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benedictpaten / marginAlign

UCSC Nanopore
MIT License
43 stars 13 forks source link

installation error #41

Closed herrroaa closed 6 years ago

herrroaa commented 6 years ago

Hi, I installed marginAlign, I did a test run (make test) and it was successful, please see below the final part of the test run result. However, when I try to call marginAlign it returns -bash: marginAlign: command not found

`.AverageReadIdentity 0.795369618446 MedianReadIdentity 0.795369618446 MinReadIdentity 0.720926843486 MaxReadIdentity 0.869812393405 ValuesReadIdentity 0.869812393405 0.720926843486 AverageAlignmentIdentity 0.509266537938 MedianAlignmentIdentity 0.509266537938 MinAlignmentIdentity 0.417804478427 MaxAlignmentIdentity 0.60072859745 ValuesAlignmentIdentity 0.417804478427 0.60072859745 AverageReadCoverage 0.901063009589 MedianReadCoverage 0.901063009589 MinReadCoverage 0.860682016905 MaxReadCoverage 0.941444002274 ValuesReadCoverage 0.941444002274 0.860682016905 AverageMismatchesPerAlignedBase 0.119232100001 MedianMismatchesPerAlignedBase 0.119232100001 MinMismatchesPerAlignedBase 0.0760869565217 MaxMismatchesPerAlignedBase 0.162377243481 ValuesMismatchesPerAlignedBase 0.0760869565217 0.162377243481 AverageDeletionsPerReadBase 0.0574880045021 MedianDeletionsPerReadBase 0.0574880045021 MinDeletionsPerReadBase 0.0458937198068 MaxDeletionsPerReadBase 0.0690822891974 ValuesDeletionsPerReadBase 0.0458937198068 0.0690822891974 AverageInsertionsPerReadBase 0.0392299405665 MedianInsertionsPerReadBase 0.0392299405665 MinInsertionsPerReadBase 0.0386048086692 MaxInsertionsPerReadBase 0.0398550724638 ValuesInsertionsPerReadBase 0.0398550724638 0.0386048086692 .

Ran 19 tests in 72.898s

OK `

mitenjain commented 6 years ago

Hello,

Are you running the executable from the marginAlign directory itself? If so, you'll probably need to run it as ./marginAlign. Could you check and try this?

Thank you.

herrroaa commented 6 years ago

Hi, It seems to work after trying ./marginAlign. Can I know why it worked after using this hidden file while it did not when I used the executable marginAlign? Also can I use marginCaller with bam files generated using any other aligners (as for example minimap2 / bwa)?

Thanks a lot

mitenjain commented 6 years ago

When you are in the base directory, you are specifying the executable by using the ./. If you add marginAlign to your $PATH then you won't need to do this. At this moment, marginAlign works with a SAM files that could have been generated by any aligner (LAST, BLASR, LASTZ, BWA, minimap2, GraphMap etc.). I will try and bring in BAM compatibility in short order.

Hope this helps. Let me know as you have more questions.