The job that was bad because of the ^M line endings got restarted and still generated a bad meta.xml. The fix I made to invoke reformat_contigs should get installed ASAP onto the server. (as I am mostly out of the loop on the MGRAST I would prefer not to be updating the code there). I have marked that job inactive as it has bogus fasta data. Also, the manually changed job 305 meta.xml had bad perms. olson@bio-ppc-head-2:~$ ls -l /vol/metagenome-48-hour/Jobs.prod/305/ meta.xml -rw-r--r-- 1 redwards metag48 2258876 Oct 22 20:05 /vol/ metagenome-48-hour/Jobs.prod/305/meta.xml I have fixed that as well.