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This will finish very quickly (likely before you begin reading this) with a final line of "Creating index HTML table...". check this using the tail command. If you instead see this output:
| No Format | ||
|---|---|---|
| Code Block | ||
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!!!!!!!!!!!!!!!!!!!!!!!> FATAL ERROR <!!!!!!!!!!!!!!!!!!!!!!!
Error running command:
[system] /opt/apps/samtools/1.3/bin/samtools sort ./03_candidate_junctions/best.unsorted.bam ./03_candidate_junctions/best
Result code: 256
FILE: libbreseq/common.h LINE: 1294
!!!!!!!!!!!!!!!!!!!!!!!> FATAL ERROR <!!!!!!!!!!!!!!!!!!!!!!!
breseq: libbreseq/common.h:92: void breseq::my_assertion_handler(bool, const char*, const char*, int, const string&): Assertion `false' failed.
Aborted
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It means that you tried to run breseq with the incorrect version of samtools loaded. Execute the following 4 commands and then retry running breseq.
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