custom_ref_db doesn't work.

[hyeiny119]

When I analyze 18S using my custom_ref_db, I get this error.

This is the parameter and custom db I made. parameters.txt (Original file name is "parameters.tsv") hikim_test_SSEQ.nds.txt (Original file name is "hikim_test_SSEQ.nds") hikim_test.fasta.txt (Original file name is "hikim_test.fasta")

So, I tested your "crest_algo_example" (http://pema/analysis_directory/custom_ref_db/crest_algo_example/). Even if I use the crest example file you uploaded, I get the same error. I have my doubts about whether your example files work well.

So what to ask for

1. Is it possible to get .fasta and .nds file of silva 132 embeded in PEMA.
2. Is it possible to get an crest example of using custom_ref_db correctly (parameters and custom db).

Thank you!

[hariszaf]

Hi @hyeiny119.

Could you please also share the pema version you re using just to make sure what to look for.

Thanks for your interest on pema.

[hariszaf]

In addition, could you also send me the log you had until the end of it ? It is my belief that the training is going fine and the issue is a bit later.

[hyeiny119]

Thank you for your prompt response. I used pema v.2.1.4. I use this command line. "$ nohup docker run -i -v /hikim/app/project/PEMA_18S/PRJNA525566_MOCK1_vsearch_dbtest:/mnt/analysis hariszaf/pema:v.2.1.4 ./pema_latest.bds > /hikim/app/project/PEMA_18S/PRJNA525566_MOCK1_vsearch_dbtest/crest_algo_example.log &"

PRJNA525566_MOCK1_vsearch_dbtest ㅤ- custom_ref_db ㅤㅤㅤ-hikim_test.fasta (hikim_test.fasta.txt) ㅤㅤㅤ-hikim_test_SSEQ.nds (hikim_test_SSEQ.nds.txt) ㅤ- mydata ㅤㅤㅤ-MOCK1_1.fastq.gz (MOCK1_1.fastq.gz) ㅤㅤㅤ-MOCK1_2.fastq.gz (MOCK1_2.fastq.gz) ㅤ- parameters.tsv (parameters.tsv.txt)

This is full logs. crest_algo_example.log hikim-custom.log

Thank you hariszf !!

[hariszaf]

@hyeiny119 thanks a lot for the feedback!

I have spotted what's the issue here and I ll try to make a new pema release by this weekend to address this.

Thanks again and I will let you know once the release is out!

[hariszaf]

Hi @hyeiny119,

would you like to give it a shot with v.2.1.5 ? You may get this by running :

docker pull hariszaf/pema:v.2.1.5 

FYI, for the time being, this version is available only as a Docker image.

Could you give it a shot and give us your feedback? Thanks again! :smiley: