I am trying toperform taxonomic analysis using workflow : Metagenomic taxonomy analysis by user mina 24. During analysis, some of jobs are paused associated with kraken/braken analysis.
Please provide possible solution for the same. Also, is their anyother workflow for taxonomic and functional analysis of shotgun data
Thank you
Shailendra
Check GTN tutorials in this section: Microbiome / Tutorial List
Check error messages for failed jobs. Click at any output from a failed job, click at Error icon and check message in the middle window. Click at Dataset details ( i ) icon, and in the middle window, in Details tab scroll down to Tool Standard Output and Tool Standard Error log files. Expand black boxes. Check the log files for error messages. Sometimes relevant information is shown under dataset name, in mini-preview. Do you see any useful hints? If not, search this forum or web for error messages.
Hope that helps.
Kind regards,
Igor
Dear Igor
Thank you for your kind response. I will follow the steps.
Are they queued (grey) or produced an error (red) ? If red, follow Igor’s advice. If grey, simply means galaxy is waiting for resources to run the job (kraken is pretty memory-heavy and can take a lot of time to run depending on reference database; might I suggest metaphlan or sylph?)