User: stu111392

gravatar for stu111392
stu11139230
Reputation:
30
Status:
New User
Location:
Germany/Kiel
Last seen:
3 years ago
Joined:
4 years ago
Email:
s********@mail.uni-kiel.de

Posts by stu111392

<prev • 28 results • page 1 of 3 • next >
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Comment: C: Megan unable to assign taxonomical information
... Maybe to you it is clear what to do to get these sam files to work but for me it is still a mystery. MEGAN can now parse files in SAM format [10]. Note, however, that SAM files usually do not contain the names of the taxa associated with the reference sequences and so one must supply suitable mappi ...
written 3.6 years ago by stu11139230
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Comment: C: malt-build and Java heap Space
... I changed it. Hope that the problem is clearer now. ...
written 3.6 years ago by stu11139230
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Comment: C: malt-build and Java heap Space
... So your suggestion would be to increase the overall amount of memory? ...
written 3.6 years ago by stu11139230
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Comment: C: malt-build and Java heap Space
... Thank you for that. I´ll try it out tomorrow.  ...
written 3.6 years ago by stu11139230
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Answer: A: malt-build and Java heap Space
... And maybe let me rephrase the question a bit. I´am not entierly sure if this is just a pure problem of RAM or a Java error and therefor I postet the question here. Because even if I give the task 100gb of RAM it says after the hash table that 75,6GB are allocated. And therefor I thought it has anoth ...
written 3.6 years ago by stu11139230
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Answer: A: malt-build and Java heap Space
... I read the manual carefully and adjusted the memory parameters  in vmop files up to 100gb RAM. This was allready done and I therefor I asked the question here. So has anyone out there a helpfull answer?  ...
written 3.6 years ago by stu11139230
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malt-build and Java heap Space
... Hey everybody, at the moment I try to index a bunch of sequences with malt. I've indexed all viral proteins from refeseq without a problem. But now I wanted to index all bacterial ref-seq sequences at once. The file is about 9.8gb great and contains 5242 sequences. I used the command: ./malt-buil ...
software error alignment sequence written 3.6 years ago by stu11139230
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Answer: A: Help with Megan
... The import of Blast output files works now if I add the GI-mapping file. Then Megan works perfectly. But if I want to import SAM files from Diamond the program is again unable to assign the reads even if I load the GI-mapping file. Is there something else I have to load to get the results out of my ...
written 3.6 years ago by stu11139230
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Megan unable to assign taxonomical information
... Hey everybody, until now I got nearly everything to work but I'am stuck with Megan which of course has a GUI (what an irony). Over a long time I tried to load blast outputs, outputs from Diamond and today even an rma file generated with malt into Megan. This file was generated mapping reads from th ...
alignment written 3.7 years ago by stu11139230 • updated 3.6 years ago by Istvan Albert ♦♦ 78k
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Comment: C: Different Problems with Velvet
... Hey, thank you for you suggestion. I'll try it out but at the moment it seem I'll try using spades for futher assemblies. By the way I asked in the Meta Velvet Google Group how to assign my reads and they should be declared as short paired. During the next days I will get access to a cluster with mu ...
written 3.8 years ago by stu11139230

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