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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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=== 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 ==
