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.

General FAQs

ERROR: Could not find umake/outputDir in currentDirectory: To work around this bug, specify an absolute path for OUT_DIR/--outdir; This is due to the aligner trying to use OUT_PREFIX to transform the output directory to an absolute path, by prepending OUT_PREFIX. But, OUT_PREFIX is a snpcall setting that sets the snpcall Makefile filename. OUT_PREFIX will be deprecated in the next release. The current OUT_PREFIX which refers to the snpcall Makefile filename will be renamed to something else.

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. This error only occurs with certain versions of perl.

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:

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 disable chr X since it may be slightly misleading due to the assumption that all samples 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

GotCloud only looks at the 2nd & 5th columns of the pedigree file (white-space delimited)

2nd column is the individual ID which should match the 1st column of the BAM_INDEX file.
5th column is the sex, use: 1 for male and 2 for female.