hello there,
I submitted a batch work for humann:
here is the log file info:
12/08/2023 09:33:31 AM - humann.humann - INFO: Running humann v3.8
12/08/2023 09:33:31 AM - humann.humann - INFO: Output files will be written to: /lustre04/scratch/zhangbin/CodeClub_V12/humann/Metaphlan_Humann_rawreads
12/08/2023 09:33:31 AM - humann.humann - INFO: Writing temp files to directory: /lustre04/scratch/zhangbin/CodeClub_V12/humann/Metaphlan_Humann_rawreads/R85_merge_reads_humann_temp
12/08/2023 09:33:31 AM - humann.utilities - INFO: File ( /lustre04/scratch/zhangbin/CodeClub_V12/metaWrap_clean_reads/merged_reads/R85_merge_reads.fastq ) is of format: fastq
12/08/2023 09:33:31 AM - humann.humann - INFO: Removing spaces from identifiers in input file
12/08/2023 09:41:35 AM - humann.utilities - DEBUG: Check software, metaphlan, for required version, 3.0
12/08/2023 09:42:23 AM - humann.utilities - INFO: Using metaphlan version 4.0
12/08/2023 09:42:23 AM - humann.utilities - DEBUG: Check software, bowtie2, for required version, 2.2
12/08/2023 09:42:23 AM - humann.utilities - INFO: Using bowtie2 version 2.5
12/08/2023 09:42:23 AM - humann.utilities - DEBUG: Check software, diamond, for required version, 2.0.15
12/08/2023 09:42:23 AM - humann.utilities - INFO: Using diamond version 2.0.15
12/08/2023 09:42:23 AM - humann.config - INFO:
Run config settings:
DATABASE SETTINGS
nucleotide database folder = /lustre04/scratch/zhangbin/chocophlan2/chocophlan/chocophlan
protein database folder = /lustre04/scratch/zhangbin/chocophlan2/chocophlan/uniref
pathways database file 1 = /home/zhangbin/Humann/lib/python3.10/site-packages/humann/data/pathways/metacyc_reactions_level4ec_only.uniref.bz2
pathways database file 2 = /home/zhangbin/Humann/lib/python3.10/site-packages/humann/data/pathways/metacyc_pathways_structured_filtered_v24_subreactions
utility mapping database folder = /lustre04/scratch/zhangbin/chocophlan2/chocophlan/utility_mapping
RUN MODES
resume = False
verbose = False
bypass prescreen = False
bypass nucleotide index = False
bypass nucleotide search = False
bypass translated search = False
translated search = diamond
threads = 1
SEARCH MODE
search mode = uniref50
nucleotide identity threshold = 0.0
translated identity threshold = 50.0
ALIGNMENT SETTINGS
bowtie2 options = --very-sensitive
diamond options = --top 1 --sensitive --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
output file format = tsv
output max decimals = 10
remove stratified output = False
remove column description output = False
log level = DEBUG
I received a failed message from the cluster, but I didn’t see any error from the humann log file. the run stopped at diamond:
12/08/2023 04:03:58 PM - humann.utilities - INFO: Execute command: /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/Compiler/gcc9/diamond/2.0.15/bin/diamond blastx --query /lustre04/scratch/zhangbin/CodeClub_V12/humann/Metaphlan_Humann_rawreads/R85_merge_reads_humann_temp/R85_merge_reads_bowtie2_unaligned.fa --evalue 1.0 --threads 1 --top 1 --sensitive --outfmt 6 --db /lustre04/scratch/zhangbin/chocophlan2/chocophlan/uniref/uniref50_201901b_full --out /lustre04/scratch/zhangbin/CodeClub_V12/humann/Metaphlan_Humann_rawreads/R85_merge_reads_humann_temp/tmpfhf_1_rv/diamond_m8_nvmiz83b --tmpdir /lustre04/scratch/zhangbin/CodeClub_V12/humann/Metaphlan_Humann_rawreads/R85_merge_reads_humann_temp/tmpfhf_1_rv
any thoughts?