maq-help Mailing List for Mapping and Assembly with Qualities
Status: Beta
Brought to you by:
lh3lh3
Menu
▾
▴
maq-help — bug report, request of new features, and help
This list is closed, nobody may subscribe to it.
| 2007 |
Jan
|
Feb
|
Mar
|
Apr
|
May
|
Jun
(6) |
Jul
(2) |
Aug
|
Sep
(3) |
Oct
(2) |
Nov
(7) |
Dec
(8) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 2008 |
Jan
(15) |
Feb
(32) |
Mar
(11) |
Apr
(21) |
May
(17) |
Jun
(57) |
Jul
(33) |
Aug
(27) |
Sep
(59) |
Oct
(22) |
Nov
(23) |
Dec
(30) |
| 2009 |
Jan
(41) |
Feb
(44) |
Mar
(41) |
Apr
(37) |
May
(72) |
Jun
(26) |
Jul
(42) |
Aug
(72) |
Sep
(23) |
Oct
(29) |
Nov
(7) |
Dec
(13) |
| 2010 |
Jan
(4) |
Feb
(3) |
Mar
(9) |
Apr
(1) |
May
(9) |
Jun
(5) |
Jul
(4) |
Aug
(3) |
Sep
(1) |
Oct
|
Nov
|
Dec
|
| 2011 |
Jan
(1) |
Feb
(2) |
Mar
(3) |
Apr
(10) |
May
(4) |
Jun
|
Jul
|
Aug
|
Sep
|
Oct
|
Nov
(1) |
Dec
|
| 2012 |
Jan
|
Feb
(2) |
Mar
(3) |
Apr
|
May
|
Jun
|
Jul
|
Aug
|
Sep
|
Oct
|
Nov
|
Dec
|
| 2013 |
Jan
|
Feb
(1) |
Mar
|
Apr
|
May
|
Jun
|
Jul
|
Aug
|
Sep
|
Oct
|
Nov
|
Dec
|
| 2015 |
Jan
|
Feb
|
Mar
|
Apr
|
May
|
Jun
|
Jul
|
Aug
(2) |
Sep
|
Oct
|
Nov
|
Dec
|
|
From: Joel M. <j_m...@lb...> - 2015-08-31 20:16:26
|
Hello, bwa and samtools/htslib are the successors to maq, I haven't tried this, well not for a long time, but 'bwa bwasw' for long queries including assembly contigs. then call variants to a vcf and 'bcftools consensus' with the vcf to generate a consensus, there will be many issues with a consensus generated this way but it's something. *http://www.htslib.org <http://www.htslib.org>* https://github.com/lh3/bwa http://bio-bwa.sourceforge.net On Mon, Aug 31, 2015 at 11:44 AM, Howard, Susanne F < Sus...@mi...> wrote: > I am completely new to MAQ. > > I have a whole plant genome assembly that has progressed to scaffolds, but > these still overlap mostly, so in reality they are not much more than > contigs, though a very few of them are much longer than contigs. I do have > a reference sequence and would like to align these contigs to the reference > and call consensus in those 85% of the genome that have coverage, without > inserting the reference sequence where I have no contig coverage (otherwise > I should be able to use GATK alternate reference maker for instance). > > This can be done by hand, but for an almost 5GB plant genome that is > really not practical. > > > > I have seen in the MAQ workflow graph that contigs can also be aligned and > a consensus called? Did I interpret the flowchart correctly? Are there any > descriptions of this step, which subroutine it uses etc? All the how-to-MAQ > pages I have found start with reads, and with the size of my genome, and > MAQ only using one processor, that is not an option. > > Does anyone have a suggestions for me? If MAQ is not suitable, maybe there > is another program I could use? > > I have seen some consensus callers, but they were for bacteria etc, so for > very small genomes. Though since I can filter the contigs by reference > chromosome, the process could be broken into pieces? > > > > If this kind of tool does not exist, can someone develop one? I know I can > have bed files and I can get the number of contigs/reads aligning to each > position of my ref seq, so it would be possible to get something like: > start consensus build when coverage at base is >1 , end consensus build > where coverage drops below threshold, and save the start and end locations > for each such area, then export the consensus pieces. Need that by > yesterday of course J J > > Thanks for any feedback, > > Susanne > > > ------------------------------------------------------------------------------ > > _______________________________________________ > maq-help mailing list > maq...@li... > https://lists.sourceforge.net/lists/listinfo/maq-help > > |
|
From: Howard, S. F <Sus...@Mi...> - 2015-08-31 18:44:24
|
I am completely new to MAQ. I have a whole plant genome assembly that has progressed to scaffolds, but these still overlap mostly, so in reality they are not much more than contigs, though a very few of them are much longer than contigs. I do have a reference sequence and would like to align these contigs to the reference and call consensus in those 85% of the genome that have coverage, without inserting the reference sequence where I have no contig coverage (otherwise I should be able to use GATK alternate reference maker for instance). This can be done by hand, but for an almost 5GB plant genome that is really not practical. I have seen in the MAQ workflow graph that contigs can also be aligned and a consensus called? Did I interpret the flowchart correctly? Are there any descriptions of this step, which subroutine it uses etc? All the how-to-MAQ pages I have found start with reads, and with the size of my genome, and MAQ only using one processor, that is not an option. Does anyone have a suggestions for me? If MAQ is not suitable, maybe there is another program I could use? I have seen some consensus callers, but they were for bacteria etc, so for very small genomes. Though since I can filter the contigs by reference chromosome, the process could be broken into pieces? If this kind of tool does not exist, can someone develop one? I know I can have bed files and I can get the number of contigs/reads aligning to each position of my ref seq, so it would be possible to get something like: start consensus build when coverage at base is >1 , end consensus build where coverage drops below threshold, and save the start and end locations for each such area, then export the consensus pieces. Need that by yesterday of course :) :) Thanks for any feedback, Susanne |
|
From: David A. <das...@ho...> - 2012-03-16 08:51:14
|
Check also FASTX-toolkit, you have a FASTQ-to-FASTA converter plus other useful tools. HTH, David From: joh...@Va... To: vc...@em...; maq...@li... Date: Wed, 14 Mar 2012 16:14:32 -0500 Subject: Re: [maq-help] consensus fastq to fasta? Hi Viren,Just tested it and it works like a charm! A million thanks! I wish I thought to ask this question months ago. Thanks again,John From: Patel, Viren [mailto:vc...@em...] Sent: Wednesday, March 14, 2012 4:10 PM To: Gibbons, John G.; 'maq...@li...' Subject: RE: consensus fastq to fasta? I have attached a Perl program I wrote ages ago... YMMV. VirenFrom: Gibbons, John G. [joh...@Va...] Sent: Wednesday, March 14, 2012 3:51 PM To: 'maq...@li...' Subject: [maq-help] consensus fastq to fasta?Hello,I have been using Maq for the last couple years and have been using a very roundabout way to get at some information that I routinely use. I typically work with Illumina population data. For phylogenomic purposes, I map my reads, call SNPs in all samples then pull out all of the variant sites from the consensus fasta file, which I generate from the consensus fastq file (with the ‘cns2fq’ command). I am not a programmer so I used a variety of sed and grep commands to produce a fasta file from the fastq file. My question is has anyone created a script to generate a fasta file from the consensus fastq file? I would be incredibly grateful for a script that could accomplish that. Thanks, John ----John G GibbonsDepartment of Biological SciencesVU Station B, Box 35-1634Vanderbilt UniversityNashville TN, 37212The Rokas LabEmail: Joh...@Va...: (615) 936-3893http://sitemason.vanderbilt.edu/people/jggibbons This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments). ------------------------------------------------------------------------------ Virtualization & Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/ _______________________________________________ maq-help mailing list maq...@li... https://lists.sourceforge.net/lists/listinfo/maq-help |
|
From: Gibbons, J. G. <joh...@Va...> - 2012-03-14 21:29:52
|
Hi Viren, Just tested it and it works like a charm! A million thanks! I wish I thought to ask this question months ago. Thanks again, John From: Patel, Viren [mailto:vc...@em...] Sent: Wednesday, March 14, 2012 4:10 PM To: Gibbons, John G.; 'maq...@li...' Subject: RE: consensus fastq to fasta? I have attached a Perl program I wrote ages ago... YMMV. Viren ________________________________ From: Gibbons, John G. [joh...@Va...] Sent: Wednesday, March 14, 2012 3:51 PM To: 'maq...@li...' Subject: [maq-help] consensus fastq to fasta? Hello, I have been using Maq for the last couple years and have been using a very roundabout way to get at some information that I routinely use. I typically work with Illumina population data. For phylogenomic purposes, I map my reads, call SNPs in all samples then pull out all of the variant sites from the consensus fasta file, which I generate from the consensus fastq file (with the 'cns2fq' command). I am not a programmer so I used a variety of sed and grep commands to produce a fasta file from the fastq file. My question is has anyone created a script to generate a fasta file from the consensus fastq file? I would be incredibly grateful for a script that could accomplish that. Thanks, John ---- John G Gibbons Department of Biological Sciences VU Station B, Box 35-1634 Vanderbilt University Nashville TN, 37212 The Rokas Lab Email: Joh...@Va...<mailto:Joh...@Va...> Tel: (615) 936-3893 http://sitemason.vanderbilt.edu/people/jggibbons ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments). |
|
From: Gibbons, J. G. <joh...@Va...> - 2012-03-14 19:51:38
|
Hello, I have been using Maq for the last couple years and have been using a very roundabout way to get at some information that I routinely use. I typically work with Illumina population data. For phylogenomic purposes, I map my reads, call SNPs in all samples then pull out all of the variant sites from the consensus fasta file, which I generate from the consensus fastq file (with the 'cns2fq' command). I am not a programmer so I used a variety of sed and grep commands to produce a fasta file from the fastq file. My question is has anyone created a script to generate a fasta file from the consensus fastq file? I would be incredibly grateful for a script that could accomplish that. Thanks, John ---- John G Gibbons Department of Biological Sciences VU Station B, Box 35-1634 Vanderbilt University Nashville TN, 37212 The Rokas Lab Email: Joh...@Va...<mailto:Joh...@Va...> Tel: (615) 936-3893 http://sitemason.vanderbilt.edu/people/jggibbons |
|
From: Joel M. <j_m...@lb...> - 2012-02-24 19:40:06
|
ask the MAQGene people you'll probably need their help
if it was i, i'd figure out where the '2> /dev/null' is and replace it with
something like '2> my.err' so you'ld have a record of what the error is.
at least while you're debugging this, and i'd get rid of the cleanup steps
where it removes the files used in that map command
rm 2844678841_split1 4145302068.00000.mismatch 4145302068.00000.1.bfq
4145302068.00000.1.fastq
you can't really see what might be wrong with those files if it deletes
them.
other than that... make sure your fastq reads are < 126 or so bases, double
check your reference fasta for weirdness,
Joel
On Fri, Feb 24, 2012 at 10:56 AM, Breton, Philippe <pb...@wu...>wrote:
> Hi Folks,
>
> I have installed MAQGene which serves as a maq front end on an 64-bit
> gentoo system. Each run I attempt excepted for the default test sequence
> ot340, yields a segmentation fault when maq map. I have pasted below the
> log from the run.
>
> /data/maqgene_current/maqgene/bin/run_maq.sh: line 44: export: `single_michael/./s_3_1_withindex_sequence.txt_CCGATTA.fastq=on': not a valid identifier
> /data/maqgene_current/maqgene/bin/run_maq.sh: line 44: export: `single_michael/./s_3_3_withindex_sequence.txt_CCGATTA.fastq=on': not a valid identifier
> Finished reading input.
> ++ echo michael/./s_3_1_withindex_sequence.txt_CCGATTA.fastq,michael/./s_3_3_withindex_sequence.txt_CCGATTA.fastq
> ++ tr , ' '
> + fastq_file_set1='michael/./s_3_1_withindex_sequence.txt_CCGATTA.fastq michael/./s_3_3_withindex_sequence.txt_CCGATTA.fastq'
> ++ cd /data/maqgene/reads
> ++ cat michael/./s_3_1_withindex_sequence.txt_CCGATTA.fastq michael/./s_3_3_withindex_sequence.txt_CCGATTA.fastq
> ++ wc -l
> ++ cut -f 1 -d ' '
> + TOTAL_LINES=86680560
> ++ echo '(86680560 / 105509888) + (86680560 % 105509888 != 0)'
> ++ bc
> + num_chunks=1
> + set +x
> make -j 2 -l 2 -C /data/maqgene/work --warn-undefined-variables -I /data/maqgene -f /data/maqgene/makefile BFA_FILE=elegans.bfa MAQGENE_GENOME_DIR=/data/maqgene/genomes reads_cksum=2844678841 map_cksum=4145302068 pileup_cksum=1488249346 cns_cksum=2226060844 umdd=50000 dmdd=1000 umid=1000 dmid=1000 max_gene_radius=50000 full_results_dir=/data/maqgene/out/example_user/Mike2_ outfile_basename=Mike2_ map_parameters=" -m 0.00001 -C 250 -n 2 -e 100 -1 0" assemble_parameters=" -N 2 -q 0 -r 0.0 -m 7 -Q 100 -p " pileup_parameters=" -Q 100 -m 7 -q 0" CHUNK_SIZE=105509888 NUM_CHUNKS=1
> Will process 86680560 lines of input in 1 chunks
> make: Entering directory `/data/maqgene/work'
> # Fri Feb 24 11:50:23 CST 2012: Removing frontend files in case this is a duplicate run ...
> rm -f /data/maqgene/out/example_user/Mike2_/Mike2__{grouped.txt,flat.txt}
> rm -f /data/maqgene/out/example_user/Mike2_/Mike2__uncovered.txt /data/maqgene/out/example_user/Mike2_/Mike2__coverage.txt /data/maqgene/out/example_user/Mike2_/Mike2__pileup.txt /data/maqgene/out/example_user/Mike2_/Mike2__log.txt /data/maqgene/out/example_user/Mike2_/Mike2__check.txt /data/maqgene/out/example_user/Mike2_/Mike2__unmapped.txt
> make: Leaving directory `/data/maqgene/work'
> make: Entering directory `/data/maqgene/work'
> /data/maqgene/makefile:73: warning: undefined variable `date'
> # : Regrouping fastq reads into chunks of size 105509888.
> split -l 105509888 -a 5 -d <(cat /data/maqgene/reads/michael/./s_3_1_withindex_sequence.txt_CCGATTA.fastq /data/maqgene/reads/michael/./s_3_3_withindex_sequence.txt_CCGATTA.fastq) 4145302068.1.fastq.
> for stem in 00000; do mv 4145302068.1.fastq.$stem 4145302068.$stem.1.fastq; done
> touch 2844678841_split1
> # Fri Feb 24 11:55:23 CST 2012: Converting fastq files to bfq ...
> /data/maqgene_current/maqgene/bin/maq sol2sanger 4145302068.00000.1.fastq /dev/stdout | \
> /data/maqgene_current/maqgene/bin/maq fastq2bfq /dev/stdin 4145302068.00000.1.bfq
> -- finish writing file '4145302068.00000.1.bfq'-- 21670140 sequences were loaded.
> # Fri Feb 24 12:07:14 CST 2012: Mapping file(s) 4145302068.00000.1.bfq
> /data/maqgene_current/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 4145302068.00000.unmapped -H 4145302068.00000.mismatch \
> 4145302068.00000.map /data/maqgene/genomes/elegans.bfa 4145302068.00000.1.bfq 2> /dev/null
> /bin/bash: line 1: 13445 *Segmentation fault* /data/maqgene_current/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 4145302068.00000.unmapped -H 4145302068.00000.mismatch 4145302068.00000.map /data/maqgene/genomes/elegans.bfa 4145302068.00000.1.bfq 2> /dev/null
> make: *** [4145302068.00000.map] Error 139
> rm 2844678841_split1 4145302068.00000.mismatch 4145302068.00000.1.bfq 4145302068.00000.1.fastq
> make: Leaving directory `/data/maqgene/work'
> make: Entering directory `/data/maqgene/work'
> make: *** No rule to make target `clean_tables'. Stop.
> make: Leaving directory `/data/maqgene/work'
>
>
> The host system is :
>
>
> bin # emerge --info
> Portage 2.1.10.44 (default/linux/amd64/10.0, gcc-4.4.5, unavailable, 3.0.6-gentoo x86_64)
> =================================================================
> System uname: Linux-3.0.6-gentoo-x86_64-Dual-Core_AMD_Opteron-tm-_Processor_2218-with-gentoo-1.12.14
> Timestamp of tree: Tue, 21 Feb 2012 00:45:01 +0000
> distcc 3.1 x86_64-pc-linux-gnu [disabled]
> app-shells/bash: 4.1_p9
> dev-lang/python: 2.4.6, 2.6.6-r2, 2.7.1-r1, 3.1.3-r1
> dev-util/cmake: 2.8.4
> dev-util/pkgconfig: 0.25-r2
> sys-apps/baselayout: 1.12.14-r1
> sys-apps/sandbox: 2.4
> sys-devel/autoconf: 2.65-r1
> sys-devel/automake: 1.11.1
> sys-devel/binutils: 2.20.1-r1
> sys-devel/gcc: 4.1.2, 4.4.5
> sys-devel/gcc-config: 1.4.1
> sys-devel/libtool: 2.2.10
> sys-devel/make: 3.81-r2
> sys-kernel/linux-headers: 2.6.36.1 (virtual/os-headers)
> sys-libs/glibc: 2.12.2
> Repositories: gentoo
> ACCEPT_KEYWORDS="amd64"
> ACCEPT_LICENSE="* -@EULA"
> CBUILD="x86_64-pc-linux-gnu"
> CFLAGS="-march=athlon64 -O2 -pipe"
> CHOST="x86_64-pc-linux-gnu"
> CONFIG_PROTECT="/etc"
> CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/php/apache2-php5.2/ext-active/ /etc/php/apache2-php5.3/ext-active/ /etc/php/cgi-php5.2/ext-active/ /etc/php/cgi-php5.3/ext-active/ /etc/php/cli-php5.2/ext-active/ /etc/php/cli-php5.3/ext-active/ /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo"
> CXXFLAGS="-march=athlon64 -O2 -pipe"
> DISTDIR="/usr/portage/distfiles"
> FEATURES="assume-digests binpkg-logs distlocks ebuild-locks fixlafiles news parallel-fetch protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch"
> FFLAGS=""
> GENTOO_MIRRORS="http://distfiles.gentoo.org"
> LDFLAGS="-Wl,-O1 -Wl,--as-needed"
> MAKEOPTS="-j3"
> PKGDIR="/usr/portage/packages"
> PORTAGE_CONFIGROOT="/"
> PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages"
> PORTAGE_TMPDIR="/var/tmp"
> PORTDIR="/usr/portage"
> PORTDIR_OVERLAY=""
> SYNC="rsync://soxsnet.wustl.edu/gentoo-portage"
> USE="X acl alsa amd64 apache2 berkdb bzip2 cdr cli cracklib crypt cups cxx dri dvd fortran gd gdbm git gpm gtk iconv ipv6 ldap mmx modules mudflap multilib mysql ncurses nls nptl nptlonly openmp pam pcre pppd readline samba session sse sse2 ssl static-libs subversion sysfs syslog tcpd unicode vhosts winbind xcb xml xorg zlib" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem ymfpci" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop empty extplug file hooks iec958 ioplug ladspa lfloat linear meter mmap_emul mulaw multi null plug rate route share shm softvol" APACHE2_MODULES="actions alias auth_basic authn_alias authn_anon authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgi cgid dav dav_fs dav_lock deflate dir disk_cache env expires ext_filter file_cache filter headers include info log_config logio mem_cache mime mime_magic negotiation rewrite setenvif speling status unique_id userdir usertrack vhost_alias" CALLIGRA_FEATURES="kexi words flow plan stage tables krita karbon braindump" CAMERAS="ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf superstar2 timing tsip tripmate tnt ubx" INPUT_DEVICES="keyboard mouse" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" PHP_TARGETS="php5-3" RUBY_TARGETS="ruby18" USERLAND="GNU" VIDEO_CARDS="radeon" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq steal rawnat logmark ipmark dhcpmac delude chaos account"
> Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, LINGUAS, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
>
>
> I have been troubleshooting this issue for several days now, and any
> help would be greatly appreciated,
>
> Thanks,
>
> Philippe
>
> PS: I am not a bioinformatician… and this may explains that!
>
>
> ------------------------------------------------------------------------------
> Virtualization & Cloud Management Using Capacity Planning
> Cloud computing makes use of virtualization - but cloud computing
> also focuses on allowing computing to be delivered as a service.
> http://www.accelacomm.com/jaw/sfnl/114/51521223/
> _______________________________________________
> maq-help mailing list
> maq...@li...
> https://lists.sourceforge.net/lists/listinfo/maq-help
>
>
|
|
From: Breton, P. <pb...@wu...> - 2012-02-24 19:31:15
|
<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=Windows-1252">
</head>
<body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">
Hi Folks,
<div><br>
</div>
<div>I have installed MAQGene which serves as a maq front end on an 64-bit gentoo system. Each run I attempt excepted for the default test sequence ot340, yields a segmentation fault when maq map. I have pasted below the log from the run.</div>
<div><br>
</div>
<div><span class="Apple-style-span" style="font-family: Times; ">
<pre style="word-wrap: break-word; white-space: pre-wrap; ">/data/maqgene_current/maqgene/bin/run_maq.sh: line 44: export: `single_michael/./s_3_1_withindex_sequence.txt_CCGATTA.fastq=on': not a valid identifier
/data/maqgene_current/maqgene/bin/run_maq.sh: line 44: export: `single_michael/./s_3_3_withindex_sequence.txt_CCGATTA.fastq=on': not a valid identifier
Finished reading input.
++ echo michael/./s_3_1_withindex_sequence.txt_CCGATTA.fastq,michael/./s_3_3_withindex_sequence.txt_CCGATTA.fastq
++ tr , ' '
+ fastq_file_set1='michael/./s_3_1_withindex_sequence.txt_CCGATTA.fastq michael/./s_3_3_withindex_sequence.txt_CCGATTA.fastq'
++ cd /data/maqgene/reads
++ cat michael/./s_3_1_withindex_sequence.txt_CCGATTA.fastq michael/./s_3_3_withindex_sequence.txt_CCGATTA.fastq
++ wc -l
++ cut -f 1 -d ' '
+ TOTAL_LINES=86680560
++ echo '(86680560 / 105509888) + (86680560 % 105509888 != 0)'
++ bc
+ num_chunks=1
+ set +x
make -j 2 -l 2 -C /data/maqgene/work --warn-undefined-variables -I /data/maqgene -f /data/maqgene/makefile BFA_FILE=elegans.bfa MAQGENE_GENOME_DIR=/data/maqgene/genomes reads_cksum=2844678841 map_cksum=4145302068 pileup_cksum=1488249346 cns_cksum=2226060844 umdd=50000 dmdd=1000 umid=1000 dmid=1000 max_gene_radius=50000 full_results_dir=/data/maqgene/out/example_user/Mike2_ outfile_basename=Mike2_ map_parameters=" -m 0.00001 -C 250 -n 2 -e 100 -1 0" assemble_parameters=" -N 2 -q 0 -r 0.0 -m 7 -Q 100 -p " pileup_parameters=" -Q 100 -m 7 -q 0" CHUNK_SIZE=105509888 NUM_CHUNKS=1
Will process 86680560 lines of input in 1 chunks
make: Entering directory `/data/maqgene/work'
# Fri Feb 24 11:50:23 CST 2012: Removing frontend files in case this is a duplicate run ...
rm -f /data/maqgene/out/example_user/Mike2_/Mike2__{grouped.txt,flat.txt}
rm -f /data/maqgene/out/example_user/Mike2_/Mike2__uncovered.txt /data/maqgene/out/example_user/Mike2_/Mike2__coverage.txt /data/maqgene/out/example_user/Mike2_/Mike2__pileup.txt /data/maqgene/out/example_user/Mike2_/Mike2__log.txt /data/maqgene/out/example_user/Mike2_/Mike2__check.txt /data/maqgene/out/example_user/Mike2_/Mike2__unmapped.txt
make: Leaving directory `/data/maqgene/work'
make: Entering directory `/data/maqgene/work'
/data/maqgene/makefile:73: warning: undefined variable `date'
# : Regrouping fastq reads into chunks of size 105509888.
split -l 105509888 -a 5 -d <(cat /data/maqgene/reads/michael/./s_3_1_withindex_sequence.txt_CCGATTA.fastq /data/maqgene/reads/michael/./s_3_3_withindex_sequence.txt_CCGATTA.fastq) 4145302068.1.fastq.
for stem in 00000; do mv 4145302068.1.fastq.$stem 4145302068.$stem.1.fastq; done
touch 2844678841_split1
# Fri Feb 24 11:55:23 CST 2012: Converting fastq files to bfq ...
/data/maqgene_current/maqgene/bin/maq sol2sanger 4145302068.00000.1.fastq /dev/stdout | \
/data/maqgene_current/maqgene/bin/maq fastq2bfq /dev/stdin 4145302068.00000.1.bfq
-- finish writing file '4145302068.00000.1.bfq'
<font class="Apple-style-span" color="#e25117">-- 21670140 sequences were loaded.
# Fri Feb 24 12:07:14 CST 2012: Mapping file(s) 4145302068.00000.1.bfq
/data/maqgene_current/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 4145302068.00000.unmapped -H 4145302068.00000.mismatch \
4145302068.00000.map /data/maqgene/genomes/elegans.bfa 4145302068.00000.1.bfq 2> /dev/null
/bin/bash: line 1: 13445 <u>Segmentation fault</u> /data/maqgene_current/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 4145302068.00000.unmapped -H 4145302068.00000.mismatch 4145302068.00000.map /data/maqgene/genomes/elegans.bfa 4145302068.00000.1.bfq 2> /dev/null
make: *** [4145302068.00000.map] Error 139</font>
rm 2844678841_split1 4145302068.00000.mismatch 4145302068.00000.1.bfq 4145302068.00000.1.fastq
make: Leaving directory `/data/maqgene/work'
make: Entering directory `/data/maqgene/work'
make: *** No rule to make target `clean_tables'. Stop.
make: Leaving directory `/data/maqgene/work'</pre>
<pre style="word-wrap: break-word; white-space: pre-wrap; "><br></pre>
<pre style="word-wrap: break-word; white-space: pre-wrap; ">The host system is : </pre>
<pre style="word-wrap: break-word; white-space: pre-wrap; "><br></pre>
<pre style="word-wrap: break-word; white-space: pre-wrap; ">bin # emerge --info
Portage 2.1.10.44 (default/linux/amd64/10.0, gcc-4.4.5, unavailable, 3.0.6-gentoo x86_64)
=================================================================
System uname: Linux-3.0.6-gentoo-x86_64-Dual-Core_AMD_Opteron-tm-_Processor_2218-with-gentoo-1.12.14
Timestamp of tree: Tue, 21 Feb 2012 00:45:01 +0000
distcc 3.1 x86_64-pc-linux-gnu [disabled]
app-shells/bash: 4.1_p9
dev-lang/python: 2.4.6, 2.6.6-r2, 2.7.1-r1, 3.1.3-r1
dev-util/cmake: 2.8.4
dev-util/pkgconfig: 0.25-r2
sys-apps/baselayout: 1.12.14-r1
sys-apps/sandbox: 2.4
sys-devel/autoconf: 2.65-r1
sys-devel/automake: 1.11.1
sys-devel/binutils: 2.20.1-r1
sys-devel/gcc: 4.1.2, 4.4.5
sys-devel/gcc-config: 1.4.1
sys-devel/libtool: 2.2.10
sys-devel/make: 3.81-r2
sys-kernel/linux-headers: 2.6.36.1 (virtual/os-headers)
sys-libs/glibc: 2.12.2
Repositories: gentoo
ACCEPT_KEYWORDS="amd64"
ACCEPT_LICENSE="* -@EULA"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=athlon64 -O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/php/apache2-php5.2/ext-active/ /etc/php/apache2-php5.3/ext-active/ /etc/php/cgi-php5.2/ext-active/ /etc/php/cgi-php5.3/ext-active/ /etc/php/cli-php5.2/ext-active/ /etc/php/cli-php5.3/ext-active/ /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo"
CXXFLAGS="-march=athlon64 -O2 -pipe"
DISTDIR="/usr/portage/distfiles"
FEATURES="assume-digests binpkg-logs distlocks ebuild-locks fixlafiles news parallel-fetch protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch"
FFLAGS=""
GENTOO_MIRRORS="<a href="http://distfiles.gentoo.org">http://distfiles.gentoo.org</a>"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
MAKEOPTS="-j3"
PKGDIR="/usr/portage/packages"
PORTAGE_CONFIGROOT="/"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY=""
SYNC="<a href="rsync://soxsnet.wustl.edu/gentoo-portage">rsync://soxsnet.wustl.edu/gentoo-portage</a>"
USE="X acl alsa amd64 apache2 berkdb bzip2 cdr cli cracklib crypt cups cxx dri dvd fortran gd gdbm git gpm gtk iconv ipv6 ldap mmx modules mudflap multilib mysql ncurses nls nptl nptlonly openmp pam pcre pppd readline samba session sse sse2 ssl static-libs subversion sysfs syslog tcpd unicode vhosts winbind xcb xml xorg zlib" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem ymfpci" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop empty extplug file hooks iec958 ioplug ladspa lfloat linear meter mmap_emul mulaw multi null plug rate route share shm softvol" APACHE2_MODULES="actions alias auth_basic authn_alias authn_anon authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgi cgid dav dav_fs dav_lock deflate dir disk_cache env expires ext_filter file_cache filter headers include info log_config logio mem_cache mime mime_magic negotiation rewrite setenvif speling status unique_id userdir usertrack vhost_alias" CALLIGRA_FEATURES="kexi words flow plan stage tables krita karbon braindump" CAMERAS="ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf superstar2 timing tsip tripmate tnt ubx" INPUT_DEVICES="keyboard mouse" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" PHP_TARGETS="php5-3" RUBY_TARGETS="ruby18" USERLAND="GNU" VIDEO_CARDS="radeon" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq steal rawnat logmark ipmark dhcpmac delude chaos account"
Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, LINGUAS, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS</pre>
</span>
<div><br>
</div>
</div>
<div>I have been troubleshooting this issue for several days now, and any help would be greatly appreciated, </div>
<div><br>
</div>
<div>Thanks,</div>
<div><br>
</div>
<div>Philippe</div>
<div><br>
</div>
<div>PS: I am not a bioinformatician… and this may explains that! </div>
</body>
</html>
|
|
From: Vibha M. <vb....@gm...> - 2011-11-25 11:52:24
|
Respected Sir
Sir we are having a problem in assembling using easyrun option ...it shows
error 842 again and again as given below... pls help me for the same...
[vb@vb Desktop]$ maq/maq.pl easyrun -d assembly est.fasta filternovel.fq
-- CMD: ln -sf /home/vibha/Desktop/est.fasta assembly/ref.bfa
-- CMD: /home/vibha/Desktop/maq/maq fastq2bfq -n 2000000
/home/vibha/Desktop/filternovel.fq assembly/read1
-- finish writing file 'assembly/read1@1.bfq'
-- 627677 sequences were loaded.
-- CMD: (cd assembly; /home/vibha/Desktop/maq/maq map -n 2 -e 70 -u
unmap1@1.txt aln1@1.map ref.bfa read1@1.bfq 2> aln1@1.map.log)
sh: line 1: 6211 Segmentation fault (core dumped)
/home/vibha/Desktop/maq/maq map -n 2 -e 70 -u unmap1@1.txt
aln1@1.mapref.bfa read1@1.bfq2> aln1@1.map.log
** fail to run command '(cd assembly; /home/vibha/Desktop/maq/maq map -n 2
-e 70 -u unmap1@1.txt aln1@1.map ref.bfa read1@1.bfq 2> aln1@1.map.log)' at
maq/maq.pl line 842.
I will be highly grateful to you.
-- Regards
Vibha Mandhan
PhD Scholar
Deptt. of Biotechnolgy
Panjab University
Chandigarh
|
|
From: Zhiqiang W. <zh...@gx...> - 2011-05-29 09:04:39
|
Hi, I am using the command "/public/sourcecode/bwa-0.5.9/bwa \ sampe -f l1_pe.sam \ cp_scalffold.fa /public/solexa/bwa_test/l1_left.sai \ /public/solexa/bwa_test/l1_right.sai \ /public/solexa/L1_align_scalffold/s_1_1_sequence.txt \ /public/solexa/L1_align_scalffold/s_1_2_sequence.txt \ " get the msg : " [bns_restore_core] fail to open file 'cp_scalffold.fa.nt.ann'. Abort! Aborted " The align process has been successfully run using the files as " cp_scalffold.fa cp_scalffold.fa.amb cp_scalffold.fa.ann cp_scalffold.fa.bwt cp_scalffold.fa.pac cp_scalffold.fa.rbwt cp_scalffold.fa.rpac cp_scalffold.fa.rsa cp_scalffold.fa.sa " If I change the file extension to cp_scalffold.fa.nt.ann, the msg turn to " [bns_restore_core] fail to open file 'cp_scalffold.fa.ann'. Abort! Aborted " I am running bwa on the Linux 2.6.18-194.el5xen kernel, X86_64,could anyone tell me how to resolve the puzzle? Great thanks -- Yours Sincerely Zhiqiang Wang |
|
From: B.M. N. <bmn...@gm...> - 2011-05-17 19:02:59
|
Hi there I have a question that is quite similar to questions that were already asked. However, reading those threads, I could not solve my problem: I want to assemble Illumina short paired end reads. I actually have data from two lanes. I managed to convert the numeric SCARF files to fastq files. I checked whether the paired reads are in the same order for the two files for each of the lanes. I also checked if there are very short reads. Both (non-pairing and short reads) were reported to cause segfaults. When I analyse the data from the first lane, I can successfully finish the maq map command. However, for the data from the second lane, maq map stops and I get a segfault. I tried different version of MAQ and even tried pre-compiled versions. The command I use is analogue to: maq map out.aln.map s_5_1.fastq s_5_2.fastq I would be very happy, if somebody can help me out! Thanks and best regards Ben --- B.M. Nitsche PhD-student Molecular Microbiology and Biotechnology Institute of Biology Leiden Leiden University Sylvius Laboratory Sylviusweg 72 2333 BE Leiden The Netherlands tel: +31 (0)71 5274826 bmn...@gm... |
|
From: Raymond W. <r-...@cb...> - 2011-05-11 08:27:18
|
Hi, Instead of downloading the source and compiling it, you should consider obtaining the binaries and (if possible), the latest 0.7.1 version. I'm guessing you can find it in Fedora's package manager. Also, it seems maq compiled correctly so the output from ./configure is actually not too helpful. Can you provide information that is more related to your problem -- the command that you ran, a *very small* sample of your input data, etc.? Ray On 06/05/11 12:09, Bhanuprakash,A (ICRISAT-IN) wrote: > I'm using maq 0.6.8 to map Illumina reads to the reference. As per the instructions I tried to install maq on fedora 14 X86_64 system and below is the o/p of the installation commands. > > > [root@agl maq-0.6.8]# ./configure > checking for a BSD-compatible install... /usr/bin/install -c > checking whether build environment is sane... yes ... > /usr/bin/install -c 'scripts/maq_eval.pl' '/usr/local/bin/maq_eval.pl' > make[1]: Nothing to be done for `install-data-am'. > make[1]: Leaving directory `/home/ngs/Desktop/softwares/maq-0.6.8' > > > I could use the options fasta2bfa,fastq2bfq but when I use map I receive a an error "Segmentation fault (core dumped)". > > Can anyone help me to overcome this error. |
|
From: Bhanuprakash,A (ICRISAT-IN) <a.b...@cg...> - 2011-05-06 03:09:44
|
Hi.
I'm using maq 0.6.8 to map Illumina reads to the reference. As per the instructions I tried to install maq on fedora 14 X86_64 system and below is the o/p of the installation commands.
[root@agl maq-0.6.8]# ./configure
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking if gcc accepts -m64... yes
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
configure: creating ./config.status
config.status: creating Makefile
config.status: creating config.h
[root@agl maq-0.6.8]# make
cd . && /bin/sh /home/ngs/Desktop/softwares/maq-0.6.8/missing --run autoheader
aclocal.m4:14: error: this file was generated for autoconf 2.61.
You have another version of autoconf. If you want to use that,
you should regenerate the build system entirely.
aclocal.m4:14: the top level
autom4te: /usr/bin/m4 failed with exit status: 63
autoheader: '/usr/bin/autom4te' failed with exit status: 63
WARNING: `autoheader' is probably too old. You should only need it if
you modified `acconfig.h' or `configure.ac'. You might want
to install the `Autoconf' and `GNU m4' packages. Grab them
from any GNU archive site.
rm -f stamp-h1
touch config.h.in
cd . && /bin/sh ./config.status config.h
config.status: creating config.h
config.status: config.h is unchanged
make all-am
make[1]: Entering directory `/home/ngs/Desktop/softwares/maq-0.6.8'
gcc -DHAVE_CONFIG_H -I. -Wall -m64 -D_FASTMAP -g -O2 -c main.c
gcc -DHAVE_CONFIG_H -I. -Wall -m64 -D_FASTMAP -g -O2 -c const.c
gcc -DHAVE_CONFIG_H -I. -Wall -m64 -D_FASTMAP -g -O2 -c seq.c
gcc -DHAVE_CONFIG_H -I. -Wall -m64 -D_FASTMAP -g -O2 -c bfa.c
g++ -DHAVE_CONFIG_H -I. -Wall -m64 -D_FASTMAP -g -O2 -c -o read.o read.cc
gcc -DHAVE_CONFIG_H -I. -Wall -m64 -D_FASTMAP -g -O2 -c fasta2bfa.c
gcc -DHAVE_CONFIG_H -I. -Wall -m64 -D_FASTMAP -g -O2 -c fastq2bfq.c
g++ -DHAVE_CONFIG_H -I. -Wall -m64 -D_FASTMAP -g -O2 -c -o merge.o merge.cc
g++ -DHAVE_CONFIG_H -I. -Wall -m64 -D_FASTMAP -g -O2 -c -o match_aux.o match_aux.cc
g++ -DHAVE_CONFIG_H -I. -Wall -m64 -D_FASTMAP -g -O2 -c -o match.o match.cc
g++ -DHAVE_CONFIG_H -I. -Wall -m64 -D_FASTMAP -g -O2 -c -o sort_mapping.o sort_mapping.cc
sort_mapping.cc: In function int ma_make_pair(const match_aux_t*, const match_info_t*, const match_info_t*, pair_info_t*):
sort_mapping.cc:59:62: warning: suggest parentheses around arithmetic in operand of ^
g++ -DHAVE_CONFIG_H -I. -Wall -m64 -D_FASTMAP -g -O2 -c -o assemble.o assemble.cc
assemble.cc: In function base_call_aux_t* assemble_cns_collect(assemble_pos_t*, const assemble_aux_t*):
assemble.cc:106:64: warning: suggest parentheses around arithmetic in operand of |
g++ -DHAVE_CONFIG_H -I. -Wall -m64 -D_FASTMAP -g -O2 -c -o pileup.o pileup.cc
g++ -DHAVE_CONFIG_H -I. -Wall -m64 -D_FASTMAP -g -O2 -c -o mapcheck.o mapcheck.cc
gcc -DHAVE_CONFIG_H -I. -Wall -m64 -D_FASTMAP -g -O2 -c get_pos.c
gcc -DHAVE_CONFIG_H -I. -Wall -m64 -D_FASTMAP -g -O2 -c assopt.c
gcc -DHAVE_CONFIG_H -I. -Wall -m64 -D_FASTMAP -g -O2 -c aux_utils.c
g++ -DHAVE_CONFIG_H -I. -Wall -m64 -D_FASTMAP -g -O2 -c -o rbcc.o rbcc.cc
g++ -DHAVE_CONFIG_H -I. -Wall -m64 -D_FASTMAP -g -O2 -c -o subsnp.o subsnp.cc
g++ -DHAVE_CONFIG_H -I. -Wall -m64 -D_FASTMAP -g -O2 -c -o pair_stat.o pair_stat.cc
g++ -DHAVE_CONFIG_H -I. -Wall -m64 -D_FASTMAP -g -O2 -c -o indel_soa.o indel_soa.cc
indel_soa.cc: In function void fill_counter(bit32_t*, int, nst_bfa1_t*, void*):
indel_soa.cc:42:44: warning: suggest parentheses around - inside <<
indel_soa.cc:56:44: warning: suggest parentheses around - inside <<
gcc -DHAVE_CONFIG_H -I. -Wall -m64 -D_FASTMAP -g -O2 -c maqmap.c
gcc -DHAVE_CONFIG_H -I. -Wall -m64 -D_FASTMAP -g -O2 -c maqmap_conv.c
g++ -DHAVE_CONFIG_H -I. -Wall -m64 -D_FASTMAP -g -O2 -c -o altchr.o altchr.cc
gcc -DHAVE_CONFIG_H -I. -Wall -m64 -D_FASTMAP -g -O2 -c submap.c
g++ -DHAVE_CONFIG_H -I. -Wall -m64 -D_FASTMAP -g -O2 -c -o rmdup.o rmdup.cc
gcc -DHAVE_CONFIG_H -I. -Wall -m64 -D_FASTMAP -g -O2 -c simulate.c
gcc -DHAVE_CONFIG_H -I. -Wall -m64 -D_FASTMAP -g -O2 -c genran.c
g++ -DHAVE_CONFIG_H -I. -Wall -m64 -D_FASTMAP -g -O2 -c -o indel_pe.o indel_pe.cc
gcc -DHAVE_CONFIG_H -I. -Wall -m64 -D_FASTMAP -g -O2 -c stdaln.c
g++ -DHAVE_CONFIG_H -I. -Wall -m64 -D_FASTMAP -g -O2 -c -o indel_call.o indel_call.cc
indel_call.cc: In function int maq_indelpe(int, char**):
indel_call.cc:86:21: warning: last.indel_info_t::coor may be used uninitialized in this function
indel_call.cc:86:21: warning: last.indel_info_t::score may be used uninitialized in this function
indel_call.cc:86:21: warning: last.indel_info_t::indelpos.assemble_indelpos_t::n_types may be used uninitialized in this function
indel_call.cc:86:21: warning: last.indel_info_t::indelpos.assemble_indelpos_t::n_ungap may be used uninitialized in this function
indel_call.cc:86:21: warning: last.indel_info_t::indelpos.assemble_indelpos_t::n_reads may be used uninitialized in this function
g++ -DHAVE_CONFIG_H -I. -Wall -m64 -D_FASTMAP -g -O2 -c -o eland2maq.o eland2maq.cc
g++ -DHAVE_CONFIG_H -I. -Wall -m64 -D_FASTMAP -g -O2 -c -o csmap2ntmap.o csmap2ntmap.cc
gcc -DHAVE_CONFIG_H -I. -Wall -m64 -D_FASTMAP -g -O2 -c break_pair.c
g++ -DHAVE_CONFIG_H -I. -Wall -m64 -D_FASTMAP -g -O2 -c -o glfgen.o glfgen.cc
glfgen.cc: In function glf1_t* glfgen1_core(assemble_pos_t*, const assemble_aux_t*, bit8_t):
glfgen.cc:43:64: warning: suggest parentheses around arithmetic in operand of |
g++ -Wall -m64 -D_FASTMAP -g -O2 -o maq main.o const.o seq.o bfa.o read.o fasta2bfa.o fastq2bfq.o merge.o match_aux.o match.o sort_mapping.o assemble.o pileup.o mapcheck.o get_pos.o assopt.o aux_utils.o rbcc.o subsnp.o pair_stat.o indel_soa.o maqmap.o maqmap_conv.o altchr.o submap.o rmdup.o simulate.o genran.o indel_pe.o stdaln.o indel_call.o eland2maq.o csmap2ntmap.o break_pair.o glfgen.o -lm -lz
make[1]: Leaving directory `/home/ngs/Desktop/softwares/maq-0.6.8'
[root@agl maq-0.6.8]# make install
make[1]: Entering directory `/home/ngs/Desktop/softwares/maq-0.6.8'
test -z "/usr/local/bin" || /bin/mkdir -p "/usr/local/bin"
/usr/bin/install -c 'maq' '/usr/local/bin/maq'
test -z "/usr/local/bin" || /bin/mkdir -p "/usr/local/bin"
/usr/bin/install -c 'scripts/maq.pl' '/usr/local/bin/maq.pl'
/usr/bin/install -c 'scripts/farm-run.pl' '/usr/local/bin/farm-run.pl'
/usr/bin/install -c 'scripts/maq_plot.pl' '/usr/local/bin/maq_plot.pl'
/usr/bin/install -c 'scripts/maq_eval.pl' '/usr/local/bin/maq_eval.pl'
make[1]: Nothing to be done for `install-data-am'.
make[1]: Leaving directory `/home/ngs/Desktop/softwares/maq-0.6.8'
I could use the options fasta2bfa,fastq2bfq but when I use map I receive a an error "Segmentation fault (core dumped)".
Can anyone help me to overcome this error.
Thanks in advance.
With Regards,
A.BhanuPrakash
|
|
From: Joel M. <j_m...@lb...> - 2011-04-28 02:40:47
|
http://sourceforge.net/projects/maq/files/maq-data/ but i would download samtools and use the wgsim tool included for generating simulated reads. Joel On Wed, Apr 27, 2011 at 7:16 PM, ShuHong Lin <shu...@gm...> wrote: > simpuars.dat |
|
From: ShuHong L. <shu...@gm...> - 2011-04-28 02:16:59
|
Hi, This is my first time to use Maq, and I want to simulate illumina sequencing reads. I followed the guideline in the help manual to simulate illumina sequencing data, and I notice that I need a simupars.dat file to simluate the data. According to the help manual, I can get *simpuars.dat* from excuting "*simutrain*" or from the Maq website, but I didn't find any related files on the Maq download page. Does anyone could tell me where I can download the file ? Thinks in advance! Alan |
|
From: Raymond W. <r-...@cb...> - 2011-04-06 02:51:30
|
Hi all, I ran MAQ twice on a particular data set, and the final results differed slightly. I understand if a read can be mapped to more than one location, then any one of the locations will be returned and the read will get a mapping quality of 0. However, in my case, I have a read X present in one result set and not present in another -- the mapping qualities are non-zero. I noticed there is a -s option to "maq map" to set the random seed (perhaps other programs have it to). Given this, I guess this behavior is normal and it doesn't have anything to do with how I am running it? For those of you who have used MAQ a lot, do you tend to fix a value to -s so that you are guaranteed the same results every time? Thank you! Ray |
|
From: Joel M. <j_m...@lb...> - 2011-04-06 02:34:34
|
maq.pl statmap *.map.log Joel On Tue, Apr 5, 2011 at 7:06 PM, Raymond Wan <r-...@cb...>wrote: > > Hi Jon, > > > On 15/03/11 06:21, Durkin, Jonathan wrote: > > After I run maq.pl easyrun with paired-end data, it gives the following > > output to the screen: > > > > Total reads: > > Total PE reads > > Total mapped PE reads > > PE reads that match mate-pair requirements with quality>30 > > PE reads that match mate-pair requirements with quality>30 > > > > Is that information saved anywhere else? I can't find any of the numbers > > in the logs, .snp files, or txt files. > > > > Also, which program of easyrun (mapmerge? assemble?) generates those > > numbers? > > > I took a glance at the source code and I can't find any of > those phrases. Strange... > > Just wondering -- are you using the (I think) latest > version: 0.7.1? > > Ray > > > > > ------------------------------------------------------------------------------ > Xperia(TM) PLAY > It's a major breakthrough. An authentic gaming > smartphone on the nation's most reliable network. > And it wants your games. > http://p.sf.net/sfu/verizon-sfdev > _______________________________________________ > maq-help mailing list > maq...@li... > https://lists.sourceforge.net/lists/listinfo/maq-help > |
|
From: Raymond W. <r-...@cb...> - 2011-04-06 02:07:16
|
Hi Jon, On 15/03/11 06:21, Durkin, Jonathan wrote: > After I run maq.pl easyrun with paired-end data, it gives the following > output to the screen: > > Total reads: > Total PE reads > Total mapped PE reads > PE reads that match mate-pair requirements with quality>30 > PE reads that match mate-pair requirements with quality>30 > > Is that information saved anywhere else? I can't find any of the numbers > in the logs, .snp files, or txt files. > > Also, which program of easyrun (mapmerge? assemble?) generates those > numbers? I took a glance at the source code and I can't find any of those phrases. Strange... Just wondering -- are you using the (I think) latest version: 0.7.1? Ray |
|
From: Raymond W. <r-...@cb...> - 2011-04-05 04:48:09
|
Hi Peter, Thank you for suggestion; yes, that worked ... none of the reads are giving this error anymore. Thank you! Ray On 04/04/11 18:01, Peter wrote: > On Mon, Apr 4, 2011 at 7:00 AM, Raymond Wan<r-...@cb...> wrote: >> I get this warning: >> >> [seq_read_fastq] Inconsistent sequence name: >> @#####!!!!!!!!#######. Continue anyway. >> -- finish writing file 'test.bfq' >> -- 2 sequences were loaded. ... > Hi, > > I would try leaving the plus line empty, it saves space and should > avoid whatever issue this parser has comparing the two: > > @test.1 HWUSI-EAS574_104864611:6:1:1018:12910 length=100 > NATCCAAGCTAACTAGGATCCTTCTCTGGAAAATGACTCTTNNNNNNAGTATTGTCTCTTTGTCTNNTTCTATTCAAAGTCAGAANNNNNNNNTGGAAAG > + > !5555;<<;;EEE;EEEE>?BBBB>EEEEEEEEEEEE<BE,!!!!!!)/02).1.BBB<B33527!!12255635?>?@@#####!!!!!!!!####### > @test.2 HWUSI-EAS574_104864611:6:1:1018:6895 length=100 > NAACTTTTGTTATTTATTAGGCAATGATACGGATTTTTTCANNNNNNTTAGTTCTTTTCCTTTTTNNTAGAATGAAATTTCCTCTNNNNNNNNAATATTG > + > !########################################!!!!!!##################!!##################!!!!!!!!####### |
|
From: Peter <pe...@ma...> - 2011-04-04 09:01:49
|
On Mon, Apr 4, 2011 at 7:00 AM, Raymond Wan <r-...@cb...> wrote: > > > Hi all, > > I'm trying to index a FASTQ data file with MAQ (fastq2bfq) > and I seem to be getting a lot of "Inconsistent sequence > name" errors. For example, with these two reads: > > > @test.1 HWUSI-EAS574_104864611:6:1:1018:12910 length=100 > NATCCAAGCTAACTAGGATCCTTCTCTGGAAAATGACTCTTNNNNNNAGTATTGTCTCTTTGTCTNNTTCTATTCAAAGTCAGAANNNNNNNNTGGAAAG > +test.1 HWUSI-EAS574_104864611:6:1:1018:12910 length=100 > !5555;<<;;EEE;EEEE>?BBBB>EEEEEEEEEEEE<BE,!!!!!!)/02).1.BBB<B33527!!12255635?>?@@#####!!!!!!!!####### > @test.2 HWUSI-EAS574_104864611:6:1:1018:6895 length=100 > NAACTTTTGTTATTTATTAGGCAATGATACGGATTTTTTCANNNNNNTTAGTTCTTTTCCTTTTTNNTAGAATGAAATTTCCTCTNNNNNNNNAATATTG > +test.2 HWUSI-EAS574_104864611:6:1:1018:6895 length=100 > !########################################!!!!!!##################!!##################!!!!!!!!####### > > > I get this warning: > > [seq_read_fastq] Inconsistent sequence name: > @#####!!!!!!!!#######. Continue anyway. > -- finish writing file 'test.bfq' > -- 2 sequences were loaded. > > Interestingly, it works fine if I change just the first read > to this: > > > @test.1 > NATCCAAGCTAACTAGGATCCTTCTCTGGAAAATGACTCTTNNNNNNAGTATTGTCTCTTTGTCTNNTTCTATTCAAAGTCAGAANNNNNNNNTGGAAAG > +test.1 > !5555;<<;;EEE;EEEE>?BBBB>EEEEEEEEEEEE<BE,!!!!!!)/02).1.BBB<B33527!!12255635?>?@@#####!!!!!!!!####### > > > I can't see anything illegal in the read or its > meta-information, though. Also, if I process just the first > read (with the meta-information intact), it reports that "2 > sequences were loaded". So, something in the header is > confusing it... > > Has anyone else encountered this before? I'm quite happy to > remove the meta-information if that is my only option. > > Thank you! > > Ray Hi, I would try leaving the plus line empty, it saves space and should avoid whatever issue this parser has comparing the two: @test.1 HWUSI-EAS574_104864611:6:1:1018:12910 length=100 NATCCAAGCTAACTAGGATCCTTCTCTGGAAAATGACTCTTNNNNNNAGTATTGTCTCTTTGTCTNNTTCTATTCAAAGTCAGAANNNNNNNNTGGAAAG + !5555;<<;;EEE;EEEE>?BBBB>EEEEEEEEEEEE<BE,!!!!!!)/02).1.BBB<B33527!!12255635?>?@@#####!!!!!!!!####### @test.2 HWUSI-EAS574_104864611:6:1:1018:6895 length=100 NAACTTTTGTTATTTATTAGGCAATGATACGGATTTTTTCANNNNNNTTAGTTCTTTTCCTTTTTNNTAGAATGAAATTTCCTCTNNNNNNNNAATATTG + !########################################!!!!!!##################!!##################!!!!!!!!####### Peter |
|
From: Raymond W. <r-...@cb...> - 2011-04-04 06:00:33
|
Hi all, I'm trying to index a FASTQ data file with MAQ (fastq2bfq) and I seem to be getting a lot of "Inconsistent sequence name" errors. For example, with these two reads: @test.1 HWUSI-EAS574_104864611:6:1:1018:12910 length=100 NATCCAAGCTAACTAGGATCCTTCTCTGGAAAATGACTCTTNNNNNNAGTATTGTCTCTTTGTCTNNTTCTATTCAAAGTCAGAANNNNNNNNTGGAAAG +test.1 HWUSI-EAS574_104864611:6:1:1018:12910 length=100 !5555;<<;;EEE;EEEE>?BBBB>EEEEEEEEEEEE<BE,!!!!!!)/02).1.BBB<B33527!!12255635?>?@@#####!!!!!!!!####### @test.2 HWUSI-EAS574_104864611:6:1:1018:6895 length=100 NAACTTTTGTTATTTATTAGGCAATGATACGGATTTTTTCANNNNNNTTAGTTCTTTTCCTTTTTNNTAGAATGAAATTTCCTCTNNNNNNNNAATATTG +test.2 HWUSI-EAS574_104864611:6:1:1018:6895 length=100 !########################################!!!!!!##################!!##################!!!!!!!!####### I get this warning: [seq_read_fastq] Inconsistent sequence name: @#####!!!!!!!!#######. Continue anyway. -- finish writing file 'test.bfq' -- 2 sequences were loaded. Interestingly, it works fine if I change just the first read to this: @test.1 NATCCAAGCTAACTAGGATCCTTCTCTGGAAAATGACTCTTNNNNNNAGTATTGTCTCTTTGTCTNNTTCTATTCAAAGTCAGAANNNNNNNNTGGAAAG +test.1 !5555;<<;;EEE;EEEE>?BBBB>EEEEEEEEEEEE<BE,!!!!!!)/02).1.BBB<B33527!!12255635?>?@@#####!!!!!!!!####### I can't see anything illegal in the read or its meta-information, though. Also, if I process just the first read (with the meta-information intact), it reports that "2 sequences were loaded". So, something in the header is confusing it... Has anyone else encountered this before? I'm quite happy to remove the meta-information if that is my only option. Thank you! Ray |
|
From: Keiran R. <kr...@sa...> - 2011-04-01 20:44:25
|
executing the program with no parameters displays the basic usage ~: maq fastq2bfq Usage: maq fastq2bfq [-n nreads] <in.fastq> <out.prefix>|<out.bfq> Also the man page: http://maq.sourceforge.net/maq-man.shtml maq fastq2bfq reads.fastq reads.bfq I don't know if you need to decompress your fastq files first though. Keiran Raine Senior Computer Biologist The Cancer Genome Project Ext: 7703 kr...@sa... On 1 Apr 2011, at 21:21, Jimmy wrote: > Hello all, > > I am new to MAQ or any aligner and please help me with these > questions: > > 1. I have a 50x2 mate-pair SOLiD library. Is MAQ aware of the > orientation of SOLiD mate-pair library or I need to change > orientation to solexa paired-end style? > 2. After running solid2fastq, I got three files: > shortname.read1.fastq.gz, shortname.read2.fast1.gz, and > shortname.single.fastq.gz. > > I don't know how to set the input to run maq fastq2bfq. I tried the > following: > maq fastq2bfq shortname shortname.bfq (trying to convert all > three files in the same time) > maq fastq2bfq shortname.read1.fastq.gz read1.bfq (trying to > convert one file at a time). > > Neither worked. How to run this maq fastq2bfq command? > > Thanks a lot! > > Guohong > Rutgers University > > > ------------------------------------------------------------------------------ > Create and publish websites with WebMatrix > Use the most popular FREE web apps or write code yourself; > WebMatrix provides all the features you need to develop and > publish your website. http://p.sf.net/sfu/ms-webmatrix-sf > _______________________________________________ > maq-help mailing list > maq...@li... > https://lists.sourceforge.net/lists/listinfo/maq-help -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. |
|
From: Jimmy <ca...@gm...> - 2011-04-01 20:21:39
|
Hello all,
I am new to MAQ or any aligner and please help me with these questions:
1. I have a 50x2 mate-pair SOLiD library. Is MAQ aware of the orientation of
SOLiD mate-pair library or I need to change orientation to solexa paired-end
style?
2. After running solid2fastq, I got three files:
shortname.read1.fastq.gz, shortname.read2.fast1.gz, and
shortname.single.fastq.gz.
I don't know how to set the input to run maq fastq2bfq. I tried the
following:
maq fastq2bfq shortname shortname.bfq (trying to convert all three
files in the same time)
maq fastq2bfq shortname.read1.fastq.gz read1.bfq (trying to convert one
file at a time).
Neither worked. How to run this maq fastq2bfq command?
Thanks a lot!
Guohong
Rutgers University
|
|
From: Durkin, J. <Jon...@AG...> - 2011-03-14 21:21:48
|
Hello all, After I run maq.pl easyrun with paired-end data, it gives the following output to the screen: Total reads: Total PE reads Total mapped PE reads PE reads that match mate-pair requirements with quality >30 PE reads that match mate-pair requirements with quality >30 Is that information saved anywhere else? I can't find any of the numbers in the logs, .snp files, or txt files. Also, which program of easyrun (mapmerge? assemble?) generates those numbers? Thank you very much for your help, Jon Durkin |
|
From: dhivya a. <dh...@gm...> - 2011-03-09 21:25:32
|
solved. This was due to an quality value when compared to the number of bases in the read sequence. This happened when converting colorspace reads to a 'mock' base sequence. thanks On Wed, Mar 9, 2011 at 12:03 PM, dhivya arasappan <dh...@gm...> wrote: > Hi, > > I'm trying to generate a random dataset using maq simutrain and maq > simulate, but I keep running into the following error: > > maq: simulate.c:214: maq_simulate_core: Assertion `size_l <= fqc->l_max && > size_r <= fqc->l_max' failed. > > > I came across this error when running simutrain using my large fastq file, > but when I trimmed the file to around 4000 lines, simutrain worked fine and > produced a simupars.data file. > > But, when I use this file to run maq simulate, this error shows up again. > > Anyone seen this before? Any idea why this error shows up and what it > means? > > Any help would be great. > > thanks > Dhivya > |
|
From: dhivya a. <dh...@gm...> - 2011-03-09 18:03:47
|
Hi, I'm trying to generate a random dataset using maq simutrain and maq simulate, but I keep running into the following error: maq: simulate.c:214: maq_simulate_core: Assertion `size_l <= fqc->l_max && size_r <= fqc->l_max' failed. I came across this error when running simutrain using my large fastq file, but when I trimmed the file to around 4000 lines, simutrain worked fine and produced a simupars.data file. But, when I use this file to run maq simulate, this error shows up again. Anyone seen this before? Any idea why this error shows up and what it means? Any help would be great. thanks Dhivya |
13 messages has been excluded from this view by a project administrator.
