Kneaddata before Humann2

[luyan...@gmail.com]

Hi, community,

I am using Humann2 to analysis my shotgun data. However, as it suggested, filtered data was suggested as the input data.

So I use the Kneaddata to filter the sequences.

Here is the code I use
kneaddata --input ../18TB_C1_L003_1.fastq --input ../18TB_C1_L003_2.fastq --reference-db /home/silva_128 --output kneaddata_output_silva132 --run-bmtagger --threads 30

However, I got the error, see below. I have searched the website, no clues. Is there anyone who can help me with this?

Thanks in advance.

04/16/2018 09:13:29 PM - kneaddata.utilities - INFO: Reformatting file sequence identifiers ...
04/16/2018 09:25:29 PM - kneaddata.utilities - INFO: READ COUNT: raw pair1 : Initial number of reads ( /home/ARG/Ublastx_stageone/example_my/data/18TB_C1_L003/18TB_C1_L003_2.fastq ): 75
04/16/2018 09:26:14 PM - kneaddata.utilities - INFO: READ COUNT: raw pair2 : Initial number of reads ( /home/ARG/Ublastx_stageone/example_my/data/18TB_C1_L003/humann2/kneaddata_output_silva132/reformatted_identi$
04/16/2018 09:26:14 PM - kneaddata.utilities - DEBUG: Checking input file to Trimmomatic : /home/ARG/Ublastx_stageone/example_my/data/18TB_C1_L003/humann2/kneaddata_output_silva132/reformatted_identifiers4z37iW_$
04/16/2018 09:26:14 PM - kneaddata.utilities - DEBUG: Checking input file to Trimmomatic : /home/ARG/Ublastx_stageone/example_my/data/18TB_C1_L003/18TB_C1_L003_2.fastq
04/16/2018 09:26:14 PM - kneaddata.utilities - INFO: Running Trimmomatic ...
04/16/2018 09:26:14 PM - kneaddata.utilities - INFO: Execute command: java -Xmx500m -d64 -jar /home/.local/bin/trimmomatic-0.33.jar PE -threads 30 -phred33 /home/ARG/Ublastx_stageone/example_my/data/18TB_C1_L003$
04/16/2018 09:26:14 PM - kneaddata.utilities - CRITICAL: Error executing: java -Xmx500m -d64 -jar /home/.local/bin/trimmomatic-0.33.jar PE -threads 30 -phred33 /home/ARG/Ublastx_stageone/example_my/data/18TB_C1_$

Error message returned from Trimmomatic :
TrimmomaticPE: Started with arguments: -threads 30 -phred33 /home/ARG/Ublastx_stageone/example_my/data/18TB_C1_L003/humann2/kneaddata_output_silva132/reformatted_identifiers4z37iW_18TB_C1_L003_1 /home/ARG/Ublast$
Exception in thread "main" java.lang.RuntimeException: Invalid FASTQ name line: #SampleID Metaphlan2_Analysis
at org.usadellab.trimmomatic.fastq.FastqParser.parseOne(FastqParser.java:67)
at org.usadellab.trimmomatic.fastq.FastqParser.parse(FastqParser.java:156)
at org.usadellab.trimmomatic.TrimmomaticPE.process(TrimmomaticPE.java:255)
at org.usadellab.trimmomatic.TrimmomaticPE.run(TrimmomaticPE.java:499)
at org.usadellab.trimmomatic.Trimmomatic.main(Trimmomatic.java:35)

[Lauren McIver]

Hi - From the error message it looks like the fastq input files you are using might be of an unexpected format. it looks like it might contain a line with "#SampleID Metaphlan2_Analysis". My suggestion would be to double check these input files are raw reads in fastq format.

Thanks,

Lauren

[luyan...@gmail.com]

Hi,
Thanks. I see.