Updated README.md with a FAQ section

README.md

@@ -33,6 +33,35 @@ lemur -i examples/example-data/example.fastq \
 
 The output in the `example-output` folder will consist of raw `relative_abundance.tsv` file with taxonomic IDs, lineage information, and inferred relative abundance (`F` column). There will also be a `relative_abundance-[rank].tsv` where the rank is specified by the `-r/--rank` flag (e.g. in the above example it will be `species`). The `*P_rgs_df*` files capture individual inferred probabilities of a given read comign from a particular taxon. 
 
+---
+
+### FAQ 
+
+**Issue:** I run my analysis on a long-read metagenome, but it crashes with the following error:
+```
+Traceback (most recent call last):
+  File "/Users/nsapoval/miniconda3/envs/lemur-test-env/bin/lemur", line 901, in <module>
+    main()
+  File "/Users/nsapoval/miniconda3/envs/lemur-test-env/bin/lemur", line 887, in main
+    run.EM_complete()
+  File "/Users/nsapoval/miniconda3/envs/lemur-test-env/bin/lemur", line 672, in EM_complete
+    self.low_abundance_threshold = 1. / n_reads
+                                   ~~~^~~~~~~~~
+ZeroDivisionError: float division by zero
+```
+
+**Solutions:** Most likely this happens due to the filtering step which be default removes all alignments shorter than 75% of the corresponding marker gene length (see `--min-aln-len-ratio` flag description in the section below).
+
+1. Produce a histogram of read lengths in your FASTQ file if there is a significant portion of the sample of length below 400-500 bps, it is very likely that the above filter removes all alignments.
+2. In the output folder, you can find a file called `P_rgs_df_raw.tsv`. It contains raw information about the alignments prior to the above filters. Verify the `aln_len` column of this file, if you see all values below 200-300 bps it means that there are no long alignments to marker genes.
+3. If either of the above holds true, the analysis results might be unreliable. However, if you wish to proceed, you can add the `--min-aln-len-ratio 0.10` flag to the run retaining all alignments of length >=10% of the target marker gene length.
+
+---
+
+If you discover any additional issues while running the tool, please use [GitHub Issues](https://github.com/treangenlab/lemur/issues) interface to report it. Common issues and solution will be added to this FAQ.
+
+---
+
 ### Parameter descriptions
 
 Main arguments: