Hi everyone,
I have run kneaddata (v0.12.0) with paired-end data and it generated a 15GB-output file with the command “–cat-final-output”, and Metaphlan and Humann run suceesfully. But when I remove the command “–cat-final-output”, size of the two output files (kneaddata_paired_1.fastq & kneaddata_paired_2.fastq) are 0. I’m not sure if there’s something wrong with my code, could anyone help with that? Thank you for your guideness.
My code:
/home/ruchenyao/anaconda3/envs/mgs/bin/kneaddata \
-i1 /home/ruchenyao/project/sIBD/data/raw_data/W0_01_R1.fq.gz \
-i2 /home/ruchenyao/project/sIBD/data/raw_data/W0_01_R2.fq.gz \
-o /home/ruchenyao/project/mgs/project/sIBD/output/W0_01 \
--output-prefix /home/ruchenyao/project/mgs/project/sIBD/output/kneaddate --serial -v \
--reference-db /home/ruchenyao/database/kneaddata_database/human_genome/ \
--run-fastqc-start --run-fastqc-end \
--trimmomatic /home/ruchenyao/software/Trimmomatic-0.39/ \
--trimmomatic-options 'SLIDINGWINDOW:4:20 MINLEN:50' \
-t 4 --bowtie2-options '--very-sensitive --dovetail' --remove-intermediate-output > /home/ruchenyao/project/mgs/project/sIBD/script/kneaddata/W0_01.sh
Screenshot of the output file:
Lat few lines of the log file:
08/30/2024 09:14:08 PM - kneaddata.utilities - INFO: READ COUNT: decontaminated hg37dec_v0.1 pair1 : Total reads after removing those found in reference database ( /home/ruchenyao/project/mgs/project/sIBD/output/kneaddate_hg37dec_v0.1_bowtie2_paired_clean_1.fastq ): 0.0
08/30/2024 09:14:08 PM - kneaddata.utilities - INFO: READ COUNT: decontaminated hg37dec_v0.1 pair2 : Total reads after removing those found in reference database ( /home/ruchenyao/project/mgs/project/sIBD/output/kneaddate_hg37dec_v0.1_bowtie2_paired_clean_2.fastq ): 0.0
08/30/2024 09:14:08 PM - kneaddata.utilities - INFO: READ COUNT: final pair1 : Total reads after merging results from multiple databases ( /home/ruchenyao/project/mgs/project/sIBD/output/kneaddate_paired_1.fastq ): 0.0
08/30/2024 09:14:08 PM - kneaddata.utilities - INFO: READ COUNT: final pair2 : Total reads after merging results from multiple databases ( /home/ruchenyao/project/mgs/project/sIBD/output/kneaddate_paired_2.fastq ): 0.0
08/30/2024 09:14:08 PM - kneaddata.utilities - WARNING: Unable to remove file: /home/ruchenyao/project/mgs/project/sIBD/output/kneaddate_hg37dec_v0.1_bowtie2_paired_clean_1.fastq
08/30/2024 09:14:08 PM - kneaddata.utilities - WARNING: Unable to remove file: /home/ruchenyao/project/mgs/project/sIBD/output/kneaddate_hg37dec_v0.1_bowtie2_paired_clean_2.fastq
08/30/2024 09:14:34 PM - kneaddata.utilities - INFO: READ COUNT: decontaminated hg37dec_v0.1 orphan1 : Total reads after removing those found in reference database ( /home/ruchenyao/project/mgs/project/sIBD/output/kneaddate_hg37dec_v0.1_bowtie2_unmatched_1_clean.fastq ): 22324475.0
08/30/2024 09:14:57 PM - kneaddata.utilities - INFO: READ COUNT: final orphan1 : Total reads after merging results from multiple databases ( /home/ruchenyao/project/mgs/project/sIBD/output/kneaddate_unmatched_1.fastq ): 22324475.0
08/30/2024 09:14:57 PM - kneaddata.utilities - WARNING: Unable to remove file: /home/ruchenyao/project/mgs/project/sIBD/output/kneaddate_hg37dec_v0.1_bowtie2_unmatched_1_clean.fastq
08/30/2024 09:15:23 PM - kneaddata.utilities - INFO: READ COUNT: decontaminated hg37dec_v0.1 orphan2 : Total reads after removing those found in reference database ( /home/ruchenyao/project/mgs/project/sIBD/output/kneaddate_hg37dec_v0.1_bowtie2_unmatched_2_clean.fastq ): 22236068.0
08/30/2024 09:15:48 PM - kneaddata.utilities - INFO: READ COUNT: final orphan2 : Total reads after merging results from multiple databases ( /home/ruchenyao/project/mgs/project/sIBD/output/kneaddate_unmatched_2.fastq ): 22236068.0
08/30/2024 09:15:48 PM - kneaddata.utilities - WARNING: Unable to remove file: /home/ruchenyao/project/mgs/project/sIBD/output/kneaddate_hg37dec_v0.1_bowtie2_unmatched_2_clean.fastq
08/30/2024 09:15:59 PM - kneaddata.utilities - DEBUG: Checking input file to fastqc : /home/ruchenyao/project/mgs/project/sIBD/output/kneaddate_paired_1.fastq
08/30/2024 09:15:59 PM - kneaddata.utilities - DEBUG: Checking input file to fastqc : /home/ruchenyao/project/mgs/project/sIBD/output/kneaddate_paired_2.fastq
08/30/2024 09:15:59 PM - kneaddata.utilities - DEBUG: Checking input file to fastqc : /home/ruchenyao/project/mgs/project/sIBD/output/kneaddate_unmatched_1.fastq
08/30/2024 09:15:59 PM - kneaddata.utilities - DEBUG: Checking input file to fastqc : /home/ruchenyao/project/mgs/project/sIBD/output/kneaddate_unmatched_2.fastq
08/30/2024 09:15:59 PM - kneaddata.utilities - INFO: Running fastqc …
08/30/2024 09:15:59 PM - kneaddata.utilities - INFO: Execute command: /home/ruchenyao/anaconda3/envs/mgs/bin/fastqc /home/ruchenyao/project/mgs/project/sIBD/output/kneaddate_paired_1.fastq /home/ruchenyao/project/mgs/project/sIBD/output/kneaddate_paired_2.fastq /home/ruchenyao/project/mgs/project/sIBD/output/kneaddate_unmatched_1.fastq /home/ruchenyao/project/mgs/project/sIBD/output/kneaddate_unmatched_2.fastq --threads 4 --outdir /home/ruchenyao/project/mgs/project/sIBD/output/W0_01/fastqc --extract
08/30/2024 09:19:48 PM - kneaddata.utilities - DEBUG: b’null\nnull\nnull\nnull\nStarted analysis of kneaddate_paired_1.fastq\nAnalysis complete for kneaddate_paired_1.fastq\nStarted analysis of kneaddate_paired_2.fastq\nAnalysis complete for kneaddate_paired_2.fastq\nStarted analysis of kneaddate_unmatched_1.fastq\nStarted analysis of kneaddate_unmatched_2.fastq\nApprox 5% complete for kneaddate_unmatched_1.fastq\nApprox 5% complete for kneaddate_unmatched_2.fastq\nApprox 10% complete for kneaddate_unmatched_1.fastq\nApprox 10% complete for kneaddate_unmatched_2.fastq\nApprox 15% complete for kneaddate_unmatched_1.fastq\nApprox 15% complete for kneaddate_unmatched_2.fastq\nApprox 20% complete for kneaddate_unmatched_1.fastq\nApprox 20% complete for kneaddate_unmatched_2.fastq\nApprox 25% complete for kneaddate_unmatched_1.fastq\nApprox 25% complete for kneaddate_unmatched_2.fastq\nApprox 30% complete for kneaddate_unmatched_2.fastq\nApprox 30% complete for kneaddate_unmatched_1.fastq\nApprox 35% complete for kneaddate_unmatched_2.fastq\nApprox 35% complete for kneaddate_unmatched_1.fastq\nApprox 40% complete for kneaddate_unmatched_2.fastq\nApprox 40% complete for kneaddate_unmatched_1.fastq\nApprox 45% complete for kneaddate_unmatched_2.fastq\nApprox 45% complete for kneaddate_unmatched_1.fastq\nApprox 50% complete for kneaddate_unmatched_2.fastq\nApprox 50% complete for kneaddate_unmatched_1.fastq\nApprox 55% complete for kneaddate_unmatched_2.fastq\nApprox 55% complete for kneaddate_unmatched_1.fastq\nApprox 60% complete for kneaddate_unmatched_2.fastq\nApprox 60% complete for kneaddate_unmatched_1.fastq\nApprox 65% complete for kneaddate_unmatched_2.fastq\nApprox 65% complete for kneaddate_unmatched_1.fastq\nApprox 70% complete for kneaddate_unmatched_2.fastq\nApprox 70% complete for kneaddate_unmatched_1.fastq\nApprox 75% complete for kneaddate_unmatched_2.fastq\nApprox 75% complete for kneaddate_unmatched_1.fastq\nApprox 80% complete for kneaddate_unmatched_2.fastq\nApprox 80% complete for kneaddate_unmatched_1.fastq\nApprox 85% complete for kneaddate_unmatched_1.fastq\nApprox 85% complete for kneaddate_unmatched_2.fastq\nApprox 90% complete for kneaddate_unmatched_1.fastq\nApprox 90% complete for kneaddate_unmatched_2.fastq\nApprox 95% complete for kneaddate_unmatched_1.fastq\nApprox 95% complete for kneaddate_unmatched_2.fastq\nAnalysis complete for kneaddate_unmatched_1.fastq\nAnalysis complete for kneaddate_unmatched_2.fastq\n’
08/30/2024 09:19:48 PM - kneaddata.knead_data - INFO:
Final output files created:
/home/ruchenyao/project/mgs/project/sIBD/output/kneaddate_paired_1.fastq
/home/ruchenyao/project/mgs/project/sIBD/output/kneaddate_paired_2.fastq
/home/ruchenyao/project/mgs/project/sIBD/output/kneaddate_unmatched_1.fastq
/home/ruchenyao/project/mgs/project/sIBD/output/kneaddate_unmatched_2.fastq
My softwares version: kneaddata (v0.12.0), fastqc (v0.12.1), trimmomatic (v0.39)