03/05/2018 11:00:51 AM - kneaddata.knead_data - INFO: Running kneaddata v0.7.0
03/05/2018 11:00:51 AM - kneaddata.knead_data - INFO: Output files will be written to: /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main
03/05/2018 11:00:51 AM - 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/hmp2/2018-02-14/WGS/kneaddata/main/MSMA26AT.log
max_memory = 500m
remove_intermediate_output = True
fastqc_path = None
output_dir = /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/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/hmp2/2018-02-14/WGS/fastq/MSMA26AT_R1.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/fastq/MSMA26AT_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 = 4
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 = MSMA26AT
match = 2

03/05/2018 11:01:52 AM - kneaddata.utilities - INFO: READ COUNT: raw pair1 : Initial number of reads ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/fastq/MSMA26AT_R1.fastq ): 12171995
03/05/2018 11:02:40 AM - kneaddata.utilities - INFO: READ COUNT: raw pair2 : Initial number of reads ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/fastq/MSMA26AT_R2.fastq ): 12171995
03/05/2018 11:02:40 AM - kneaddata.utilities - DEBUG: Checking input file to Trimmomatic : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/fastq/MSMA26AT_R1.fastq
03/05/2018 11:02:40 AM - kneaddata.utilities - DEBUG: Checking input file to Trimmomatic : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/fastq/MSMA26AT_R2.fastq
03/05/2018 11:02:40 AM - kneaddata.utilities - INFO: Running Trimmomatic ... 
03/05/2018 11:02:40 AM - 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 4 -phred33 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/fastq/MSMA26AT_R1.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/fastq/MSMA26AT_R2.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/MSMA26AT.trimmed.1.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/MSMA26AT.trimmed.single.1.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/MSMA26AT.trimmed.2.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/MSMA26AT.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
03/05/2018 11:05:39 AM - kneaddata.utilities - DEBUG: TrimmomaticPE: Started with arguments: -threads 4 -phred33 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/fastq/MSMA26AT_R1.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/fastq/MSMA26AT_R2.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/MSMA26AT.trimmed.1.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/MSMA26AT.trimmed.single.1.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/MSMA26AT.trimmed.2.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/MSMA26AT.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: 12171995 Both Surviving: 8885371 (73.00%) Forward Only Surviving: 886479 (7.28%) Reverse Only Surviving: 510708 (4.20%) Dropped: 1889437 (15.52%)
TrimmomaticPE: Completed successfully

03/05/2018 11:05:39 AM - kneaddata.utilities - DEBUG: Checking output file from Trimmomatic : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/MSMA26AT.trimmed.1.fastq
03/05/2018 11:05:39 AM - kneaddata.utilities - DEBUG: Checking output file from Trimmomatic : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/MSMA26AT.trimmed.single.1.fastq
03/05/2018 11:05:39 AM - kneaddata.utilities - DEBUG: Checking output file from Trimmomatic : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/MSMA26AT.trimmed.2.fastq
03/05/2018 11:05:39 AM - kneaddata.utilities - DEBUG: Checking output file from Trimmomatic : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/MSMA26AT.trimmed.single.2.fastq
03/05/2018 11:05:43 AM - kneaddata.utilities - INFO: READ COUNT: trimmed pair1 : Total reads after trimming ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/MSMA26AT.trimmed.1.fastq ): 8885371
03/05/2018 11:05:50 AM - kneaddata.utilities - INFO: READ COUNT: trimmed pair2 : Total reads after trimming ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/MSMA26AT.trimmed.2.fastq ): 8885371
03/05/2018 11:05:51 AM - kneaddata.utilities - INFO: READ COUNT: trimmed orphan1 : Total reads after trimming ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/MSMA26AT.trimmed.single.1.fastq ): 886479
03/05/2018 11:05:51 AM - kneaddata.utilities - INFO: READ COUNT: trimmed orphan2 : Total reads after trimming ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/MSMA26AT.trimmed.single.2.fastq ): 510708
03/05/2018 11:05:51 AM - kneaddata.run - INFO: Decontaminating ...
03/05/2018 11:05:53 AM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/MSMA26AT.trimmed.1.fastq
03/05/2018 11:05:53 AM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/MSMA26AT.trimmed.2.fastq
03/05/2018 11:05:53 AM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/MSMA26AT.trimmed.single.1.fastq
03/05/2018 11:05:53 AM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/MSMA26AT.trimmed.single.2.fastq
03/05/2018 11:05:53 AM - kneaddata.utilities - INFO: Running bowtie2 ... 
03/05/2018 11:05:53 AM - kneaddata.utilities - INFO: Execute command: kneaddata_bowtie2_discordant_pairs --bowtie2 /n/sw/centos6/bowtie2-2.2.1/bowtie2 --threads 4 -x /n/huttenhower_lab/data/kneaddata_databases/Homo_sapiens --bowtie2-options "--very-sensitive --phred33" -1 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/MSMA26AT.trimmed.1.fastq -2 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/MSMA26AT.trimmed.2.fastq --un-pair /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/MSMA26AT_Homo_sapiens_bowtie2_paired_clean_%.fastq --al-pair /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/MSMA26AT_Homo_sapiens_bowtie2_paired_contam_%.fastq -U /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/MSMA26AT.trimmed.single.1.fastq,/n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/MSMA26AT.trimmed.single.2.fastq --un-single /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/MSMA26AT_Homo_sapiens_bowtie2_unmatched_%_clean.fastq --al-single /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/MSMA26AT_Homo_sapiens_bowtie2_unmatched_%_contam.fastq -S /dev/null
03/05/2018 11:17:52 AM - kneaddata.utilities - DEBUG: 19167929 reads; of these:
  19167929 (100.00%) were unpaired; of these:
    19155947 (99.94%) aligned 0 times
    8449 (0.04%) aligned exactly 1 time
    3533 (0.02%) aligned >1 times
0.06% overall alignment rate
pair1_aligned : 5491
pair2_aligned : 5491
orphan1_unaligned : 885988
orphan2_unaligned : 510397
orphan2_aligned : 410
pair2_unaligned : 8879781
pair1_unaligned : 8879781
orphan1_aligned : 590

03/05/2018 11:17:52 AM - kneaddata.utilities - DEBUG: Checking output file from bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/MSMA26AT_Homo_sapiens_bowtie2_paired_clean_1.fastq
03/05/2018 11:17:52 AM - kneaddata.utilities - DEBUG: Checking output file from bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/MSMA26AT_Homo_sapiens_bowtie2_paired_clean_2.fastq
03/05/2018 11:17:52 AM - kneaddata.run - INFO: Total contaminate sequences in file ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/MSMA26AT_Homo_sapiens_bowtie2_paired_contam_1.fastq ) : 5491
03/05/2018 11:17:52 AM - kneaddata.run - INFO: Total contaminate sequences in file ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/MSMA26AT_Homo_sapiens_bowtie2_paired_contam_2.fastq ) : 5491
03/05/2018 11:17:52 AM - kneaddata.run - INFO: Total contaminate sequences in file ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/MSMA26AT_Homo_sapiens_bowtie2_unmatched_1_contam.fastq ) : 590
03/05/2018 11:17:52 AM - kneaddata.run - INFO: Total contaminate sequences in file ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/MSMA26AT_Homo_sapiens_bowtie2_unmatched_2_contam.fastq ) : 410
03/05/2018 11:19:49 AM - 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/hmp2/2018-02-14/WGS/kneaddata/main/MSMA26AT_Homo_sapiens_bowtie2_paired_clean_1.fastq ): 8879781
03/05/2018 11:19:53 AM - 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/hmp2/2018-02-14/WGS/kneaddata/main/MSMA26AT_Homo_sapiens_bowtie2_paired_clean_2.fastq ): 8879781
03/05/2018 11:19:57 AM - kneaddata.utilities - INFO: READ COUNT: final pair1 : Total reads after merging results from multiple databases ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/MSMA26AT_paired_1.fastq ): 8879781
03/05/2018 11:20:00 AM - kneaddata.utilities - INFO: READ COUNT: final pair2 : Total reads after merging results from multiple databases ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/MSMA26AT_paired_2.fastq ): 8879781
03/05/2018 11:20:00 AM - kneaddata.utilities - WARNING: Unable to remove file: /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/MSMA26AT_Homo_sapiens_bowtie2_paired_clean_1.fastq
03/05/2018 11:20:00 AM - kneaddata.utilities - WARNING: Unable to remove file: /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/MSMA26AT_Homo_sapiens_bowtie2_paired_clean_2.fastq
03/05/2018 11:20:17 AM - 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/hmp2/2018-02-14/WGS/kneaddata/main/MSMA26AT_Homo_sapiens_bowtie2_unmatched_1_clean.fastq ): 885988
03/05/2018 11:20:17 AM - kneaddata.utilities - INFO: READ COUNT: final orphan1 : Total reads after merging results from multiple databases ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/MSMA26AT_unmatched_1.fastq ): 885988
03/05/2018 11:20:17 AM - kneaddata.utilities - WARNING: Unable to remove file: /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/MSMA26AT_Homo_sapiens_bowtie2_unmatched_1_clean.fastq
03/05/2018 11:20:17 AM - 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/hmp2/2018-02-14/WGS/kneaddata/main/MSMA26AT_Homo_sapiens_bowtie2_unmatched_2_clean.fastq ): 510397
03/05/2018 11:20:17 AM - kneaddata.utilities - INFO: READ COUNT: final orphan2 : Total reads after merging results from multiple databases ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/MSMA26AT_unmatched_2.fastq ): 510397
03/05/2018 11:20:17 AM - kneaddata.utilities - WARNING: Unable to remove file: /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/MSMA26AT_Homo_sapiens_bowtie2_unmatched_2_clean.fastq
03/05/2018 11:21:21 AM - kneaddata.knead_data - INFO: 
Final output file created: 
/n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/MSMA26AT.fastq