Humann 3.6 --resume

Microbial community profiling HUMAnN
1

Hello!
I am running humann 3.6 on the remote cluster. My previous run was killed due to exceeding the walltime of the job. I relaunched this sample with the same command but added --resume option. Now I can see that next to the old humann_temp directory appeared a new one, and *_metaphlan_bowtie.txt file is created.
As I understood, “–resume” option did not work. Is it right?

Here is a current log:

11/29/2022 01:38:08 PM - humann.humann - INFO: Running humann v3.6

11/29/2022 01:38:08 PM - humann.humann - INFO: Output files will be written to: /work/Biobakery4/Humann/s84

11/29/2022 01:38:08 PM - humann.humann - INFO: Writing temp files to directory: /work/Biobakery4/Humann/s84/s84_humann_temp_iuqbiodr

11/29/2022 01:38:08 PM - humann.utilities - INFO: File ( /work/Biobakery4/s84.fq.gz ) is of format: fastq.gz

11/29/2022 01:38:08 PM - humann.utilities - INFO: Decompressing gzipped file ...

11/29/2022 01:50:21 PM - humann.utilities - DEBUG: Check software, metaphlan, for required version, 3.0

11/29/2022 01:50:22 PM - humann.utilities - INFO: Using metaphlan version 4.0

11/29/2022 01:50:22 PM - humann.utilities - DEBUG: Check software, bowtie2, for required version, 2.2

11/29/2022 01:50:22 PM - humann.utilities - INFO: Using bowtie2 version 2.5

11/29/2022 01:50:22 PM - humann.humann - INFO: Search mode set to uniref90 because a uniref90 translated search database is selected

11/29/2022 01:50:22 PM - humann.utilities - DEBUG: Check software, diamond, for required version, 2.0.15

11/29/2022 01:50:22 PM - humann.utilities - INFO: Using diamond version 2.0.15

11/29/2022 01:50:22 PM - humann.config - INFO:

Run config settings:

DATABASE SETTINGS

nucleotide database folder = /work/Databases/Humann3_6/chocophlan/chocophlan

protein database folder = /work/Databases/Humann3_6/uniref90/uniref

pathways database file 1 = /home/username/miniconda3/envs/biobakery4/lib/python3.7/site-packages/humann/data/pathways/metacyc_reactions_level4ec_only.uniref.bz2

pathways database file 2 = /home/username/miniconda3/envs/biobakery4/lib/python3.7/site-packages/humann/data/pathways/metacyc_pathways_structured_filtered_v24

utility mapping database folder = /work/Databases/Humann3_6/mapping/utility_mapping

RUN MODES

resume = True

verbose = False

bypass prescreen = False

bypass nucleotide index = False

bypass nucleotide search = False

bypass translated search = False

translated search = diamond

threads = 4

SEARCH MODE

search mode = uniref90

nucleotide identity threshold = 0.0

translated identity threshold = 80.0

ALIGNMENT SETTINGS

bowtie2 options = --very-sensitive

diamond options = --top 1 --outfmt 6

evalue threshold = 1.0

prescreen threshold = 0.01

translated subject coverage threshold = 50.0

translated query coverage threshold = 90.0

nucleotide subject coverage threshold = 50.0

nucleotide query coverage threshold = 90.0

PATHWAYS SETTINGS

minpath = on

xipe = off

gap fill = on

INPUT AND OUTPUT FORMATS

input file format = fastq.gz

output file format = tsv

output max decimals = 10

remove stratified output = False

remove column description output = False

log level = DEBUG

11/29/2022 01:50:22 PM - humann.store - DEBUG: Initialize Alignments class instance to minimize memory use

11/29/2022 01:50:22 PM - humann.store - DEBUG: Initialize Reads class instance to minimize memory use

11/29/2022 01:50:41 PM - humann.humann - INFO: Load pathways database part 1: /home/username/miniconda3/envs/biobakery4/lib/python3.7/site-packages/humann/data/pathways/metacyc_reactions_level4ec_only.uniref.bz2

11/29/2022 01:50:41 PM - humann.humann - INFO: Load pathways database part 2: /home/username/miniconda3/envs/biobakery4/lib/python3.7/site-packages/humann/data/pathways/metacyc_pathways_structured_filtered_v24

11/29/2022 01:50:41 PM - humann.search.prescreen - INFO: Running metaphlan ........

11/29/2022 01:50:41 PM - humann.utilities - DEBUG: Using software: /home/username/miniconda3/envs/biobakery4/bin/metaphlan

11/29/2022 01:50:41 PM - humann.utilities - INFO: Execute command: /home/username/miniconda3/envs/biobakery4/bin/metaphlan /work/Biobakery4/Humann/s84/s84_humann_temp_iuqbiodr/tmpbau_wyn3/tmp6f4iup_h --index mpa_vJan21_CHOCOPhlAnSGB_202103 --bowtie2db /work/Databases//MetaPhlan4 -o /work/Biobakery4/Humann/s84/s84_humann_temp_iuqbiodr/s84_metaphlan_bugs_list.tsv --input_type fastq --bowtie2out /work/Biobakery4/Humann/s84/s84_humann_temp_iuqbiodr/s84_metaphlan_bowtie2.txt --nproc 4
2

This topic can be deleted.
–resume option is working and second “temp” folder is created. Initially I thought that second folder means that resume option was not recognized, but since all my samples finished this time in time I suppose that all works as it supposed to.

3

Glad this ended up producing the desired outputs! I’m happy to leave this topic up for other people who might encounter a similar issue in the future.