gtdbtk.exceptions.PplacerException

[B-1991-ing]

Dear GTDB-Tk support team,

I am running the gtdbtk classify_wf command line below, but error occurred. According to your experience, what could be the reason?

The gtdbtk classify_wf command line
filtered_output_dir=/home/projects/XXX/people/binson/Previous_pipeline/stats_output/outliers_output_cov_corr_080_cov_perc_50/filtered_out/
out_dir=/home/projects/XXX/people/binson/Previous_pipeline/classify_wf/
gtdbtk classify_wf --cpus 28 -x fa --genome_dir ${filtered_output_dir} --out_dir ${out_dir}

Error

Error file
Attached file - classify_wf_err.txt.
classify_wf_err.txt

/home/projects/env_10000/people/binson/Previous_pipeline/classify_wf/classify/intermediate_results/pplacer/pplacer.bac120.out
pplacer.bac120.out.txt

Best,

Bing

[B-1991-ing]

Dear GTDB-Tk support team,

My error seems like similar with questions below.

Similar questions
PplacerException Error
#352
Pplacer error (ValueError) on last step: not a memory issue?
#275
Issue with pplacer #256
Error in Pplacer step, classify_wf #239
An issue when running classify_wf #238
EXCEPTION: PplacerException #217

So, I submitted job using nodes=3:ppn=24,mem=120gb on 70 MAGs.

Command line
qsub -W group_list=env_10000 -A env_10000 -l nodes=2:ppn=16,mem=300gb,walltime=12:00:00 ./scripts/runmetawrappipeline.sh

But, "FileNotFoundError" happened.

Error file
classify_wf.err.txt

Log file
classify_wf.log.txt

Best,

Bing

[B-1991-ing]

Dear GTDB-Tk support team,

Updated

Error
"FileNotFoundError" (screenshot above)
It's same error with Running earlier version of GTDB in GTDB-Tk. No such file or directory: '/markers/pfam/individual_hmms/PF01868.17.hmm' #333.

Solution
module load gtdbtk/2.0.0
/home/databases/gtdbtk/release202/ classify_wf --cpus 16 -x fa --genome_dir ${filtered_output_dir} --out_dir ${out_dir}

Finally, it works.

Best,

Bing