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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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Error executing process > 'read_correction (2)' #29

Open anilchauhanhp9 opened 3 years ago

anilchauhanhp9 commented 3 years ago

Hi, i ran the pipeline on my oqn data set using following command

nextflow /home/hamlab/NanoCLUST/main.nf --reads '/home/hamlab/Nanopore/nanofilt_trimmed_barecode01.fastq' --db '/home/hamlab/NanoCLUST/db/blastdb' --tax '/home/hamlab/NanoCLUST/db/taxdb' -profile conda

the pipeline works as Run Name : awesome_plateau Reads : /home/hamlab/Nanopore/nanofilt_trimmed_barecode01.fastq Max Resources : 128 GB memory, 16 cpus, 10d time per job Output dir : ./results Launch dir : /home/hamlab/Nanopore Working dir : /home/hamlab/Nanopore/work Script dir : /home/hamlab/NanoCLUST User : hamlab Config Profile : conda

[- ] process > QC - [- ] process > fastqc - [- ] process > kmer_freqs - executor > local (1) [be/62e2a0] process > QC (1) [100%] 1 of 1 ✔ [- ] process > fastqc - [- ] process > kmer_freqs - executor > local (2) [be/62e2a0] process > QC (1) [100%] 1 of 1 ✔ [- ] process > fastqc - [- ] process > kmer_freqs - executor > local (2) [be/62e2a0] process > QC (1) [100%] 1 of 1 ✔ [- ] process > fastqc - [- ] process > kmer_freqs - executor > local (3) [be/62e2a0] process > QC (1) [100%] 1 of 1 ✔ executor > local (4) [be/62e2a0] process > QC (1) [100%] 1 of 1 ✔ executor > local (4) [be/62e2a0] process > QC (1) [100%] 1 of 1 ✔ executor > local (8) [be/62e2a0] process > QC (1) [100%] 1 of 1 ✔ [ce/6e7260] process > fastqc (1) [100%] 1 of 1 ✔ [52/c6994a] process > kmer_freqs (1) [100%] 1 of 1 ✔ [65/c93866] process > read_clustering (1) [100%] 1 of 1 ✔ [1a/98e4b2] process > split_by_cluster (1) [100%] 1 of 1 ✔ [f1/f29d75] process > read_correction (2) [ 0%] 0 of 2 [- ] process > draft_selection - [- ] process > racon_pass - [- ] process > medaka_pass - [- ] process > consensus_classification - [- ] process > join_results - [- ] process > get_abundances - [- ] process > plot_abundances - [52/0c3775] process > output_documentation [100%] 1 of 1 ✔

After that it has this error Error executing process > 'read_correction (2)' Caused by: Process read_correction (2) terminated with an error exit status (1) Command executed: head -n$(( 100*4 )) 1.fastq > subset.fastq canu -correct -p corrected_reads -nanopore-raw subset.fastq genomeSize=1.5k stopOnLowCoverage=1 minInputCoverage=2 minReadLength=500 minOverlapLength=200 gunzip corrected_reads.correctedReads.fasta.gz READ_COUNT=$(( $(awk '{print $1/2}' <(wc -l corrected_reads.correctedReads.fasta)) )) cat 1.log > 1_racon.log echo -n ";100;$READ_COUNT;" >> 1_racon.log && cp 1_racon.log 1racon.log Command exit status: 1 Command output: (empty) Command error: /home/hamlab/Nanopore/work/conda/read_correction--9838d2d8e8d06bacfda88b353ba23513/bin/sqStoreDumpMetaData \ -S ./corrected_reads.seqStore **** executor > local (8) [be/62e2a0] process > QC (1) [100%] 1 of 1 ✔ [ce/6e7260] process > fastqc (1) [100%] 1 of 1 ✔ [52/c6994a] process > kmer_freqs (1) [100%] 1 of 1 ✔ [65/c93866] process > read_clustering (1) [100%] 1 of 1 ✔ [1a/98e4b2] process > split_by_cluster (1) [100%] 1 of 1 ✔ [f1/f29d75] process > read_correction (2) [ 50%] 1 of 2, failed: 1 [- ] process > draft_selection - [- ] process > racon_pass - [- ] process > medaka_pass - [- ] process > consensus_classification - [- ] process > join_results - [- ] process > get_abundances - [- ] process > plot_abundances - [52/0c3775] process > output_documentation [100%] 1 of 1 ✔ can you help me in resolving the issue Thanks