03/21/2018 01:14:57 PM - kneaddata.knead_data - INFO: Running kneaddata v0.7.0
03/21/2018 01:14:57 PM - kneaddata.knead_data - INFO: Output files will be written to: /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main
03/21/2018 01:14:57 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/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7.log
max_memory = 500m
remove_intermediate_output = True
fastqc_path = None
output_dir = /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main
trf_path = None
remove_temp_output = True
reference_db = /n/huttenhower_lab/data/kneaddata_databases/Homo_sapiens /n/huttenhower_lab/data/kneaddata_databases/ribosomal_RNA/SILVA_128_LSUParc_SSUParc_ribosomal_RNA /n/huttenhower_lab/data/kneaddata_databases/transcriptome/human_hg38_refMrna
input = /n/regal/huttenhower_lab/carze/data/hmp2/workflow/deposition/HMP2/2018-03-20/MTX/PSMB4MC7_R1.fastq.gz /n/regal/huttenhower_lab/carze/data/hmp2/workflow/deposition/HMP2/2018-03-20/MTX/PSMB4MC7_R2.fastq.gz
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 = ILLUMINACLIP:/n/home07/carze/.local/bin/Trimmomatic-0.36/adapters/TruSeq3-PE-2.fa:2:30:10:8:TRUE SLIDINGWINDOW:4:20 MINLEN:50
output_prefix = PSMB4MC7
match = 2

03/21/2018 01:14:57 PM - kneaddata.utilities - INFO: Decompressing gzipped file ...
03/21/2018 01:15:45 PM - kneaddata.utilities - INFO: Decompressed file created: /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/decompressed_8Ty9ZZ_PSMB4MC7_R1.fastq
03/21/2018 01:15:45 PM - kneaddata.utilities - INFO: Decompressing gzipped file ...
03/21/2018 01:16:43 PM - kneaddata.utilities - INFO: Decompressed file created: /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/decompressed_RJnJSz_PSMB4MC7_R2.fastq
03/21/2018 01:16:43 PM - kneaddata.utilities - INFO: Reformatting file sequence identifiers ...
03/21/2018 01:18:10 PM - kneaddata.utilities - INFO: Reformatting file sequence identifiers ...
03/21/2018 01:19:53 PM - kneaddata.utilities - INFO: READ COUNT: raw pair1 : Initial number of reads ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/reformatted_identifiers8ERMpv_decompressed_8Ty9ZZ_PSMB4MC7_R1 ): 30835772
03/21/2018 01:20:10 PM - kneaddata.utilities - INFO: READ COUNT: raw pair2 : Initial number of reads ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/reformatted_identifierscL12F5_decompressed_RJnJSz_PSMB4MC7_R2 ): 30835772
03/21/2018 01:20:10 PM - kneaddata.utilities - DEBUG: Checking input file to Trimmomatic : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/reformatted_identifiers8ERMpv_decompressed_8Ty9ZZ_PSMB4MC7_R1
03/21/2018 01:20:10 PM - kneaddata.utilities - DEBUG: Checking input file to Trimmomatic : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/reformatted_identifierscL12F5_decompressed_RJnJSz_PSMB4MC7_R2
03/21/2018 01:20:10 PM - kneaddata.utilities - INFO: Running Trimmomatic ... 
03/21/2018 01:20:10 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 4 -phred33 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/reformatted_identifiers8ERMpv_decompressed_8Ty9ZZ_PSMB4MC7_R1 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/reformatted_identifierscL12F5_decompressed_RJnJSz_PSMB4MC7_R2 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7.trimmed.1.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7.trimmed.single.1.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7.trimmed.2.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7.trimmed.single.2.fastq ILLUMINACLIP:/n/home07/carze/.local/bin/Trimmomatic-0.36/adapters/TruSeq3-PE-2.fa:2:30:10:8:TRUE SLIDINGWINDOW:4:20 MINLEN:50
03/21/2018 01:29:57 PM - kneaddata.utilities - DEBUG: TrimmomaticPE: Started with arguments: -threads 4 -phred33 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/reformatted_identifiers8ERMpv_decompressed_8Ty9ZZ_PSMB4MC7_R1 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/reformatted_identifierscL12F5_decompressed_RJnJSz_PSMB4MC7_R2 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7.trimmed.1.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7.trimmed.single.1.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7.trimmed.2.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7.trimmed.single.2.fastq ILLUMINACLIP:/n/home07/carze/.local/bin/Trimmomatic-0.36/adapters/TruSeq3-PE-2.fa:2:30:10:8:TRUE SLIDINGWINDOW:4:20 MINLEN:50
Using PrefixPair: 'TACACTCTTTCCCTACACGACGCTCTTCCGATCT' and 'GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT'
Using Long Clipping Sequence: 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC'
Using Long Clipping Sequence: 'TACACTCTTTCCCTACACGACGCTCTTCCGATCT'
Using Long Clipping Sequence: 'GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT'
Using Long Clipping Sequence: 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA'
ILLUMINACLIP: Using 1 prefix pairs, 4 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences
Input Read Pairs: 30835772 Both Surviving: 21828018 (70.79%) Forward Only Surviving: 5138567 (16.66%) Reverse Only Surviving: 607681 (1.97%) Dropped: 3261506 (10.58%)
TrimmomaticPE: Completed successfully

03/21/2018 01:29:57 PM - kneaddata.utilities - DEBUG: Checking output file from Trimmomatic : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7.trimmed.1.fastq
03/21/2018 01:29:57 PM - kneaddata.utilities - DEBUG: Checking output file from Trimmomatic : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7.trimmed.single.1.fastq
03/21/2018 01:29:57 PM - kneaddata.utilities - DEBUG: Checking output file from Trimmomatic : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7.trimmed.2.fastq
03/21/2018 01:29:57 PM - kneaddata.utilities - DEBUG: Checking output file from Trimmomatic : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7.trimmed.single.2.fastq
03/21/2018 01:30:22 PM - kneaddata.utilities - INFO: READ COUNT: trimmed pair1 : Total reads after trimming ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7.trimmed.1.fastq ): 21828018
03/21/2018 01:30:49 PM - kneaddata.utilities - INFO: READ COUNT: trimmed pair2 : Total reads after trimming ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7.trimmed.2.fastq ): 21828018
03/21/2018 01:31:02 PM - kneaddata.utilities - INFO: READ COUNT: trimmed orphan1 : Total reads after trimming ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7.trimmed.single.1.fastq ): 5138567
03/21/2018 01:31:03 PM - kneaddata.utilities - INFO: READ COUNT: trimmed orphan2 : Total reads after trimming ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7.trimmed.single.2.fastq ): 607681
03/21/2018 01:31:03 PM - kneaddata.run - INFO: Decontaminating ...
03/21/2018 01:31:05 PM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7.trimmed.1.fastq
03/21/2018 01:31:05 PM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7.trimmed.2.fastq
03/21/2018 01:31:05 PM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7.trimmed.single.1.fastq
03/21/2018 01:31:05 PM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7.trimmed.single.2.fastq
03/21/2018 01:31:05 PM - kneaddata.utilities - INFO: Running bowtie2 ... 
03/21/2018 01:31:05 PM - 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/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7.trimmed.1.fastq -2 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7.trimmed.2.fastq --un-pair /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7_Homo_sapiens_bowtie2_paired_clean_%.fastq --al-pair /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7_Homo_sapiens_bowtie2_paired_contam_%.fastq -U /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7.trimmed.single.1.fastq,/n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7.trimmed.single.2.fastq --un-single /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7_Homo_sapiens_bowtie2_unmatched_%_clean.fastq --al-single /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7_Homo_sapiens_bowtie2_unmatched_%_contam.fastq -S /dev/null
03/21/2018 02:08:46 PM - kneaddata.utilities - DEBUG: 49402284 reads; of these:
  49402284 (100.00%) were unpaired; of these:
    48062665 (97.29%) aligned 0 times
    171427 (0.35%) aligned exactly 1 time
    1168192 (2.36%) aligned >1 times
2.71% overall alignment rate
pair1_aligned : 326271
pair2_aligned : 326271
orphan1_unaligned : 4531733
orphan2_unaligned : 589308
orphan2_aligned : 49308
pair2_unaligned : 21470812
pair1_unaligned : 21470812
orphan1_aligned : 637769

03/21/2018 02:08:46 PM - kneaddata.utilities - DEBUG: Checking output file from bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7_Homo_sapiens_bowtie2_paired_clean_1.fastq
03/21/2018 02:08:46 PM - kneaddata.utilities - DEBUG: Checking output file from bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7_Homo_sapiens_bowtie2_paired_clean_2.fastq
03/21/2018 02:08:46 PM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7.trimmed.1.fastq
03/21/2018 02:08:46 PM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7.trimmed.2.fastq
03/21/2018 02:08:46 PM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7.trimmed.single.1.fastq
03/21/2018 02:08:46 PM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7.trimmed.single.2.fastq
03/21/2018 02:08:46 PM - kneaddata.utilities - INFO: Running bowtie2 ... 
03/21/2018 02:08:46 PM - 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/ribosomal_RNA/SILVA_128_LSUParc_SSUParc_ribosomal_RNA --bowtie2-options "--very-sensitive --phred33" -1 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7_Homo_sapiens_bowtie2_paired_clean_1.fastq -2 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7_Homo_sapiens_bowtie2_paired_clean_2.fastq --un-pair /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_paired_clean_%.fastq --al-pair /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_paired_contam_%.fastq -U /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7_Homo_sapiens_bowtie2_unmatched_1_clean.fastq,/n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7_Homo_sapiens_bowtie2_unmatched_2_clean.fastq --un-single /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_unmatched_%_clean.fastq --al-single /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_unmatched_%_contam.fastq -S /dev/null
03/21/2018 02:50:09 PM - kneaddata.utilities - DEBUG: 48062665 reads; of these:
  48062665 (100.00%) were unpaired; of these:
    48028670 (99.93%) aligned 0 times
    1660 (0.00%) aligned exactly 1 time
    32335 (0.07%) aligned >1 times
0.07% overall alignment rate
pair1_aligned : 929
pair2_aligned : 929
orphan1_unaligned : 4538765
orphan2_unaligned : 587395
orphan2_aligned : 20541
pair2_unaligned : 21451255
pair1_unaligned : 21451255
orphan1_aligned : 11596

03/21/2018 02:50:09 PM - kneaddata.utilities - DEBUG: Checking output file from bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_paired_clean_1.fastq
03/21/2018 02:50:09 PM - kneaddata.utilities - DEBUG: Checking output file from bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_paired_clean_2.fastq
03/21/2018 02:50:09 PM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7.trimmed.1.fastq
03/21/2018 02:50:09 PM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7.trimmed.2.fastq
03/21/2018 02:50:09 PM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7.trimmed.single.1.fastq
03/21/2018 02:50:09 PM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7.trimmed.single.2.fastq
03/21/2018 02:50:09 PM - kneaddata.utilities - INFO: Running bowtie2 ... 
03/21/2018 02:50:09 PM - 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/transcriptome/human_hg38_refMrna --bowtie2-options "--very-sensitive --phred33" -1 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_paired_clean_1.fastq -2 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_paired_clean_2.fastq --un-pair /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7_human_hg38_refMrna_bowtie2_paired_clean_%.fastq --al-pair /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7_human_hg38_refMrna_bowtie2_paired_contam_%.fastq -U /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_unmatched_1_clean.fastq,/n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_unmatched_2_clean.fastq --un-single /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7_human_hg38_refMrna_bowtie2_unmatched_%_clean.fastq --al-single /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7_human_hg38_refMrna_bowtie2_unmatched_%_contam.fastq -S /dev/null
03/21/2018 03:11:07 PM - kneaddata.utilities - DEBUG: 48028670 reads; of these:
  48028670 (100.00%) were unpaired; of these:
    48017317 (99.98%) aligned 0 times
    4553 (0.01%) aligned exactly 1 time
    6800 (0.01%) aligned >1 times
0.02% overall alignment rate
pair1_aligned : 1682
pair2_aligned : 1682
orphan1_unaligned : 4535383
orphan2_unaligned : 584068
orphan2_aligned : 3967
pair2_unaligned : 21448933
pair1_unaligned : 21448933
orphan1_aligned : 4022

03/21/2018 03:11:08 PM - kneaddata.utilities - DEBUG: Checking output file from bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7_human_hg38_refMrna_bowtie2_paired_clean_1.fastq
03/21/2018 03:11:08 PM - kneaddata.utilities - DEBUG: Checking output file from bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7_human_hg38_refMrna_bowtie2_paired_clean_2.fastq
03/21/2018 03:11:08 PM - kneaddata.run - INFO: Total contaminate sequences in file ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7_Homo_sapiens_bowtie2_paired_contam_1.fastq ) : 326271
03/21/2018 03:11:09 PM - kneaddata.run - INFO: Total contaminate sequences in file ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7_Homo_sapiens_bowtie2_paired_contam_2.fastq ) : 326271
03/21/2018 03:11:11 PM - kneaddata.run - INFO: Total contaminate sequences in file ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7_Homo_sapiens_bowtie2_unmatched_1_contam.fastq ) : 637769
03/21/2018 03:11:12 PM - kneaddata.run - INFO: Total contaminate sequences in file ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7_Homo_sapiens_bowtie2_unmatched_2_contam.fastq ) : 49308
03/21/2018 03:11:13 PM - kneaddata.run - INFO: Total contaminate sequences in file ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_paired_contam_1.fastq ) : 929
03/21/2018 03:11:13 PM - kneaddata.run - INFO: Total contaminate sequences in file ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_paired_contam_2.fastq ) : 929
03/21/2018 03:11:13 PM - kneaddata.run - INFO: Total contaminate sequences in file ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_unmatched_1_contam.fastq ) : 11596
03/21/2018 03:11:13 PM - kneaddata.run - INFO: Total contaminate sequences in file ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_unmatched_2_contam.fastq ) : 20541
03/21/2018 03:11:13 PM - kneaddata.run - INFO: Total contaminate sequences in file ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7_human_hg38_refMrna_bowtie2_paired_contam_1.fastq ) : 1682
03/21/2018 03:11:13 PM - kneaddata.run - INFO: Total contaminate sequences in file ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7_human_hg38_refMrna_bowtie2_paired_contam_2.fastq ) : 1682
03/21/2018 03:11:13 PM - kneaddata.run - INFO: Total contaminate sequences in file ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7_human_hg38_refMrna_bowtie2_unmatched_1_contam.fastq ) : 4022
03/21/2018 03:11:13 PM - kneaddata.run - INFO: Total contaminate sequences in file ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7_human_hg38_refMrna_bowtie2_unmatched_2_contam.fastq ) : 3967
03/21/2018 03:12:19 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/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7_Homo_sapiens_bowtie2_paired_clean_1.fastq ): 21470812
03/21/2018 03:13:10 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/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7_Homo_sapiens_bowtie2_paired_clean_2.fastq ): 21470812
03/21/2018 03:14:05 PM - kneaddata.utilities - INFO: READ COUNT: decontaminated SILVA_128_LSUParc_SSUParc_ribosomal_RNA pair1 : Total reads after removing those found in reference database ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_paired_clean_1.fastq ): 21451255
03/21/2018 03:15:46 PM - kneaddata.utilities - INFO: READ COUNT: decontaminated SILVA_128_LSUParc_SSUParc_ribosomal_RNA pair2 : Total reads after removing those found in reference database ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_paired_clean_2.fastq ): 21451255
03/21/2018 03:16:53 PM - kneaddata.utilities - INFO: READ COUNT: decontaminated human_hg38_refMrna pair1 : Total reads after removing those found in reference database ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7_human_hg38_refMrna_bowtie2_paired_clean_1.fastq ): 21448933
03/21/2018 03:18:16 PM - kneaddata.utilities - INFO: READ COUNT: decontaminated human_hg38_refMrna pair2 : Total reads after removing those found in reference database ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7_human_hg38_refMrna_bowtie2_paired_clean_2.fastq ): 21448933
03/21/2018 04:04:31 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/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7_paired_1.fastq ): 21448933
03/21/2018 04:06:08 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/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7_paired_2.fastq ): 21448933
03/21/2018 04:07:24 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/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7_Homo_sapiens_bowtie2_unmatched_1_clean.fastq ): 4531733
03/21/2018 04:07:41 PM - kneaddata.utilities - INFO: READ COUNT: decontaminated SILVA_128_LSUParc_SSUParc_ribosomal_RNA orphan1 : Total reads after removing those found in reference database ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_unmatched_1_clean.fastq ): 4538765
03/21/2018 04:08:58 PM - kneaddata.utilities - INFO: READ COUNT: decontaminated human_hg38_refMrna orphan1 : Total reads after removing those found in reference database ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7_human_hg38_refMrna_bowtie2_unmatched_1_clean.fastq ): 4535383
03/21/2018 04:09:41 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/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7_unmatched_1.fastq ): 4519034
03/21/2018 04:10:14 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/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7_Homo_sapiens_bowtie2_unmatched_2_clean.fastq ): 589308
03/21/2018 04:10:16 PM - kneaddata.utilities - INFO: READ COUNT: decontaminated SILVA_128_LSUParc_SSUParc_ribosomal_RNA orphan2 : Total reads after removing those found in reference database ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_unmatched_2_clean.fastq ): 587395
03/21/2018 04:10:24 PM - kneaddata.utilities - INFO: READ COUNT: decontaminated human_hg38_refMrna orphan2 : Total reads after removing those found in reference database ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7_human_hg38_refMrna_bowtie2_unmatched_2_clean.fastq ): 584068
03/21/2018 04:10:37 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/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7_unmatched_2.fastq ): 581249
03/21/2018 04:28:20 PM - kneaddata.knead_data - INFO: 
Final output file created: 
/n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/PSMB4MC7.fastq