BOWTIE2 errors in the pipeline about paleomix HOT 8 CLOSED

I can't really read the YAML file you copy/pasted (if you need to include files to a github issue, then just include them as attachments), but it looks like you've tried to override options but omitted the Options key. I'm guessing that your YAML file looks something like this:

Z2_align:
  Z2_align:
    Z2_align:
      Bowtie2:
        MinQuality: 30

But what you'd actually want is something like the following, corresponding to the Options section at the top of the file:

Z2_align:
  Z2_align:
    Z2_align:
      Options:
        Aligners:
          Bowtie2:
            MinQuality: 30

I am guessing that you just want to map all your samples with Bowtie2. In that case you're better off just changing appropriate option in the Options section at the top of the YAML file, rather than trying to override options for a specific sample. The Options listed at the top of file apply to all samples, unless specifically overridden, and you generally don't need to set options for specific samples/library/etc. unless your data is heterogeneous.

However, I also noticed that the copy pasted YAML appears to be from the trim pipeline. If you created your YAML file using paleomix trim makefile, then I'd suggest creating a new one using paleomix bam makefile instead. The trim pipeline just runs the first step of the BAM pipeline and is intended for the case where all you want to do is to trim/merge your reads. Because of that the YAML template doesn't include any of the mapping options. If you instead make a YAML file with paleomix bam makefile then it'll also include all the mapping options, including the options that lets you pick Bowtie2 instead of BWA.

from paleomix.

from paleomix.

Dear Mikkel,

No you're right, it's a zipped fasta and not a fastq. I tried gunzip -v and the output file isn't functional still. Do you know of another way? Thank you so much for your help, I really appreciate it! My supervisor is on annual leave and I'm scratching my head a bit.

Best,

Roz

from paleomix.

Hi Roz,

It's a bit hard to say from where I'm sitting.
Why isn't the output file functional? Did it extract correctly or did you get any errors? Is the output a FASTA file or something else?
If the genome is something you've downloaded from a public website then I can take a look at it if you share the URL.

Cheers,
Mikkel

from paleomix.

Dear Mikkel,

When I use the genome.fna.gz file I receive this error:

Error reading makefiles: Path for prefix 'millet_genome' does not end with .fasta:
   '~/align.bowtie2/GCA_002895445.2_ASM289544v2_genomic.fna.gz'

I then tried to unzip the file using gunzip. This gives a .fasta file but the colour of the file has changed indicating it's no longer the same type of file. I tried with this file anyway and got:

Reference FASTA file does not exist: '~/align.bowtie2/GCA_002895445.2_ASM289544v2_genomic.fasta'

It's this millet genome
https://www.ncbi.nlm.nih.gov/genome?LinkName=bioproject_genome&from_uid=431363

Thanks!
Roz

from paleomix.

gunzip removes the .gz extension as part of the decompression process, so your FASTA is mostly likely named GCA_002895445.2_ASM289544v2_genomic.fna.gz now (ending with .fna). You'll need to rename it so that it ends with .fasta.

I'm also not sure off the top of my head if the pipeline supports ~/ in paths in the YAML file, so you'll probably need use the full path.

from paleomix.

Hi Mikkel,

Yes my file path was the problem!! Thank you so much. I can't promise I won't be back with more silly questions, but you'll be featuring in my acknowledgments :) If you're particularly interested in my results I can also send them over at the end of the project. I'm in the Archaeology Dept. at Cambridge.

Thanks again, paleomix is really impressive work!

from paleomix.

Hi Roz,

I'm glad that you got it working and thank you for the acknowledgments.
Feel free to open new issues if you run into any other problems.

I also appreciate your offer, but millet aDNA is a bit outside my current areas of interest.
But best of luck with your project!

Cheers,
Mikkel

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