GotCloud: FAQs - Revision history

Mktrost: /* Variant Calling Pipeline FAQs */

2015-06-23T14:54:30Z

Variant Calling Pipeline FAQs

@@ Line 101: / Line 101: @@
 ::#* 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
 == Tutorial FAQs ==

Mktrost: /* Variant Calling Pipeline FAQs */

2015-03-02T14:50:25Z

Variant Calling Pipeline FAQs

← Older revision		Revision as of 10:50, 2 March 2015
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	== 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
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	::::20299969		::::20299969
	::::20299994		::::20299994


	=== Does Not Run ===		=== Does Not Run ===

Mktrost: /* Compiling FAQs */

2015-02-26T20:49:11Z

Compiling FAQs

@@ Line 10: / Line 10: @@
 ; How do I compile
 : <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
@@ Line 24: / Line 25: @@
+;mkdir -p premo/build; cd premo/build; cmake ..<br />/bin/sh<nowiki>: cmake:</nowiki> command not found<br />make<nowiki>:</nowiki> *** [premo] Error 127
 ;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.

Mktrost: /* Compiling FAQs */

2015-02-26T20:38:56Z

Compiling FAQs

← Older revision		Revision as of 16:38, 26 February 2015
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	;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		;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		: 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/~~Makeifle~~</code>		:* Modify: <code>gotcloud/src/samtools/Makefile</code> and <code>gotcloud/src/samtools-hybrid/Makefile</code>
	:*# Replace:		:*# Replace:
	:*#: <code>-D_CURSES_LIB=1</code>		:*#: <code>-D_CURSES_LIB=1</code>

Mktrost: /* Compiling FAQs */

2015-02-26T20:38:37Z

Compiling FAQs

@@ Line 10: / Line 10: @@
 ; How do I compile
 : <pre>cd src/; make;</pre>
 ;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.

Mktrost: /* Version Problems */

2015-02-26T20:30:25Z

Version Problems

← Older revision		Revision as of 16:30, 26 February 2015
Line 61:		Line 61:

	= Version Problems =		= Version Problems =

			== Prior to Version 1.16 ==
			; perl is not found in <code>/usr/bin/perl</code>
			: Modify all of the .pl scripts in gotcloud/, gotcloud/bin/, and gotcloud/scripts/
			:* If the first line contains: <code>#!/usr/bin/perl</code>
			:** Replace it with: <code>#!/usr/bin/env perl</code>
			:* Also, remove <code>-w</code> if it occurs on that first line of the perl scripts.
			:** If it is not already specified in the script, add the following line later in the script: <code>use warnings;</code>
			: This issues has been fixed in version 1.16.

	== Version 1.08 ==		== Version 1.08 ==

Mktrost: /* Variant Calling Pipeline FAQs */

2015-01-19T14:39:41Z

Variant Calling Pipeline FAQs

@@ Line 45: / Line 45: @@
 ::::20299969
 ::::20299994
 == Tutorial FAQs ==

Mktrost: /* Alignment Pipeline FAQs */

2014-09-29T15:58:47Z

Alignment Pipeline FAQs

← Older revision		Revision as of 11:58, 29 September 2014
Line 19:		Line 19:

	== Alignment Pipeline FAQs ==		== Alignment Pipeline FAQs ==
			; Error "read <> mapped to 'chr1' at POS 0 to -1, flag 69,0 has BIN 4680 but should be 266824".<br />        "Fix it by using BAM->SAM->BAM to force a recalculation of the BIN field."<br />        "Fail to index the BAM file"
			:This error appears to be due to BWA reference files that do not match the version of BWA used to run GotCloud align. Run the following to regenerate the BWA reference files with the GotCloud version of BWA.
			::<pre>gotcloud/bin/bwa index path/to/your/ref.fa</pre>

	== Variant Calling Pipeline FAQs ==		== Variant Calling Pipeline FAQs ==

Mktrost: /* Targetted/Exome */

2014-09-08T20:09:00Z

Targetted/Exome

← Older revision		Revision as of 16:09, 8 September 2014
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	:Further Explanation of the issue<nowiki>:</nowiki>		:Further Explanation of the issue<nowiki>:</nowiki>
	::The SAMTOOLS_VIEW_TARGET_ONLY set to TRUE tells our pipeline to pass to SAMTOOLS view all of the regions in the BED file that fall into a single segment of our processing.		::The SAMTOOLS_VIEW_TARGET_ONLY set to TRUE tells our pipeline to pass to SAMTOOLS view all of the regions in the BED file that fall into a single segment of our processing.
	::It appears that samtools view will then go through each of those regions independently and one a ta time, selecting just the records that fall within that region.		::It appears that samtools view will then go through each of those regions independently and one at a time, selecting just the records that fall within that region.
	::A problem occurs if records fall within multiple regions from the BED file. Since samtools view process the regions independently, it will write those records multiple times and they will end up out of order.		::A problem occurs if records fall within multiple regions from the BED file. Since samtools view process the regions independently, it will write those records multiple times and they will end up out of order.

Mktrost: /* Variant Calling Pipeline FAQs */

2014-08-25T21:08:46Z

Variant Calling Pipeline FAQs

← Older revision		Revision as of 17:08, 25 August 2014
Line 21:		Line 21:

	== Variant Calling Pipeline FAQs ==		== Variant Calling Pipeline FAQs ==
			=== 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

			: This error occurs if you have <code>SAMTOOLS_VIEW_TARGET_ONLY = TRUE</code> in your configuration file and a read(s) in your BAM file overlaps multiple regions in your BED file.
			: To fix this, set<nowiki>:</nowiki>
			:: <pre>SAMTOOLS_VIEW_TARGET_ONLY = FALSE</pre>
			:Further Explanation of the issue<nowiki>:</nowiki>
			::The SAMTOOLS_VIEW_TARGET_ONLY set to TRUE tells our pipeline to pass to SAMTOOLS view all of the regions in the BED file that fall into a single segment of our processing.
			::It appears that samtools view will then go through each of those regions independently and one a ta time, selecting just the records that fall within that region.
			::A problem occurs if records fall within multiple regions from the BED file. Since samtools view process the regions independently, it will write those records multiple times and they will end up out of order.

			::For example<nowiki>:</nowiki>
			::: If we have BED with regions chr20 20300049-20300050 and chr20 20300052-20300053
			:::The resulting call to samtools view looks like this:
			::: <pre>gotcloud/bin/samtools-hybrid view -q 20 -F 0x0704 bamFile.bam 20:20300049-20300050 20:20300052-20300053</pre>

			:::Say there are reads at positions 20299969 and 20299994 that are each 76 bases long, they will end up being output twice by the samtools view call and in this order:
			::::20299969
			::::20299994
			::::20299969
			::::20299994

	== Tutorial FAQs ==		== Tutorial FAQs ==