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MISO: Mixture of Isoforms model for RNA-Seq isoform quantitation
http://genes.mit.edu/burgelab/miso/index.html
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Batch-logs file not being created #96

Open hershbc opened 7 years ago

hershbc commented 7 years ago

Hello, My name is Courtney, I'm a graduate student at the Cleveland Clinic in Rick Padgett's lab. I'm very excited to use MISO but the program is getting stuck when I try to use it. My indexed bam files were created and sorted in galaxy, then downloaded and saved into the folder in which I run MISO. I was able to use the compute insert length on these files, and I was also able to view it using samtools, which is what the documentation suggested to check upon getting 0 alignments. MISO is installed on our building server, so I did check the our UNIX guy that it is the most up-to-date version. I showed him the error code I was getting and he deduced that the program is trying to make a file with ":" in the filename and therefore it is not being made. I don't know how to get around this since it isn't any of the files that I am providing that have this notation. If you have any idea how this can be solved, please let me know. Thank you, Courtney

[hershbc@cognac2 ~]$ cd padgetrlab/courtney/MISO/tryagain [hershbc@cognac2 tryagain]$ /usr/local/bin/miso --run indexed rnaseq/Galaxy29-[Sort_on_data_11].bam --output-dir output --read-len 151 --paired-end 184 28.6 MISO (Mixture of Isoforms model) Probabilistic analysis of RNA-Seq data for detecting differential isoforms Use --help argument to view options.

Using MISO settings file: /usr/local/lib/python2.7/site-packages/misopy/settings/miso_settings.txt Computing Psi values...

roryk commented 7 years ago

Hi Courtney,

Does the directory "output" ever get made?

hershbc commented 7 years ago

Hi Rory, Thanks for the quick reply! Yes the output folder is being made. Inside that folder batch-genes, batch-logs, cluster_scripts, logs, scripts_output, and summary folders are being made. Batch genes contains 4 text files, batch logs is empty, cluster_scripts is empty. Logs has 5 .log files in it. Scripts is empty and summary has output.miso_summary in it. When I go a step further and run the miso summary program, it shows up with 0 alignments.