04/23/2018 11:01:07 AM - kneaddata.knead_data - INFO: Running kneaddata v0.7.0
04/23/2018 11:01:07 AM - kneaddata.knead_data - INFO: Output files will be written to: /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main
04/23/2018 11:01:07 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/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT.log
max_memory = 500m
remove_intermediate_output = True
fastqc_path = None
output_dir = /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/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/HMP2/2018-04-23/MTX/HSM7J4OT_R1.fastq.gz /n/regal/huttenhower_lab/carze/data/hmp2/workflow/deposition/HMP2/2018-04-23/MTX/HSM7J4OT_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 = 8
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 = HSM7J4OT
match = 2

04/23/2018 11:01:07 AM - kneaddata.utilities - INFO: Decompressing gzipped file ...
04/23/2018 11:01:38 AM - kneaddata.utilities - INFO: Decompressed file created: /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/decompressed_Rqoc5j_HSM7J4OT_R1.fastq
04/23/2018 11:01:38 AM - kneaddata.utilities - INFO: Decompressing gzipped file ...
04/23/2018 11:02:09 AM - kneaddata.utilities - INFO: Decompressed file created: /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/decompressed_JqaBCZ_HSM7J4OT_R2.fastq
04/23/2018 11:02:09 AM - kneaddata.utilities - INFO: Reformatting file sequence identifiers ...
04/23/2018 11:03:13 AM - kneaddata.utilities - INFO: Reformatting file sequence identifiers ...
04/23/2018 11:05:23 AM - kneaddata.utilities - INFO: READ COUNT: raw pair1 : Initial number of reads ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/reformatted_identifiers9jQuTA_decompressed_Rqoc5j_HSM7J4OT_R1 ): 21074337
04/23/2018 11:05:42 AM - kneaddata.utilities - INFO: READ COUNT: raw pair2 : Initial number of reads ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/reformatted_identifiersu82q0Z_decompressed_JqaBCZ_HSM7J4OT_R2 ): 21074337
04/23/2018 11:05:42 AM - kneaddata.utilities - DEBUG: Checking input file to Trimmomatic : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/reformatted_identifiers9jQuTA_decompressed_Rqoc5j_HSM7J4OT_R1
04/23/2018 11:05:42 AM - kneaddata.utilities - DEBUG: Checking input file to Trimmomatic : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/reformatted_identifiersu82q0Z_decompressed_JqaBCZ_HSM7J4OT_R2
04/23/2018 11:05:42 AM - kneaddata.utilities - INFO: Running Trimmomatic ... 
04/23/2018 11:05:42 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 8 -phred33 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/reformatted_identifiers9jQuTA_decompressed_Rqoc5j_HSM7J4OT_R1 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/reformatted_identifiersu82q0Z_decompressed_JqaBCZ_HSM7J4OT_R2 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT.trimmed.1.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT.trimmed.single.1.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT.trimmed.2.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT.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
04/23/2018 11:12:56 AM - kneaddata.utilities - DEBUG: TrimmomaticPE: Started with arguments: -threads 8 -phred33 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/reformatted_identifiers9jQuTA_decompressed_Rqoc5j_HSM7J4OT_R1 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/reformatted_identifiersu82q0Z_decompressed_JqaBCZ_HSM7J4OT_R2 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT.trimmed.1.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT.trimmed.single.1.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT.trimmed.2.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT.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: 21074337 Both Surviving: 4562468 (21.65%) Forward Only Surviving: 7884594 (37.41%) Reverse Only Surviving: 1253354 (5.95%) Dropped: 7373921 (34.99%)
TrimmomaticPE: Completed successfully

04/23/2018 11:12:56 AM - kneaddata.utilities - DEBUG: Checking output file from Trimmomatic : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT.trimmed.1.fastq
04/23/2018 11:12:56 AM - kneaddata.utilities - DEBUG: Checking output file from Trimmomatic : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT.trimmed.single.1.fastq
04/23/2018 11:12:56 AM - kneaddata.utilities - DEBUG: Checking output file from Trimmomatic : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT.trimmed.2.fastq
04/23/2018 11:12:56 AM - kneaddata.utilities - DEBUG: Checking output file from Trimmomatic : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT.trimmed.single.2.fastq
04/23/2018 11:13:01 AM - kneaddata.utilities - INFO: READ COUNT: trimmed pair1 : Total reads after trimming ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT.trimmed.1.fastq ): 4562468
04/23/2018 11:13:07 AM - kneaddata.utilities - INFO: READ COUNT: trimmed pair2 : Total reads after trimming ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT.trimmed.2.fastq ): 4562468
04/23/2018 11:13:28 AM - kneaddata.utilities - INFO: READ COUNT: trimmed orphan1 : Total reads after trimming ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT.trimmed.single.1.fastq ): 7884594
04/23/2018 11:13:34 AM - kneaddata.utilities - INFO: READ COUNT: trimmed orphan2 : Total reads after trimming ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT.trimmed.single.2.fastq ): 1253354
04/23/2018 11:13:34 AM - kneaddata.run - INFO: Decontaminating ...
04/23/2018 11:13:39 AM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT.trimmed.1.fastq
04/23/2018 11:13:39 AM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT.trimmed.2.fastq
04/23/2018 11:13:39 AM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT.trimmed.single.1.fastq
04/23/2018 11:13:39 AM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT.trimmed.single.2.fastq
04/23/2018 11:13:39 AM - kneaddata.utilities - INFO: Running bowtie2 ... 
04/23/2018 11:13:39 AM - kneaddata.utilities - INFO: Execute command: kneaddata_bowtie2_discordant_pairs --bowtie2 /n/sw/centos6/bowtie2-2.2.1/bowtie2 --threads 8 -x /n/huttenhower_lab/data/kneaddata_databases/Homo_sapiens --bowtie2-options "--very-sensitive --phred33" -1 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT.trimmed.1.fastq -2 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT.trimmed.2.fastq --un-pair /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT_Homo_sapiens_bowtie2_paired_clean_%.fastq --al-pair /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT_Homo_sapiens_bowtie2_paired_contam_%.fastq -U /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT.trimmed.single.1.fastq,/n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT.trimmed.single.2.fastq --un-single /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT_Homo_sapiens_bowtie2_unmatched_%_clean.fastq --al-single /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT_Homo_sapiens_bowtie2_unmatched_%_contam.fastq -S /dev/null
04/23/2018 12:08:16 PM - kneaddata.utilities - DEBUG: 18262884 reads; of these:
  18262884 (100.00%) were unpaired; of these:
    2017483 (11.05%) aligned 0 times
    514445 (2.82%) aligned exactly 1 time
    15730956 (86.14%) aligned >1 times
88.95% overall alignment rate
pair1_aligned : 3739914
pair2_aligned : 3739914
orphan1_unaligned : 503785
orphan2_unaligned : 597074
orphan2_aligned : 1020522
pair2_unaligned : 458312
pair1_unaligned : 458312
orphan1_aligned : 7745051

04/23/2018 12:08:16 PM - kneaddata.utilities - DEBUG: Checking output file from bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT_Homo_sapiens_bowtie2_paired_clean_1.fastq
04/23/2018 12:08:16 PM - kneaddata.utilities - DEBUG: Checking output file from bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT_Homo_sapiens_bowtie2_paired_clean_2.fastq
04/23/2018 12:08:16 PM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT.trimmed.1.fastq
04/23/2018 12:08:16 PM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT.trimmed.2.fastq
04/23/2018 12:08:16 PM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT.trimmed.single.1.fastq
04/23/2018 12:08:16 PM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT.trimmed.single.2.fastq
04/23/2018 12:08:16 PM - kneaddata.utilities - INFO: Running bowtie2 ... 
04/23/2018 12:08:16 PM - kneaddata.utilities - INFO: Execute command: kneaddata_bowtie2_discordant_pairs --bowtie2 /n/sw/centos6/bowtie2-2.2.1/bowtie2 --threads 8 -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/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT_Homo_sapiens_bowtie2_paired_clean_1.fastq -2 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT_Homo_sapiens_bowtie2_paired_clean_2.fastq --un-pair /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_paired_clean_%.fastq --al-pair /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_paired_contam_%.fastq -U /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT_Homo_sapiens_bowtie2_unmatched_1_clean.fastq,/n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT_Homo_sapiens_bowtie2_unmatched_2_clean.fastq --un-single /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_unmatched_%_clean.fastq --al-single /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_unmatched_%_contam.fastq -S /dev/null
04/23/2018 12:13:50 PM - kneaddata.utilities - DEBUG: 2017483 reads; of these:
  2017483 (100.00%) were unpaired; of these:
    1569075 (77.77%) aligned 0 times
    31437 (1.56%) aligned exactly 1 time
    416971 (20.67%) aligned >1 times
22.23% overall alignment rate
pair1_aligned : 11054
pair2_aligned : 11054
orphan1_unaligned : 379583
orphan2_unaligned : 337346
orphan2_aligned : 280913
pair2_unaligned : 426073
pair1_unaligned : 426073
orphan1_aligned : 145387

04/23/2018 12:13:50 PM - kneaddata.utilities - DEBUG: Checking output file from bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_paired_clean_1.fastq
04/23/2018 12:13:50 PM - kneaddata.utilities - DEBUG: Checking output file from bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_paired_clean_2.fastq
04/23/2018 12:13:50 PM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT.trimmed.1.fastq
04/23/2018 12:13:50 PM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT.trimmed.2.fastq
04/23/2018 12:13:50 PM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT.trimmed.single.1.fastq
04/23/2018 12:13:50 PM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT.trimmed.single.2.fastq
04/23/2018 12:13:50 PM - kneaddata.utilities - INFO: Running bowtie2 ... 
04/23/2018 12:13:50 PM - kneaddata.utilities - INFO: Execute command: kneaddata_bowtie2_discordant_pairs --bowtie2 /n/sw/centos6/bowtie2-2.2.1/bowtie2 --threads 8 -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/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_paired_clean_1.fastq -2 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_paired_clean_2.fastq --un-pair /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT_human_hg38_refMrna_bowtie2_paired_clean_%.fastq --al-pair /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT_human_hg38_refMrna_bowtie2_paired_contam_%.fastq -U /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_unmatched_1_clean.fastq,/n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_unmatched_2_clean.fastq --un-single /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT_human_hg38_refMrna_bowtie2_unmatched_%_clean.fastq --al-single /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT_human_hg38_refMrna_bowtie2_unmatched_%_contam.fastq -S /dev/null
04/23/2018 12:15:34 PM - kneaddata.utilities - DEBUG: 1569075 reads; of these:
  1569075 (100.00%) were unpaired; of these:
    1440733 (91.82%) aligned 0 times
    16107 (1.03%) aligned exactly 1 time
    112235 (7.15%) aligned >1 times
8.18% overall alignment rate
pair1_aligned : 900
pair2_aligned : 900
orphan1_unaligned : 370230
orphan2_unaligned : 221681
orphan2_aligned : 116427
pair2_unaligned : 424411
pair1_unaligned : 424411
orphan1_aligned : 10115

04/23/2018 12:15:34 PM - kneaddata.utilities - DEBUG: Checking output file from bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT_human_hg38_refMrna_bowtie2_paired_clean_1.fastq
04/23/2018 12:15:34 PM - kneaddata.utilities - DEBUG: Checking output file from bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT_human_hg38_refMrna_bowtie2_paired_clean_2.fastq
04/23/2018 12:15:38 PM - kneaddata.run - INFO: Total contaminate sequences in file ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT_Homo_sapiens_bowtie2_paired_contam_1.fastq ) : 3739914
04/23/2018 12:15:44 PM - kneaddata.run - INFO: Total contaminate sequences in file ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT_Homo_sapiens_bowtie2_paired_contam_2.fastq ) : 3739914
04/23/2018 12:15:52 PM - kneaddata.run - INFO: Total contaminate sequences in file ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT_Homo_sapiens_bowtie2_unmatched_1_contam.fastq ) : 7745051
04/23/2018 12:15:53 PM - kneaddata.run - INFO: Total contaminate sequences in file ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT_Homo_sapiens_bowtie2_unmatched_2_contam.fastq ) : 1020522
04/23/2018 12:15:53 PM - kneaddata.run - INFO: Total contaminate sequences in file ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_paired_contam_1.fastq ) : 11054
04/23/2018 12:15:53 PM - kneaddata.run - INFO: Total contaminate sequences in file ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_paired_contam_2.fastq ) : 11054
04/23/2018 12:15:53 PM - kneaddata.run - INFO: Total contaminate sequences in file ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_unmatched_1_contam.fastq ) : 145387
04/23/2018 12:15:53 PM - kneaddata.run - INFO: Total contaminate sequences in file ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_unmatched_2_contam.fastq ) : 280913
04/23/2018 12:15:53 PM - kneaddata.run - INFO: Total contaminate sequences in file ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT_human_hg38_refMrna_bowtie2_paired_contam_1.fastq ) : 900
04/23/2018 12:15:53 PM - kneaddata.run - INFO: Total contaminate sequences in file ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT_human_hg38_refMrna_bowtie2_paired_contam_2.fastq ) : 900
04/23/2018 12:15:53 PM - kneaddata.run - INFO: Total contaminate sequences in file ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT_human_hg38_refMrna_bowtie2_unmatched_1_contam.fastq ) : 10115
04/23/2018 12:15:53 PM - kneaddata.run - INFO: Total contaminate sequences in file ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT_human_hg38_refMrna_bowtie2_unmatched_2_contam.fastq ) : 116427
04/23/2018 12:15:55 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/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT_Homo_sapiens_bowtie2_paired_clean_1.fastq ): 458312
04/23/2018 12:15:56 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/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT_Homo_sapiens_bowtie2_paired_clean_2.fastq ): 458312
04/23/2018 12:15:56 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/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_paired_clean_1.fastq ): 426073
04/23/2018 12:15:56 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/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_paired_clean_2.fastq ): 426073
04/23/2018 12:15:57 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/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT_human_hg38_refMrna_bowtie2_paired_clean_1.fastq ): 424411
04/23/2018 12:15:57 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/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT_human_hg38_refMrna_bowtie2_paired_clean_2.fastq ): 424411
04/23/2018 12:16:04 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/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT_paired_1.fastq ): 424411
04/23/2018 12:16:04 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/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT_paired_2.fastq ): 424411
04/23/2018 12:16:04 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/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT_Homo_sapiens_bowtie2_unmatched_1_clean.fastq ): 503785
04/23/2018 12:16:04 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/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_unmatched_1_clean.fastq ): 379583
04/23/2018 12:16:04 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/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT_human_hg38_refMrna_bowtie2_unmatched_1_clean.fastq ): 370230
04/23/2018 12:16:08 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/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT_unmatched_1.fastq ): 368820
04/23/2018 12:16:08 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/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT_Homo_sapiens_bowtie2_unmatched_2_clean.fastq ): 597074
04/23/2018 12:16:08 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/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_unmatched_2_clean.fastq ): 337346
04/23/2018 12:16:08 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/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT_human_hg38_refMrna_bowtie2_unmatched_2_clean.fastq ): 221681
04/23/2018 12:16:12 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/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT_unmatched_2.fastq ): 206789
04/23/2018 12:16:14 PM - kneaddata.knead_data - INFO: 
Final output file created: 
/n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM7J4OT.fastq