Difference between revisions of "Frequently Asked Questions"
From SHORE wiki
(→When trying to run the precompiled SHORE binary it says something like locale::facet::_S_create_c_locale name not valid.) |
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| + | ===Does SHORE include the SHORE''map'' package for mutation mapping?=== | ||
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| + | No. [http://1001genomes.org/software/shoremap.html SHORE''map''] is an add-on that is distributed as a separate package. However, SHORE''map'' requires the output of [[shore consensus]] as an input. | ||
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===What happened if I received a ''bad write'' error?=== | ===What happened if I received a ''bad write'' error?=== | ||
* <code>read/write failure --- bad write</code> | * <code>read/write failure --- bad write</code> | ||
Revision as of 13:53, 15 May 2012
Does SHORE include the SHOREmap package for mutation mapping?
No. SHOREmap is an add-on that is distributed as a separate package. However, SHOREmap requires the output of shore consensus as an input.
What happened if I received a bad write error?
-
read/write failure --- bad write
-
thread N: error - bad write
terminate called after throwing an instance of 'std::ios_base::failure'
These errors indicate a failure writing to disk, usually after running out of disk space either in the temporary file directory or in your output directory.
To reduce disk space requirements for read import and alignment, try adding the -B switch to shore import, e. g. shore import -B 1000000 ...; or provide an alternate temporary file directory with sufficient disk space, e. g. shore -T /very_large_tmp mapflowcell ....
When trying to run the precompiled SHORE binary it says something like locale::facet::_S_create_c_locale name not valid.
As a workaround, set the current locale to C by doing
export LC_ALL=C
Alternatively, this problem can be fixed by compiling shore using the source package.
