NoneType

[ErikaGress]

Hi Brant

I using the workflow to mapping and pahsing. I used Trimmomatic to trim the reads (i.e. not Illumiprocessor) but I edited the name of the reads to be what Snakefile expects <line 25, in get_fq1 expects '{}-READ1.fastq.gz'.> I am putting the absolute paths on my mapping.conf but still getting the errro below.

Error:
TypeError: 'NoneType' object is not subscriptable
Wildcards:
sample=None
Traceback:
File "/home/erikagress/miniconda3/envs/phyluce-1.7.3/phyluce/workflows/mapping/Snakefile", line 25, in get_fq1

Thank you!

[brantfaircloth]

If you take a look at this file, you'll see the format that gets run for the tests of the workflow. This config file uses relative paths (so these are relative to the current files location). Perhaps check to ensure your formatting aligns with this.

[ErikaGress]

I changed to relative paths and double checked formatting aligns but still getting the same error. Not sure if I'd have to go back to beginning and use Illuminprocessor instead. Not sure why, I have the reads in this format "{}-READ1.fastq.gz (and READ2).

[ErikaGress]

Hi Brant
Still haven't solved the issue above so...

I am using the data from your Tutorial 1 to check the workflow. I followed it exactly (including using illumiprocessor). Note: I had to put the reads into its own sample/spp folder because they all together otherwise.
I am now getting this error:
MissingInputException in line 39 of /home/erikagress/miniconda3/envs/phyluce-1.7.3/phyluce/workflows/mapping/Snakefile:
Missing input files for rule copy_and_build_index:
../spades-assemblies/contigs/alligator_mississippiensis.contigs.fasta

I also tried using UCE contigs only (which is what I want to do for my reads) so I ran the contig matiching and exploded the fastas by taxon. I even renamed the directory to bev'contigs' (instead of 'exploded.fastas') and renamed the files to be .contigs.fasta (instead of unaligned.fasta). Is that how you would do it if you wanted to use UCE contigs only?
However, I get the same error:
MissingInputException in line 39 of /home/erikagress/miniconda3/envs/phyluce-1.7.3/phyluce/workflows/mapping/Snakefile:
Missing input files for rule copy_and_build_index:
../taxon-sets/all/contigs/alligator_mississippiensis.contigs.fasta

My mapping.config.yaml below. I am following your example including '-' or '_'
reads:
alligator-mississippiensis: ../raw-fastq/alligator-mississippiensis
gallus-gallus: ../raw-fastq/gallus-gallus

contigs:
alligator-mississippiensis: ../spades-assemblies/contigs/alligator_mississippiensis.contigs.fasta
gallus-gallus: ../spades-assemblies/contigs/gallus_gallus.contigs.fasta

Do you have any suggestions?

Thank you