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