See the logs below. It starts right after prepare_s3_checkouts.
[Tue, 26 Feb 2013 01:38:03 +0000] DEBUG: STDERR:
[Tue, 26 Feb 2013 01:38:03 +0000] DEBUG: ---- End output of git init; git add .; git commit -m 'Create temporary repository from downloaded contents.' ----
[Tue, 26 Feb 2013 01:38:03 +0000] DEBUG: Ran git init; git add .; git commit -m 'Create temporary repository from downloaded contents.' returned 0
[Tue, 26 Feb 2013 01:38:03 +0000] INFO: Ran execute[create git repository] successfully
[Tue, 26 Feb 2013 01:38:03 +0000] DEBUG: Processing scm[Download Custom Cookbooks] on mynode-00.localdomain
[Tue, 26 Feb 2013 01:38:03 +0000] INFO: Cloning repo /tmp/opsworks20130226-834-1e0sh27/archive.d to /opt/aws/opsworks/current/site-cookbooks
[Tue, 26 Feb 2013 01:38:03 +0000] DEBUG: Executing git clone /tmp/opsworks20130226-834-1e0sh27/archive.d /opt/aws/opsworks/current/site-cookbooks
[Tue, 26 Feb 2013 01:38:03 +0000] DEBUG: ---- Begin output of git clone /tmp/opsworks20130226-834-1e0sh27/archive.d /opt/aws/opsworks/current/site-cookbooks ----
[Tue, 26 Feb 2013 01:38:03 +0000] DEBUG: STDOUT: Cloning into '/opt/aws/opsworks/current/site-cookbooks'...
done.
[Tue, 26 Feb 2013 01:38:03 +0000] DEBUG: STDERR:
[Tue, 26 Feb 2013 01:38:03 +0000] DEBUG: ---- End output of git clone /tmp/opsworks20130226-834-1e0sh27/archive.d /opt/aws/opsworks/current/site-cookbooks ----
[Tue, 26 Feb 2013 01:38:03 +0000] DEBUG: Ran git clone /tmp/opsworks20130226-834-1e0sh27/archive.d /opt/aws/opsworks/current/site-cookbooks returned 0
[Tue, 26 Feb 2013 01:38:03 +0000] DEBUG: Executing git ls-remote /tmp/opsworks20130226-834-1e0sh27/archive.d HEAD
[Tue, 26 Feb 2013 01:38:03 +0000] DEBUG: Executing git ls-remote /tmp/opsworks20130226-834-1e0sh27/archive.d HEAD
[Tue, 26 Feb 2013 01:38:03 +0000] DEBUG: ---- Begin output of git ls-remote /tmp/opsworks20130226-834-1e0sh27/archive.d HEAD ----
[Tue, 26 Feb 2013 01:38:03 +0000] DEBUG: STDOUT: 183e5968347b2c5eb192855230937507f55f32b3 HEAD
[Tue, 26 Feb 2013 01:38:03 +0000] DEBUG: STDERR:
[Tue, 26 Feb 2013 01:38:03 +0000] DEBUG: ---- End output of git ls-remote /tmp/opsworks20130226-834-1e0sh27/archive.d HEAD ----
[Tue, 26 Feb 2013 01:38:03 +0000] DEBUG: Ran git ls-remote /tmp/opsworks20130226-834-1e0sh27/archive.d HEAD returned 0
[Tue, 26 Feb 2013 01:38:03 +0000] INFO: Checking out branch: HEAD reference: 183e5968347b2c5eb192855230937507f55f32b3
[Tue, 26 Feb 2013 01:38:03 +0000] DEBUG: Executing git checkout -b deploy 183e5968347b2c5eb192855230937507f55f32b3
[Tue, 26 Feb 2013 01:38:04 +0000] DEBUG: ---- Begin output of git checkout -b deploy 183e5968347b2c5eb192855230937507f55f32b3 ----
[Tue, 26 Feb 2013 01:38:04 +0000] DEBUG: STDOUT:
[Tue, 26 Feb 2013 01:38:04 +0000] DEBUG: STDERR: Switched to a new branch 'deploy'
[Tue, 26 Feb 2013 01:38:04 +0000] DEBUG: ---- End output of git checkout -b deploy 183e5968347b2c5eb192855230937507f55f32b3 ----
[Tue, 26 Feb 2013 01:38:04 +0000] DEBUG: Ran git checkout -b deploy 183e5968347b2c5eb192855230937507f55f32b3 returned 0
[Tue, 26 Feb 2013 01:38:04 +0000] INFO: Enabling git submodules
[Tue, 26 Feb 2013 01:38:04 +0000] DEBUG: Executing git submodule init && git submodule update
[Tue, 26 Feb 2013 01:38:04 +0000] DEBUG: ---- Begin output of git submodule init && git submodule update ----
[Tue, 26 Feb 2013 01:38:04 +0000] DEBUG: STDOUT:
[Tue, 26 Feb 2013 01:38:04 +0000] DEBUG: STDERR: No submodule mapping found in .gitmodules for path 'mongodb'
[Tue, 26 Feb 2013 01:38:04 +0000] DEBUG: ---- End output of git submodule init && git submodule update ----
[Tue, 26 Feb 2013 01:38:04 +0000] DEBUG: Ran git submodule init && git submodule update returned 1
[Tue, 26 Feb 2013 01:38:04 +0000] ERROR: scm[Download Custom Cookbooks] (/opt/aws/opsworks/releases/20130225142901_104/cookbooks/opsworks_custom_cookbooks/recipes/checkout.rb:27:in `from_file') had an error:
git submodule init && git submodule update returned 1, expected 0
---- Begin output of git submodule init && git submodule update ----
STDOUT: STDERR: No submodule mapping found in .gitmodules for path 'mongodb'
---- End output of git submodule init && git submodule update ----
/opt/aws/opsworks/releases/20130225142901_104/vendor/bundle/ruby/1.8/gems/chef-0.9.15.3/bin/../lib/chef/mixin/command.rb:184:in `handle_command_failures'
/opt/aws/opsworks/releases/20130225142901_104/vendor/bundle/ruby/1.8/gems/chef-0.9.15.3/bin/../lib/chef/mixin/command.rb:131:in `run_command'
/opt/aws/opsworks/releases/20130225142901_104/vendor/bundle/ruby/1.8/gems/chef-0.9.15.3/bin/../lib/chef/provider/git.rb:128:in `enable_submodules'
/opt/aws/opsworks/releases/20130225142901_104/vendor/bundle/ruby/1.8/gems/chef-0.9.15.3/bin/../lib/chef/provider/git.rb:44:in `action_checkout'
/opt/aws/opsworks/releases/20130225142901_104/vendor/bundle/ruby/1.8/gems/chef-0.9.15.3/bin/../lib/chef/resource.rb:406:in `send'
/opt/aws/opsworks/releases/20130225142901_104/vendor/bundle/ruby/1.8/gems/chef-0.9.15.3/bin/../lib/chef/resource.rb:406:in `run_action'
/opt/aws/opsworks/releases/20130225142901_104/vendor/bundle/ruby/1.8/gems/chef-0.9.15.3/bin/../lib/chef/runner.rb:53:in `run_action'
/opt/aws/opsworks/releases/20130225142901_104/vendor/bundle/ruby/1.8/gems/chef-0.9.15.3/bin/../lib/chef/runner.rb:89:in `converge'
/opt/aws/opsworks/releases/20130225142901_104/vendor/bundle/ruby/1.8/gems/chef-0.9.15.3/bin/../lib/chef/runner.rb:89:in `each'
/opt/aws/opsworks/releases/20130225142901_104/vendor/bundle/ruby/1.8/gems/chef-0.9.15.3/bin/../lib/chef/runner.rb:89:in `converge'
/opt/aws/opsworks/releases/20130225142901_104/vendor/bundle/ruby/1.8/gems/chef-0.9.15.3/bin/../lib/chef/resource_collection.rb:94:in `execute_each_resource'
/opt/aws/opsworks/releases/20130225142901_104/vendor/bundle/ruby/1.8/gems/chef-0.9.15.3/bin/../lib/chef/resource_collection/stepable_iterator.rb:116:in `call'
/opt/aws/opsworks/releases/20130225142901_104/vendor/bundle/ruby/1.8/gems/chef-0.9.15.3/bin/../lib/chef/resource_collection/stepable_iterator.rb:116:in `call_iterator_block'
/opt/aws/opsworks/releases/20130225142901_104/vendor/bundle/ruby/1.8/gems/chef-0.9.15.3/bin/../lib/chef/resource_collection/stepable_iterator.rb:85:in `step'
/opt/aws/opsworks/releases/20130225142901_104/vendor/bundle/ruby/1.8/gems/chef-0.9.15.3/bin/../lib/chef/resource_collection/stepable_iterator.rb:104:in `iterate'
/opt/aws/opsworks/releases/20130225142901_104/vendor/bundle/ruby/1.8/gems/chef-0.9.15.3/bin/../lib/chef/resource_collection/stepable_iterator.rb:55:in `each_with_index'
/opt/aws/opsworks/releases/20130225142901_104/vendor/bundle/ruby/1.8/gems/chef-0.9.15.3/bin/../lib/chef/resource_collection.rb:92:in `execute_each_resource'
/opt/aws/opsworks/releases/20130225142901_104/vendor/bundle/ruby/1.8/gems/chef-0.9.15.3/bin/../lib/chef/runner.rb:84:in `converge'
/opt/aws/opsworks/releases/20130225142901_104/vendor/bundle/ruby/1.8/gems/chef-0.9.15.3/bin/../lib/chef/client.rb:268:in `converge'
/opt/aws/opsworks/releases/20130225142901_104/vendor/bundle/ruby/1.8/gems/chef-0.9.15.3/bin/../lib/chef/client.rb:158:in `run'
/opt/aws/opsworks/releases/20130225142901_104/vendor/bundle/ruby/1.8/gems/chef-0.9.15.3/bin/../lib/chef/application/solo.rb:190:in `run_application'
/opt/aws/opsworks/releases/20130225142901_104/vendor/bundle/ruby/1.8/gems/chef-0.9.15.3/bin/../lib/chef/application/solo.rb:181:in `loop'
/opt/aws/opsworks/releases/20130225142901_104/vendor/bundle/ruby/1.8/gems/chef-0.9.15.3/bin/../lib/chef/application/solo.rb:181:in `run_application'
/opt/aws/opsworks/releases/20130225142901_104/vendor/bundle/ruby/1.8/gems/chef-0.9.15.3/bin/../lib/chef/application.rb:62:in `run'
/opt/aws/opsworks/releases/20130225142901_104/vendor/bundle/ruby/1.8/gems/chef-0.9.15.3/bin/chef-solo:25
/opt/aws/opsworks/current/bin/chef-solo:16:in `load'
/opt/aws/opsworks/current/bin/chef-solo:16