Error with run_humann_nonhost Rule

When running the HoMi pipeline with the default latest setting for the metaphlan database index, meaning the parameter for the rule metaphlan_index=get_metaphlan_index_name(config) is "latest", I received the following error with the run_humann_nonhost rule:

rule run_humann_nonhost: input: data/metaphlan_db, data/humann_dbs/chocophlan, data/humann_dbs/uniref, Zim4.f5.0.r10.0.nonhost.concat/7_ZIM143.fq.gz output: Zim4.f5.0.r10.0.nonhost.humann/7_ZIM143/7_ZIM143_pathabundance.tsv, Zim4.f5.0.r10.0.nonhost.humann/7_ZIM143/7_ZIM143_pathcoverage.tsv, Zim4.f5.0.r10.0.nonhost.humann/7_ZIM143/7_ZIM143_genefamilies.tsv, Zim4.f5.0.r10.0.nonhost.humann/7_ZIM143/7_ZIM143_humann_temp/7_ZIM143_metaphlan_bugs_list.tsv jobid: 0 reason: Forced execution wildcards: sample=7_ZIM143 threads: 32 resources: mem_mb=64000, mem_mib=61036, disk_mb=5830, disk_mib=5560, tmpdir=/scratch/alpine/joconnor@xsede.org, partition=amilan, runtime=1434, slurm=

mkdir -p Zim4.f5.0.r10.0.nonhost.humann

if [ "latest" = "latest" ]; then
  # read index name form the latest file
  metaphlan_db_name="$(<data/metaphlan_db//latest)"

  humann -i Zim4.f5.0.r10.0.nonhost.concat/7_ZIM143.fq.gz -o Zim4.f5.0.r10.0.nonhost.humann/7_ZIM143       --threads 32 --search-mode uniref90       --metaphlan-options "--bowtie2db data/metaphlan_db/"       

else
  humann -i Zim4.f5.0.r10.0.nonhost.concat/7_ZIM143.fq.gz -o Zim4.f5.0.r10.0.nonhost.humann/7_ZIM143       --threads 32 --search-mode uniref90       --metaphlan-options "--bowtie2db data/metaphlan_db/ --index latest"       

fi

Activating conda environment: ../../../../../projects/.xsede.org/joconnor/.snakemake/conda/9421bbfdb9a1863fa8a7cbc3b664de75_ /usr/bin/bash: line 5: data/metaphlan_db//latest: No such file or directory

When this is resolved with manual installation https://github.com/sterrettJD/HoMi/issues/86 and specifying the index in the config by adding metaphlan_index_name: mpa_vOct22_CHOCOPhlAnSGB_202212, I run into the following error. This is because there is no mpa_pkl file.

rule run_humann_nonhost: input: data/metaphlan_db, data/humann_dbs/chocophlan, data/humann_dbs/uniref, Zim4.f5.0.r10.0.nonhost.concat/12_ZIM159.fq.gz output: Zim4.f5.0.r10.0.nonhost.humann/12_ZIM159/12_ZIM159_pathabundance.tsv, Zim4.f5.0.r10.0.nonhost.humann/12_ZIM159/12_ZIM159_pathcoverage.tsv, Zim4.f5.0.r10.0.nonhost.humann/12_ZIM159/12_ZIM159_genefamilies.tsv, Zim4.f5.0.r10.0.nonhost.humann/12_ZIM159/12_ZIM159_humann_temp/12_ZIM159_metaphlan_bugs_list.tsv jobid: 0 reason: Forced execution wildcards: sample=12_ZIM159 threads: 32 resources: mem_mb=64000, mem_mib=61036, disk_mb=6983, disk_mib=6660, tmpdir=/scratch/alpine/joconnor@xsede.org, partition=amilan, runtime=1434, slurm=

mkdir -p Zim4.f5.0.r10.0.nonhost.humann

if [ "mpa_vOct22_CHOCOPhlAnSGB_202212" = "latest" ]; then
  # read index name form the latest file
  metaphlan_db_name="$(<data/metaphlan_db//mpa_vOct22_CHOCOPhlAnSGB_202212)"

  humann -i Zim4.f5.0.r10.0.nonhost.concat/12_ZIM159.fq.gz -o Zim4.f5.0.r10.0.nonhost.humann/12_ZIM159       --threads 32 --search-mode uniref90       --metaphlan-options "--bowtie2db data/metaphlan_db/"       

else
  humann -i Zim4.f5.0.r10.0.nonhost.concat/12_ZIM159.fq.gz -o Zim4.f5.0.r10.0.nonhost.humann/12_ZIM159       --threads 32 --search-mode uniref90       --metaphlan-options "--bowtie2db data/metaphlan_db/ --index mpa_vOct22_CHOCOPhlAnSGB_202212"       

fi

Activating conda environment: ../../../../../projects/.xsede.org/joconnor/.snakemake/conda/9421bbfdb9a1863fa8a7cbc3b664de75 CRITICAL ERROR: Error executing: /projects/.xsede.org/joconnor/.snakemake/conda/9421bbfdb9a1863fa8a7cbc3b664de75/bin/metaphlan /gpfs/alpine1/scratch/joconnor@xsede.org/HoMi/Zim4.f5.0.r10.0.nonhost.humann/12_ZIM159/12_ZIM159_humann_temp/tmp0kf_hp61/tmppkme36_s --bowtie2db data/metaphlan_db/ --index mpa_vOct22_CHOCOPhlAnSGB_202212 -o /gpfs/alpine1/scratch/joconnor@xsede.org/HoMi/Zim4.f5.0.r10.0.nonhost.humann/12_ZIM159/12_ZIM159_humann_temp/12_ZIM159_metaphlan_bugs_list.tsv --input_type fastq --bowtie2out /gpfs/alpine1/scratch/joconnor@xsede.org/HoMi/Zim4.f5.0.r10.0.nonhost.humann/12_ZIM159/12_ZIM159_humann_temp/12_ZIM159_metaphlan_bowtie2.txt --nproc 32

Error message returned from metaphlan : Error: Unable to find the mpa_pkl file at: mpa_pklExiting...

sterrettJD / HoMi

Error with run_humann_nonhost Rule #87