12/16/2021 02:13:49 PM - kneaddata.knead_data - INFO: Running kneaddata v0.10.0 12/16/2021 02:13:49 PM - kneaddata.knead_data - INFO: Output files will be written to: /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1 12/16/2021 02:13:49 PM - kneaddata.knead_data - DEBUG: Running with the following arguments: verbose = False input = /home/yanhz/data2t/meishan7/00.rawdata/S1R1/S1R1_L1_1.fq.gz /home/yanhz/data2t/meishan7/00.rawdata/S1R1/S1R1_L1_2.fq.gz output_dir = /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1 reference_db = /home/yanhz/data2t/kneaddataDB/human_hg38_refMrna /home/yanhz/data2t/kneaddataDB/hg37dec_v0.1 bypass_trim = False output_prefix = S1R1_L1_1_kneaddata threads = 4 processes = 4 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 = /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/S1R1_L1_1_kneaddata.log trimmomatic_path = /home/yanhz/miniconda2/envs/kneaddata/bin/trimmomatic-0.33.jar run_trim_repetitive = False max_memory = 500m trimmomatic_options = None sequencer_source = NexteraPE bowtie2_path = /home/yanhz/miniconda2/envs/kneaddata/bin/bowtie2 bowtie2_options = --very-sensitive-local --phred33 decontaminate_pairs = strict reorder = False serial = True bmtagger_path = None trf_path = /home/yanhz/miniconda2/envs/kneaddata/bin/trf match = 2 mismatch = 7 delta = 7 pm = 80 pi = 10 minscore = 50 maxperiod = 500 fastqc_path = None remove_temp_output = True discordant = True 12/16/2021 02:13:49 PM - kneaddata.utilities - INFO: Decompressing gzipped file ... 12/16/2021 02:16:11 PM - kneaddata.utilities - INFO: Decompressed file created: /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/decompressed_4r_c5wr3_S1R1_L1_1.fq 12/16/2021 02:16:11 PM - kneaddata.utilities - INFO: Decompressing gzipped file ... 12/16/2021 02:18:05 PM - kneaddata.utilities - INFO: Decompressed file created: /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/decompressed_z20qf7cy_S1R1_L1_2.fq 12/16/2021 02:18:05 PM - kneaddata.utilities - INFO: Reformatting file sequence identifiers ... 12/16/2021 02:20:17 PM - kneaddata.utilities - INFO: Reformatting file sequence identifiers ... 12/16/2021 02:23:44 PM - kneaddata.utilities - INFO: READ COUNT: raw pair1 : Initial number of reads ( /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/reformatted_identifiersky_8kq96_decompressed_4r_c5wr3_S1R1_L1_1 ): 77827844.0 12/16/2021 02:24:21 PM - kneaddata.utilities - INFO: READ COUNT: raw pair2 : Initial number of reads ( /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/reformatted_identifiersx5m6s3wu_decompressed_z20qf7cy_S1R1_L1_2 ): 77827844.0 12/16/2021 02:24:21 PM - kneaddata.utilities - DEBUG: Checking input file to Trimmomatic : /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/reformatted_identifiersky_8kq96_decompressed_4r_c5wr3_S1R1_L1_1 12/16/2021 02:24:21 PM - kneaddata.utilities - DEBUG: Checking input file to Trimmomatic : /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/reformatted_identifiersx5m6s3wu_decompressed_z20qf7cy_S1R1_L1_2 12/16/2021 02:24:21 PM - kneaddata.utilities - INFO: Running Trimmomatic ... 12/16/2021 02:24:21 PM - kneaddata.utilities - INFO: Execute command: java -Xmx500m -jar /home/yanhz/miniconda2/envs/kneaddata/bin/trimmomatic-0.33.jar PE -threads 4 -phred33 /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/reformatted_identifiersky_8kq96_decompressed_4r_c5wr3_S1R1_L1_1 /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/reformatted_identifiersx5m6s3wu_decompressed_z20qf7cy_S1R1_L1_2 /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/S1R1_L1_1_kneaddata.trimmed.1.fastq /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/S1R1_L1_1_kneaddata.trimmed.single.1.fastq /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/S1R1_L1_1_kneaddata.trimmed.2.fastq /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/S1R1_L1_1_kneaddata.trimmed.single.2.fastq MINLEN:60 ILLUMINACLIP:/home/yanhz/miniconda2/envs/kneaddata/lib/python3.9/site-packages/kneaddata/adapters/NexteraPE-PE.fa:2:30:10:8:TRUE SLIDINGWINDOW:4:20 MINLEN:75 12/16/2021 02:39:13 PM - kneaddata.utilities - DEBUG: b"TrimmomaticPE: Started with arguments: -threads 4 -phred33 /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/reformatted_identifiersky_8kq96_decompressed_4r_c5wr3_S1R1_L1_1 /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/reformatted_identifiersx5m6s3wu_decompressed_z20qf7cy_S1R1_L1_2 /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/S1R1_L1_1_kneaddata.trimmed.1.fastq /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/S1R1_L1_1_kneaddata.trimmed.single.1.fastq /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/S1R1_L1_1_kneaddata.trimmed.2.fastq /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/S1R1_L1_1_kneaddata.trimmed.single.2.fastq MINLEN:60 ILLUMINACLIP:/home/yanhz/miniconda2/envs/kneaddata/lib/python3.9/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: 77827844 Both Surviving: 72013849 (92.53%) Forward Only Surviving: 2541749 (3.27%) Reverse Only Surviving: 1680797 (2.16%) Dropped: 1591449 (2.04%)\nTrimmomaticPE: Completed successfully\n" 12/16/2021 02:39:13 PM - kneaddata.utilities - DEBUG: Checking output file from Trimmomatic : /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/S1R1_L1_1_kneaddata.trimmed.1.fastq 12/16/2021 02:39:13 PM - kneaddata.utilities - DEBUG: Checking output file from Trimmomatic : /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/S1R1_L1_1_kneaddata.trimmed.single.1.fastq 12/16/2021 02:39:13 PM - kneaddata.utilities - DEBUG: Checking output file from Trimmomatic : /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/S1R1_L1_1_kneaddata.trimmed.2.fastq 12/16/2021 02:39:13 PM - kneaddata.utilities - DEBUG: Checking output file from Trimmomatic : /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/S1R1_L1_1_kneaddata.trimmed.single.2.fastq 12/16/2021 02:40:03 PM - kneaddata.utilities - INFO: READ COUNT: trimmed pair1 : Total reads after trimming ( /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/S1R1_L1_1_kneaddata.trimmed.1.fastq ): 72013849.0 12/16/2021 02:40:51 PM - kneaddata.utilities - INFO: READ COUNT: trimmed pair2 : Total reads after trimming ( /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/S1R1_L1_1_kneaddata.trimmed.2.fastq ): 72013849.0 12/16/2021 02:40:53 PM - kneaddata.utilities - INFO: READ COUNT: trimmed orphan1 : Total reads after trimming ( /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/S1R1_L1_1_kneaddata.trimmed.single.1.fastq ): 2541749.0 12/16/2021 02:40:54 PM - kneaddata.utilities - INFO: READ COUNT: trimmed orphan2 : Total reads after trimming ( /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/S1R1_L1_1_kneaddata.trimmed.single.2.fastq ): 1680797.0 12/16/2021 03:14:40 PM - kneaddata.utilities - DEBUG: Checking input file to trf : /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/S1R1_L1_1_kneaddata.trimmed.2.fasta 12/16/2021 03:14:40 PM - kneaddata.utilities - DEBUG: Checking input file to trf : /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/S1R1_L1_1_kneaddata.trimmed.1.fasta 12/16/2021 03:14:40 PM - kneaddata.utilities - INFO: Running trf ... 12/16/2021 03:14:40 PM - kneaddata.utilities - INFO: Running trf ... 12/16/2021 03:14:40 PM - kneaddata.utilities - INFO: Execute command: kneaddata_trf_parallel --input /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/S1R1_L1_1_kneaddata.trimmed.1.fasta --output /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/S1R1_L1_1_kneaddata.trimmed.1.fasta.trf.parameters.2.7.7.80.10.50.500.dat --trf-path /home/yanhz/miniconda2/envs/kneaddata/bin/trf --trf-options '2 7 7 80 10 50 500 -h -ngs' --nproc 4 12/16/2021 03:14:40 PM - kneaddata.utilities - INFO: Execute command: kneaddata_trf_parallel --input /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/S1R1_L1_1_kneaddata.trimmed.2.fasta --output /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/S1R1_L1_1_kneaddata.trimmed.2.fasta.trf.parameters.2.7.7.80.10.50.500.dat --trf-path /home/yanhz/miniconda2/envs/kneaddata/bin/trf --trf-options '2 7 7 80 10 50 500 -h -ngs' --nproc 4 12/16/2021 04:52:02 PM - kneaddata.utilities - DEBUG: 0 12/16/2021 04:52:02 PM - kneaddata.utilities - DEBUG: Checking output file from trf : /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/S1R1_L1_1_kneaddata.trimmed.1.fasta.trf.parameters.2.7.7.80.10.50.500.dat 12/16/2021 04:52:54 PM - kneaddata.utilities - DEBUG: 0 12/16/2021 04:52:54 PM - kneaddata.utilities - DEBUG: Checking output file from trf : /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/S1R1_L1_1_kneaddata.trimmed.2.fasta.trf.parameters.2.7.7.80.10.50.500.dat 12/16/2021 04:55:59 PM - kneaddata.run - INFO: Total number of sequences with repeats removed from file ( /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/S1R1_L1_1_kneaddata.trimmed.1.fastq ): 4893262 12/16/2021 04:58:56 PM - kneaddata.run - INFO: Total number of sequences with repeats removed from file ( /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/S1R1_L1_1_kneaddata.trimmed.2.fastq ): 4853920 12/16/2021 04:59:34 PM - kneaddata.utilities - DEBUG: Checking input file to trf : /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/S1R1_L1_1_kneaddata.trimmed.single.1.fasta 12/16/2021 04:59:34 PM - kneaddata.utilities - INFO: Running trf ... 12/16/2021 04:59:34 PM - kneaddata.utilities - INFO: Execute command: kneaddata_trf_parallel --input /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/S1R1_L1_1_kneaddata.trimmed.single.1.fasta --output /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/S1R1_L1_1_kneaddata.trimmed.single.1.fasta.trf.parameters.2.7.7.80.10.50.500.dat --trf-path /home/yanhz/miniconda2/envs/kneaddata/bin/trf --trf-options '2 7 7 80 10 50 500 -h -ngs' --nproc 4 12/16/2021 05:03:26 PM - kneaddata.utilities - DEBUG: 0 12/16/2021 05:03:26 PM - kneaddata.utilities - DEBUG: Checking output file from trf : /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/S1R1_L1_1_kneaddata.trimmed.single.1.fasta.trf.parameters.2.7.7.80.10.50.500.dat 12/16/2021 05:03:31 PM - kneaddata.run - INFO: Total number of sequences with repeats removed from file ( /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/S1R1_L1_1_kneaddata.trimmed.single.1.fastq ): 488123 12/16/2021 05:03:55 PM - kneaddata.utilities - DEBUG: Checking input file to trf : /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/S1R1_L1_1_kneaddata.trimmed.single.2.fasta 12/16/2021 05:03:55 PM - kneaddata.utilities - INFO: Running trf ... 12/16/2021 05:03:55 PM - kneaddata.utilities - INFO: Execute command: kneaddata_trf_parallel --input /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/S1R1_L1_1_kneaddata.trimmed.single.2.fasta --output /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/S1R1_L1_1_kneaddata.trimmed.single.2.fasta.trf.parameters.2.7.7.80.10.50.500.dat --trf-path /home/yanhz/miniconda2/envs/kneaddata/bin/trf --trf-options '2 7 7 80 10 50 500 -h -ngs' --nproc 4 12/16/2021 05:06:51 PM - kneaddata.utilities - DEBUG: 0 12/16/2021 05:06:51 PM - kneaddata.utilities - DEBUG: Checking output file from trf : /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/S1R1_L1_1_kneaddata.trimmed.single.2.fasta.trf.parameters.2.7.7.80.10.50.500.dat 12/16/2021 05:06:53 PM - kneaddata.run - INFO: Total number of sequences with repeats removed from file ( /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/S1R1_L1_1_kneaddata.trimmed.single.2.fastq ): 309205 12/16/2021 05:06:53 PM - kneaddata.run - INFO: Decontaminating ... 12/16/2021 05:06:53 PM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/S1R1_L1_1_kneaddata.repeats.removed.1.fastq 12/16/2021 05:06:53 PM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/S1R1_L1_1_kneaddata.repeats.removed.1.fastq 12/16/2021 05:06:53 PM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/S1R1_L1_1_kneaddata.repeats.removed.2.fastq 12/16/2021 05:06:53 PM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/S1R1_L1_1_kneaddata.repeats.removed.2.fastq 12/16/2021 05:06:53 PM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/S1R1_L1_1_kneaddata.repeats.removed.unmatched.1.fastq 12/16/2021 05:06:53 PM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/S1R1_L1_1_kneaddata.repeats.removed.unmatched.1.fastq 12/16/2021 05:06:53 PM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/S1R1_L1_1_kneaddata.repeats.removed.unmatched.2.fastq 12/16/2021 05:06:53 PM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/S1R1_L1_1_kneaddata.repeats.removed.unmatched.2.fastq 12/16/2021 05:06:53 PM - kneaddata.utilities - INFO: Running bowtie2 ... 12/16/2021 05:06:53 PM - kneaddata.utilities - INFO: Running bowtie2 ... 12/16/2021 05:06:53 PM - kneaddata.utilities - INFO: Execute command: kneaddata_bowtie2_discordant_pairs --bowtie2 /home/yanhz/miniconda2/envs/kneaddata/bin/bowtie2 --threads 4 -x /home/yanhz/data2t/kneaddataDB/human_hg38_refMrna --mode strict --bowtie2-options "--very-sensitive-local --phred33" -1 /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/S1R1_L1_1_kneaddata.repeats.removed.1.fastq -2 /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/S1R1_L1_1_kneaddata.repeats.removed.2.fastq --un-pair /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/S1R1_L1_1_kneaddata_human_hg38_refMrna_bowtie2_paired_clean_%.fastq --al-pair /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/S1R1_L1_1_kneaddata_human_hg38_refMrna_bowtie2_paired_contam_%.fastq -U /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/S1R1_L1_1_kneaddata.repeats.removed.unmatched.1.fastq,/home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/S1R1_L1_1_kneaddata.repeats.removed.unmatched.2.fastq --un-single /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/S1R1_L1_1_kneaddata_human_hg38_refMrna_bowtie2_unmatched_%_clean.fastq --al-single /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/S1R1_L1_1_kneaddata_human_hg38_refMrna_bowtie2_unmatched_%_contam.fastq -S /dev/null 12/16/2021 05:06:53 PM - kneaddata.utilities - INFO: Execute command: kneaddata_bowtie2_discordant_pairs --bowtie2 /home/yanhz/miniconda2/envs/kneaddata/bin/bowtie2 --threads 4 -x /home/yanhz/data2t/kneaddataDB/hg37dec_v0.1 --mode strict --bowtie2-options "--very-sensitive-local --phred33" -1 /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/S1R1_L1_1_kneaddata_human_hg38_refMrna_bowtie2_paired_clean_1.fastq -2 /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/S1R1_L1_1_kneaddata_human_hg38_refMrna_bowtie2_paired_clean_2.fastq --un-pair /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/S1R1_L1_1_kneaddata_hg37dec_v0.1_bowtie2_paired_clean_%.fastq --al-pair /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/S1R1_L1_1_kneaddata_hg37dec_v0.1_bowtie2_paired_contam_%.fastq -U /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/S1R1_L1_1_kneaddata_human_hg38_refMrna_bowtie2_unmatched_1_clean.fastq,/home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/S1R1_L1_1_kneaddata_human_hg38_refMrna_bowtie2_unmatched_2_clean.fastq --un-single /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/S1R1_L1_1_kneaddata_hg37dec_v0.1_bowtie2_unmatched_%_clean.fastq --al-single /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/S1R1_L1_1_kneaddata_hg37dec_v0.1_bowtie2_unmatched_%_contam.fastq -S /dev/null 12/16/2021 05:06:53 PM - kneaddata.utilities - CRITICAL: Error executing: kneaddata_bowtie2_discordant_pairs --bowtie2 /home/yanhz/miniconda2/envs/kneaddata/bin/bowtie2 --threads 4 -x /home/yanhz/data2t/kneaddataDB/hg37dec_v0.1 --mode strict --bowtie2-options "--very-sensitive-local --phred33" -1 /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/S1R1_L1_1_kneaddata_human_hg38_refMrna_bowtie2_paired_clean_1.fastq -2 /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/S1R1_L1_1_kneaddata_human_hg38_refMrna_bowtie2_paired_clean_2.fastq --un-pair /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/S1R1_L1_1_kneaddata_hg37dec_v0.1_bowtie2_paired_clean_%.fastq --al-pair /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/S1R1_L1_1_kneaddata_hg37dec_v0.1_bowtie2_paired_contam_%.fastq -U /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/S1R1_L1_1_kneaddata_human_hg38_refMrna_bowtie2_unmatched_1_clean.fastq,/home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/S1R1_L1_1_kneaddata_human_hg38_refMrna_bowtie2_unmatched_2_clean.fastq --un-single /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/S1R1_L1_1_kneaddata_hg37dec_v0.1_bowtie2_unmatched_%_clean.fastq --al-single /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/S1R1_L1_1_kneaddata_hg37dec_v0.1_bowtie2_unmatched_%_contam.fastq -S /dev/null Error message returned from bowtie2 : stat: Bad file descriptor Warning: Could not open read file "/home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/S1R1_L1_1_kneaddata_human_hg38_refMrna_bowtie2_paired_clean_1.fastq" for reading; skipping... stat: Bad file descriptor Warning: Could not open read file "/home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/S1R1_L1_1_kneaddata_human_hg38_refMrna_bowtie2_paired_clean_2.fastq" for reading; skipping... stat: Bad file descriptor Warning: Could not open read file "/home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/S1R1_L1_1_kneaddata_human_hg38_refMrna_bowtie2_unmatched_1_clean.fastq" for reading; skipping... stat: Bad file descriptor Warning: Could not open read file "/home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/S1R1_L1_1_kneaddata_human_hg38_refMrna_bowtie2_unmatched_2_clean.fastq" for reading; skipping... Error: No input read files were valid (ERR): bowtie2-align exited with value 1 Unable to run bowtie2: /home/yanhz/miniconda2/envs/kneaddata/bin/bowtie2 --threads 4 -x /home/yanhz/data2t/kneaddataDB/hg37dec_v0.1 -S /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/_temp.sam8e6c3r8_kneaddata_ --no-head -U /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/S1R1_L1_1_kneaddata_human_hg38_refMrna_bowtie2_paired_clean_1.fastq,/home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/S1R1_L1_1_kneaddata_human_hg38_refMrna_bowtie2_paired_clean_2.fastq,/home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/S1R1_L1_1_kneaddata_human_hg38_refMrna_bowtie2_unmatched_1_clean.fastq,/home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/S1R1_L1_1_kneaddata_human_hg38_refMrna_bowtie2_unmatched_2_clean.fastq --very-sensitive-local --phred33 12/16/2021 06:08:45 PM - kneaddata.utilities - DEBUG: b'137705734 reads; of these:\n 137705734 (100.00%) were unpaired; of these:\n 137438829 (99.81%) aligned 0 times\n 27712 (0.02%) aligned exactly 1 time\n 239193 (0.17%) aligned >1 times\n0.19% overall alignment rate\npair1_aligned : 186958\npair2_aligned : 186958\npair1_unaligned : 64334143\npair2_unaligned : 64334143\norphan1_aligned : 14150\norphan2_aligned : 12509\norphan1_unaligned : 4638962\norphan2_unaligned : 3997911\n' 12/16/2021 06:08:45 PM - kneaddata.utilities - DEBUG: Checking output file from bowtie2 : /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/S1R1_L1_1_kneaddata_human_hg38_refMrna_bowtie2_paired_clean_1.fastq 12/16/2021 06:08:45 PM - kneaddata.utilities - DEBUG: Checking output file from bowtie2 : /home/yanhz/Documents/tools/kneaddata/kneaddata_S1R1/S1R1_L1_1_kneaddata_human_hg38_refMrna_bowtie2_paired_clean_2.fastq