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Description of bugMy Command is: ./metaspades.py --pe1-1 /home/user/Desktop/data/HLP/dataRfoodW/READ_QC/R384/final_pure_reads384_1.fastq --pe1-2 /home/user/Desktop/data/HLP/dataRfoodW/READ_QC/R384/final_pure_reads384_2.fastq -o /data2/FL/ASSEMBLY/ASSEMBLYWR384 -t 40 The scaffolds.fasta file is in the output file. But that said SPAdes pipeline finished WITH WARNINGS! So what should I do to solve this warning. spades.logparams.txtSPAdes versionSPAdes 3.15.2 Operating SystemLInux-5.8.0-53-generic-x86_64-with-debian-bullseye-sid Python VersionPython 3.6.13 Method of SPAdes installationmanual No errors reported in spades.log
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Well, as stated in the warning – the insert size is quite small and your paired end reads do almost overlap. The only way to "fix" this warning is to re-sequence your data with wider insert / fragment length used during the library preparation. You may want to forward this question to your sequencing / wet lab facility. |
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Well, as stated in the warning – the insert size is quite small and your paired end reads do almost overlap. The only way to "fix" this warning is to re-sequence your data with wider insert / fragment length used during the library preparation. You may want to forward this question to your sequencing / wet lab facility.