Platanus assembler : unable to start contig assembly, any problem with the command?

Question: Platanus assembler : unable to start contig assembly, any problem with the command?

13 months ago by

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!

platanus • 765 views

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modified 13 months ago by Selenocysteine • 510 • written 13 months ago by johnnytam100 • 100

13 months ago by

Selenocysteine • 510

Dublin, Ireland

Selenocysteine • 510 wrote:

This error means that the call is not correctly formatted. I don't know this assembler, but I would guess that you forgot to put a flag before the number 2 close to the end?

ADD COMMENT • link written 13 months ago by Selenocysteine • 510

Solved, actually it's the opposite, I delete the 2, which was originally present in the example given by the manual :

Platanus assemble –o Pxut –f ./DRR02167[34]_[12].fastq –t 16 –m 128 2> assemble.log

Thank you!

ADD REPLY • link modified 13 months ago • written 13 months ago by johnnytam100 • 100

In the example, they use 2> assemble.log to redirect stderror to a file. In your original command you made a mistake by typing a space between 2 and >. That's why removing 2 helped. Alternatively, removing the space should fix this as well.

ADD REPLY • link written 11 weeks ago by al-ash • 70

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