copy missing default_files directory for PICRUSt2

[laraPPr]

(created using eb --new-pr)

[casparvl]

@boegelbot please test @ generoso

[boegelbot]

@casparvl: Request for testing this PR well received on login1

PR test command 'EB_PR=18459 EB_ARGS= EB_CONTAINER= /opt/software/slurm/bin/sbatch --job-name test_PR_18459 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

• exit code: 0
• output:

Submitted batch job 11386

Test results coming soon (I hope)...

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Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

[casparvl]

@boegelbot please test @ jsc-zen2

[boegelbot]

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
cns8 - Linux Rocky Linux 8.5, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/boegelbot/8dcb196159cc37d0c5083c8a94905502 for a full test report.

[casparvl]

@boegelbot please test @ generoso

[boegelbot]

@casparvl: Request for testing this PR well received on login1

PR test command 'EB_PR=18459 EB_ARGS= EB_CONTAINER= /opt/software/slurm/bin/sbatch --job-name test_PR_18459 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

• exit code: 0
• output:

Submitted batch job 11388

Test results coming soon (I hope)...

- notification for comment with ID 1665651083 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

[boegelbot]

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
cns8 - Linux Rocky Linux 8.5, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/boegelbot/172403051fe0b93f0202a2e17b5fde8e for a full test report.

[boegel]

Test report by @boegel
SUCCESS
Build succeeded for 2 out of 2 (1 easyconfigs in total)
node3106.skitty.os - Linux RHEL 8.6, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz (skylake_avx512), Python 3.6.8
See https://gist.github.com/boegel/4cddec85c8e47c57e89b86f872b62e76 for a full test report.

[boegel]

Going in, thanks @laraPPr!

[sitinurmilah]

I'am a newbie running picrust2, i have the same problem with this topic, but i can't understand what should I do. I use WSL ubuntu and get this error result.

picrust2_pipeline.py -s study_seqs.fna -i study_seqs.biom -o picrust2_out_pipeline -p 1
No FASTA file found in specified directory. Expected to find one of:
/home/buah2023/miniconda3/envs/picrust2/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.fna.gz
/home/buah2023/miniconda3/envs/picrust2/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.fasta.gz
/home/buah2023/miniconda3/envs/picrust2/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.fna
/home/buah2023/miniconda3/envs/picrust2/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.fasta

In addition to the missing FASTA file, the following expected file(s) could not be found:
/home/buah2023/miniconda3/envs/picrust2/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.tre
/home/buah2023/miniconda3/envs/picrust2/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.hmm
/home/buah2023/miniconda3/envs/picrust2/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.model

Error - missing at least one of the four reference files in this specified directory: /home/buah2023/miniconda3/envs/picrust2/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref

Please someone can help me?