missingcataloginfastaformat

[Marco Crotti]

Hello everyone,

I am struggling to solve this issue. I am running Stacks v. 2.1 on single end reads. I ran ustacks, cstacks and sstacks separately. For ustacks I used the attached scripts that I found on github. For cstacks I ran the following command:

cstacks -o ./example -s ./example/T2116 -s ./example/T3131 -s ./example/T3134 -s ./example/T3559 -s ./example/T3636 -s ./example/T3755 -s ./example/T3782 -s ./example/T3784 -s ./example/T3840 -s ./example/T3841 -s ./example/T4036 -s ./example/T4050 -s ./example/T4076 -s ./example/T4167 -s ./example/T4178 -s ./example/T4383 -s ./example/T4384 -s ./example/T4385 -s ./example/T4386 -s ./example/T4424 -s ./example/T4425 -s ./example/T4426 -s ./example/T4427 -s ./example/T4428 -s ./example/T4795 -s ./example/T4796 -s ./example/T4982 -s ./example/T5105 -s ./example/T5144 -s ./example/T5145 -s ./example/T5303 -s ./example/T5304 -s ./example/T5305 -s ./example/T5306 -s ./example/T5307 -s ./example/T5488 -s ./example/T5609 -s ./example/T5952 -s ./example/T5954 -s ./example/T6121 -s ./example/T6125 -s ./example/T6133 -s ./example/T6134 -s ./example/T6135 -s ./example/T6136 -n 4 -p 15

And for sstacks the following command:

sstacks -P ./example -M ./pop_map.txt -p 8

Now I want to run populations to generate phylip files, but I am missing the catalog.fa.gz, I only have the catalog.alleles.tsv.gz, catalog.snps.tsv.gz, and catalog.tags.tsv.gz files. What did I miss when running the above commands? What should I do to generate a catalog.fasta.gz file?

Thank you very much for your help.

Marco

[Marco Crotti]

I just ran the denovo_map.pl script with 5 samples, and the catalog.fasta.gz file is indeed created, so it seems it's a feature of the denovo_map.pl script. How can I tell populations to look for the other catalog files?

[Nicolas Rochette]

Hi Marco,

Please see the updated manual (on the Stacks website).

Best,

Nicolas

On 8/1/18 7:53 AM, Marco Crotti wrote:

I just ran the denovo_map.pl script with 5 samples, and the catalog.fasta.gz file is indeed created, so it seems it's a feature of the denovo_map.pl script. How can I tell populations to look for the other catalog files?

--
Stacks website: http://catchenlab.life.illinois.edu/stacks/
---
You received this message because you are subscribed to the Google Groups "Stacks" group.
To unsubscribe from this group and stop receiving emails from it, send an email to stacks-users...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/stacks-users/429b3737-85d1-413c-97d5-ae7f39259712%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

[Marco Crotti]

Hi Nicolas,

Yeah I figured it out, didn't realise I had to do the tsv2bam and gstack steps with the new Stacks version, all solved now and it's working. Thanks