Question: Platanus assembler : unable to start contig assembly, any problem with the command?
0
johnnytam100 • 100 wrote:
I used the following command in hope to start the contig assembly using Platanus :
/data/tam/script/platanus/platanus assemble -f /data/tam/genome/reads/kmer_containing_reads/TTN_3TTN_TTNR1_for_contig/step4_TTN_3TTN_TTNR1_master.fastq -o 1d_TTN_3TTN_TTNR1_for_contig_platanus -m 128 -t 16 2 > assemble.log
However, the following message regarding the usage of option appeared.
Platanus version: 1.2.4
/data/tam/script/platanus/platanus assemble -f /data/tam/genome/reads/kmer_containing_reads/TTN_3TTN_TTNR1_for_contig/step4_TTN_3TTN_TTNR1_master.fastq -o 1d_TTN_3TTN_TTNR1_for_contig_platanus -m 128 -t 16 2
Usage platanus assemble [Options]
Options:
-o STR : prefix of output files (default 1d_TTN_3TTN_TTNR1_for_contig_platanus, length <= 200)
-f FILE1 [FILE2 ...] : reads file (fasta or fastq, number <= 100)
-k INT : initial k-mer size (default 32)
-s INT : step size of k-mer extension (>= 1, default 10)
-n INT : initial k-mer coverage cutoff (default 0, 0 means auto)
-c INT : minimun k-mer coverage (default 2)
-a FLOAT : k-mer extension safety level (default 10.0)
-u FLOAT : maximum difference for bubble crush (identity, default 0.1)
-d FLOAT : maximum difference for branch cutting (coverage ratio, default 0.5)
-e FLOAT : k-mer coverage depth (k = initial k-mer size specified by -k) of homozygous region (default auto)
-t INT : number of threads (<= 100, default 16)
-m INT : memory limit for making kmer distribution (GB, >=1, default 128)
-tmp DIR : directory for temporary files (default .)
Outputs:
PREFIX_contig.fa
PREFIX_contigBubble.fa
PREFIX_kmerFrq.tsv
Anything wrong with my command?
Thank you!
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modified 3.3 years ago
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Selenocysteine • 600
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written
3.3 years ago by
johnnytam100 • 100