Troubleshooting, common issues, and recommendations

###### tags: `hybpiper_wiki` # Troubleshooting, common issues, and recommendations **CJJ/MJ: ToDo** - CJJ I think the details below can all be deleted. - Section on target file creation - NewTargets and other options. - Section on how to improve gene recovery (with caveats) e.g. BLASTx eValue, cov_cutoff, single-cell mode, etc. - ... ------------------ In most cases, issues with HybPiper can be identified by investigating which stage of HybPiper failed: mapping (BWA or BLAST), distribution of reads/targets, assembly (SPAdes), exon extraction (Exonerate). Saving the output of HybPiper to a file is the best way to identify problems. Here are some common issues and how to solve them: --- `parallel: command not found` One or more of the dependencies may be missing from the user's `$PATH`. Check to see that the dependencies are in the correct place with: `reads_first.py --check_depend` If you are running HybPiper on a Cluster, it is a good idea to also run this command as a submitted job-- the `$PATH` may be different for submitted vs. interactive jobs. --- `ImportError: No module named importlib` `ImportError: No module named argparse` Both of these errors suggest that HybPiper was called with an earlier version of Python. HybPiper requires Python 2.7.x (and Python 3 support is coming soon!). If multiple versions of Python are on your system, ensure that the correct version is being called by HybPiper. --- ``` protname = hitname[1] Index Error: list index out of range ``` This error occurs during the distribution of reads/targets. Typically, it means the target FASTA file is not properly formatted. Sequences in the target file should be named in the format `>Source-GeneName`. This allows for multiple orthologous sequences to be used for each gene. Please see the [Tutorial](Tutorial) and the example dataset for a full explanation of target file format. --- --- `option --cov-cutoff not recognized` This error is caused by an older version of SPAdes, which does not support the `--cov-cutoff` option. HybPiper requires SPAdes 3.5 or higher. ---