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Code Block
titleCount the number of successful alignmentsCheck for failed alignment tasks
grep -L 'completed successfully' *.align.log

The -L option tells grep to only print the filenames that don't contain the pattern. Perfect! To see what might happen happens in the case of failure, create try it on a dummy file that doesn't contain the success that message:

Code Block
languagebashtitleCount the number of successful alignments
echo 'dummy log' > dummy.align.log
grep -L 'completed successfully' *.align.logaln_script.cmds

Checking alignment statistics



That information is in the *.iszinfo.txt files, on the line labeled Mode.

The median value is th 3rd value in the 5 fivnum values; it is the 6th 7th whitespace-separated field on the Mode line.