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Bug: failing to index new fasta files for filtering for some step combinations

The pipeline fails to create an index for FASTAs given for read filtering for some combinations of steps, e.g. if using only preprocessing or preprocessing taxonomy. Apparently, the rule required to build the indices is not included in those cases.

IMP version: 47a4181a

Config:

steps: "preprocessing taxonomy"
preprocessing_filtering: true
mem:
  normal_mem_per_core_gb: 8
  big_mem_total_gb: 120
  big_mem_cores: 5
  big_mem_per_core_gb: 24
tmp_dir: tmp
raws: 
  Metagenomics: "/mnt/isilon/projects/ecosystem_biology/sofunmoni/raw/metat/fastq/G-AN-AL6-150_capp_SOFUNMONI_NHM_S5_R1_001.fastq.gz"
sample: test
outputdir: "/mnt/lscratch/users/vgalata/tmp/filt_test"
db_path: "/mnt/lscratch/users/vgalata/tmp/imp3_dbs"
filtering:
  filter: "PhiX EiseniaAndrei EiseniaFetida"

Databases folder structure:

adapters -> /work/projects/ecosystem_biology/local_tools/IMP3/databases/adapters
minikraken2 -> /work/projects/ecosystem_biology/local_tools/IMP3/databases/minikraken2
filtering/EiseniaAndrei.fa
filtering/EiseniaFetida.fa
filtering/PhiX.fa -> /work/projects/ecosystem_biology/local_tools/IMP3/databases/filtering/PhiX.fa
filtering/PhiX.fa.amb -> /work/projects/ecosystem_biology/local_tools/IMP3/databases/filtering/PhiX.fa.amb
filtering/PhiX.fa.ann -> /work/projects/ecosystem_biology/local_tools/IMP3/databases/filtering/PhiX.fa.ann
filtering/PhiX.fa.bwt -> /work/projects/ecosystem_biology/local_tools/IMP3/databases/filtering/PhiX.fa.bwt
filtering/PhiX.fa.pac -> /work/projects/ecosystem_biology/local_tools/IMP3/databases/filtering/PhiX.fa.pac
filtering/PhiX.fa.sa -> /work/projects/ecosystem_biology/local_tools/IMP3/databases/filtering/PhiX.fa.sa

CMD:

# on a bigmem node with 5 cores
snakemake -s Snakefile -rpn --jobs 5 --configfile myconfig.yaml --use-conda

Error message:

MissingInputException in line 26 of /mnt/lscratch/users/vgalata/tmp/imp3/workflow/rules/Preprocessing/filtering.smk:
Missing input files for rule mg_filtering:
/mnt/lscratch/users/vgalata/tmp/imp3_dbs/filtering/EiseniaAndrei.fa.pac
/mnt/lscratch/users/vgalata/tmp/imp3_dbs/filtering/EiseniaAndrei.fa.bwt
/mnt/lscratch/users/vgalata/tmp/imp3_dbs/filtering/EiseniaAndrei.fa.ann
/mnt/lscratch/users/vgalata/tmp/imp3_dbs/filtering/EiseniaAndrei.fa.amb
/mnt/lscratch/users/vgalata/tmp/imp3_dbs/filtering/EiseniaAndrei.fa.sa
/mnt/lscratch/users/vgalata/tmp/imp3_dbs/filtering/EiseniaAndrei.fa
Edited by Valentina Galata