kaichop
commented
5 years ago The input file is corrupted or incomplete, so that a SNP has only A allele and not B allele. You can do a "tail" command to check the last a few lines of the file.
On Wed, Oct 31, 2018 at 8:20 AM Hernán Morales Durand < notifications@github.com> wrote:
Hello,
I am running an issue in generate_affy_geno_cluster.pl using latest PennCNV to perform Affymetrix based analysis:
/usr/bin/perl /usr/local/bin/generate_affy_geno_cluster.pl \ ax_output/AxiomGT1.calls.txt \ ax_output/AxiomGT1.confidences.txt \ ax_output/quant-norm.pm-only.med-polish.expr.summary.txt \ -locfile penncnv_output/Run1_AxiomGT1.cleaned.pfb \ -sexfile clean_gender_file.txt \ -out ax_output/AxiomGT1.genocluster
This is the command output:
NOTICE: The --confidence_threshold argument is automatically set as 0.01 (default for Affymetrix Power Tools calling) NOTICE: Reading marker-location-file penncnv_output/Run1_AxiomGT1.cleaned.pfb ... Done with 19981 markers! NOTICE: A total of 119 males and 71 females are found in the signal file axoutput/quant-norm.pm-only.med-polish.expr.summary.txt Use of uninitialized value $ in substitution (s///) at /usr/local/bin/ generate_affy_genocluster.pl line 138, line 1303830. Use of uninitialized value $ in split at /usr/local/bin/ generate_affy_geno_cluster.pl line 139, line 1303830. Use of uninitialized value $sig_psid in string eq at /usr/local/bin/ generate_affy_geno_cluster.pl line 141, line 1303830. Use of uninitialized value $sig_psid in concatenation (.) or string at /usr/local/bin/generate_affy_genocluster.pl line 141, line 1303830. Use of uninitialized value $ in concatenation (.) or string at /usr/local/bin/generate_affy_geno_cluster.pl line 141, line 1303830. Error: Found probeset A allele but not B allele in signal file ax_output/quant-norm.pm-only.med-polish.expr.summary.txt line 1303355 (genofile line 1) for marker AX-18000609: <> at /usr/local/bin/ generate_affy_geno_cluster.pl line 141 main::generateAffyGenoCluster('ax_output/AxiomGT1.calls.txt', 'ax_output/AxiomGT1.confidences.txt', 'ax_output/quant-norm.pm-only.med-polish.expr.summary.txt', 'HASH(0xc59738)', 'HASH(0xc59270)') called at /usr/local/bin/ generate_affy_geno_cluster.pl line 41 done.
I don't know under which circumstances this behavior is expected. Any idea what's happening?
This is my perl environment
$ perl -V Summary of my perl5 (revision 5 version 14 subversion 2) configuration:
Platform: osname=linux, osvers=4.9.0-2-amd64, archname=x86_64-linux-gnu-thread-multi uname='linux tatooine 4.9.0-2-amd64 #1 https://github.com/WGLab/PennCNV/pull/1 smp debian 4.9.13-1 (2017-02-27) x86_64 gnulinux ' config_args='-Dusethreads -Duselargefiles -Dccflags=-DDEBIAN -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Dldflags= -Wl,-z,relro -Dlddlflags=-shared -Wl,-z,relro -Dcccdlflags=-fPIC -Darchname=x86_64-linux-gnu -Dprefix=/usr -Dprivlib=/usr/share/perl/5.14 -Darchlib=/usr/lib /perl/5.14 -Dvendorprefix=/usr -Dvendorlib=/usr/share/perl5 -Dvendorarch=/usr/lib/perl5 -Dsiteprefix=/usr/local -Dsitelib=/usr/local/share/perl/5.14.2 -Dsitearch=/usr/l ocal/lib/perl/5.14.2 -Dman1dir=/usr/share/man/man1 -Dman3dir=/usr/share/man/man3 -Dsiteman1dir=/usr/local/man/man1 -Dsiteman3dir=/usr/local/man/man3 -Dusesitecustomize -Duse64bitint -Dman1ext=1 -Dman3ext=3perl -Dpager=/usr/bin/sensible-pager -Uafs -Ud_csh -Ud_ualarm -Uusesfio -Uusenm -Ui_libutil -DDEBUGGING=-g -Doptimize=-O2 -Duseshrp lib -Dlibperl=libperl.so.5.14.2 -des' hint=recommended, useposix=true, d_sigaction=define useithreads=define, usemultiplicity=define useperlio=define, d_sfio=undef, uselargefiles=define, usesocks=undef use64bitint=define, use64bitall=define, uselongdouble=undef usemymalloc=n, bincompat5005=undef Compiler: cc='cc', ccflags ='-D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fstack-protector -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64', optimize='-O2 -g', cppflags='-D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fstack-protector -fno-strict-aliasing -pipe -I/usr/local/include' ccversion='', gccversion='4.7.2', gccosandvers='' [125/162] intsize=4, longsize=8, ptrsize=8, doublesize=8, byteorder=12345678 d_longlong=define, longlongsize=8, d_longdbl=define, longdblsize=16 ivtype='long', ivsize=8, nvtype='double', nvsize=8, Off_t='off_t', lseeksize=8 alignbytes=8, prototype=define Linker and Libraries: ld='cc', ldflags =' -fstack-protector -L/usr/local/lib' libpth=/usr/local/lib /lib/x86_64-linux-gnu /lib/../lib /usr/lib/x86_64-linux-gnu /usr/lib/../lib /lib /usr/lib libs=-lgdbm -lgdbm_compat -ldb -ldl -lm -lpthread -lc -lcrypt perllibs=-ldl -lm -lpthread -lc -lcrypt libc=, so=so, useshrplib=true, libperl=libperl.so.5.14.2 gnulibc_version='2.13' Dynamic Linking: dlsrc=dl_dlopen.xs, dlext=so, d_dlsymun=undef, ccdlflags='-Wl,-E' cccdlflags='-fPIC', lddlflags='-shared -L/usr/local/lib -fstack-protector'
Characteristics of this binary (from libperl): Compile-time options: MULTIPLICITY PERL_DONT_CREATE_GVSV PERL_IMPLICIT_CONTEXT PERL_MALLOC_WRAP PERL_PRESERVE_IVUV USE_64_BIT_ALL USE_64_BIT_INT USE_ITHREADS USE_LARGE_FILES USE_PERLIO USE_PERL_ATOF USE_REENTRANT_API USE_SITECUSTOMIZE [103/162] Locally applied patches: DEBPKG:debian/arm_thread_stress_timeout - http://bugs.debian.org/501970 Raise the timeout of ext/threads/shared/t/stress.t to accommodate slower build hosts DEBPKG:debian/cpan_definstalldirs - Provide a sensible INSTALLDIRS default for modules installed from CPAN. DEBPKG:debian/db_file_ver - http://bugs.debian.org/340047 Remove overly restrictive DB_File version check. DEBPKG:debian/doc_info - Replace generic man(1) instructions with Debian-specific information. DEBPKG:debian/enc2xs_inc - http://bugs.debian.org/290336 Tweak enc2xs to follow symlinks and ignore missing @inc https://github.com/inc directories. DEBPKG:debian/errno_ver - http://bugs.debian.org/343351 Remove Errno version check due to upgrade problems with long-running processes. DEBPKG:debian/libperl_embed_doc - http://bugs.debian.org/186778 Note that libperl-dev package is required for embedded linking DEBPKG:fixes/respect_umask - Respect umask during installation DEBPKG:debian/writable_site_dirs - Set umask approproately for site install directories DEBPKG:debian/extutils_set_libperl_path - EU:MM: Set location of libperl.a to /usr/lib DEBPKG:debian/no_packlist_perllocal - Don't install .packlist or perllocal.pod for perl or vendor DEBPKG:debian/prefix_changes - Fiddle with
PREFIX and variables written to the makefile DEBPKG:debian/fakeroot - Postpone LD_LIBRARY_PATH evaluation to the binary targets. DEBPKG:debian/instmodsh_doc - Debian policy doesn't install .packlist files for core or vendor. DEBPKG:debian/ld_run_path - Remove standard libs from LD_RUN_PATH as per Debian policy. DEBPKG:debian/libnet_config_path - Set location of libnet.cfg to /etc/perl/Net as /usr may not be writable. DEBPKG:debian/m68k_thread_stress - http://bugs.debian.org/517938 http://bugs.debian.org/517938 http://bugs.debian.org/495826 http://bugs.debian.org/495826 Disable some threads tests on m68k for now due to missing TLS. DEBPKG:debian/mod_paths - Tweak @inc https://github.com/inc ordering for Debian DEBPKG:debian/module_build_man_extensions - http://bugs.debian.org/479460 http://bugs.debian.org/479460 Adjust Module::Build manual page extensions for the Debian Perl policy DEBPKG:debian/prune_libs - http://bugs.debian.org/128355 http://bugs.debian.org/128355 Prune the list of libraries wanted to what we actually need. DEBPKG:fixes/net_smtp_docs - [rt.cpan.org http://rt.cpan.org #36038] http://bugs.debian.org/100195 http://bugs.debian.org/100195 Document the Net::SMTP 'Port' option [81/162] DEBPKG:debian/perlivp - http://bugs.debian.org/510895 http://bugs.debian.org/510895 Make perlivp skip include directories in /usr/local DEBPKG:debian/cpanplus_definstalldirs - http://bugs.debian.org/533707 http://bugs.debian.org/533707 Configure CPANPLUS to use the site directories by default. DEBPKG:debian/cpanplus_config_path - Save local versions of CPANPLUS::Config::System into /etc/perl. DEBPKG:debian/deprecate-with-apt - http://bugs.debian.org/580034 http://bugs.debian.org/580034 Point users to Debian packages of deprecated core modules DEBPKG:fixes/hurd-ccflags - [a190e64] http://bugs.debian.org/587901 http://bugs.debian.org/587901 [perl #92244] Make hints/gnu.sh append to $ccflags rather than overriding them DEBPKG:debian/squelch-locale-warnings - http://bugs.debian.org/508764 http://bugs.debian.org/508764 Squelch locale warnings in Debian package maintainer scripts DEBPKG:debian/skip-upstream-git-tests - Skip tests specific to the upstream Git repository DEBPKG:fixes/extutils-cbuilder-cflags - [011e8fb] http://bugs.debian.org/624460 http://bugs.debian.org/624460 [perl #89478] Append CFLAGS and LDFLAGS to their Config.pm counterparts in EU::C Builder DEBPKG:fixes/module-build-home-directory - http://bugs.debian.org/624850 http://bugs.debian.org/624850 [rt.cpan.org http://rt.cpan.org #67893] Fix failing tilde test when run under a UID without a passwd entry DEBPKG:debian/patchlevel - http://bugs.debian.org/567489 http://bugs.debian.org/567489 List packaged patches for 5.14.2-21+deb7u5 in patchlevel.h DEBPKG:fixes/h2ph-multiarch - [e7ec705] http://bugs.debian.org/625808 http://bugs.debian.org/625808 [perl #90122] Make h2ph correctly search gcc include directories DEBPKG:fixes/index-tainting - [3b36395] http://bugs.debian.org/291450 http://bugs.debian.org/291450 [perl #64804] RT 64804: tainting with index() of a constant DEBPKG:fixes/document_makemaker_ccflags - http://bugs.debian.org/628522 http://bugs.debian.org/628522 [rt.cpan.org http://rt.cpan.org #68613] Document that CCFLAGS should include $Config{ccflags} DEBPKG:fixes/sys-syslog-socket-timeout-kfreebsd.patch - http://bugs.debian.org/627821 http://bugs.debian.org/627821 [rt.cpan.org http://rt.cpan.org #69997] Use a socket timeout on GNU/kFreeBSD to catch ICMP po rt unreachable messages DEBPKG:fixes/hurd-hints - http://bugs.debian.org/636609 http://bugs.debian.org/636609 Improve general GNU hints, needed for GNU/Hurd. DEBPKG:fixes/pod_fixes - [7698aed] http://bugs.debian.org/637816 http://bugs.debian.org/637816 Fix typos in several pod/perl.pod files DEBPKG:debian/find_html2text - http://bugs.debian.org/640479 Configure CPAN::Distribution with correct name of html2text DEBPKG:fixes/digest_eval_hole - http://bugs.debian.org/644108 Close the eval "require $module" security hole in Digest->new($algorithm) DEBPKG:fixes/hurd-ndbm - [f0d0a20] [perl #102680] http://bugs.debian.org/645989 Add GNU/Hurd hints for NDBM_File DEBPKG:fixes/sysconf.t-posix - [8040185] [perl #102888] http://bugs.debian.org/646016 Fix hang in ext/POSIX/t/sysconf.t on GNU/Hurd [59/162] DEBPKG:fixes/hurd-largefile - [1fda587] [perl #103014] http://bugs.debian.org/645790 enable LFS on GNU/Hurd DEBPKG:debian/hurd_test_todo_syslog - http://bugs.debian.org/650093 Disable failing GNU/Hurd tests in cpan/Sys-Syslog/t/syslog.t DEBPKG:fixes/hurd_skip_itimer_virtual - [rt.cpan.org #72754] http://bugs.debian.org/650094 Skip interval timer tests in Time::HiRes on GNU/Hurd DEBPKG:debian/hurd_test_skip_sigdispatch - http://bugs.debian.org/650188 Disable failing GNU/Hurd tests op/sigdispatch.t DEBPKG:debian/hurd_test_skip_stack - http://bugs.debian.org/650175 Disable failing GNU/Hurd tests dist/threads/t/stack.t DEBPKG:debian/hurd_test_skip_pipe - http://bugs.debian.org/650187 Disable failing GNU/Hurd tests io/pipe.t DEBPKG:debian/hurd_test_skip_io_pipe - http://bugs.debian.org/650096 Disable failing GNU/Hurd tests dist/IO/t/io_pipe.t DEBPKG:fixes/manpage_name_CPAN - http://bugs.debian.org/650448 [ rt.cpan.org #73396] cpan/CPAN: add NAME headings in modules with POD DEBPKG:fixes/manpage_name_CPANPLUS - http://bugs.debian.org/650450 [ rt.cpan.org #73398] cpan/CPANPLUS: add NAME headings in modules with POD DEBPKG:fixes/manpage_name_Test-Harness - http://bugs.debian.org/650451 [ rt.cpan.org #73399] cpan/Test-Harness: add NAME headings in modules with POD DEBPKG:fixes/manpage_name_Term-UI - http://bugs.debian.org/650452 [ rt.cpan.org #73400] cpan/Term-UI: add NAME headings in modules with POD DEBPKG:fixes/podlators_ae_ligature_fallback - http://bugs.debian.org/652851 Fix the ASCII fallback string for AE DEBPKG:fixes/fsf_postal_address - [de89470] Update references to the FSF's postal address DEBPKG:fixes/cpan_module_pod_fixes - [perl #106870] [rt.cpan.org #73447] [ rt.cpan.org #73446] Fix POD formatting in Term-Cap and Pod-Parser DEBPKG:fixes/cgi_no_shellwords_pl - Use Text::ParseWords instead of shellwords.pl DEBPKG:fixes/path_max_fallback - [perl #109262] http://bugs.debian.org/656869 Don't use _POSIX_PATH_MAX as a fallback PATH_MAX DEBPKG:debian/makemaker-pasthru - http://bugs.debian.org/660195 [ rt.cpan.org #28632] Make EU::MM pass LD through to recursive Makefile.PL invocations DEBPKG:fixes/propagate_tainted_errors.patch - http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=663158 [perl #111654] properly propagate tainted errors DEBPKG:debian/perl5db-x-terminal-emulator.patch - http://bugs.debian.org/668490 Invoke x-terminal-emulator rather than xterm in perl5db.pl DEBPKG:fixes/socket_cache_propagate - http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=659075 [rt.cpan.org
61577] [perl #112736] sockdomain and socktype undef on newly accepted
sockets DEBPKG:fixes/ipc_open3 - [perl #114454] http://bugs.debian.org/683894 IPC::Open3::open3(..., '-') broken [37/162] DEBPKG:fixes/string_repeat_overrun - http://bugs.debian.org/689314 [b675304] avoid calling memset with a negative count DEBPKG:debian/cpan-missing-site-dirs - http://bugs.debian.org/688842 Fix CPAN::FirstTime defaults with nonexisting site dirs if a parent is writable DEBPKG:fixes/kfreebsd-overrides - http://bugs.debian.org/689713 [perl
115324] [7dc6565] Remove unnecessary overrides in gnukfreebsd and
gnuknetbsd hints. DEBPKG:fixes/tainted-smartmatch - [be88a5c] http://bugs.debian.org/690571 [perl #93590] $tainted ~~ [...] failing DEBPKG:fixes/regexp-matching-starter - [6e634c5] http://bugs.debian.org/690975 [perl #101710] Regression with /i, latin1 chars. DEBPKG:fixes/regexp-matching-fold - [399fb9c] http://bugs.debian.org/690976 regexec.c: Fix "\x{FB01}\x{FB00}" =~ /ff/i DEBPKG:fixes/regexp-matching-opposite-case - [dc91d5a] http://bugs.debian.org/690979 [perl #101970] /[[:lower:]]/i matches upper case DEBPKG:fixes/reading-glob-copy-handle - [fd1564b] http://bugs.debian.org/629363 [perl #92258] <$fh> hangs on a glob copy DEBPKG:fixes/smartmatch-rhs-precedence - http://bugs.debian.org/691102 [011be0b] Enforce Any ~~ Object smartmatch precedence DEBPKG:fixes/perlcheat-update - http://bugs.debian.org/691112 [ab0ae0a] Update PerlCheat to 5.14 DEBPKG:fixes/cgi-cr-escaping - http://bugs.debian.org/693420 CR escaping for P3P and Set-Cookie headers DEBPKG:fixes/maketext-code-execution - [1735f6f] http://bugs.debian.org/695224 Fix misparsing of maketext strings. DEBPKG:fixes/storable-security-warning - [664f237] http://bugs.debian.org/695223 add a note about security concerns in Storable DEBPKG:fixes/digest-sha-doublefree - [rt.cpan.org #82655] http://bugs.debian.org/698172 [a8c6ff7] Fix a double-free bug in Digest::SHA DEBPKG:fixes/64bitint-signedness-wraparound - http://bugs.debian.org/698320 [94e529c] Avoid wraparound when casting unsigned size_t to signed ssize_t. DEBPKG:fixes/stdin-sigchld - http://bugs.debian.org/700171 [perl #116621] [be48bbe] add a couple missing LEAVEs in perlio_async_run() DEBPKG:fixes/hsplit-rehash - [d59e31f] http://bugs.debian.org/702296 Prevent premature hsplit() calls, and only trigger REHASH after hsplit() DEBPKG:fixes/encode-memleak - http://bugs.debian.org/702416 [5814803] Encode: Fixed a memory leak that occurred in the UTF-8 encoding. DEBPKG:fixes/threads_shared_elements_crash - [perl #119089] http://bugs.debian.org/718438 threads::shared should not crash if shared elements outlive their aggr egate. DEBPKG:fixes/perlbug-patchlist - [3541c11] http://bugs.debian.org/710842 [perl #118433] Make perlbug look up the list of local patches at run time DEBPKG:fixes/digest_sha_double_free - [ee8c6f4] [rt.cpan.org #86295] http://bugs.debian.org/711206 maint-5.18: Digest-SHA crash fix in 5.85 [15/162] DEBPKG:fixes/pl_eval_start_use_after_free - [eae139f] [perl #115992] PL_eval_start use-after-free DEBPKG:fixes/regcomp_fix_segv - [ebb390a] [perl #115994] fix segv in regcomp.c:S_join_exact() DEBPKG:fixes/list_util_off_by_two - [623a911] fix off-by-two error in List::Util DEBPKG:fixes/sdbm_off_by_one - [7f5f08b] [perl #111586] sdbm.c: fix off-by-one access to global ".dir" DEBPKG:fixes/socket_unpack_sockaddr_un_heap_buffer_overflow - [e508642] [perl #111594] Socket::unpack_sockaddr_un heap-buffer-overflow DEBPKG:fixes/data_dump_infinite_recurse - [19be3be] don't recurse infinitely in Data::Dumper DEBPKG:debian/kfreebsd-softupdates - https://bugs.debian.org/796798 =?UTF-8?q?kFreeBSD=2010=20(possibly=20only=20with=20softupdates?= =?UTF-8?q?=20enabled)=20ma y=20defer=0Acalculating=20the=20mtime=20for=20m?= DEBPKG:fixes/CVE-2016-2381_duplicate_env - remove duplicate environment variables from environ DEBPKG:fixes/CVE-2016-1238/remove-dot-when-loading - [perl #127834] (perl
127834) remove . from the end of @inc https://github.com/inc if
complex modules are loaded DEBPKG:fixes/CVE-2016-1238/remove-dot-in-padwalker - [perl #127834] perl5db.pl: ensure PadWalker is loaded from standard paths DEBPKG:fixes/CVE-2016-1238/remove-dot-in-dist - [perl #127834] dist/: remove . from @inc https://github.com/inc when loading optional modules DEBPKG:fixes/CVE-2016-1238/remove-dot-in-cpan - [perl #127834] cpan/: remove . from @inc https://github.com/inc when loading optional modules DEBPKG:debian/CVE-2016-1238/test-suite-without-dot - [perl #127810] Patch unit tests to explicitly insert "." into @inc https://github.com/inc when needed. DEBPKG:debian/CVE-2016-1238/eumm-without-dot - [perl #127810] Add PERL_USE_UNSAFE_INC support to EU::MM for fortify_inc support. DEBPKG:debian/CVE-2016-1238/cpan-without-dot - [perl #127810] Set PERL_USE_UNSAFE_INC for cpan usage DEBPKG:debian/CVE-2016-1238/sitecustomize-in-etc - Look for sitecustomize.pl in /etc/perl rather than sitelib on Debian systems DEBPKG:debian/CVE-2016-1238/mb-without-dot - Make Module::Build set PERL_USE_UNSAFE_INC DEBPKG:debian/CVE-2016-1238/remove-inc-test - Remove test for '.' in @inc https://github.com/inc as it might not be DEBPKG:fixes/xsloader-eval - [rt.cpan.org #115808] https://bugs.debian.org/829578 =?UTF-8?q?Don=E2=80=99t=20let=20XSLoader=20load=20relative=20path?= =?UTF-8?q? s?= DEBPKG:fixes/file_path_chmod_race - https://bugs.debian.org/863870 [ rt.cpan.org #121951] Prevent directory chmod race attack. DEBPKG:fixes/extutils_file_path_compat - Correct the order of tests of chmod(). (#294) Built under linux Compiled at Jun 5 2017 18:24:09 @inc https://github.com/inc: /etc/perl /usr/local/lib/perl/5.14.2 /usr/local/share/perl/5.14.2 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.14 /usr/share/perl/5.14 /usr/local/lib/site_perl .
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hernanmd
Hello,
I am running an issue in generate_affy_geno_cluster.pl using latest PennCNV to perform Affymetrix based analysis:
This is the command output:
I don't know under which circumstances this behavior is expected. Any idea what's happening?
This is my perl environment