I'm trying to run AlignGraph using this command:
AlignGraph --read1 AM_1P.fa --read2 AM_2P.fa --contig Am_assembly_47.scafSeq.fa --genome AMgenomic.fa --distanceLow 11 --distanceHigh 283 --extendedContig AM_extended.fa --remainingContig AM_remaining.fa --kMer 47
The program does not run, instead printing only this output:
AlignGraph: algorithm for secondary de novo genome assembly guided by closely related references
By Ergude Bao, CS Department, UC-Riverside. All Rights Reserved
AlignGraph --read1 reads_1.fa --read2 reads_2.fa --contig contigs.fa --genome genome.fa --distanceLow distanceLow --distanceHigh distancehigh --extendedContig extendedContigs.fa --remainingContig remainingContigs.fa [--kMer k --insertVariation insertVariation --covereage coverage --part p --ratioCheck --iterativeMap --misassemblyRemoval --resume]
Inputs:
--read1 is the the first pair of PE DNA reads in fasta format
--read2 is the the second pair of PE DNA reads in fasta format
--contig is the initial contigs in fasta format
--genome is the reference genome in fasta format
--distanceLow is the lower bound of alignment distance between the first and second pairs of PE DNA reads (recommended: max{insert length - 1000, single read length}) . . .
I am on a linux cluster environment with all the files in the same directory. Any help troubleshooting this issue would be appreciated!
Hello,
I'm trying to run AlignGraph using this command: AlignGraph --read1 AM_1P.fa --read2 AM_2P.fa --contig Am_assembly_47.scafSeq.fa --genome AMgenomic.fa --distanceLow 11 --distanceHigh 283 --extendedContig AM_extended.fa --remainingContig AM_remaining.fa --kMer 47
The program does not run, instead printing only this output:
AlignGraph: algorithm for secondary de novo genome assembly guided by closely related references By Ergude Bao, CS Department, UC-Riverside. All Rights Reserved
AlignGraph --read1 reads_1.fa --read2 reads_2.fa --contig contigs.fa --genome genome.fa --distanceLow distanceLow --distanceHigh distancehigh --extendedContig extendedContigs.fa --remainingContig remainingContigs.fa [--kMer k --insertVariation insertVariation --covereage coverage --part p --ratioCheck --iterativeMap --misassemblyRemoval --resume] Inputs: --read1 is the the first pair of PE DNA reads in fasta format --read2 is the the second pair of PE DNA reads in fasta format --contig is the initial contigs in fasta format --genome is the reference genome in fasta format --distanceLow is the lower bound of alignment distance between the first and second pairs of PE DNA reads (recommended: max{insert length - 1000, single read length}) . . .
I am on a linux cluster environment with all the files in the same directory. Any help troubleshooting this issue would be appreciated!