10/06/2020 09:56:18 AM - kneaddata.knead_data - INFO: Running kneaddata v0.7.10
10/06/2020 09:56:18 AM - kneaddata.knead_data - INFO: Output files will be written to: /exports/mm-run/bacteriologie/quinten/kneaddata_test/nursing_home_test
10/06/2020 09:56:18 AM - kneaddata.knead_data - DEBUG: Running with the following arguments: 
verbose = True
input = /exports/mm-run/bacteriologie/CMAT/20190002_Nursinghome/20200323_NH_metagenomics/raw_fastq/H75MHDSXY_103997-001-007_TTGATCCG-GTGAGCTT_L001_R1.fastq.gz /exports/mm-run/bacteriologie/CMAT/20190002_Nursinghome/20200323_NH_metagenomics/raw_fastq/H75MHDSXY_103997-001-007_TTGATCCG-GTGAGCTT_L001_R3.fastq.gz
output_dir = /exports/mm-run/bacteriologie/quinten/kneaddata_test/nursing_home_test
reference_db = /exports/mm-run/bacteriologie/quinten/Databases/kneaddata_dbs/hg37dec_v0.1
bypass_trim = False
output_prefix = H75MHDSXY_103997-001-007_TTGATCCG-GTGAGCTT_L001_R1_kneaddata
threads = 16
processes = 1
trimmomatic_quality_scores = -phred33
bmtagger = False
bypass_trf = False
fastqc_start = False
fastqc_end = False
store_temp_output = False
remove_intermediate_output = False
cat_final_output = False
log_level = DEBUG
log = /exports/mm-run/bacteriologie/quinten/kneaddata_test/nursing_home_test/H75MHDSXY_103997-001-007_TTGATCCG-GTGAGCTT_L001_R1_kneaddata.log
trimmomatic_path = /exports/mm-run/bacteriologie/quinten/tools/miniconda3/envs/kneaddata/bin/trimmomatic-0.33.jar
max_memory = 500m
trimmomatic_options = None
sequencer_source = NexteraPE
bowtie2_path = /exports/mm-run/bacteriologie/quinten/tools/miniconda3/envs/kneaddata/bin/bowtie2
bowtie2_options = --very-sensitive --phred33
no_discordant = False
reorder = False
serial = False
bmtagger_path = None
trf_path = /exports/mm-run/bacteriologie/quinten/tools/miniconda3/envs/kneaddata/bin/trf
match = 2
mismatch = 7
delta = 7
pm = 80
pi = 10
minscore = 50
maxperiod = 500
fastqc_path = None
remove_temp_output = True

10/06/2020 09:56:18 AM - kneaddata.utilities - INFO: Decompressing gzipped file ...
10/06/2020 09:56:29 AM - kneaddata.utilities - INFO: Decompressed file created: /exports/mm-run/bacteriologie/quinten/kneaddata_test/nursing_home_test/decompressed_u6j0g2b0_H75MHDSXY_103997-001-007_TTGATCCG-GTGAGCTT_L001_R1.fastq
10/06/2020 09:56:29 AM - kneaddata.utilities - INFO: Decompressing gzipped file ...
10/06/2020 09:56:40 AM - kneaddata.utilities - INFO: Decompressed file created: /exports/mm-run/bacteriologie/quinten/kneaddata_test/nursing_home_test/decompressed_jiz3p8dv_H75MHDSXY_103997-001-007_TTGATCCG-GTGAGCTT_L001_R3.fastq
10/06/2020 09:56:40 AM - kneaddata.utilities - INFO: Reformatting file sequence identifiers ...
10/06/2020 09:56:50 AM - kneaddata.utilities - INFO: Reordering read identifiers ...
10/06/2020 09:57:28 AM - kneaddata.utilities - INFO: READ COUNT: raw pair1 : Initial number of reads ( /exports/mm-run/bacteriologie/quinten/kneaddata_test/nursing_home_test/reordered_9m0u9t3w_decompressed_jiz3p8dv_H75MHDSXY_103997-001-007_TTGATCCG-GTGAGCTT_L001_R3 ): 2540009.0
10/06/2020 09:57:35 AM - kneaddata.utilities - INFO: READ COUNT: raw pair2 : Initial number of reads ( /exports/mm-run/bacteriologie/quinten/kneaddata_test/nursing_home_test/reordered_yg7pad5f_reformatted_identifiersatibd3_z_decompressed_u6j0g2b0_H75MHDSXY_103997-001-007_TTGATCCG-GTGAGCTT_L001_R1 ): 2540009.0
10/06/2020 09:57:35 AM - kneaddata.utilities - DEBUG: Checking input file to Trimmomatic : /exports/mm-run/bacteriologie/quinten/kneaddata_test/nursing_home_test/reordered_yg7pad5f_reformatted_identifiersatibd3_z_decompressed_u6j0g2b0_H75MHDSXY_103997-001-007_TTGATCCG-GTGAGCTT_L001_R1
10/06/2020 09:57:35 AM - kneaddata.utilities - DEBUG: Checking input file to Trimmomatic : /exports/mm-run/bacteriologie/quinten/kneaddata_test/nursing_home_test/reordered_9m0u9t3w_decompressed_jiz3p8dv_H75MHDSXY_103997-001-007_TTGATCCG-GTGAGCTT_L001_R3
10/06/2020 09:57:35 AM - kneaddata.utilities - INFO: Running Trimmomatic ... 
10/06/2020 09:57:35 AM - kneaddata.utilities - INFO: Execute command: java -Xmx500m -jar /exports/mm-run/bacteriologie/quinten/tools/miniconda3/envs/kneaddata/bin/trimmomatic-0.33.jar PE -threads 16 -phred33 /exports/mm-run/bacteriologie/quinten/kneaddata_test/nursing_home_test/reordered_yg7pad5f_reformatted_identifiersatibd3_z_decompressed_u6j0g2b0_H75MHDSXY_103997-001-007_TTGATCCG-GTGAGCTT_L001_R1 /exports/mm-run/bacteriologie/quinten/kneaddata_test/nursing_home_test/reordered_9m0u9t3w_decompressed_jiz3p8dv_H75MHDSXY_103997-001-007_TTGATCCG-GTGAGCTT_L001_R3 /exports/mm-run/bacteriologie/quinten/kneaddata_test/nursing_home_test/H75MHDSXY_103997-001-007_TTGATCCG-GTGAGCTT_L001_R1_kneaddata.trimmed.1.fastq /exports/mm-run/bacteriologie/quinten/kneaddata_test/nursing_home_test/H75MHDSXY_103997-001-007_TTGATCCG-GTGAGCTT_L001_R1_kneaddata.trimmed.single.1.fastq /exports/mm-run/bacteriologie/quinten/kneaddata_test/nursing_home_test/H75MHDSXY_103997-001-007_TTGATCCG-GTGAGCTT_L001_R1_kneaddata.trimmed.2.fastq /exports/mm-run/bacteriologie/quinten/kneaddata_test/nursing_home_test/H75MHDSXY_103997-001-007_TTGATCCG-GTGAGCTT_L001_R1_kneaddata.trimmed.single.2.fastq ILLUMINACLIP:/exports/mm-run/bacteriologie/quinten/tools/miniconda3/envs/kneaddata/lib/python3.8/site-packages/kneaddata/adapters/NexteraPE-PE.fa:2:30:10:8:TRUE SLIDINGWINDOW:4:20 MINLEN:75
"10/06/2020 09:57:49 AM - kneaddata.utilities - DEBUG: b""TrimmomaticPE: Started with arguments: -threads 16 -phred33 /exports/mm-run/bacteriologie/quinten/kneaddata_test/nursing_home_test/reordered_yg7pad5f_reformatted_identifiersatibd3_z_decompressed_u6j0g2b0_H75MHDSXY_103997-001-007_TTGATCCG-GTGAGCTT_L001_R1 /exports/mm-run/bacteriologie/quinten/kneaddata_test/nursing_home_test/reordered_9m0u9t3w_decompressed_jiz3p8dv_H75MHDSXY_103997-001-007_TTGATCCG-GTGAGCTT_L001_R3 /exports/mm-run/bacteriologie/quinten/kneaddata_test/nursing_home_test/H75MHDSXY_103997-001-007_TTGATCCG-GTGAGCTT_L001_R1_kneaddata.trimmed.1.fastq /exports/mm-run/bacteriologie/quinten/kneaddata_test/nursing_home_test/H75MHDSXY_103997-001-007_TTGATCCG-GTGAGCTT_L001_R1_kneaddata.trimmed.single.1.fastq /exports/mm-run/bacteriologie/quinten/kneaddata_test/nursing_home_test/H75MHDSXY_103997-001-007_TTGATCCG-GTGAGCTT_L001_R1_kneaddata.trimmed.2.fastq /exports/mm-run/bacteriologie/quinten/kneaddata_test/nursing_home_test/H75MHDSXY_103997-001-007_TTGATCCG-GTGAGCTT_L001_R1_kneaddata.trimmed.single.2.fastq ILLUMINACLIP:/exports/mm-run/bacteriologie/quinten/tools/miniconda3/envs/kneaddata/lib/python3.8/site-packages/kneaddata/adapters/NexteraPE-PE.fa:2:30:10:8:TRUE SLIDINGWINDOW:4:20 MINLEN:75\nUsing PrefixPair: 'AGATGTGTATAAGAGACAG' and 'AGATGTGTATAAGAGACAG'\nUsing Long Clipping Sequence: 'GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG'\nUsing Long Clipping Sequence: 'TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG'\nUsing Long Clipping Sequence: 'CTGTCTCTTATACACATCTCCGAGCCCACGAGAC'\nUsing Long Clipping Sequence: 'CTGTCTCTTATACACATCTGACGCTGCCGACGA'\nILLUMINACLIP: Using 1 prefix pairs, 4 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences\nInput Read Pairs: 2540009 Both Surviving: 2162954 (85.16%) Forward Only Surviving: 213649 (8.41%) Reverse Only Surviving: 62405 (2.46%) Dropped: 101001 (3.98%)\nTrimmomaticPE: Completed successfully\n"""
10/06/2020 09:57:49 AM - kneaddata.utilities - DEBUG: Checking output file from Trimmomatic : /exports/mm-run/bacteriologie/quinten/kneaddata_test/nursing_home_test/H75MHDSXY_103997-001-007_TTGATCCG-GTGAGCTT_L001_R1_kneaddata.trimmed.1.fastq
10/06/2020 09:57:49 AM - kneaddata.utilities - DEBUG: Checking output file from Trimmomatic : /exports/mm-run/bacteriologie/quinten/kneaddata_test/nursing_home_test/H75MHDSXY_103997-001-007_TTGATCCG-GTGAGCTT_L001_R1_kneaddata.trimmed.single.1.fastq
10/06/2020 09:57:49 AM - kneaddata.utilities - DEBUG: Checking output file from Trimmomatic : /exports/mm-run/bacteriologie/quinten/kneaddata_test/nursing_home_test/H75MHDSXY_103997-001-007_TTGATCCG-GTGAGCTT_L001_R1_kneaddata.trimmed.2.fastq
10/06/2020 09:57:49 AM - kneaddata.utilities - DEBUG: Checking output file from Trimmomatic : /exports/mm-run/bacteriologie/quinten/kneaddata_test/nursing_home_test/H75MHDSXY_103997-001-007_TTGATCCG-GTGAGCTT_L001_R1_kneaddata.trimmed.single.2.fastq
10/06/2020 09:57:55 AM - kneaddata.utilities - INFO: READ COUNT: trimmed pair1 : Total reads after trimming ( /exports/mm-run/bacteriologie/quinten/kneaddata_test/nursing_home_test/H75MHDSXY_103997-001-007_TTGATCCG-GTGAGCTT_L001_R1_kneaddata.trimmed.1.fastq ): 2162954.0
10/06/2020 09:57:56 AM - kneaddata.utilities - INFO: READ COUNT: trimmed pair2 : Total reads after trimming ( /exports/mm-run/bacteriologie/quinten/kneaddata_test/nursing_home_test/H75MHDSXY_103997-001-007_TTGATCCG-GTGAGCTT_L001_R1_kneaddata.trimmed.2.fastq ): 2162954.0
10/06/2020 09:57:57 AM - kneaddata.utilities - INFO: READ COUNT: trimmed orphan1 : Total reads after trimming ( /exports/mm-run/bacteriologie/quinten/kneaddata_test/nursing_home_test/H75MHDSXY_103997-001-007_TTGATCCG-GTGAGCTT_L001_R1_kneaddata.trimmed.single.1.fastq ): 213649.0
10/06/2020 09:57:57 AM - kneaddata.utilities - INFO: READ COUNT: trimmed orphan2 : Total reads after trimming ( /exports/mm-run/bacteriologie/quinten/kneaddata_test/nursing_home_test/H75MHDSXY_103997-001-007_TTGATCCG-GTGAGCTT_L001_R1_kneaddata.trimmed.single.2.fastq ): 62405.0
10/06/2020 09:58:45 AM - kneaddata.utilities - DEBUG: Checking input file to trf : /exports/mm-run/bacteriologie/quinten/kneaddata_test/nursing_home_test/H75MHDSXY_103997-001-007_TTGATCCG-GTGAGCTT_L001_R1_kneaddata.trimmed.1.fasta
10/06/2020 09:58:45 AM - kneaddata.utilities - INFO: Running trf ... 
10/06/2020 09:58:45 AM - kneaddata.utilities - INFO: Execute command: /exports/mm-run/bacteriologie/quinten/tools/miniconda3/envs/kneaddata/bin/trf /exports/mm-run/bacteriologie/quinten/kneaddata_test/nursing_home_test/H75MHDSXY_103997-001-007_TTGATCCG-GTGAGCTT_L001_R1_kneaddata.trimmed.1.fasta 2 7 7 80 10 50 500 -h -ngs
10/06/2020 10:04:48 AM - kneaddata.utilities - DEBUG: 0
10/06/2020 10:04:48 AM - kneaddata.utilities - DEBUG: Checking output file from trf : /exports/mm-run/bacteriologie/quinten/kneaddata_test/nursing_home_test/H75MHDSXY_103997-001-007_TTGATCCG-GTGAGCTT_L001_R1_kneaddata.trimmed.1.fasta.trf.parameters.2.7.7.80.10.50.500.dat
10/06/2020 10:04:48 AM - kneaddata.utilities - DEBUG: Checking input file to trf : /exports/mm-run/bacteriologie/quinten/kneaddata_test/nursing_home_test/H75MHDSXY_103997-001-007_TTGATCCG-GTGAGCTT_L001_R1_kneaddata.trimmed.2.fasta
10/06/2020 10:04:48 AM - kneaddata.utilities - INFO: Running trf ... 
10/06/2020 10:04:48 AM - kneaddata.utilities - INFO: Execute command: /exports/mm-run/bacteriologie/quinten/tools/miniconda3/envs/kneaddata/bin/trf /exports/mm-run/bacteriologie/quinten/kneaddata_test/nursing_home_test/H75MHDSXY_103997-001-007_TTGATCCG-GTGAGCTT_L001_R1_kneaddata.trimmed.2.fasta 2 7 7 80 10 50 500 -h -ngs
10/06/2020 10:11:01 AM - kneaddata.utilities - DEBUG: 0
10/06/2020 10:11:01 AM - kneaddata.utilities - DEBUG: Checking output file from trf : /exports/mm-run/bacteriologie/quinten/kneaddata_test/nursing_home_test/H75MHDSXY_103997-001-007_TTGATCCG-GTGAGCTT_L001_R1_kneaddata.trimmed.2.fasta.trf.parameters.2.7.7.80.10.50.500.dat
10/06/2020 10:11:05 AM - kneaddata.run - INFO: Total number of sequences with repeats removed from file ( /exports/mm-run/bacteriologie/quinten/kneaddata_test/nursing_home_test/H75MHDSXY_103997-001-007_TTGATCCG-GTGAGCTT_L001_R1_kneaddata.trimmed.1.fastq ): 10400
10/06/2020 10:11:10 AM - kneaddata.run - INFO: Total number of sequences with repeats removed from file ( /exports/mm-run/bacteriologie/quinten/kneaddata_test/nursing_home_test/H75MHDSXY_103997-001-007_TTGATCCG-GTGAGCTT_L001_R1_kneaddata.trimmed.2.fastq ): 12554
10/06/2020 10:11:15 AM - kneaddata.utilities - DEBUG: Checking input file to trf : /exports/mm-run/bacteriologie/quinten/kneaddata_test/nursing_home_test/H75MHDSXY_103997-001-007_TTGATCCG-GTGAGCTT_L001_R1_kneaddata.trimmed.single.1.fasta
10/06/2020 10:11:15 AM - kneaddata.utilities - INFO: Running trf ... 
10/06/2020 10:11:15 AM - kneaddata.utilities - INFO: Execute command: /exports/mm-run/bacteriologie/quinten/tools/miniconda3/envs/kneaddata/bin/trf /exports/mm-run/bacteriologie/quinten/kneaddata_test/nursing_home_test/H75MHDSXY_103997-001-007_TTGATCCG-GTGAGCTT_L001_R1_kneaddata.trimmed.single.1.fasta 2 7 7 80 10 50 500 -h -ngs
10/06/2020 10:11:49 AM - kneaddata.utilities - DEBUG: 0
10/06/2020 10:11:49 AM - kneaddata.utilities - DEBUG: Checking output file from trf : /exports/mm-run/bacteriologie/quinten/kneaddata_test/nursing_home_test/H75MHDSXY_103997-001-007_TTGATCCG-GTGAGCTT_L001_R1_kneaddata.trimmed.single.1.fasta.trf.parameters.2.7.7.80.10.50.500.dat
10/06/2020 10:11:49 AM - kneaddata.run - INFO: Total number of sequences with repeats removed from file ( /exports/mm-run/bacteriologie/quinten/kneaddata_test/nursing_home_test/H75MHDSXY_103997-001-007_TTGATCCG-GTGAGCTT_L001_R1_kneaddata.trimmed.single.1.fastq ): 1056
10/06/2020 10:11:50 AM - kneaddata.utilities - DEBUG: Checking input file to trf : /exports/mm-run/bacteriologie/quinten/kneaddata_test/nursing_home_test/H75MHDSXY_103997-001-007_TTGATCCG-GTGAGCTT_L001_R1_kneaddata.trimmed.single.2.fasta
10/06/2020 10:11:50 AM - kneaddata.utilities - INFO: Running trf ... 
10/06/2020 10:11:50 AM - kneaddata.utilities - INFO: Execute command: /exports/mm-run/bacteriologie/quinten/tools/miniconda3/envs/kneaddata/bin/trf /exports/mm-run/bacteriologie/quinten/kneaddata_test/nursing_home_test/H75MHDSXY_103997-001-007_TTGATCCG-GTGAGCTT_L001_R1_kneaddata.trimmed.single.2.fasta 2 7 7 80 10 50 500 -h -ngs
10/06/2020 10:12:01 AM - kneaddata.utilities - DEBUG: 0
10/06/2020 10:12:01 AM - kneaddata.utilities - DEBUG: Checking output file from trf : /exports/mm-run/bacteriologie/quinten/kneaddata_test/nursing_home_test/H75MHDSXY_103997-001-007_TTGATCCG-GTGAGCTT_L001_R1_kneaddata.trimmed.single.2.fasta.trf.parameters.2.7.7.80.10.50.500.dat
10/06/2020 10:12:01 AM - kneaddata.run - INFO: Total number of sequences with repeats removed from file ( /exports/mm-run/bacteriologie/quinten/kneaddata_test/nursing_home_test/H75MHDSXY_103997-001-007_TTGATCCG-GTGAGCTT_L001_R1_kneaddata.trimmed.single.2.fastq ): 433
10/06/2020 10:12:01 AM - kneaddata.run - INFO: Decontaminating ...
10/06/2020 10:12:01 AM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /exports/mm-run/bacteriologie/quinten/kneaddata_test/nursing_home_test/H75MHDSXY_103997-001-007_TTGATCCG-GTGAGCTT_L001_R1_kneaddata.repeats.removed.1.fastq
10/06/2020 10:12:01 AM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /exports/mm-run/bacteriologie/quinten/kneaddata_test/nursing_home_test/H75MHDSXY_103997-001-007_TTGATCCG-GTGAGCTT_L001_R1_kneaddata.repeats.removed.2.fastq
10/06/2020 10:12:01 AM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /exports/mm-run/bacteriologie/quinten/kneaddata_test/nursing_home_test/H75MHDSXY_103997-001-007_TTGATCCG-GTGAGCTT_L001_R1_kneaddata.repeats.removed.unmatched.1.fastq
10/06/2020 10:12:01 AM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /exports/mm-run/bacteriologie/quinten/kneaddata_test/nursing_home_test/H75MHDSXY_103997-001-007_TTGATCCG-GTGAGCTT_L001_R1_kneaddata.repeats.removed.unmatched.2.fastq
10/06/2020 10:12:01 AM - kneaddata.utilities - INFO: Running bowtie2 ... 
"10/06/2020 10:12:01 AM - kneaddata.utilities - INFO: Execute command: kneaddata_bowtie2_discordant_pairs --bowtie2 /exports/mm-run/bacteriologie/quinten/tools/miniconda3/envs/kneaddata/bin/bowtie2 --threads 16 -x /exports/mm-run/bacteriologie/quinten/Databases/kneaddata_dbs/hg37dec_v0.1 --bowtie2-options ""--very-sensitive --phred33"" -1 /exports/mm-run/bacteriologie/quinten/kneaddata_test/nursing_home_test/H75MHDSXY_103997-001-007_TTGATCCG-GTGAGCTT_L001_R1_kneaddata.repeats.removed.1.fastq -2 /exports/mm-run/bacteriologie/quinten/kneaddata_test/nursing_home_test/H75MHDSXY_103997-001-007_TTGATCCG-GTGAGCTT_L001_R1_kneaddata.repeats.removed.2.fastq --un-pair /exports/mm-run/bacteriologie/quinten/kneaddata_test/nursing_home_test/H75MHDSXY_103997-001-007_TTGATCCG-GTGAGCTT_L001_R1_kneaddata_hg37dec_v0.1_bowtie2_paired_clean_%.fastq --al-pair /exports/mm-run/bacteriologie/quinten/kneaddata_test/nursing_home_test/H75MHDSXY_103997-001-007_TTGATCCG-GTGAGCTT_L001_R1_kneaddata_hg37dec_v0.1_bowtie2_paired_contam_%.fastq -U /exports/mm-run/bacteriologie/quinten/kneaddata_test/nursing_home_test/H75MHDSXY_103997-001-007_TTGATCCG-GTGAGCTT_L001_R1_kneaddata.repeats.removed.unmatched.1.fastq,/exports/mm-run/bacteriologie/quinten/kneaddata_test/nursing_home_test/H75MHDSXY_103997-001-007_TTGATCCG-GTGAGCTT_L001_R1_kneaddata.repeats.removed.unmatched.2.fastq --un-single /exports/mm-run/bacteriologie/quinten/kneaddata_test/nursing_home_test/H75MHDSXY_103997-001-007_TTGATCCG-GTGAGCTT_L001_R1_kneaddata_hg37dec_v0.1_bowtie2_unmatched_%_clean.fastq --al-single /exports/mm-run/bacteriologie/quinten/kneaddata_test/nursing_home_test/H75MHDSXY_103997-001-007_TTGATCCG-GTGAGCTT_L001_R1_kneaddata_hg37dec_v0.1_bowtie2_unmatched_%_contam.fastq -S /dev/null"
"10/06/2020 10:14:03 AM - kneaddata.utilities - DEBUG: b'4577519 reads; of these:\n  4577519 (100.00%) were unpaired; of these:\n    4576737 (99.98%) aligned 0 times\n    557 (0.01%) aligned exactly 1 time\n    225 (0.00%) aligned >1 times\n0.02% overall alignment rate\npair1_aligned : 0\npair2_aligned : 0\npair1_unaligned : 0\npair2_unaligned : 0\norphan1_aligned : 747\norphan2_aligned : 35\norphan1_unaligned : 4351695\norphan2_unaligned : 225042\n'"
10/06/2020 10:14:03 AM - kneaddata.utilities - DEBUG: Checking output file from bowtie2 : /exports/mm-run/bacteriologie/quinten/kneaddata_test/nursing_home_test/H75MHDSXY_103997-001-007_TTGATCCG-GTGAGCTT_L001_R1_kneaddata_hg37dec_v0.1_bowtie2_paired_clean_1.fastq
10/06/2020 10:14:03 AM - kneaddata.utilities - DEBUG: Checking output file from bowtie2 : /exports/mm-run/bacteriologie/quinten/kneaddata_test/nursing_home_test/H75MHDSXY_103997-001-007_TTGATCCG-GTGAGCTT_L001_R1_kneaddata_hg37dec_v0.1_bowtie2_paired_clean_2.fastq
10/06/2020 10:14:03 AM - kneaddata.run - INFO: Total contaminate sequences in file ( /exports/mm-run/bacteriologie/quinten/kneaddata_test/nursing_home_test/H75MHDSXY_103997-001-007_TTGATCCG-GTGAGCTT_L001_R1_kneaddata_hg37dec_v0.1_bowtie2_paired_contam_1.fastq ) : 0.0
10/06/2020 10:14:03 AM - kneaddata.run - INFO: Total contaminate sequences in file ( /exports/mm-run/bacteriologie/quinten/kneaddata_test/nursing_home_test/H75MHDSXY_103997-001-007_TTGATCCG-GTGAGCTT_L001_R1_kneaddata_hg37dec_v0.1_bowtie2_paired_contam_2.fastq ) : 0.0
10/06/2020 10:14:03 AM - kneaddata.run - INFO: Total contaminate sequences in file ( /exports/mm-run/bacteriologie/quinten/kneaddata_test/nursing_home_test/H75MHDSXY_103997-001-007_TTGATCCG-GTGAGCTT_L001_R1_kneaddata_hg37dec_v0.1_bowtie2_unmatched_1_contam.fastq ) : 747.0
10/06/2020 10:14:03 AM - kneaddata.run - INFO: Total contaminate sequences in file ( /exports/mm-run/bacteriologie/quinten/kneaddata_test/nursing_home_test/H75MHDSXY_103997-001-007_TTGATCCG-GTGAGCTT_L001_R1_kneaddata_hg37dec_v0.1_bowtie2_unmatched_2_contam.fastq ) : 35.0
10/06/2020 10:14:03 AM - kneaddata.utilities - INFO: READ COUNT: decontaminated hg37dec_v0.1 pair1 : Total reads after removing those found in reference database ( /exports/mm-run/bacteriologie/quinten/kneaddata_test/nursing_home_test/H75MHDSXY_103997-001-007_TTGATCCG-GTGAGCTT_L001_R1_kneaddata_hg37dec_v0.1_bowtie2_paired_clean_1.fastq ): 0.0
10/06/2020 10:14:03 AM - kneaddata.utilities - INFO: READ COUNT: decontaminated hg37dec_v0.1 pair2 : Total reads after removing those found in reference database ( /exports/mm-run/bacteriologie/quinten/kneaddata_test/nursing_home_test/H75MHDSXY_103997-001-007_TTGATCCG-GTGAGCTT_L001_R1_kneaddata_hg37dec_v0.1_bowtie2_paired_clean_2.fastq ): 0.0
10/06/2020 10:14:03 AM - kneaddata.utilities - INFO: READ COUNT: final pair1 : Total reads after merging results from multiple databases ( /exports/mm-run/bacteriologie/quinten/kneaddata_test/nursing_home_test/H75MHDSXY_103997-001-007_TTGATCCG-GTGAGCTT_L001_R1_kneaddata_paired_1.fastq ): 0.0
10/06/2020 10:14:03 AM - kneaddata.utilities - INFO: READ COUNT: final pair2 : Total reads after merging results from multiple databases ( /exports/mm-run/bacteriologie/quinten/kneaddata_test/nursing_home_test/H75MHDSXY_103997-001-007_TTGATCCG-GTGAGCTT_L001_R1_kneaddata_paired_2.fastq ): 0.0
10/06/2020 10:14:03 AM - kneaddata.utilities - WARNING: Unable to remove file: /exports/mm-run/bacteriologie/quinten/kneaddata_test/nursing_home_test/H75MHDSXY_103997-001-007_TTGATCCG-GTGAGCTT_L001_R1_kneaddata_hg37dec_v0.1_bowtie2_paired_clean_1.fastq
10/06/2020 10:14:03 AM - kneaddata.utilities - WARNING: Unable to remove file: /exports/mm-run/bacteriologie/quinten/kneaddata_test/nursing_home_test/H75MHDSXY_103997-001-007_TTGATCCG-GTGAGCTT_L001_R1_kneaddata_hg37dec_v0.1_bowtie2_paired_clean_2.fastq
10/06/2020 10:14:07 AM - kneaddata.utilities - INFO: READ COUNT: decontaminated hg37dec_v0.1 orphan1 : Total reads after removing those found in reference database ( /exports/mm-run/bacteriologie/quinten/kneaddata_test/nursing_home_test/H75MHDSXY_103997-001-007_TTGATCCG-GTGAGCTT_L001_R1_kneaddata_hg37dec_v0.1_bowtie2_unmatched_1_clean.fastq ): 4351695.0
10/06/2020 10:14:18 AM - kneaddata.utilities - INFO: READ COUNT: final orphan1 : Total reads after merging results from multiple databases ( /exports/mm-run/bacteriologie/quinten/kneaddata_test/nursing_home_test/H75MHDSXY_103997-001-007_TTGATCCG-GTGAGCTT_L001_R1_kneaddata_unmatched_1.fastq ): 4351695.0
10/06/2020 10:14:18 AM - kneaddata.utilities - WARNING: Unable to remove file: /exports/mm-run/bacteriologie/quinten/kneaddata_test/nursing_home_test/H75MHDSXY_103997-001-007_TTGATCCG-GTGAGCTT_L001_R1_kneaddata_hg37dec_v0.1_bowtie2_unmatched_1_clean.fastq
10/06/2020 10:14:19 AM - kneaddata.utilities - INFO: READ COUNT: decontaminated hg37dec_v0.1 orphan2 : Total reads after removing those found in reference database ( /exports/mm-run/bacteriologie/quinten/kneaddata_test/nursing_home_test/H75MHDSXY_103997-001-007_TTGATCCG-GTGAGCTT_L001_R1_kneaddata_hg37dec_v0.1_bowtie2_unmatched_2_clean.fastq ): 225042.0
10/06/2020 10:14:19 AM - kneaddata.utilities - INFO: READ COUNT: final orphan2 : Total reads after merging results from multiple databases ( /exports/mm-run/bacteriologie/quinten/kneaddata_test/nursing_home_test/H75MHDSXY_103997-001-007_TTGATCCG-GTGAGCTT_L001_R1_kneaddata_unmatched_2.fastq ): 225042.0
10/06/2020 10:14:19 AM - kneaddata.utilities - WARNING: Unable to remove file: /exports/mm-run/bacteriologie/quinten/kneaddata_test/nursing_home_test/H75MHDSXY_103997-001-007_TTGATCCG-GTGAGCTT_L001_R1_kneaddata_hg37dec_v0.1_bowtie2_unmatched_2_clean.fastq
10/06/2020 10:14:19 AM - kneaddata.knead_data - INFO: 
Final output files created: 
/exports/mm-run/bacteriologie/quinten/kneaddata_test/nursing_home_test/H75MHDSXY_103997-001-007_TTGATCCG-GTGAGCTT_L001_R1_kneaddata_paired_1.fastq
/exports/mm-run/bacteriologie/quinten/kneaddata_test/nursing_home_test/H75MHDSXY_103997-001-007_TTGATCCG-GTGAGCTT_L001_R1_kneaddata_paired_2.fastq
/exports/mm-run/bacteriologie/quinten/kneaddata_test/nursing_home_test/H75MHDSXY_103997-001-007_TTGATCCG-GTGAGCTT_L001_R1_kneaddata_unmatched_1.fastq
/exports/mm-run/bacteriologie/quinten/kneaddata_test/nursing_home_test/H75MHDSXY_103997-001-007_TTGATCCG-GTGAGCTT_L001_R1_kneaddata_unmatched_2.fastq