3,045
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to search→Variant Calling Pipeline FAQs
; How do I compile
; How do I compile
: <pre>cd src/; make;</pre>
: <pre>cd src/; make;</pre>
;bam_tview_curses.c<nowiki>:5:20: error: curses.h: No such file or directory</nowiki><br />bam_tview_curses.c<nowiki>:7:2: warning: #warning "_CURSES_LIB=1 but NCURSES_VERSION not defined; tview is NOT compiled"</nowiki><br />bam_tview_curses.c<nowiki>:287:2: warning: #warning "No curses library is available; tview with curses is disabled."</nowiki><br />make[2]<nowiki>:</nowiki> *** [bam_tview_curses.o] Error 1<br />make[2]<nowiki>:</nowiki> Leaving directory `/group/onel-lab/GeneticResources/bin/gotcloud/1.16/gotcloud-gotcloud.1.16/src/samtools'<br />make[1]<nowiki>:</nowiki> *** [all-recur] Error 1<br />make[1]<nowiki>:</nowiki> Leaving directory `/group/onel-lab/GeneticResources/bin/gotcloud/1.16/gotcloud-gotcloud.1.16/src/samtools'<br />make<nowiki>:</nowiki> *** [samtools] Error 2
: This error is due to curses not being installed on your machine. To fix this error, you need to disable curses in samtools & samtools-hybrid
:* Modify: <code>gotcloud/src/samtools/Makefile</code> and <code>gotcloud/src/samtools-hybrid/Makefile</code>
:*# Replace:
:*#: <code>-D_CURSES_LIB=1</code>
:*#: with:
:*#: <code>-D_CURSES_LIB=0</code>
:*# Replace:
:*#: <code>LIBCURSES= -lcurses # -lXCurses</code>
:*#: with:
:*#: <code>LIBCURSES= # -lcurses # -lXCurses</code>
;mkdir -p premo/build; cd premo/build; cmake ..<br />/bin/sh<nowiki>: cmake:</nowiki> command not found<br />make<nowiki>:</nowiki> *** [premo] Error 127
: This occurs if you do not have cmake installed on your machine.
:* Since premo is not used by default, just remove premo from the build
:** premo is only used for the mosaik aligner (non-default) and for MEI calling (which is not yet implemented)
:* Modify: <code>gotcloud/src/Makefile</code>
:** Remove <code>premo</code> from the <code>EXES = </code>... line
; <nowiki>bed.cpp:62: error: call of overloaded ‘to_string(int32_t&)’ is ambiguous</nowiki><br /><nowiki>/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.h:2604: note: candidates are: std::string std::to_string(long long int)</nowiki><br /><nowiki>/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.h:2610: note: std::string std::to_string(long long unsigned int)</nowiki><br /><nowiki>/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.h:2616: note: std::string std::to_string(long double)</nowiki><br /><nowiki>make[1]: *** [bed.o] Error 1</nowiki><br /><nowiki>make[1]: Leaving directory `/group/onel-lab/GeneticResources/bin/gotcloud/1.16/gotcloud-gotcloud.1.16/src/vt'</nowiki><br /><nowiki>make: *** [vt] Error 2</nowiki>
: std::to_string is defined in c++11. However, not all compilers have updated to accept all overloads of to_string.
:* You need to cast the integer to an overload that is defined:
:** Edit line 62 of <code>gotcloud/src/vt/bed.cpp</code>
:**:From:
:**::<code>return this->chrom + ":" + std::to_string(this->start1) + "-" + std::to_string(this->end1);</code>
:**:To:
:**::<code>return this->chrom + ":" + std::to_string(static_cast<long long>(this->start1)) + "-" + std::to_string(static_cast<long long>(this->end1));</code>
;CMake Error<nowiki>:</nowiki> The current CMakeCache.txt directory /path1/gotcloud/src/premo/build/CMakeCache.txt is different than the directory /path2/gotcloud/src/premo/build where CMakeCache.txt was created. This may result in binaries being created in the wrong place. If you are not sure, reedit the CMakeCache.txt<br /><nowiki>CMake Error: The source "/path1/gotcloud/src/premo/CMakeLists.txt" does not match the source "/path2/gotcloud/src/premo/CMakeLists.txt" used to generate cache. Re-run cmake with a different source directory.
;CMake Error<nowiki>:</nowiki> The current CMakeCache.txt directory /path1/gotcloud/src/premo/build/CMakeCache.txt is different than the directory /path2/gotcloud/src/premo/build where CMakeCache.txt was created. This may result in binaries being created in the wrong place. If you are not sure, reedit the CMakeCache.txt<br /><nowiki>CMake Error: The source "/path1/gotcloud/src/premo/CMakeLists.txt" does not match the source "/path2/gotcloud/src/premo/CMakeLists.txt" used to generate cache. Re-run cmake with a different source directory.
== Variant Calling Pipeline FAQs ==
== Variant Calling Pipeline FAQs ==
; make<nowiki>: *** [outdir/vcfs/chr20/chr20.hardfiltered.vcf.gz.OK] Error 1</nowiki>
: Check the log file at: <code>outdir/vcfs/chr20/chr20.hardfiltered.sites.vcf.summary.log</code>
: If it says:
:: '''[tabix] the index file either does not exist or is older than the vcf file. Please reindex.<br />ERROR: vcf-summary, failed to open ''/path/to/refVcf.vcf.gz'', exit code: 1'''
: It means that your VCF file is newer than the associated index (.tbi) file.
:* If you are using a downloaded set of reference files, and the time stamps are similar, you just need to mark the .tbi file as newer (replace with the correct .tbi file):
:** <code>touch ''/path/to/refVcf.vcf.gz.tbi''</code>
:* If you are using your own reference files, and you think your vcf file is newer than your .tbi file, regenerate the .tbi file using (replace with the correct .vcf.gz file):
:** <code>gotcloud/bin/tabix -f /path/to/refVcf.vcf.gz</code>
=== Targetted/Exome ===
=== Targetted/Exome ===
; Exiting due to ERROR<nowiki>:</nowiki><br /> INVALID_SORT<nowiki>:</nowiki> ERROR<nowiki>:</nowiki> File is not coordinate sorted at record 1003<br /> PreviousRecord was 1<nowiki>:</nowiki>15347, but this record is 1<nowiki>:</nowiki>15328
; Exiting due to ERROR<nowiki>:</nowiki><br /> INVALID_SORT<nowiki>:</nowiki> ERROR<nowiki>:</nowiki> File is not coordinate sorted at record 1003<br /> PreviousRecord was 1<nowiki>:</nowiki>15347, but this record is 1<nowiki>:</nowiki>15328
::::20299969
::::20299969
::::20299994
::::20299994
=== Does Not Run ===
=== Does Not Run ===
::#* gotcloud/bin/genomestrip.pl - you only need to update this one if you want to run genomestrip
::#* gotcloud/bin/genomestrip.pl - you only need to update this one if you want to run genomestrip
::#* gotcloud/scripts/bed-diff.pl - you only need to update this one if you plan to run bed-diff.pl
::#* gotcloud/scripts/bed-diff.pl - you only need to update this one if you plan to run bed-diff.pl
== ldrefine Pipeline FAQs ==
; make<nowiki>: *** [outdir/beagle/chr#/split/bgl.#.chr#.PASS.#.vcf.gz.tbi] Error 1</nowiki>
: Check the log file at: <code>outdir/beagle/chr#/split/bgl.#.err</code>
: If it says:
:: '''Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: -2'''
::: '''at phaser.j.a(Unknown Source)<br /> at phaser.j.c(Unknown Source)<br /> at phaser.h.a(Unknown Source)<br /> at phaser.E.a(Unknown Source)<br /> at phaser.Y.a(Unknown Source)<br /> at phaser.PhaseMain.<init>(Unknown Source)<br /> at phaser.PhaseMain.main(Unknown Source)'''
: You need to change the seed for running beagle.
:* In your configuration file, set:
:** <code>BEAGLE = java -Xmx4g -jar $(BIN_DIR)/beagle.20101226.jar seed=993470 gprobs=true niterations=50 lowmem=true</code>
:* If it fails again, change the seed in the above command to something else, and rerun.
== Tutorial FAQs ==
== Tutorial FAQs ==
