Hi Experts, I am using Rsubread align using following comand-
align (index="my_index",
readfile1 = "SRR123456_1.fastq" ,readfile2= "SRR123456_2.fastq",
type="rna",input_format = "FASTQ",
minFragLength=35,maxFragLength=151,useAnnotation="TRUE",
nthreads=64,
annot.ext = "my_annotation.gtf.gz",
isGTF = "TRUE",
sortReadsByCoordinates = "TRUE", output_format = "BAM")
here i have asigned 64 threads but in console, i see only 40 threads, I dont know why ? can you guys please explain. All i want to have fast alignment using all my threads. The cpu has – 12 cores which goes to 24 threads, but i was playing around nthreads parameter of align and came up this is the max number that it allows, again i dont know why/how ?
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==== ___ | | | | _ <| _ /| __| / / | | | |
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Rsubread 2.6.4
//================================= setting ==================================\
|| ||
|| Function : Read alignment (RNA-Seq) ||
|| Input file 1 : SRR123456_1.fastq ||
|| Input file 2 : SRR123456_2.fastq ||
|| Output file : SRR123456_1.fastq.subread.BAM (BAM), Sorted ||
|| Index name : my_index ||
|| ||
|| ------------------------------------ ||
|| ||
|| Threads : 40 ||
|| Phred offset : 33 ||
|| # of extracted subreads : 10 ||
|| Min read1 vote : 3 ||
|| Min read2 vote : 1 ||
|| Max fragment size : 151 ||
|| Min fragment size : 35 ||
|| Max mismatches : 3 ||
|| Max indel length : 5 ||
|| Report multi-mapping reads : yes ||
|| Max alignments per multi-mapping read : 1 ||
|| Annotations : GCF_000000000.1_ASM0000v1_geno ... ||
|| ||
\============================================================================//
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