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wdecoster / nanoQC

Quality control tools for nanopore sequencing data
GNU General Public License v3.0
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nanoQC was not making html output report #19

Open nzhou-Irhs opened 4 months ago

nzhou-Irhs commented 4 months ago

I used 'pip install nanoQC' to install nanoQC, it looks well done.

DNAseq of ONT: nanoQC -o outdir SRR26318748.fastq.gz RNAseq of ONT: nanoQC --rna -o outdir SRR26318747.fastq.gz

Both programs ran without interruption and error messages， however, the nanoQC was not making html output report, and only the *.log file was written to the designated output directory.

I used python3, and updated Bokeh with "pip install broken -U",

the nohup.out report is like this: 2024-03-18 05:01:35,829 NanoQC started. 2024-03-18 05:09:32,971 Note: NumExpr detected 32 cores but "NUMEXPR_MAX_THREADS" not set, so enforcing safe limit of 8. 2024-03-18 05:09:32,971 NumExpr defaulting to 8 threads. 2024-03-18 05:09:33,275 Extracting nucleotides and quality scores. 2024-03-18 05:24:01,328 Using 8843207 reads with a minimum length of 200bp for plotting 2024-03-18 05:24:01,328 Creating plots... 2024-03-18 06:04:20,422 Per base sequence content and quality completed. NanoQC.log (END)

wdecoster commented 4 months ago

The log file is incomplete so nanoQC did not finish as it should. Could you run it without nohup and try to capture the error message?

Maybe something like nanoQC --rna -o outdir SRR26318747.fastq.gz 2> nanoqc-error.err