# Kneaddata paired output ordering or interleaving **URL:** \ **Category:** KneadData\ **Created:** [March 24, 2021, 3:45pm UTC](https://forum.biobakery.org/t/kneaddata-paired-output-ordering-or-interleaving/1843 "2021-03-24T15:45:25Z")\ **Posts on this page:** 2\ **Page:** 1
**Author:** ![kochja](https://avatars.discourse-cdn.com/v4/letter/k/dfb087/32.png) [@kochja](https://forum.biobakery.org/u/kochja)\ **Post date:** [March 24, 2021, 3:45pm UTC](https://forum.biobakery.org/t/kneaddata-paired-output-ordering-or-interleaving/1843/1 "2021-03-24T15:45:25Z")
I have run kneaddata 0.7.4 on my metagenomics data. I have \*paired\_1.fastq and \*paired\_2.fastq for each sample. If I look at each of these fastq files, the reads do not appear to be in matching order (e.g. forward read 1, forward read 2, etc in file 1 and reverse read 1, reverse read 2, etc in file 2). I will post the head of each file for one sample below. How can I go about pairing these read correctly if this is the case? Can I interleave these two files and what script/program would work? I am trying to take this qc and decontaminated data into a metagenomics assembly pipeline. Thanks! **Head of file 1:** @J00107:235:HFWNCBBXY:1:1101:2859:1173:N:0:NAGGCATG+ATAGAGAG#0/1 GTGTTATTATGATTGATGAGGCTCATGAAAGAACTCTTTACACAGACATTATTTTGGGTCTTTTAAAAAAGGTTGGTCTTTTTCACTGGGAAGTGTCATTTTACGATTTTTTTTCTGTGGCATATATCTGTCTCTTATACACATCTCCGAG + AAFFFJJJJJJJJJJAJJJJJJJJJJJJJJJJJJJJJJJJJJJJF-FJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJAF @J00107:235:HFWNCBBXY:1:1101:4868:1173:N:0:NAGGCATG+ATAGAGAG#0/1 GAAGGTGGTGAGACCTTTGAGGCGTGCTGACCCACAGGTATGGTGAAAGAGATAATAGCAAAACCTTGTATTATCTGGGATAGCTTTCTTCACCTGTCTCTTATACACATCTCCGAGCCCACGAGACTAGGCATGATCTCGTATGCCGTCT + AAFFFJJJJJFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJFJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJAFJJJJJJJJJJFJF @J00107:235:HFWNCBBXY:1:1101:4929:1173:N:0:NAGGCATG+ATAGAGAG#0/1 AACCTAACAAGAGGTACTGTACTAATGGAGCAATCAAAGGAAACTAATGATTGGTACTGCTTTACTCGCTTATGGCCAATGATTTAACTCCACACTATATCTACCAACATTTTTTCAAAAACACACCTTTCAGTTCATGTTAATGCTGTCT **Head of file 2:** @J00107:235:HFWNCBBXY:1:1101:13210:1173:N:0:NAGGCATG+ATAGAGAG#0/2 GATAACTTGGGAGGATCTTAACTATAAGGGTACTTGTGTTAGTAGAATAGTGGGCCTATAAAC + AAAFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @J00107:235:HFWNCBBXY:1:1101:13758:1173:N:0:NAGGCATG+ATAGAGAG#0/2 TCCATACCCTATGAGGTCCTTGTCCCATCCATTTAATCGATTTACACTTCGTTTCAGGGTATTTAAATGAGATTCCTACAAAGTCTTTATTCCTTAATTCTTTAGCTATTGGGCCTACTTCCAATCCCAACAAACCATTTTGCTCTAATTT + AAFFFJJJJJJJJJFJFJJJJJJFJJJAJJJJFJJJJJJJJJJJJJJFFJJFFJJJJJFJFFFFFJJFJJJFJJJJJJJJJJJJJJJJJJFJJJFFFJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJAJJJJ @J00107:235:HFWNCBBXY:1:1101:16315:1173:N:0:NAGGCATG+ATAGAGAG#0/2 GTATAGTACATCATGATAAGGGGAGGGCTGGTATGGTACATAATGATAAGGGGAGGAGTAGTATCTGTCTCTTATACACATCTGACGCTGCCGACGAATAGAGAGGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAA **Here is an abbreviated log output of kneaddata:** 08/08/2020 04:05:04 PM - kneaddata.knead\_data - INFO: Running kneaddata v0.7.4 08/08/2020 04:05:04 PM - kneaddata.knead\_data - INFO: Output files will be written to: /nfs0/IB/Weis\_Lab/kochja/MicrOA/raw\_metagenome/raw\_data/kneaddata\_out2 08/08/2020 04:05:04 PM - kneaddata.knead\_data - DEBUG: Running with the following arguments: verbose = True input = /nfs0/IB/Weis\_Lab/kochja/MicrOA/raw\_metagenome/raw\_data/lane1-s001-indexN706-S502-TAGGCATG-ATAGAGAG-Sample-1\_S1\_L001\_R1\_001.fastq.gz /nfs0/IB/Weis\_Lab/kochja/MicrOA/raw\_metagenome/raw\_data/lane1-s001-indexN706-S502-TAGGCATG-ATAGAGAG-Sample-1\_S1\_L001\_R2\_001.fastq.gz output\_dir = /nfs0/IB/Weis\_Lab/kochja/MicrOA/raw\_metagenome/raw\_data/kneaddata\_out2 reference\_db = /nfs0/IB/Weis\_Lab/kochja/MicrOA/raw\_metagenome/raw\_data/anthopleura\_genome\_db /nfs0/IB/Weis\_Lab/kochja/MicrOA/raw\_metagenome/raw\_data/breviolum\_minutum\_db /nfs0/IB/Weis\_Lab/kochja/MicrOA/raw\_metagenome/raw\_data/SILVA\_128\_LSUParc\_SSUParc\_ribosomal\_RNA /nfs0/IB/Weis\_Lab/kochja/MicrOA/raw\_metagenome/raw\_data/hg37dec\_v0.1 /nfs0/IB/Weis\_Lab/kochja/MicrOA/raw\_metagenome/raw\_data/human\_hg38\_refMrna bypass\_trim = False output\_prefix = lane1-s001-indexN706-S502-TAGGCATG-ATAGAGAG-Sample-1\_S1\_L001\_R1\_001\_kneaddata threads = 5 processes = 1 trimmomatic\_quality\_scores = -phred33 bmtagger = False trf = False fastqc\_start = False fastqc\_end = False store\_temp\_output = False remove\_intermediate\_output = False cat\_final\_output = False log\_level = DEBUG log = /nfs0/IB/Weis\_Lab/kochja/MicrOA/raw\_metagenome/raw\_data/kneaddata\_out2/lane1-s001-indexN706-S502-TAGGCATG-ATAGAGAG-Sample-1\_S1\_L001\_R1\_001\_kneaddata.log trimmomatic\_path = /nfs0/IB/Weis\_Lab/kochja/opt/conda/envs/humann3.1/bin/trimmomatic-0.33.jar max\_memory = 500m trimmomatic\_options = SLIDINGWINDOW:4:25 MINLEN:50 bowtie2\_path = /nfs0/IB/Weis\_Lab/kochja/opt/conda/envs/humann3.1/bin/bowtie2 bowtie2\_options = --very-sensitive --dovetail --phred33 no\_discordant = False reorder = False serial = False bmtagger\_path = None trf\_path = None match = 2 mismatch = 7 delta = 7 pm = 80 pi = 10 minscore = 50 maxperiod = 500 fastqc\_path = None remove\_temp\_output = True ``` 08/08/2020 04:05:04 PM - kneaddata.utilities - INFO: Decompressing gzipped file ... 08/08/2020 04:06:37 PM - kneaddata.utilities - INFO: Decompressed file created: /nfs0/IB/Weis_Lab/kochja/MicrOA/raw_metagenome/raw_data/kneaddata_out2/decompressed_dkmn7uv3_lane1-s001-indexN706-S502-TAGGCATG-ATAGAGAG-Sample-1_S1_L001_R1_001.fastq 08/08/2020 04:06:37 PM - kneaddata.utilities - INFO: Decompressing gzipped file ... 08/08/2020 04:08:14 PM - kneaddata.utilities - INFO: Decompressed file created: /nfs0/IB/Weis_Lab/kochja/MicrOA/raw_metagenome/raw_data/kneaddata_out2/decompressed_9hod5u1j_lane1-s001-indexN706-S502-TAGGCATG-ATAGAGAG-Sample-1_S1_L001_R2_001.fastq 08/08/2020 04:08:16 PM - kneaddata.utilities - INFO: Reformatting file sequence identifiers ... 08/08/2020 04:10:29 PM - kneaddata.utilities - INFO: Reformatting file sequence identifiers ... 08/08/2020 04:15:03 PM - kneaddata.utilities - INFO: READ COUNT: raw pair1 : Initial number of reads ( /nfs0/IB/Weis_Lab/kochja/MicrOA/raw_metagenome/raw_data/kneaddata_out2/reformatted_identifiers28pjg7p9_decompressed_dkmn7uv3_lane1-s001-indexN706-S502-TAGGCATG-ATAGAGAG-Sample-1_S1_L001_R1_001 ): 17659800.0 08/08/2020 04:15:26 PM - kneaddata.utilities - INFO: READ COUNT: raw pair2 : Initial number of reads ( /nfs0/IB/Weis_Lab/kochja/MicrOA/raw_metagenome/raw_data/kneaddata_out2/reformatted_identifiersq2mceagx_decompressed_9hod5u1j_lane1-s001-indexN706-S502-TAGGCATG-ATAGAGAG-Sample-1_S1_L001_R2_001 ): 17659800.0 ``` … 08/08/2020 07:46:28 PM - kneaddata.utilities - INFO: READ COUNT: decontaminated anthopleura\_genome\_db orphan2 : Total reads after removing those found in reference database ( /nfs0/IB/Weis\_Lab/kochja/MicrOA/raw\_metagenome/raw\_data/kneaddata\_out2/lane1-s001-indexN706-S502-TAGGCATG-ATAGAGAG-Sample-1\_S1\_L001\_R1\_001\_kneaddata\_SILVA\_128\_LSUParc\_SSUParc\_ribosomal\_RNA\_bowtie2\_unmatched\_2\_clean.fastq ): 355073.0 08/08/2020 07:46:37 PM - kneaddata.utilities - INFO: READ COUNT: decontaminated breviolum\_minutum\_db orphan2 : Total reads after removing those found in reference database ( /nfs0/IB/Weis\_Lab/kochja/MicrOA/raw\_metagenome/raw\_data/kneaddata\_out2/lane1-s001-indexN706-S502-TAGGCATG-ATAGAGAG-Sample-1\_S1\_L001\_R1\_001\_kneaddata\_anthopleura\_genome\_db\_bowtie2\_unmatched\_2\_clean.fastq ): 801714.0 08/08/2020 07:46:41 PM - kneaddata.utilities - INFO: READ COUNT: decontaminated SILVA\_128\_LSUParc\_SSUParc\_ribosomal\_RNA orphan2 : Total reads after removing those found in reference database ( /nfs0/IB/Weis\_Lab/kochja/MicrOA/raw\_metagenome/raw\_data/kneaddata\_out2/lane1-s001-indexN706-S502-TAGGCATG-ATAGAGAG-Sample-1\_S1\_L001\_R1\_001\_kneaddata\_breviolum\_minutum\_db\_bowtie2\_unmatched\_2\_clean.fastq ): 381086.0 08/08/2020 07:46:45 PM - kneaddata.utilities - INFO: READ COUNT: decontaminated hg37dec\_v0.1 orphan2 : Total reads after removing those found in reference database ( /nfs0/IB/Weis\_Lab/kochja/MicrOA/raw\_metagenome/raw\_data/kneaddata\_out2/lane1-s001-indexN706-S502-TAGGCATG-ATAGAGAG-Sample-1\_S1\_L001\_R1\_001\_kneaddata\_hg37dec\_v0.1\_bowtie2\_unmatched\_2\_clean.fastq ): 367332.0 08/08/2020 07:46:47 PM - kneaddata.utilities - INFO: READ COUNT: decontaminated human\_hg38\_refMrna orphan2 : Total reads after removing those found in reference database ( /nfs0/IB/Weis\_Lab/kochja/MicrOA/raw\_metagenome/raw\_data/kneaddata\_out2/lane1-s001-indexN706-S502-TAGGCATG-ATAGAGAG-Sample-1\_S1\_L001\_R1\_001\_kneaddata\_human\_hg38\_refMrna\_bowtie2\_unmatched\_2\_clean.fastq ): 359875.0 08/08/2020 07:46:57 PM - kneaddata.utilities - INFO: READ COUNT: final orphan2 : Total reads after merging results from multiple databases ( /nfs0/IB/Weis\_Lab/kochja/MicrOA/raw\_metagenome/raw\_data/kneaddata\_out2/lane1-s001-indexN706-S502-TAGGCATG-ATAGAGAG-Sample-1\_S1\_L001\_R1\_001\_kneaddata\_unmatched\_2.fastq ): 115693.0 08/08/2020 07:47:04 PM - kneaddata.knead\_data - INFO: Final output files created: /nfs0/IB/Weis\_Lab/kochja/MicrOA/raw\_metagenome/raw\_data/kneaddata\_out2/lane1-s001-indexN706-S502-TAGGCATG-ATAGAGAG-Sample-1\_S1\_L001\_R1\_001\_kneaddata\_paired\_1.fastq /nfs0/IB/Weis\_Lab/kochja/MicrOA/raw\_metagenome/raw\_data/kneaddata\_out2/lane1-s001-indexN706-S502-TAGGCATG-ATAGAGAG-Sample-1\_S1\_L001\_R1\_001\_kneaddata\_paired\_2.fastq /nfs0/IB/Weis\_Lab/kochja/MicrOA/raw\_metagenome/raw\_data/kneaddata\_out2/lane1-s001-indexN706-S502-TAGGCATG-ATAGAGAG-Sample-1\_S1\_L001\_R1\_001\_kneaddata\_unmatched\_1.fastq /nfs0/IB/Weis\_Lab/kochja/MicrOA/raw\_metagenome/raw\_data/kneaddata\_out2/lane1-s001-indexN706-S502-TAGGCATG-ATAGAGAG-Sample-1\_S1\_L001\_R1\_001\_kneaddata\_unmatched\_2.fastq ---
**Author:** ![timyerg](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/timyerg/32/959_2.png) [@timyerg](https://forum.biobakery.org/u/timyerg)\ **Post date:** [March 24, 2021, 8:59pm UTC](https://forum.biobakery.org/t/kneaddata-paired-output-ordering-or-interleaving/1843/2 "2021-03-24T20:59:49Z")
Hi! I think you should use `--reorder` option while running kneaddata