Revision as of 09:35, 19 July 2013

GotCloud Frequently Asked Questions (FAQs)

This page hopes to answer some of the FAQs about GotCloud.

If you cannot find the answer to your question here, please contact us.

Type of arg 1 to keys must be hash (not hash element) at gotcloud/bin/Conf.pm line 155, near "}) " Compilation failed in require at gotcloud/bin/align.pl line 56.

To fix this bug, you need to edit gotcloud/bin/Conf.pm, line 155.

Change

foreach my $key (keys $CONF_HASH{$section}) {

to

foreach my $key (keys %{$CONF_HASH{$section}}) {

Illegal division by zero at gotcloud/scripts/vcf-summary line 388.
make: *** [vcfs/chrY/chrY.hardfiltered.vcf.gz.OK] Error 255
make: *** Waiting for unfinished jobs....
Commands finished in xxxxx secs WITH ERRORS. Check the logs: The current version does not gracefully handle a chromosome with no variants.; By default, GotCloud assumes all samples are female, producing no chr Y variants, which will produce this error.

Work arounds:

* Disable Chromosome Y by adding the following to your configuration file:

CHRS = 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X

You may also want to remove the X from the end, since it may be slightly misleading since it assumes all people are female.

* Specify a pedigree file that tells GotCloud which individuals are Male & which are Female by adding the following to your configuration file:

PED_INDEX = pedigreeFile.ped

@@ Line 24: / Line 24: @@
 : To fix this bug, you need to edit gotcloud/bin/Conf.pm, line 155.
 :Change
-<syntaxhighlight lang="perl">foreach my $key (keys $CONF_HASH{$section}) {</syntaxhighlight>
+:<syntaxhighlight lang="perl">foreach my $key (keys $CONF_HASH{$section}) {</syntaxhighlight>
 :to
-<syntaxhighlight lang="perl">foreach my $key (keys %{$CONF_HASH{$section}}) {</syntaxhighlight>
+:<syntaxhighlight lang="perl">foreach my $key (keys %{$CONF_HASH{$section}}) {</syntaxhighlight>
+;Illegal division by zero at gotcloud/scripts/vcf-summary line 388.<br />make<nowiki>:</nowiki> *** [vcfs/chrY/chrY.hardfiltered.vcf.gz.OK] Error 255<br />make<nowiki>:</nowiki> *** Waiting for unfinished jobs....<br />Commands finished in xxxxx secs WITH ERRORS.  Check the logs
+: The current version does not gracefully handle a chromosome with no variants.
+: By default, GotCloud assumes all samples are female, producing no chr Y variants, which will produce this error.
+: Work arounds:
+:: * Disable Chromosome Y by adding the following to your configuration file:
+::: <pre>CHRS = 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X</pre>
+::: You may also want to remove the X from the end, since it may be slightly misleading since it assumes all people are female.
+:: * Specify a pedigree file that tells GotCloud which individuals are Male & which are Female by adding the following to your configuration file:
+::: <pre>PED_INDEX = pedigreeFile.ped</pre>