voutcn / megahit

Ultra-fast and memory-efficient (meta-)genome assembler
http://www.ncbi.nlm.nih.gov/pubmed/25609793
GNU General Public License v3.0
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== Error == system call for: "['']" finished abnormally, OS return value: 2 #352

Open MaxBai0123 opened 1 year ago

MaxBai0123 commented 1 year ago

Hi~I rerun metaspades in a new machine, which memory has 512G, indeed, it worked, but I meet another error "Sorry, current version of metaSPAdes can work either with single library (paired-end only) or in hybrid paired-end + (TSLR or PacBio or Nanopore) mode." Is metaSPADES cannot assemble multiple sets of paired-end sequences? Can I solve this problem by merge all paired-end sequences into one sequence file? my input code: time spades.py --meta -o /project01/workspace/Metagenome/R1rawdata/result/metaspades --pe1-1 /project01/workspace/Metagenome/R1rawdata/result/trimmomatic/R1.224d.R1.paired.fq.gz --pe2-1 /project01/workspace/Metagenome/R1rawdata/result/trimmomatic/R1.496d.R1.paired.fq.gz --pe3-1 /project01/workspace/Metagenome/R1rawdata/result/trimmomatic/R1.590d.10G.R1.paired.fq.gz --pe1-2 /project01/workspace/Metagenome/R1rawdata/result/trimmomatic/R1.224d.R2.paired.fq.gz --pe2-2 /project01/workspace/Metagenome/R1rawdata/result/trimmomatic/R1.496d.R2.paired.fq.gz --pe3-2 /project01/workspace/Metagenome/R1rawdata/result/trimmomatic/R1.590d.10G.R2.paired.fq.gz -k 21,33,55,77,99,127 -m 400 -t 20 --phred-offset 33