hi Iam having this error executor > local (180) [- ] NFCORE_TAXPROFILERtaxprofilerUNTAR - [ad/a9b04e] NFCORE_TAXPROFILERtaxprofilerFASTQC (ZHC0098) | 394 of 394, cached: 394 ✔️ [- ] NFC…RtaxprofilerSHORTREAD_PREPROCESSINGSHORTREAD FASTPFASTP_SINGLE - [1c/cd37e5] NFC…LERSHORTREAD PREPROCESSINGSHORTREAD_FASTP:FASTP_PAIRED (ZHC0098) | 394 of 394, cached: 394 ✔️ [f8/79a01e] NFC…LERtaxprofilerSHORTREAD_PREPROCESSING:FASTQC_PROCESSED (MRH5162) | 325 of 394, cached: 281 [91/f3d462] NFC…OFILERtaxprofilerPROFILING:KRAKEN2_KRAKEN2 (db1|kraken2|HLH4044) | 95 of 788, cached: 1 [e1/cbb9ba] NFCORE_TAXPROFILERtaxprofilerPROFILING:BRACKEN_BRACKEN (db2|HZH4088) | 41 of 46 [- ] NFCORE_TAXPROFILERtaxprofilerMULTIQC - -[nf-core/taxprofiler] Pipeline completed with errors- ERROR ~ Error executing process > 'NFCORE_TAXPROFILERtaxprofilerSHORTREAD_PREPROCESSING:FASTQC_PROCESSED (MRH5191)' Caused by: Process

NFCORE_TAXPROFILER:taxprofiler:SHORTREAD_PREPROCESSING:FASTQC_PROCESSED (MRH5191)

terminated with an error exit status (1) Command executed: printf "%s %s\n" MRH5191_MRH5191_1.fastp.fastq.gz MRH5191_MRH5191_processed_1.gz MRH5191_MRH5191_2.fastp.fastq.gz MRH5191_MRH5191_processed_2.gz | while read old_name new_name; do [ -f "${new_name}" ] || ln -s $old_name $new_name done fastqc \ --quiet \ --threads 6 \ --memory 6144 \ MRH5191_MRH5191_processed_1.gz MRH5191_MRH5191_processed_2.gz cat <-END_VERSIONS versions.yml "NFCORE_TAXPROFILERtaxprofilerSHORTREAD_PREPROCESSING:FASTQC_PROCESSED": fastqc: $( fastqc --version | sed '/FastQC v/!d; s/.*v//' ) END_VERSIONS Command exit status: 1 Command output: application/gzip application/gzip Command error: application/gzip Failed to process MRH5191_MRH5191_processed_1.gz java.io.EOFException at java.base/java.util.zip.GZIPInputStream.readUByte(GZIPInputStream.java:268) at java.base/java.util.zip.GZIPInputStream.readUShort(GZIPInputStream.java:258) at java.base/java.util.zip.GZIPInputStream.readHeader(GZIPInputStream.java:164) at java.base/java.util.zip.GZIPInputStream.init(GZIPInputStream.java:79) at java.base/java.util.zip.GZIPInputStream.init(GZIPInputStream.java:91) at uk.ac.babraham.FastQC.Utilities.MultiMemberGZIPInputStream.init(MultiMemberGZIPInputStream.java:37) at uk.ac.babraham.FastQC.Sequence.FastQFile.init(FastQFile.java:84) at uk.ac.babraham.FastQC.Sequence.SequenceFactory.getSequenceFile(SequenceFactory.java:106) at uk.ac.babraham.FastQC.Sequence.SequenceFactory.getSequenceFile(SequenceFactory.java:62) at uk.ac.babraham.FastQC.Analysis.OfflineRunner.processFile(OfflineRunner.java:163) at uk.ac.babraham.FastQC.Analysis.OfflineRunner.init(OfflineRunner.java:125) at uk.ac.babraham.FastQC.FastQCApplication.main(FastQCApplication.java:316) application/gzip Failed to process MRH5191_MRH5191_processed_2.gz java.io.EOFException at java.base/java.util.zip.GZIPInputStream.readUByte(GZIPInputStream.java:268) at java.base/java.util.zip.GZIPInputStream.readUShort(GZIPInputStream.java:258) at java.base/java.util.zip.GZIPInputStream.readHeader(GZIPInputStream.java:164) at java.base/java.util.zip.GZIPInputStream.init(GZIPInputStream.java:79) at java.base/java.util.zip.GZIPInputStream.init(GZIPInputStream.java:91) at uk.ac.babraham.FastQC.Utilities.MultiMemberGZIPInputStream.init(MultiMemberGZIPInputStream.java:37) at uk.ac.babraham.FastQC.Sequence.FastQFile.init(FastQFile.java:84) at uk.ac.babraham.FastQC.Sequence.SequenceFactory.getSequenceFile(SequenceFactory.java:106) at uk.ac.babraham.FastQC.Sequence.SequenceFactory.getSequenceFile(SequenceFactory.java:62) at uk.ac.babraham.FastQC.Analysis.OfflineRunner.processFile(OfflineRunner.java:163) at uk.ac.babraham.FastQC.Analysis.OfflineRunner.init(OfflineRunner.java:125) at uk.ac.babraham.FastQC.FastQCApplication.main(FastQCApplication.java:316) Work dir: /tank/lmapunda/ARI/taxoprofile/work/7d/198e2f959b9c3a1f621892cfa4e5e0 Container: /tank/lmapunda/ARI/work/singularity/depot.galaxyproject.org-singularity-fastqc-0.12.1--hdfd78af_0.img Tip: when you have fixed the problem you can continue the execution adding the option

-resume

to the run command line -- Check '.nextflow.log' file for details ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting -- Check '.nextflow.log' file for details here is my command

nextflow run nf-core/taxprofiler -r 1.2.6 -profile singularity --input data/Metadata.csv --databases data/databases.csv --outdir ./ARI_results/ --perform_shortread_qc --run_kraken2 --run_bracken

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Based on`Failed to process MRH5191_MRH5191_processed_1.gz` and

java.io.EOFException
 	at java.base/java.util.zip.GZIPInputStream.readUByte(GZIPInputStream.java:268)

This looks to me like your input files are corrupted somehow, either FASTQC expects a

fastq.gz

like suffix, or the file itself is not gzpiped?

Thank you! I will work on that sample and rerun the pipeline