Hello, I’m running shotgun samples through kneaddata v0.12.0. However, 4 of those samples failed running kneaddata.
Their fastq files have a larger size (7-15GB) than the rest of the samples (~2GB)
Wondering is there a limit input file size when running kneaddata? tks
Below is the log file of one failed samples:
05/14/2024 09:08:34 PM - kneaddata.knead_data - INFO: Running kneaddata v0.12.0
05/14/2024 09:08:34 PM - kneaddata.knead_data - INFO: Output files will be written to: /OLY1/output/kneaddata
05/14/2024 09:08:34 PM - kneaddata.knead_data - DEBUG: Running with the following arguments:
verbose = False
input1 = ./input/OLY1.R1.fastq.gz
input2 = ./input/OLY1.R2.fastq.gz
unpaired = None
output_dir = /OLY1/output/kneaddata
scratch_dir =
reference_db = /opt/metaphlan4/biobakery_workflows_databases/kneaddata_db_human_genome/hg37dec_v0.1
bypass_trim = False
output_prefix = OLY1
threads = 70
processes = 1
trimmomatic_quality_scores = -phred33
bmtagger = False
bypass_trf = True
run_trf = False
fastqc_start = False
fastqc_end = False
store_temp_output = False
remove_intermediate_output = False
cat_final_output = True
log_level = DEBUG
log = /OLY1/output/kneaddata/OLY1.log
trimmomatic_path = /Trimmomatic-0.39/trimmomatic-0.39.jar
run_trim_repetitive = False
max_memory = 500m
trimmomatic_options = None
sequencer_source = NexteraPE
bowtie2_path = /data/conda/bin/bowtie2
bowtie2_options = --very-sensitive-local --phred33
decontaminate_pairs = strict
reorder = False
serial = False
bmtagger_path = None
trf_path = None
match = 2
mismatch = 7
delta = 7
pm = 80
pi = 10
minscore = 50
maxperiod = 500
fastqc_path = None
remove_temp_output = True
input = /OLY1/input/OLY1.R1.fastq.gz /OLY1/input/OLY1.R2.fastq.gz
discordant = True
05/14/2024 09:08:34 PM - kneaddata.utilities - INFO: Decompressing gzipped file …
05/14/2024 09:11:46 PM - kneaddata.utilities - INFO: Decompressed file created: /OLY1/output/kneaddata/decompressed_3584h9s6_OLY1.R1.fastq
05/14/2024 09:11:46 PM - kneaddata.utilities - INFO: Decompressing gzipped file …
05/14/2024 09:15:52 PM - kneaddata.utilities - INFO: Decompressed file created: /OLY1/output/kneaddata/decompressed_9om1vmdq_OLY1.R2.fastq
05/14/2024 09:15:52 PM - kneaddata.utilities - INFO: Reformatting file sequence identifiers …
05/14/2024 09:22:57 PM - kneaddata.utilities - INFO: Reformatting file sequence identifiers …
05/14/2024 09:29:57 PM - kneaddata.utilities - INFO: Reordering read identifiers …