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genomicsITER / NanoCLUST

NanoCLUST is an analysis pipeline for UMAP-based classification of amplicon-based full-length 16S rRNA nanopore reads
MIT License
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Fail process > fastqc (1) #36

Open icotto25 opened 3 years ago

icotto25 commented 3 years ago

Hello,

I am getting the following error running (nextflow run main.nf -profile test,conda). Can you please help me to fix this issue?

Thank you,

Irmarie

N E X T F L O W ~ version 21.04.0 Launching main.nf [fabulous_darwin] - revision: 5e0f88a799

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NanoCLUST v1.0dev

Run Name : fabulous_darwin Reads : /scratch/icotto25/shotgun_time_series/16S_May2021/NanoCLUST/test_datasets/mock4_run3bc08_5000.fastq Max Resources : 128 GB memory, 16 cpus, 10d time per job Output dir : ./results Launch dir : /scratch/icotto25/shotgun_time_series/16S_May2021/NanoCLUST Working dir : /scratch/icotto25/shotgun_time_series/16S_May2021/NanoCLUST/work Script dir : /scratch/icotto25/shotgun_time_series/16S_May2021/NanoCLUST User : icotto25 Config Profile : test,conda Config Description: Minimal test dataset to check pipeline function

executor > local (5) executor > local (5) executor > local (5) [c8/177787] process > QC (1) [100%] 1 of 1 ✔ executor > local (5) [c8/177787] process > QC (1) [100%] 1 of 1 ✔ [1a/4e6673] process > fastqc (1) [100%] 1 of 1, failed: 1 ✘ [49/bc700b] process > kmer_freqs (1) [100%] 1 of 1 ✔ [55/c689e9] process > read_clustering (1) [100%] 1 of 1, failed: 1 ✘ [- ] process > split_by_cluster - [- ] process > read_correction - [- ] process > draft_selection - [- ] process > racon_pass - [- ] process > medaka_pass - [- ] process > consensus_classification - [- ] process > join_results - [- ] process > get_abundances - [- ] process > plot_abundances - [07/3f35b0] process > output_documentation [100%] 1 of 1 ✔ Execution cancelled -- Finishing pending tasks before exit [nf-core/nanoclust] Pipeline completed with errors Error executing process > 'fastqc (1)'

Caused by: Process fastqc (1) terminated with an error exit status (127)

Command executed:

fastqc -q mock4_run3bc08_5000_qced_reads_set.fastq

Command exit status: 127

Command output: (empty)

Command error: .command.sh: line 2: fastqc: command not found

Work dir: /scratch/icotto25/shotgun_time_series/16S_May2021/NanoCLUST/work/1a/4e6673c56c84743a12d46b1aaf57aa

Tip: when you have fixed the problem you can continue the execution adding the option -resume to the run command line

mghayour commented 3 years ago

We have same problem here, could u fix it ?

minamikawasaki-ab commented 1 year ago

I have the same problem too.