---
# System prepended metadata

title: 'Troubleshooting, common issues, and recommendations'
tags: [hybpiper_wiki]

---

###### 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.
- ...


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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:

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`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.

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`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.

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```
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.

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`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.

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