hello,
i have set the minimum coverage at 40 with kmar size at 35 of a bacteria
and i get this output:
861 Rank 0: the minimum coverage is 40
862 Rank 0: the peak coverage is 8
863 Rank 0: Assembler panic: no peak observed in the k-mer coverage
distribution.
864 Rank 0: to deal with the sequencing error rate, try to lower the k-mer
length (-k)
865 Rank 15: sent 50519 messages, received 50520 messages.
866 Rank 14: sent 50583 messages, received 50584 messages.
867 Rank 13: sent 50504 messages, received 50505 messages.
868 Rank 12: sent 50565 messages, received 50566 messages.
869 Rank 11: sent 50318 messages, received 50319 messages.
870 Rank 10: sent 50318 messages, received 50319 messages.
871 Rank 9: sent 50328 messages, received 50329 messages.
872 Rank 8: sent 50590 messages, received 50591 messages.
873 Rank 7: sent 50494 messages, received 50495 messages.
874 Rank 6: sent 50421 messages, received 50422 messages.
875 Rank 5: sent 50401 messages, received 50402 messages.
876 Rank 4: sent 72261 messages, received 72262 messages.
877 Rank 3: sent 118348 messages, received 118349 messages.
878 Rank 2: sent 118723 messages, received 118724 messages.
879 Rank 1: sent 118452 messages, received 118453 messages.
880 Rank 0: sent 118589 messages, received 118573 messages.
how can i set the average coverage? Because all the papers i see have
examined at coverage of N50, N40 , N30
also by this output i want to ask you if i'm running in parallel, the Rank
symbolize the spesific CPU/ task??
i gave this commant:
14 srun ~/Ray-1.7/Ray -n 16 -k 35 -minimumCoverage 40 \
15 -p ~/Staphylococcus_aureus/frag_1.fastq
~/Staphylococcus_aureus/frag_2.fastq\
16 -p ~/Staphylococcus_aureus/shortjump_1.fastq
~/Staphylococcus_aureus/shortjump_2.fastq\
17 -o Staphy1635c40
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