Difference between revisions of "Frequently Asked Questions"
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===Does SHORE include the SHORE''map'' package for mutation mapping?=== | ===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. | 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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To reduce disk space requirements for read import and alignment, try adding the <code>-B</code> switch to [[shore import]], e. g. <code>shore import -B 1000000 ...</code>; or provide an alternate temporary file directory with sufficient disk space, e. g. <code>shore -T /very_large_tmp mapflowcell ...</code>. | To reduce disk space requirements for read import and alignment, try adding the <code>-B</code> switch to [[shore import]], e. g. <code>shore import -B 1000000 ...</code>; or provide an alternate temporary file directory with sufficient disk space, e. g. <code>shore -T /very_large_tmp mapflowcell ...</code>. | ||
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| + | ===When trying to run the precompiled (statically linked) SHORE binary, it aborts with a message like ''locale::facet::_S_create_c_locale name not valid''.=== | ||
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| + | This issue is caused by the ''Boost'' C++ library. | ||
| + | As a workaround, set the current locale to ''C'' by doing | ||
| + | export LC_ALL=C'' | ||
| + | Alternatively, this problem can be fixed by [[Downloading_and_Installing_SHORE#Installing_SHORE_using_the_source_files|compiling shore using the source package]]. | ||
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| + | ===I generated SAM files using ''shore convert'', but now ''SAMtools'' states that the CIGAR strings are invalid=== | ||
| + | SHORE uses the CIGAR characters ''='' and ''X'' to indicate a match or mismatch, respectively. This format is only understood by recent versions of ''SAMtools'' (>= version 0.18). | ||
Latest revision as of 09:09, 7 October 2013
Contents
- 1 Does SHORE include the SHOREmap package for mutation mapping?
- 2 What happened if I received a bad write error?
- 3 When trying to run the precompiled (statically linked) SHORE binary, it aborts with a message like locale::facet::_S_create_c_locale name not valid.
- 4 I generated SAM files using shore convert, but now SAMtools states that the CIGAR strings are invalid
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 (statically linked) SHORE binary, it aborts with a message like locale::facet::_S_create_c_locale name not valid.
This issue is caused by the Boost C++ library. 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.
I generated SAM files using shore convert, but now SAMtools states that the CIGAR strings are invalid
SHORE uses the CIGAR characters = and X to indicate a match or mismatch, respectively. This format is only understood by recent versions of SAMtools (>= version 0.18).
