# No reads in the "Final output files created" **URL:** \ **Category:** KneadData\ **Created:** [April 6, 2022, 8:02pm UTC](https://forum.biobakery.org/t/no-reads-in-the-final-output-files-created/3419 "2022-04-06T20:02:54Z")\ **Posts on this page:** 3\ **Page:** 1
**Author:** ![Rabindra](https://avatars.discourse-cdn.com/v4/letter/r/8e8cbc/32.png) [@Rabindra](https://forum.biobakery.org/u/Rabindra)\ **Post date:** [April 6, 2022, 8:02pm UTC](https://forum.biobakery.org/t/no-reads-in-the-final-output-files-created/3419/1 "2022-04-06T20:02:54Z")
Dear forum members, I am not getting any reads in the final steps of Kneaddata. It works well with the demo data but does not work with my own data. Please see the line count in the output files. I have also pasted the log file at the end. Any suggestion would be highly appreciated. $ wc -l \*fastq 0 s34\_R1\_kneaddata\_hg37dec\_v0.1\_bowtie2\_paired\_contam\_1.fastq 0 s34\_R1\_kneaddata\_hg37dec\_v0.1\_bowtie2\_paired\_contam\_2.fastq 2492 s34\_R1\_kneaddata\_hg37dec\_v0.1\_bowtie2\_unmatched\_1\_contam.fastq 2540 s34\_R1\_kneaddata\_hg37dec\_v0.1\_bowtie2\_unmatched\_2\_contam.fastq 0 s34\_R1\_kneaddata\_paired\_1.fastq 0 s34\_R1\_kneaddata\_paired\_2.fastq 345088 s34\_R1\_kneaddata.repeats.removed.1.fastq 344964 s34\_R1\_kneaddata.repeats.removed.2.fastq 10592 s34\_R1\_kneaddata.repeats.removed.unmatched.1.fastq 7668 s34\_R1\_kneaddata.repeats.removed.unmatched.2.fastq 346168 s34\_R1\_kneaddata.trimmed.1.fastq 346168 s34\_R1\_kneaddata.trimmed.2.fastq 10612 s34\_R1\_kneaddata.trimmed.single.1.fastq 7720 s34\_R1\_kneaddata.trimmed.single.2.fastq 353188 s34\_R1\_kneaddata\_unmatched\_1.fastq 350092 s34\_R1\_kneaddata\_unmatched\_2.fastq 2127292 total log file: 04/04/2022 12:47:54 PM - kneaddata.knead\_data - INFO: Running kneaddata v0.10.0 04/04/2022 12:47:54 PM - kneaddata.knead\_data - INFO: Output files will be written to: /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output 04/04/2022 12:47:54 PM - kneaddata.knead\_data - DEBUG: Running with the following arguments: verbose = False input1 = s34\_R1.fastq input2 = s34\_R2.fastq unpaired = None output\_dir = /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output reference\_db = /N/slate/rmandal/kneaddatabase/hg37dec\_v0.1 bypass\_trim = False output\_prefix = s34\_R1\_kneaddata threads = 1 processes = 1 trimmomatic\_quality\_scores = -phred33 bmtagger = False bypass\_trf = False run\_trf = False fastqc\_start = False fastqc\_end = False store\_temp\_output = False remove\_intermediate\_output = False cat\_final\_output = False log\_level = DEBUG log = /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output/s34\_R1\_kneaddata.log trimmomatic\_path = /N/u/rmandal/Carbonate/.local/bin/trimmomatic-0.33.jar run\_trim\_repetitive = False max\_memory = 500m trimmomatic\_options = None sequencer\_source = NexteraPE bowtie2\_path = /N/u/rmandal/Carbonate/.local/bin/bowtie2 bowtie2\_options = --very-sensitive-local --phred33 decontaminate\_pairs = strict reorder = False serial = False bmtagger\_path = None trf\_path = /N/u/rmandal/Carbonate/.local/bin/trf match = 2 mismatch = 7 delta = 7 pm = 80 pi = 10 minscore = 50 maxperiod = 500 fastqc\_path = None remove\_temp\_output = True input = /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/s34\_R1.fastq /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/s34\_R2.fastq discordant = True 04/04/2022 12:47:54 PM - kneaddata.utilities - INFO: Reformatting file sequence identifiers … 04/04/2022 12:47:55 PM - kneaddata.utilities - INFO: Reformatting file sequence identifiers … 04/04/2022 12:47:55 PM - kneaddata.utilities - INFO: Reordering read identifiers … 04/04/2022 12:47:57 PM - kneaddata.utilities - INFO: READ COUNT: raw pair1 : Initial number of reads ( /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output/reordered\_n1ymom5c\_reformatted\_identifiersqe83rdy8\_s34\_R1 ): 100000.0 04/04/2022 12:47:57 PM - kneaddata.utilities - INFO: READ COUNT: raw pair2 : Initial number of reads ( /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output/reordered\_5qwugmx9\_reformatted\_identifiersfsonvs4e\_s34\_R2 ): 100000.0 04/04/2022 12:47:57 PM - kneaddata.utilities - DEBUG: Checking input file to Trimmomatic : /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output/reordered\_n1ymom5c\_reformatted\_identifiersqe83rdy8\_s34\_R1 04/04/2022 12:47:57 PM - kneaddata.utilities - DEBUG: Checking input file to Trimmomatic : /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output/reordered\_5qwugmx9\_reformatted\_identifiersfsonvs4e\_s34\_R2 04/04/2022 12:47:57 PM - kneaddata.utilities - INFO: Running Trimmomatic … 04/04/2022 12:47:57 PM - kneaddata.utilities - INFO: Execute command: java -Xmx500m -jar /N/u/rmandal/Carbonate/.local/bin/trimmomatic-0.33.jar PE -threads 1 -phred33 /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output/reordered\_n1ymom5c\_reformatted\_identifiersqe83rdy8\_s34\_R1 /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output/reordered\_5qwugmx9\_reformatted\_identifiersfsonvs4e\_s34\_R2 /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output/s34\_R1\_kneaddata.trimmed.1.fastq /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output/s34\_R1\_kneaddata.trimmed.single.1.fastq /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output/s34\_R1\_kneaddata.trimmed.2.fastq /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output/s34\_R1\_kneaddata.trimmed.single.2.fastq MINLEN:60 ILLUMINACLIP:/N/u/rmandal/Carbonate/.local/lib/python3.6/site-packages/kneaddata/adapters/NexteraPE-PE.fa:2:30:10:8:TRUE SLIDINGWINDOW:4:20 MINLEN:75 04/04/2022 12:48:00 PM - kneaddata.utilities - DEBUG: b"TrimmomaticPE: Started with arguments: -threads 1 -phred33 /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output/reordered\_n1ymom5c\_reformatted\_identifiersqe83rdy8\_s34\_R1 /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output/reordered\_5qwugmx9\_reformatted\_identifiersfsonvs4e\_s34\_R2 /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output/s34\_R1\_kneaddata.trimmed.1.fastq /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output/s34\_R1\_kneaddata.trimmed.single.1.fastq /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output/s34\_R1\_kneaddata.trimmed.2.fastq /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output/s34\_R1\_kneaddata.trimmed.single.2.fastq MINLEN:60 ILLUMINACLIP:/N/u/rmandal/Carbonate/.local/lib/python3.6/site-packages/kneaddata/adapters/NexteraPE-PE.fa:2:30:10:8:TRUE SLIDINGWINDOW:4:20 MINLEN:75\nUsing PrefixPair: ‘AGATGTGTATAAGAGACAG’ and ‘AGATGTGTATAAGAGACAG’\nUsing Long Clipping Sequence: ‘GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG’\nUsing Long Clipping Sequence: ‘TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG’\nUsing Long Clipping Sequence: ‘CTGTCTCTTATACACATCTCCGAGCCCACGAGAC’\nUsing Long Clipping Sequence: ‘CTGTCTCTTATACACATCTGACGCTGCCGACGA’\nILLUMINACLIP: Using 1 prefix pairs, 4 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences\nInput Read Pairs: 100000 Both Surviving: 86542 (86.54%) Forward Only Surviving: 2653 (2.65%) Reverse Only Surviving: 1930 (1.93%) Dropped: 8875 (8.88%)\nTrimmomaticPE: Completed successfully\n" 04/04/2022 12:48:00 PM - kneaddata.utilities - DEBUG: Checking output file from Trimmomatic : /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output/s34\_R1\_kneaddata.trimmed.1.fastq 04/04/2022 12:48:00 PM - kneaddata.utilities - DEBUG: Checking output file from Trimmomatic : /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output/s34\_R1\_kneaddata.trimmed.single.1.fastq 04/04/2022 12:48:00 PM - kneaddata.utilities - DEBUG: Checking output file from Trimmomatic : /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output/s34\_R1\_kneaddata.trimmed.2.fastq 04/04/2022 12:48:00 PM - kneaddata.utilities - DEBUG: Checking output file from Trimmomatic : /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output/s34\_R1\_kneaddata.trimmed.single.2.fastq 04/04/2022 12:48:00 PM - kneaddata.utilities - INFO: READ COUNT: trimmed pair1 : Total reads after trimming ( /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output/s34\_R1\_kneaddata.trimmed.1.fastq ): 86542.0 04/04/2022 12:48:00 PM - kneaddata.utilities - INFO: READ COUNT: trimmed pair2 : Total reads after trimming ( /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output/s34\_R1\_kneaddata.trimmed.2.fastq ): 86542.0 04/04/2022 12:48:00 PM - kneaddata.utilities - INFO: READ COUNT: trimmed orphan1 : Total reads after trimming ( /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output/s34\_R1\_kneaddata.trimmed.single.1.fastq ): 2653.0 04/04/2022 12:48:00 PM - kneaddata.utilities - INFO: READ COUNT: trimmed orphan2 : Total reads after trimming ( /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output/s34\_R1\_kneaddata.trimmed.single.2.fastq ): 1930.0 04/04/2022 12:48:02 PM - kneaddata.utilities - DEBUG: Checking input file to trf : /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output/s34\_R1\_kneaddata.trimmed.1.fasta 04/04/2022 12:48:02 PM - kneaddata.utilities - INFO: Running trf … 04/04/2022 12:48:02 PM - kneaddata.utilities - INFO: Execute command: kneaddata\_trf\_parallel --input /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output/s34\_R1\_kneaddata.trimmed.1.fasta --output /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output/s34\_R1\_kneaddata.trimmed.1.fasta.trf.parameters.2.7.7.80.10.50.500.dat --trf-path /N/u/rmandal/Carbonate/.local/bin/trf --trf-options ‘2 7 7 80 10 50 500 -h -ngs’ --nproc 1 04/04/2022 12:48:16 PM - kneaddata.utilities - DEBUG: 0 04/04/2022 12:48:16 PM - kneaddata.utilities - DEBUG: Checking output file from trf : /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output/s34\_R1\_kneaddata.trimmed.1.fasta.trf.parameters.2.7.7.80.10.50.500.dat 04/04/2022 12:48:16 PM - kneaddata.utilities - DEBUG: Checking input file to trf : /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output/s34\_R1\_kneaddata.trimmed.2.fasta 04/04/2022 12:48:16 PM - kneaddata.utilities - INFO: Running trf … 04/04/2022 12:48:16 PM - kneaddata.utilities - INFO: Execute command: kneaddata\_trf\_parallel --input /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output/s34\_R1\_kneaddata.trimmed.2.fasta --output /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output/s34\_R1\_kneaddata.trimmed.2.fasta.trf.parameters.2.7.7.80.10.50.500.dat --trf-path /N/u/rmandal/Carbonate/.local/bin/trf --trf-options ‘2 7 7 80 10 50 500 -h -ngs’ --nproc 1 04/04/2022 12:48:30 PM - kneaddata.utilities - DEBUG: 0 04/04/2022 12:48:30 PM - kneaddata.utilities - DEBUG: Checking output file from trf : /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output/s34\_R1\_kneaddata.trimmed.2.fasta.trf.parameters.2.7.7.80.10.50.500.dat 04/04/2022 12:48:30 PM - kneaddata.run - INFO: Total number of sequences with repeats removed from file ( /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output/s34\_R1\_kneaddata.trimmed.1.fastq ): 270 04/04/2022 12:48:30 PM - kneaddata.run - INFO: Total number of sequences with repeats removed from file ( /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output/s34\_R1\_kneaddata.trimmed.2.fastq ): 301 04/04/2022 12:48:30 PM - kneaddata.utilities - DEBUG: Checking input file to trf : /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output/s34\_R1\_kneaddata.trimmed.single.1.fasta 04/04/2022 12:48:30 PM - kneaddata.utilities - INFO: Running trf … 04/04/2022 12:48:30 PM - kneaddata.utilities - INFO: Execute command: kneaddata\_trf\_parallel --input /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output/s34\_R1\_kneaddata.trimmed.single.1.fasta --output /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output/s34\_R1\_kneaddata.trimmed.single.1.fasta.trf.parameters.2.7.7.80.10.50.500.dat --trf-path /N/u/rmandal/Carbonate/.local/bin/trf --trf-options ‘2 7 7 80 10 50 500 -h -ngs’ --nproc 1 04/04/2022 12:48:32 PM - kneaddata.utilities - DEBUG: 0 04/04/2022 12:48:32 PM - kneaddata.utilities - DEBUG: Checking output file from trf : /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output/s34\_R1\_kneaddata.trimmed.single.1.fasta.trf.parameters.2.7.7.80.10.50.500.dat 04/04/2022 12:48:32 PM - kneaddata.run - INFO: Total number of sequences with repeats removed from file ( /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output/s34\_R1\_kneaddata.trimmed.single.1.fastq ): 5 04/04/2022 12:48:32 PM - kneaddata.utilities - DEBUG: Checking input file to trf : /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output/s34\_R1\_kneaddata.trimmed.single.2.fasta 04/04/2022 12:48:32 PM - kneaddata.utilities - INFO: Running trf … 04/04/2022 12:48:32 PM - kneaddata.utilities - INFO: Execute command: kneaddata\_trf\_parallel --input /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output/s34\_R1\_kneaddata.trimmed.single.2.fasta --output /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output/s34\_R1\_kneaddata.trimmed.single.2.fasta.trf.parameters.2.7.7.80.10.50.500.dat --trf-path /N/u/rmandal/Carbonate/.local/bin/trf --trf-options ‘2 7 7 80 10 50 500 -h -ngs’ --nproc 1 04/04/2022 12:48:33 PM - kneaddata.utilities - DEBUG: 0 04/04/2022 12:48:33 PM - kneaddata.utilities - DEBUG: Checking output file from trf : /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output/s34\_R1\_kneaddata.trimmed.single.2.fasta.trf.parameters.2.7.7.80.10.50.500.dat 04/04/2022 12:48:34 PM - kneaddata.run - INFO: Total number of sequences with repeats removed from file ( /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output/s34\_R1\_kneaddata.trimmed.single.2.fastq ): 13 04/04/2022 12:48:34 PM - kneaddata.run - INFO: Decontaminating … 04/04/2022 12:48:34 PM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output/s34\_R1\_kneaddata.repeats.removed.1.fastq 04/04/2022 12:48:34 PM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output/s34\_R1\_kneaddata.repeats.removed.2.fastq 04/04/2022 12:48:34 PM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output/s34\_R1\_kneaddata.repeats.removed.unmatched.1.fastq 04/04/2022 12:48:34 PM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output/s34\_R1\_kneaddata.repeats.removed.unmatched.2.fastq 04/04/2022 12:48:34 PM - kneaddata.utilities - INFO: Running bowtie2 … 04/04/2022 12:48:34 PM - kneaddata.utilities - INFO: Execute command: kneaddata\_bowtie2\_discordant\_pairs --bowtie2 /N/u/rmandal/Carbonate/.local/bin/bowtie2 --threads 1 -x /N/slate/rmandal/kneaddatabase/hg37dec\_v0.1 --mode strict --bowtie2-options “–very-sensitive-local --phred33” -1 /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output/s34\_R1\_kneaddata.repeats.removed.1.fastq -2 /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output/s34\_R1\_kneaddata.repeats.removed.2.fastq --un-pair /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output/s34\_R1\_kneaddata\_hg37dec\_v0.1\_bowtie2\_paired\_clean\_%.fastq --al-pair /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output/s34\_R1\_kneaddata\_hg37dec\_v0.1\_bowtie2\_paired\_contam\_%.fastq -U /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output/s34\_R1\_kneaddata.repeats.removed.unmatched.1.fastq,/N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output/s34\_R1\_kneaddata.repeats.removed.unmatched.2.fastq --un-single /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output/s34\_R1\_kneaddata\_hg37dec\_v0.1\_bowtie2\_unmatched\_%_clean.fastq --al-single /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output/s34\_R1\_kneaddata\_hg37dec\_v0.1\_bowtie2\_unmatched_%\_contam.fastq -S /dev/null 04/04/2022 12:48:59 PM - kneaddata.utilities - DEBUG: b’177078 reads; of these:\n 177078 (100.00%) were unpaired; of these:\n 175820 (99.29%) aligned 0 times\n 1062 (0.60%) aligned exactly 1 time\n 196 (0.11%) aligned \>1 times\n0.71% overall alignment rate\npair1\_aligned : 0\npair2\_aligned : 0\npair1\_unaligned : 0\npair2\_unaligned : 0\norphan1\_aligned : 623\norphan2\_aligned : 635\norphan1\_unaligned : 88297\norphan2\_unaligned : 87523\n’ 04/04/2022 12:48:59 PM - kneaddata.utilities - DEBUG: Checking output file from bowtie2 : /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output/s34\_R1\_kneaddata\_hg37dec\_v0.1\_bowtie2\_paired\_clean\_1.fastq 04/04/2022 12:48:59 PM - kneaddata.utilities - DEBUG: Checking output file from bowtie2 : /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output/s34\_R1\_kneaddata\_hg37dec\_v0.1\_bowtie2\_paired\_clean\_2.fastq 04/04/2022 12:48:59 PM - kneaddata.run - INFO: Total contaminate sequences in file ( /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output/s34\_R1\_kneaddata\_hg37dec\_v0.1\_bowtie2\_paired\_contam\_1.fastq ) : 0.0 04/04/2022 12:48:59 PM - kneaddata.run - INFO: Total contaminate sequences in file ( /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output/s34\_R1\_kneaddata\_hg37dec\_v0.1\_bowtie2\_paired\_contam\_2.fastq ) : 0.0 04/04/2022 12:48:59 PM - kneaddata.run - INFO: Total contaminate sequences in file ( /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output/s34\_R1\_kneaddata\_hg37dec\_v0.1\_bowtie2\_unmatched\_1\_contam.fastq ) : 623.0 04/04/2022 12:48:59 PM - kneaddata.run - INFO: Total contaminate sequences in file ( /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output/s34\_R1\_kneaddata\_hg37dec\_v0.1\_bowtie2\_unmatched\_2\_contam.fastq ) : 635.0 04/04/2022 12:48:59 PM - kneaddata.utilities - INFO: READ COUNT: decontaminated hg37dec\_v0.1 pair1 : Total reads after removing those found in reference database ( /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output/s34\_R1\_kneaddata\_hg37dec\_v0.1\_bowtie2\_paired\_clean\_1.fastq ): 0.0 04/04/2022 12:48:59 PM - kneaddata.utilities - INFO: READ COUNT: decontaminated hg37dec\_v0.1 pair2 : Total reads after removing those found in reference database ( /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output/s34\_R1\_kneaddata\_hg37dec\_v0.1\_bowtie2\_paired\_clean\_2.fastq ): 0.0 04/04/2022 12:48:59 PM - kneaddata.utilities - INFO: READ COUNT: final pair1 : Total reads after merging results from multiple databases ( /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output/s34\_R1\_kneaddata\_paired\_1.fastq ): 0.0 04/04/2022 12:48:59 PM - kneaddata.utilities - INFO: READ COUNT: final pair2 : Total reads after merging results from multiple databases ( /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output/s34\_R1\_kneaddata\_paired\_2.fastq ): 0.0 04/04/2022 12:48:59 PM - kneaddata.utilities - WARNING: Unable to remove file: /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output/s34\_R1\_kneaddata\_hg37dec\_v0.1\_bowtie2\_paired\_clean\_1.fastq 04/04/2022 12:48:59 PM - kneaddata.utilities - WARNING: Unable to remove file: /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output/s34\_R1\_kneaddata\_hg37dec\_v0.1\_bowtie2\_paired\_clean\_2.fastq 04/04/2022 12:48:59 PM - kneaddata.utilities - INFO: READ COUNT: decontaminated hg37dec\_v0.1 orphan1 : Total reads after removing those found in reference database ( /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output/s34\_R1\_kneaddata\_hg37dec\_v0.1\_bowtie2\_unmatched\_1\_clean.fastq ): 88297.0 04/04/2022 12:48:59 PM - kneaddata.utilities - INFO: READ COUNT: final orphan1 : Total reads after merging results from multiple databases ( /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output/s34\_R1\_kneaddata\_unmatched\_1.fastq ): 88297.0 04/04/2022 12:48:59 PM - kneaddata.utilities - WARNING: Unable to remove file: /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output/s34\_R1\_kneaddata\_hg37dec\_v0.1\_bowtie2\_unmatched\_1\_clean.fastq 04/04/2022 12:48:59 PM - kneaddata.utilities - INFO: READ COUNT: decontaminated hg37dec\_v0.1 orphan2 : Total reads after removing those found in reference database ( /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output/s34\_R1\_kneaddata\_hg37dec\_v0.1\_bowtie2\_unmatched\_2\_clean.fastq ): 87523.0 04/04/2022 12:49:00 PM - kneaddata.utilities - INFO: READ COUNT: final orphan2 : Total reads after merging results from multiple databases ( /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output/s34\_R1\_kneaddata\_unmatched\_2.fastq ): 87523.0 04/04/2022 12:49:00 PM - kneaddata.utilities - WARNING: Unable to remove file: /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output/s34\_R1\_kneaddata\_hg37dec\_v0.1\_bowtie2\_unmatched\_2\_clean.fastq 04/04/2022 12:49:00 PM - kneaddata.knead\_data - INFO: Final output files created: /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output/s34\_R1\_kneaddata\_paired\_1.fastq /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output/s34\_R1\_kneaddata\_paired\_2.fastq /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output/s34\_R1\_kneaddata\_unmatched\_1.fastq /N/project/mandal-mouseMalaria/heba-Diabetes/test-workflow/smallFile/knead-small-output/s34\_R1\_kneaddata\_unmatched\_2.fastq Thanks, Rabindra ---
**Author:** ![Hafiz\_Muhammad\_Talha](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/hafiz_muhammad_talha/32/1387_2.png) [@Hafiz\_Muhammad\_Talha](https://forum.biobakery.org/u/Hafiz_Muhammad_Talha)\ **Post date:** [April 14, 2022, 6:14am UTC](https://forum.biobakery.org/t/no-reads-in-the-final-output-files-created/3419/2 "2022-04-14T06:14:36Z")
were you able to resolve this ? if so, kindly help me as well. ---
**Author:** ![jorondo1](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/jorondo1/32/1312_2.png) [@jorondo1](https://forum.biobakery.org/u/jorondo1)\ **Post date:** [April 14, 2022, 2:59pm UTC](https://forum.biobakery.org/t/no-reads-in-the-final-output-files-created/3419/3 "2022-04-14T14:59:45Z")
04/04/2022 12:48:59 PM - kneaddata.utilities - DEBUG: b’177078 reads; of these:\n **177078 (100.00%) were unpaired**; of these:\n 175820 (99.29%) aligned 0 times\n 1062 (0.60%) aligned exactly 1 time\n 196 (0.11%) aligned \>1 times\n0.71% overall alignment rate\npair1\_aligned : 0\npair2\_aligned : 0\npair1\_unaligned : 0\npair2\_unaligned : 0\norphan1\_aligned : 623\norphan2\_aligned : 635\norphan1\_unaligned : 88297\norphan2\_unaligned : 87523\n ` this is telling us the reads are not paired is reordered\_n1ymom5c\_reformatted\_identifiersqe83rdy8\_s34\_R1 truly the pair to reordered\_5qwugmx9\_reformatted\_identifiersfsonvs4e\_s34\_R2 ? Maybe checking your input data might reveal something… hope it helps