The bioBakery help forum

Error: Unable to find the mpa_pkl file at: mpa_pklExiting

Microbial community profiling MetaPhlAn
#1

Hi.
I’ve installed metaphlan 3 using this command:

conda create --name mpa -c bioconda python=3.7 metaphlan

Then I’ve installed the database using this command:

mkdir -p $WORK_DIR/mpa_db metaphlan --install --bowtie2db $WORK_DIR/mpa_db

Inside the directory mpd_db I can find these files:

-rw-rw-r-- 1 dpietruc interactive 342M Jun 30 2020 mpa_v30_CHOCOPhlAn_201901.fna.bz2
-rw-r–r-- 1 dpietruc interactive 26 Jan 19 14:26 mpa_latest
-rw-r–r-- 1 dpietruc interactive 367M Jan 19 14:27 mpa_v30_CHOCOPhlAn_201901.tar
-rw-r–r-- 1 dpietruc interactive 64 Jan 19 14:27 mpa_v30_CHOCOPhlAn_201901.md5
-rw-rw-r-- 1 dpietruc interactive 286M Jan 19 14:28 mpa_v30_CHOCOPhlAn_201901.4.bt2
-rw-rw-r-- 1 dpietruc interactive 9.9M Jan 19 14:28 mpa_v30_CHOCOPhlAn_201901.3.bt2
-rw-rw-r-- 1 dpietruc interactive 286M Jan 19 14:35 mpa_v30_CHOCOPhlAn_201901.2.bt2
-rw-rw-r-- 1 dpietruc interactive 601M Jan 19 14:35 mpa_v30_CHOCOPhlAn_201901.1.bt2
-rw-rw-r-- 1 dpietruc interactive 286M Jan 19 14:43 mpa_v30_CHOCOPhlAn_201901.rev.2.bt2
-rw-rw-r-- 1 dpietruc interactive 601M Jan 19 14:43 mpa_v30_CHOCOPhlAn_201901.rev.1.bt2

However, when I run the command:

metaphlan $Name_file_forward,$Name_file_reverse --bowtie2db $WORK_DIR/mpa_db/ --input_type fastq --read_min_len 30 --bowtie2out $Bam --input_type fastq --nproc 8 --stat_q 0.01 -t rel_ab_w_read_stats > $Out

I get this error:

Error: Unable to find the mpa_pkl file at: mpa_pklExiting...

Can you help me to solve this problem? Thanks in advance!

#2

Have you tried unpacking mpa_v30_CHOCOPhlAn_201901.tar?

#3

Thanks, I’ve unpacked the file and now it’s working!

#4

Hi, I have unpacked mpa_v30_CHOCOPhlAn_201901.tar but still get the same error when I run the command:
‘metaphlan unmapped.ASD001_r1.fastq,unmapped.ASD001_r2.fastq --bowtie2db /home/yanz/miniconda3/envs/biosoftware/lib/python3.6/site-packages/metaphlan/metaphlan_databases --nproc 12 --input_type fastq -o unmapped_metagenome.txt’
‘Error: Unable to find the mpa_pkl file at: mpa_pklExiting…’

can anyone help me :frowning:

#5

Have you built the database using bowtie2-build or metaphlan --install?
Can you post there the output of ls -l /home/yanz/miniconda3/envs/biosoftware/lib/python3.6/site-packages/metaphlan/metaphlan_databases ?