02/13/2018 02:29:09 PM - kneaddata.knead_data - INFO: Running kneaddata v0.7.0
02/13/2018 02:29:09 PM - kneaddata.knead_data - INFO: Output files will be written to: /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2017-11-17/WGS/kneaddata/main
02/13/2018 02:29:09 PM - kneaddata.knead_data - DEBUG: Running with the following arguments: 
verbose = False
bmtagger_path = None
minscore = 50
bowtie2_path = /n/sw/centos6/bowtie2-2.2.1/bowtie2
maxperiod = 500
no_discordant = False
serial = True
fastqc_start = False
bmtagger = False
cat_final_output = True
log_level = DEBUG
log = /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2017-11-17/WGS/kneaddata/main/MSM9VZP1.log
max_memory = 500m
remove_intermediate_output = True
fastqc_path = None
output_dir = /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2017-11-17/WGS/kneaddata/main
trf_path = None
remove_temp_output = True
reference_db = /n/huttenhower_lab/data/kneaddata_databases/Homo_sapiens
input = /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2017-11-17/WGS/fastq/MSM9VZP1_R1.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2017-11-17/WGS/fastq/MSM9VZP1_R2.fastq
pi = 10
reorder = False
pm = 80
trimmomatic_path = /n/huttenhower_lab/tools/kneaddata/bin_v0.7.0_devel/trimmomatic-0.33.jar
store_temp_output = False
mismatch = 7
threads = 6
delta = 7
bowtie2_options = --very-sensitive --phred33
bypass_trim = False
processes = 1
trimmomatic_quality_scores = -phred33
fastqc_end = False
trf = False
trimmomatic_options = None
output_prefix = MSM9VZP1
match = 2

02/13/2018 02:30:12 PM - kneaddata.utilities - INFO: READ COUNT: raw pair1 : Initial number of reads ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2017-11-17/WGS/fastq/MSM9VZP1_R1.fastq ): 26337572
02/13/2018 02:31:37 PM - kneaddata.utilities - INFO: READ COUNT: raw pair2 : Initial number of reads ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2017-11-17/WGS/fastq/MSM9VZP1_R2.fastq ): 26337572
02/13/2018 02:31:37 PM - kneaddata.utilities - DEBUG: Checking input file to Trimmomatic : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2017-11-17/WGS/fastq/MSM9VZP1_R1.fastq
02/13/2018 02:31:37 PM - kneaddata.utilities - DEBUG: Checking input file to Trimmomatic : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2017-11-17/WGS/fastq/MSM9VZP1_R2.fastq
02/13/2018 02:31:37 PM - kneaddata.utilities - INFO: Running Trimmomatic ... 
02/13/2018 02:31:37 PM - kneaddata.utilities - INFO: Execute command: java -Xmx500m -d64 -jar /n/huttenhower_lab/tools/kneaddata/bin_v0.7.0_devel/trimmomatic-0.33.jar PE -threads 6 -phred33 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2017-11-17/WGS/fastq/MSM9VZP1_R1.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2017-11-17/WGS/fastq/MSM9VZP1_R2.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2017-11-17/WGS/kneaddata/main/MSM9VZP1.trimmed.1.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2017-11-17/WGS/kneaddata/main/MSM9VZP1.trimmed.single.1.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2017-11-17/WGS/kneaddata/main/MSM9VZP1.trimmed.2.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2017-11-17/WGS/kneaddata/main/MSM9VZP1.trimmed.single.2.fastq ILLUMINACLIP:/n/huttenhower_lab/tools/kneaddata/lib_v0.7.0_devel/kneaddata/adapters/NexteraPE-PE.fa:2:30:10:8:TRUE SLIDINGWINDOW:4:20 MINLEN:50
02/13/2018 02:36:23 PM - kneaddata.utilities - DEBUG: TrimmomaticPE: Started with arguments: -threads 6 -phred33 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2017-11-17/WGS/fastq/MSM9VZP1_R1.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2017-11-17/WGS/fastq/MSM9VZP1_R2.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2017-11-17/WGS/kneaddata/main/MSM9VZP1.trimmed.1.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2017-11-17/WGS/kneaddata/main/MSM9VZP1.trimmed.single.1.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2017-11-17/WGS/kneaddata/main/MSM9VZP1.trimmed.2.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2017-11-17/WGS/kneaddata/main/MSM9VZP1.trimmed.single.2.fastq ILLUMINACLIP:/n/huttenhower_lab/tools/kneaddata/lib_v0.7.0_devel/kneaddata/adapters/NexteraPE-PE.fa:2:30:10:8:TRUE SLIDINGWINDOW:4:20 MINLEN:50
Using PrefixPair: 'AGATGTGTATAAGAGACAG' and 'AGATGTGTATAAGAGACAG'
Using Long Clipping Sequence: 'GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG'
Using Long Clipping Sequence: 'TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG'
Using Long Clipping Sequence: 'CTGTCTCTTATACACATCTGACGCTGCCGACGA'
Using Long Clipping Sequence: 'CTGTCTCTTATACACATCTCCGAGCCCACGAGAC'
ILLUMINACLIP: Using 1 prefix pairs, 4 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences
Input Read Pairs: 26337572 Both Surviving: 17529274 (66.56%) Forward Only Surviving: 1956626 (7.43%) Reverse Only Surviving: 1401291 (5.32%) Dropped: 5450381 (20.69%)
TrimmomaticPE: Completed successfully

02/13/2018 02:36:23 PM - kneaddata.utilities - DEBUG: Checking output file from Trimmomatic : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2017-11-17/WGS/kneaddata/main/MSM9VZP1.trimmed.1.fastq
02/13/2018 02:36:23 PM - kneaddata.utilities - DEBUG: Checking output file from Trimmomatic : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2017-11-17/WGS/kneaddata/main/MSM9VZP1.trimmed.single.1.fastq
02/13/2018 02:36:23 PM - kneaddata.utilities - DEBUG: Checking output file from Trimmomatic : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2017-11-17/WGS/kneaddata/main/MSM9VZP1.trimmed.2.fastq
02/13/2018 02:36:23 PM - kneaddata.utilities - DEBUG: Checking output file from Trimmomatic : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2017-11-17/WGS/kneaddata/main/MSM9VZP1.trimmed.single.2.fastq
02/13/2018 02:38:48 PM - kneaddata.utilities - INFO: READ COUNT: trimmed pair1 : Total reads after trimming ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2017-11-17/WGS/kneaddata/main/MSM9VZP1.trimmed.1.fastq ): 17529274
02/13/2018 02:39:29 PM - kneaddata.utilities - INFO: READ COUNT: trimmed pair2 : Total reads after trimming ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2017-11-17/WGS/kneaddata/main/MSM9VZP1.trimmed.2.fastq ): 17529274
02/13/2018 02:39:33 PM - kneaddata.utilities - INFO: READ COUNT: trimmed orphan1 : Total reads after trimming ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2017-11-17/WGS/kneaddata/main/MSM9VZP1.trimmed.single.1.fastq ): 1956626
02/13/2018 02:39:41 PM - kneaddata.utilities - INFO: READ COUNT: trimmed orphan2 : Total reads after trimming ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2017-11-17/WGS/kneaddata/main/MSM9VZP1.trimmed.single.2.fastq ): 1401291
02/13/2018 02:39:41 PM - kneaddata.run - INFO: Decontaminating ...
02/13/2018 02:39:43 PM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2017-11-17/WGS/kneaddata/main/MSM9VZP1.trimmed.1.fastq
02/13/2018 02:39:43 PM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2017-11-17/WGS/kneaddata/main/MSM9VZP1.trimmed.2.fastq
02/13/2018 02:39:43 PM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2017-11-17/WGS/kneaddata/main/MSM9VZP1.trimmed.single.1.fastq
02/13/2018 02:39:43 PM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2017-11-17/WGS/kneaddata/main/MSM9VZP1.trimmed.single.2.fastq
02/13/2018 02:39:43 PM - kneaddata.utilities - INFO: Running bowtie2 ... 
02/13/2018 02:39:43 PM - kneaddata.utilities - INFO: Execute command: kneaddata_bowtie2_discordant_pairs --bowtie2 /n/sw/centos6/bowtie2-2.2.1/bowtie2 --threads 6 -x /n/huttenhower_lab/data/kneaddata_databases/Homo_sapiens --bowtie2-options "--very-sensitive --phred33" -1 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2017-11-17/WGS/kneaddata/main/MSM9VZP1.trimmed.1.fastq -2 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2017-11-17/WGS/kneaddata/main/MSM9VZP1.trimmed.2.fastq --un-pair /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2017-11-17/WGS/kneaddata/main/MSM9VZP1_Homo_sapiens_bowtie2_paired_clean_%.fastq --al-pair /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2017-11-17/WGS/kneaddata/main/MSM9VZP1_Homo_sapiens_bowtie2_paired_contam_%.fastq -U /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2017-11-17/WGS/kneaddata/main/MSM9VZP1.trimmed.single.1.fastq,/n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2017-11-17/WGS/kneaddata/main/MSM9VZP1.trimmed.single.2.fastq --un-single /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2017-11-17/WGS/kneaddata/main/MSM9VZP1_Homo_sapiens_bowtie2_unmatched_%_clean.fastq --al-single /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2017-11-17/WGS/kneaddata/main/MSM9VZP1_Homo_sapiens_bowtie2_unmatched_%_contam.fastq -S /dev/null
02/13/2018 04:39:24 PM - kneaddata.utilities - DEBUG: 38416465 reads; of these:
  38416465 (100.00%) were unpaired; of these:
    23691754 (61.67%) aligned 0 times
    11473520 (29.87%) aligned exactly 1 time
    3251191 (8.46%) aligned >1 times
38.33% overall alignment rate
pair1_aligned : 6674008
pair2_aligned : 6674008
orphan1_unaligned : 1237150
orphan2_unaligned : 882208
orphan2_aligned : 588151
pair2_unaligned : 10786198
pair1_unaligned : 10786198
orphan1_aligned : 788544

02/13/2018 04:39:24 PM - kneaddata.utilities - DEBUG: Checking output file from bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2017-11-17/WGS/kneaddata/main/MSM9VZP1_Homo_sapiens_bowtie2_paired_clean_1.fastq
02/13/2018 04:39:24 PM - kneaddata.utilities - DEBUG: Checking output file from bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2017-11-17/WGS/kneaddata/main/MSM9VZP1_Homo_sapiens_bowtie2_paired_clean_2.fastq
02/13/2018 04:39:31 PM - kneaddata.run - INFO: Total contaminate sequences in file ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2017-11-17/WGS/kneaddata/main/MSM9VZP1_Homo_sapiens_bowtie2_paired_contam_1.fastq ) : 6674008
02/13/2018 04:39:39 PM - kneaddata.run - INFO: Total contaminate sequences in file ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2017-11-17/WGS/kneaddata/main/MSM9VZP1_Homo_sapiens_bowtie2_paired_contam_2.fastq ) : 6674008
02/13/2018 04:39:40 PM - kneaddata.run - INFO: Total contaminate sequences in file ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2017-11-17/WGS/kneaddata/main/MSM9VZP1_Homo_sapiens_bowtie2_unmatched_1_contam.fastq ) : 788544
02/13/2018 04:39:46 PM - kneaddata.run - INFO: Total contaminate sequences in file ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2017-11-17/WGS/kneaddata/main/MSM9VZP1_Homo_sapiens_bowtie2_unmatched_2_contam.fastq ) : 588151
02/13/2018 04:40:05 PM - kneaddata.utilities - INFO: READ COUNT: decontaminated Homo_sapiens pair1 : Total reads after removing those found in reference database ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2017-11-17/WGS/kneaddata/main/MSM9VZP1_Homo_sapiens_bowtie2_paired_clean_1.fastq ): 10786198
02/13/2018 04:40:16 PM - kneaddata.utilities - INFO: READ COUNT: decontaminated Homo_sapiens pair2 : Total reads after removing those found in reference database ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2017-11-17/WGS/kneaddata/main/MSM9VZP1_Homo_sapiens_bowtie2_paired_clean_2.fastq ): 10786198
02/13/2018 04:40:21 PM - kneaddata.utilities - INFO: READ COUNT: final pair1 : Total reads after merging results from multiple databases ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2017-11-17/WGS/kneaddata/main/MSM9VZP1_paired_1.fastq ): 10786198
02/13/2018 04:40:25 PM - kneaddata.utilities - INFO: READ COUNT: final pair2 : Total reads after merging results from multiple databases ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2017-11-17/WGS/kneaddata/main/MSM9VZP1_paired_2.fastq ): 10786198
02/13/2018 04:40:25 PM - kneaddata.utilities - WARNING: Unable to remove file: /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2017-11-17/WGS/kneaddata/main/MSM9VZP1_Homo_sapiens_bowtie2_paired_clean_1.fastq
02/13/2018 04:40:25 PM - kneaddata.utilities - WARNING: Unable to remove file: /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2017-11-17/WGS/kneaddata/main/MSM9VZP1_Homo_sapiens_bowtie2_paired_clean_2.fastq
02/13/2018 04:40:26 PM - kneaddata.utilities - INFO: READ COUNT: decontaminated Homo_sapiens orphan1 : Total reads after removing those found in reference database ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2017-11-17/WGS/kneaddata/main/MSM9VZP1_Homo_sapiens_bowtie2_unmatched_1_clean.fastq ): 1237150
02/13/2018 04:40:26 PM - kneaddata.utilities - INFO: READ COUNT: final orphan1 : Total reads after merging results from multiple databases ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2017-11-17/WGS/kneaddata/main/MSM9VZP1_unmatched_1.fastq ): 1237150
02/13/2018 04:40:26 PM - kneaddata.utilities - WARNING: Unable to remove file: /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2017-11-17/WGS/kneaddata/main/MSM9VZP1_Homo_sapiens_bowtie2_unmatched_1_clean.fastq
02/13/2018 04:40:27 PM - kneaddata.utilities - INFO: READ COUNT: decontaminated Homo_sapiens orphan2 : Total reads after removing those found in reference database ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2017-11-17/WGS/kneaddata/main/MSM9VZP1_Homo_sapiens_bowtie2_unmatched_2_clean.fastq ): 882208
02/13/2018 04:40:27 PM - kneaddata.utilities - INFO: READ COUNT: final orphan2 : Total reads after merging results from multiple databases ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2017-11-17/WGS/kneaddata/main/MSM9VZP1_unmatched_2.fastq ): 882208
02/13/2018 04:40:27 PM - kneaddata.utilities - WARNING: Unable to remove file: /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2017-11-17/WGS/kneaddata/main/MSM9VZP1_Homo_sapiens_bowtie2_unmatched_2_clean.fastq
02/13/2018 04:40:56 PM - kneaddata.knead_data - INFO: 
Final output file created: 
/n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2017-11-17/WGS/kneaddata/main/MSM9VZP1.fastq