: ./inc/fa.h:109:9: note: expected ‘char **’ but argument is of type ‘char (*)[512]’ boolean faMixedSpeedReadNext(struct lineFile *lf, DNA **retDna, int *retSize, char **retName, DNA **faFastBuf, unsigned *faFastBufSize); ^~~~~~~~~~~~~~~~~~~~ gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o dnaMarkov.o lib/dnaMarkov.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o dnaseq.o lib/dnaseq.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o dnautil.o lib/dnautil.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o dnaMotif.o lib/dnaMotif.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o dtdParse.o lib/dtdParse.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o dystring.o lib/dystring.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o emblParse.o lib/emblParse.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o errabort.o lib/errabort.c lib/errabort.c: In function ‘getThreadVars’: lib/errabort.c:345:5: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(STDERR_FILENO, errMsg, strlen(errMsg)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o errCatch.o lib/errCatch.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o fa.o lib/fa.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o ffAli.o lib/ffAli.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o ffScore.o lib/ffScore.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o filePath.o lib/filePath.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o fixColor.o lib/fixColor.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o flydna.o lib/flydna.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o fof.o lib/fof.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o fuzzyShow.o lib/fuzzyShow.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o gapCalc.o lib/gapCalc.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o gdf.o lib/gdf.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o gemfont.o lib/gemfont.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o gfNet.o lib/gfNet.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o gff.o lib/gff.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o gfxPoly.o lib/gfxPoly.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o gifcomp.o lib/gifcomp.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o gifdecomp.o lib/gifdecomp.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o gifLabel.o lib/gifLabel.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o gifread.o lib/gifread.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o gifwrite.o lib/gifwrite.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o hash.o lib/hash.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o hex.o lib/hex.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o histogram.o lib/histogram.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o hmmPfamParse.o lib/hmmPfamParse.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o hmmstats.o lib/hmmstats.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o htmlPage.o lib/htmlPage.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o htmshell.o lib/htmshell.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o https.o lib/https.c lib/https.c:27:13: warning: ‘openssl_locking_callback’ defined but not used [-Wunused-function] static void openssl_locking_callback(int mode, int n, const char * file, int line) ^~~~~~~~~~~~~~~~~~~~~~~~ lib/https.c:22:22: warning: ‘openssl_id_callback’ defined but not used [-Wunused-function] static unsigned long openssl_id_callback(void) ^~~~~~~~~~~~~~~~~~~ gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o internet.o lib/internet.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o intExp.o lib/intExp.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o jointalign.o lib/jointalign.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o jpegSize.o lib/jpegSize.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o keys.o lib/keys.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o kxTok.o lib/kxTok.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o linefile.o lib/linefile.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o localmem.o lib/localmem.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o log.o lib/log.c lib/log.c: In function ‘logDaemonize’: lib/log.c:344:5: warning: ignoring return value of ‘dup’, declared with attribute warn_unused_result [-Wunused-result] dup(nullFd); // Stdout goes also to /dev/null ^~~~~~~~~~~ lib/log.c:345:5: warning: ignoring return value of ‘dup’, declared with attribute warn_unused_result [-Wunused-result] dup(nullFd); // Stderr goes also to /dev/null ^~~~~~~~~~~ gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o maf.o lib/maf.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o mafFromAxt.o lib/mafFromAxt.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o mafScore.o lib/mafScore.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o md5.o lib/md5.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o memalloc.o lib/memalloc.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o memgfx.o lib/memgfx.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o mgCircle.o lib/mgCircle.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o mgPolygon.o lib/mgPolygon.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o mime.o lib/mime.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o net.o lib/net.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o nib.o lib/nib.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o nibTwo.o lib/nibTwo.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o nt4.o lib/nt4.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o obscure.o lib/obscure.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o oldGff.o lib/oldGff.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o oligoTm.o lib/oligoTm.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o options.o lib/options.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o osunix.o lib/osunix.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o pairHmm.o lib/pairHmm.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o phyloTree.o lib/phyloTree.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o pipeline.o lib/pipeline.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o portimpl.o lib/portimpl.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o pscmGfx.o lib/pscmGfx.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o psGfx.o lib/psGfx.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o psl.o lib/psl.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o pslGenoShow.o lib/pslGenoShow.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o pslShow.o lib/pslShow.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o pslTbl.o lib/pslTbl.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o pslTransMap.o lib/pslTransMap.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o psPoly.o lib/psPoly.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o pthreadWrap.o lib/pthreadWrap.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o qa.o lib/qa.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o quickHeap.o lib/quickHeap.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o quotedP.o lib/quotedP.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o ra.o lib/ra.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o rangeTree.o lib/rangeTree.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o rbTree.o lib/rbTree.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o repMask.o lib/repMask.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o rle.o lib/rle.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o rnautil.o lib/rnautil.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o rudp.o lib/rudp.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o scoreWindow.o lib/scoreWindow.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o seqOut.o lib/seqOut.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o seqStats.o lib/seqStats.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o servBrcMcw.o lib/servBrcMcw.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o servcis.o lib/servcis.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o servCrunx.o lib/servCrunx.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o servcl.o lib/servcl.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o servmsII.o lib/servmsII.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o servpws.o lib/servpws.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o shaRes.o lib/shaRes.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o slog.o lib/slog.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o snof.o lib/snof.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o snofmake.o lib/snofmake.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o snofsig.o lib/snofsig.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o spacedColumn.o lib/spacedColumn.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o spacedSeed.o lib/spacedSeed.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o spaceSaver.o lib/spaceSaver.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o sqlNum.o lib/sqlNum.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o sqlList.o lib/sqlList.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o subText.o lib/subText.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o synQueue.o lib/synQueue.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o tabRow.o lib/tabRow.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o textOut.o lib/textOut.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o tokenizer.o lib/tokenizer.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o trix.o lib/trix.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o twoBit.o lib/twoBit.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o udc.o lib/udc.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o verbose.o lib/verbose.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o vGfx.o lib/vGfx.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o wildcmp.o lib/wildcmp.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o wormdna.o lib/wormdna.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o xa.o lib/xa.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o xAli.o lib/xAli.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o xap.o lib/xap.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o xmlEscape.o lib/xmlEscape.c gcc -O -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I./inc -I./htslib -c -o xp.o lib/xp.c ar rcus jkweb.a aliType.o apacheLog.o asParse.o axt.o axtAffine.o base64.o bits.o binRange.o blastOut.o blastParse.o boxClump.o boxLump.o bPlusTree.o cda.o chain.o chainBlock.o chainConnect.o chainToAxt.o chainToPsl.o cheapcgi.o codebias.o colHash.o common.o correlate.o dgRange.o diGraph.o dlist.o dnaLoad.o dnaMarkov.o dnaseq.o dnautil.o dnaMotif.o dtdParse.o dystring.o emblParse.o errabort.o errCatch.o fa.o ffAli.o ffScore.o filePath.o fixColor.o flydna.o fof.o fuzzyShow.o gapCalc.o gdf.o gemfont.o gfNet.o gff.o gfxPoly.o gifcomp.o gifdecomp.o gifLabel.o gifread.o gifwrite.o hash.o hex.o histogram.o hmmPfamParse.o hmmstats.o htmlPage.o htmshell.o https.o internet.o intExp.o jointalign.o jpegSize.o keys.o kxTok.o linefile.o localmem.o log.o maf.o mafFromAxt.o mafScore.o md5.o memalloc.o memgfx.o mgCircle.o mgPolygon.o mime.o net.o nib.o nibTwo.o nt4.o obscure.o oldGff.o oligoTm.o options.o osunix.o pairHmm.o phyloTree.o pipeline.o portimpl.o pscmGfx.o psGfx.o psl.o pslGenoShow.o pslShow.o pslTbl.o pslTransMap.o psPoly.o pthreadWrap.o qa.o quickHeap.o quotedP.o ra.o rangeTree.o rbTree.o repMask.o rle.o rnautil.o rudp.o scoreWindow.o seqOut.o seqStats.o servBrcMcw.o servcis.o servCrunx.o servcl.o servmsII.o servpws.o shaRes.o slog.o snof.o snofmake.o snofsig.o spacedColumn.o spacedSeed.o spaceSaver.o sqlNum.o sqlList.o subText.o synQueue.o tabRow.o textOut.o tokenizer.o trix.o twoBit.o udc.o verbose.o vGfx.o wildcmp.o wormdna.o xa.o xAli.o xap.o xmlEscape.o xp.o ar: u' modifier ignored since D' is the default (see U')
cd htslib && make
make[1]: Entering directory '/home/gina/programs/icebert-pblat-2 (1).1-0-g652d3b3/icebert-pblat-652d3b3/htslib'
cc -DKNETFILE_HOOKS -DUCSC_CRAM -I. -c -o kfunc.o kfunc.c
cc -DKNETFILE_HOOKS -DUCSC_CRAM -I. -c -o knetfile.o knetfile.c
cc -DKNETFILE_HOOKS -DUCSC_CRAM -I. -c -o kstring.o kstring.c
cc -DKNETFILE_HOOKS -DUCSC_CRAM -I. -c -o bgzf.o bgzf.c
cc -DKNETFILE_HOOKS -DUCSC_CRAM -I. -c -o faidx.o faidx.c
cc -DKNETFILE_HOOKS -DUCSC_CRAM -I. -c -o hfile.o hfile.c
cc -DKNETFILE_HOOKS -DUCSC_CRAM -I. -c -o hfile_net.o hfile_net.c
echo '#define HTS_VERSION "1.3"' > version.h
cc -DKNETFILE_HOOKS -DUCSC_CRAM -I. -c -o hts.o hts.c
cc -DKNETFILE_HOOKS -DUCSC_CRAM -I. -c -o md5.o md5.c
cc -DKNETFILE_HOOKS -DUCSC_CRAM -I. -c -o regidx.o regidx.c
cc -DKNETFILE_HOOKS -DUCSC_CRAM -I. -c -o sam.o sam.c
cc -DKNETFILE_HOOKS -DUCSC_CRAM -I. -c -o synced_bcf_reader.o synced_bcf_reader.c
cc -DKNETFILE_HOOKS -DUCSC_CRAM -I. -c -o vcf_sweep.o vcf_sweep.c
cc -DKNETFILE_HOOKS -DUCSC_CRAM -I. -c -o tbx.o tbx.c
cc -DKNETFILE_HOOKS -DUCSC_CRAM -I. -c -o vcf.o vcf.c
cc -DKNETFILE_HOOKS -DUCSC_CRAM -I. -c -o vcfutils.o vcfutils.c
cc -DKNETFILE_HOOKS -DUCSC_CRAM -I. -c -o cram/cram_codecs.o cram/cram_codecs.c
cc -DKNETFILE_HOOKS -DUCSC_CRAM -I. -c -o cram/cram_decode.o cram/cram_decode.c
cc -DKNETFILE_HOOKS -DUCSC_CRAM -I. -c -o cram/cram_encode.o cram/cram_encode.c
cc -DKNETFILE_HOOKS -DUCSC_CRAM -I. -c -o cram/cram_external.o cram/cram_external.c
cc -DKNETFILE_HOOKS -DUCSC_CRAM -I. -c -o cram/cram_index.o cram/cram_index.c
cc -DKNETFILE_HOOKS -DUCSC_CRAM -I. -c -o cram/cram_io.o cram/cram_io.c
cc -DKNETFILE_HOOKS -DUCSC_CRAM -I. -c -o cram/cram_samtools.o cram/cram_samtools.c
cc -DKNETFILE_HOOKS -DUCSC_CRAM -I. -c -o cram/cram_stats.o cram/cram_stats.c
cc -DKNETFILE_HOOKS -DUCSC_CRAM -I. -c -o cram/files.o cram/files.c
cc -DKNETFILE_HOOKS -DUCSC_CRAM -I. -c -o cram/mFILE.o cram/mFILE.c
cc -DKNETFILE_HOOKS -DUCSC_CRAM -I. -c -o cram/open_trace_file.o cram/open_trace_file.c
cc -DKNETFILE_HOOKS -DUCSC_CRAM -I. -c -o cram/pooled_alloc.o cram/pooled_alloc.c
cc -DKNETFILE_HOOKS -DUCSC_CRAM -I. -c -o cram/rANS_static.o cram/rANS_static.c
cc -DKNETFILE_HOOKS -DUCSC_CRAM -I. -c -o cram/sam_header.o cram/sam_header.c
cc -DKNETFILE_HOOKS -DUCSC_CRAM -I. -c -o cram/string_alloc.o cram/string_alloc.c
cc -DKNETFILE_HOOKS -DUCSC_CRAM -I. -c -o cram/thread_pool.o cram/thread_pool.c
cc -DKNETFILE_HOOKS -DUCSC_CRAM -I. -c -o cram/vlen.o cram/vlen.c
cc -DKNETFILE_HOOKS -DUCSC_CRAM -I. -c -o cram/zfio.o cram/zfio.c
ar -rc libhts.a kfunc.o knetfile.o kstring.o bgzf.o faidx.o hfile.o hfile_net.o hts.o md5.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o cram/thread_pool.o cram/vlen.o cram/zfio.o
ranlib libhts.a
make[1]: Leaving directory '/home/gina/programs/icebert-pblat-2 (1).1-0-g652d3b3/icebert-pblat-652d3b3/htslib'
gcc -O -Wall -o pblat blat.o jkOwnLib.a jkweb.a htslib/libhts.a -lm -lpthread -lz -lssl -lcrypto
rm -f *.o *.a

AddressSanitizer: heap-buffer-overflow (Out-of-Bound Write) at lib/fa.c:483

When pblat is compiled with AddressSanitizer, it reports a out-of-bound write buffer overflow error at lib/fa.c:483.

./pblat -threads=1 ./pblat-report/01.fa pblat-report/astral-scopdom-seqres-all-test.fa /tmp/pblat-c.psl

=================================================================
==29050==ERROR: AddressSanitizer: heap-buffer-overflow on address 0x7f44b1e8e800 at pc 0x0000005e1b69 bp 0x7ffcfec890f0 sp 0x7ffcfec890e8
WRITE of size 1 at 0x7f44b1e8e800 thread T0
    #0 0x5e1b68 in faMixedSpeedReadNext /home/exp/work/pblat/lib/fa.c:483:39
    #1 0x5e3ac7 in faReadAllMixableInLf /home/exp/work/pblat/lib/fa.c:583:18
    #2 0x5e3890 in faReadAllSeqMixable /home/exp/work/pblat/lib/fa.c:606:26
    #3 0x5e3890 in faReadAllMixed /home/exp/work/pblat/lib/fa.c:650
    #4 0x555406 in gfClientSeqList /home/exp/work/pblat/jkOwnLib/gfClientLib.c:194:14
    #5 0x5123bf in blat /home/exp/work/pblat/blatSrc/blat.c:711:17
    #6 0x51405b in main /home/exp/work/pblat/blatSrc/blat.c:947:5
    #7 0x7f44b0e50b96 in __libc_start_main /build/glibc-OTsEL5/glibc-2.27/csu/../csu/libc-start.c:310
    #8 0x41d9d9 in _start (/home/exp/work/pblat-asan/pblat+0x41d9d9)

0x7f44b1e8e800 is located 0 bytes to the right of 131072-byte region [0x7f44b1e6e800,0x7f44b1e8e800)
allocated by thread T0 here:
    #0 0x4d3030 in malloc (/home/exp/work/pblat-asan/pblat+0x4d3030)
    #1 0x607987 in needHugeMem /home/exp/work/pblat/lib/memalloc.c:136:11
    #2 0x5e3ac7 in faReadAllMixableInLf /home/exp/work/pblat/lib/fa.c:583:18
    #3 0x5e3890 in faReadAllSeqMixable /home/exp/work/pblat/lib/fa.c:606:26
    #4 0x5e3890 in faReadAllMixed /home/exp/work/pblat/lib/fa.c:650
    #5 0x555406 in gfClientSeqList /home/exp/work/pblat/jkOwnLib/gfClientLib.c:194:14
    #6 0x5123bf in blat /home/exp/work/pblat/blatSrc/blat.c:711:17
    #7 0x51405b in main /home/exp/work/pblat/blatSrc/blat.c:947:5
    #8 0x7f44b0e50b96 in __libc_start_main /build/glibc-OTsEL5/glibc-2.27/csu/../csu/libc-start.c:310

SUMMARY: AddressSanitizer: heap-buffer-overflow /home/exp/work/pblat/lib/fa.c:483:39 in faMixedSpeedReadNext
Shadow bytes around the buggy address:
  0x0fe9163c9cb0: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00
  0x0fe9163c9cc0: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00
  0x0fe9163c9cd0: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00
  0x0fe9163c9ce0: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00
  0x0fe9163c9cf0: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00
=>0x0fe9163c9d00:[fa]fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa
  0x0fe9163c9d10: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa
  0x0fe9163c9d20: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa
  0x0fe9163c9d30: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa
  0x0fe9163c9d40: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa
  0x0fe9163c9d50: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa
Shadow byte legend (one shadow byte represents 8 application bytes):
  Addressable:           00
  Partially addressable: 01 02 03 04 05 06 07 
  Heap left redzone:       fa
  Freed heap region:       fd
  Stack left redzone:      f1
  Stack mid redzone:       f2
  Stack right redzone:     f3
  Stack after return:      f5
  Stack use after scope:   f8
  Global redzone:          f9
  Global init order:       f6
  Poisoned by user:        f7
  Container overflow:      fc
  Array cookie:            ac
  Intra object redzone:    bb
  ASan internal:           fe
  Left alloca redzone:     ca
  Right alloca redzone:    cb
==29050==ABORTING

Since this specifies only one thread, it may also affect the original blat; however I'm not able to compile that, so only report here. Please see the attached files for details.

pblat-report.zip

compile error: undefined reference to `gzgetc_'

gcc -O -Wall  -o pblat blat.o jkOwnLib.a jkweb.a htslib/libhts.a  -lm -lpthread -lssl -lcrypto -lz
htslib/libhts.a(zfio.o): In function `zfpeek':
zfio.c:(.text+0x1c8): undefined reference to `gzgetc_'