Hi Theo,If the manifest is the same as from your first mail, then the problem might be that you didn't define your PEs properly.
In your manifest, it should be (at least): readgroup = Someunpairediontorrentreads *autopairing* data = /home/Wriddhiman/M_Series_Assembly/Raw_Fastq/M10_8.fastq technology = iontor Andrej On 04/09/2014 02:20 PM, Theo.Allnutt@xxxxxxxx wrote:
Hi, ok, I think I fixed the file not opening problem, though don't know how. I put eveything in the same folder and that seemed to work. Then I got the dreaded NFS warning, which is wrong because I'm using a VirtualBox Linux shared folder, not an NFS. I fixed that with the suggested switch, but then got the error: * MIRA found duplicate read names in your data (see log above for more info). * * * * This should never, never be! * * * * You may have loaded a file more than once in the manifest or * * reads may be present multiple times across your input file(s). * * Either way: fix that! However, I ahve checked and none of the reads have the same name. There are paired reads with same name then /1 or /2 appended (by sff_extract). Is this the problem Has the required format changed since 3.xx? Thanks. -----Original Message----- From: mira_talk-bounce@xxxxxxxxxxxxx [mailto:mira_talk-bounce@xxxxxxxxxxxxx] On Behalf Of Bastien Chevreux Sent: Wednesday, 9 April 2014 5:49 PM To: mira_talk@xxxxxxxxxxxxx Subject: [mira_talk] Re: 4 won't run!On April 9, 2014 at 9:05 AM Theo.Allnutt@xxxxxxxx wrote: Every time I run Mira 4, I get a file not found error: Looking for files named in data ...Data '/path/is/definitely/correct/paired1.fastq' was not found (neither as file nor as directory) or led to a read error. What could be wrong? Its driving me mad, have tried with several different files. [...] data = /path/is/definitely/correct/paired1.fastqAs first approximation, I would still guess there's a typo somewhere (I know, I know, you checked). If you type "ls " and then copy/paste (no typing, really mouse-only copy/paste) the full path from the "data=" line of the manifest into your terminal and then hit RETURN, does this work? Should that work we'd have to move on to more esoteric explanations like "is MIRA run as another user which might not have the same access permissions as you" and similar things. Hope that helps, Bastien -- You have received this mail because you are subscribed to the mira_talk mailing list. For information on how to subscribe or unsubscribe, please visit http://www.chevreux.org/mira_mailinglists.html b��j��yǢ��m�+&j)[yƮ�쨹���r��y�h�����jY&j)b� b��h�)ߢ���*'�xh��,���&ޢ�����r��z�^jǯ�ȭ��i��0��^���Ɗ��h�jf��)��+-�fl===