Charles Bridges

After consultation with my HPC support staff I have gotten metassemble wrapper to run using python2. Still working out the kinks, will let you know how it goes. Thanks!

Hello, I've taken Wences' advice to use the python wrapper to run the sample dataset instead of using the step-by-step script. I've run into the issue that Metassembler v1.5 requires python3, but the metassemble.py wrapper seems to be written using python2 syntax. I cannot load both python2 and python3 on my HPC cluster. Am I missing something? How do users reconcile this? Thank you! Charles

Thank you Wences. I've replaced the directory paths appropriately, and most of the program is running as expected. Now, I'm not sure if the program has run to completion. Based on the description of directories that should be created found in the Manual, I believe the program is hung up after the asseMerge or meta2fasta. I have directory /M1/, which contains 19 or so files including B.A.fasta, but around 8 of those files are 0 bytes. I'm also lacking the M1/Metassembly/ directory, and my stdout file...

Hello, When running the sample data on an HPC cluster, the assembly fails. The /MergePipline folder is created with directories /A.CEstat and /B.CEstat, each of those contain /BWTaln directories containing files (which look to be appropriate size), but the /A.ce or /B.ce directories are empty. /BWTaln/A.mtp.2k.err (and B..err) show 92-93% alignment rate. /MergePipeline/M1 directory is empty. I've written the stdout and sterr to files, which I'll paste below. The main error seems to be that metassembler...

Hi, I'm trying to figure out how to use a single, interleaved paired-end library in metassembler. I'm running the latest release of Bowtie2, v2.3.2 which allows the user to use a single library using the parameter --interleaved. Will metassembler pass this parameter to Bowtie2? How is this written in the metassembler config file under the [global] section? I imagine something like: bowtie2_interleaved Thanks for your help.