AlignGraph doesn't response but i have what it needs

Question

[Calvin]

This is the command line i was running AlignGraph --read1 W_S1_L001_R1_001.fasta --read2 W_S1_L001_R2_001.fasta --contigs 04.break.broken_assembly.fa --genome sequence.fasta.txt --distanceLow 300 --distanceHigh 1300 --extendedContig S.Pneu_extendedContigs.fa --remainingContigs S.Pneu_remainingContigs.fa And when i press enter, it gives me this which is manual page and there is no error message.

I have install bowtie2 and pblat and set their variable path How can i solve this ?

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}) --distanceHigh is the upper bound of alignment distance between the first and second pairs of PE DNA reads (recommended: insert length + 1000) Outputs: --extendedContig is the extended contig file in fasta format --remainingContig is the not extended initial contig file in fasta format

Options: --kMer is the k-mer size (default: 5) --insertVariation is the small variation of insert length (default: 50) --coverage is the minimum coverage to keep a path in de Bruijn graph (default: 20) --part is the number of parts a chromosome is divided into when it is loaded to reduce memory requirement (default: 1) --fastMap calls NUCMER to make fast but less sensitive and accurate contig alignment instead of BLAT (default: none) --ratioCheck checks read alignment ratio to the reference beforehand and warns if the ratio is too low; may take a little more time (default: none) --iterativeMap aligns reads to one chromosome and then another rather than directly to the genome, which increases sensitivity while loses precision (default: none) --misassemblyRemoval detects and then breaks at or removes misassembed regions (default: none) --resume resumes the previous unfinished running from several checkpoints (default: none)

Answer 1

[Sej Modha]

I think you have a typo in the --contig parameter, it's not --contigs.

[Calvin]

i corrected it. it still doesn't work

[Sej Modha]

You should check your command again, there is another typo in --remainingContig You are typing --remainingContig**s** instead with an extra s. Normally when you get such syntax error, it is advisable that you make sure that there are no typos in your command before posting them on the web!