Error with PathConsensus ...

[marcovth]

Hello ...

I have been running this script ...

#!/bin/bash 

set -eu 

contigs=$1 

reads1=$2

reads2=$3 

k=$4 

output=$5 

bwa index $contigs 

bwa mem -a -t16 -S -P -k$k $contigs $reads1 $reads2 | gzip > $contigs.sam.gz 

abyss-longseqdist -k$k  $contigs.sam.gz | grep -v "l=" > $contigs.dist.dot 

abyss-scaffold -v -k$k -s200- -n1 -g $contigs.path.dot $contigs $contigs.dist.dot > $contigs.path 

PathConsensus -v -k$k -p1 -s ${contigs}2 -g ${contigs}2.adj -o ${contigs}2.path $contigs $contigs $contigs.path 

cat $contigs ${contigs}2.fa | MergeContigs -v -k$k -o $output - ${contigs}2.adj ${contigs}2.path 

However, with PathConsensus I am getting the following error ...

PathConsensus -v -k 25 -p1 -s Cgriseus17AGY.seq2 -g Cgriseus17AGY.seq2.adj -o Cgriseus17AGY.seq2.path Cgriseus17AGY.seq Cgriseus17AGY.seq Cgriseus17AGY.seq.path 

Reading `Cgriseus17AGY.seq'...

error: Expected `=' and saw `r'

What could be wrong with my Cgriseus17AGY.seq file?

This file are these fasta files concatenated into a single file ...

http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=APMK01#contigs

Thanks for any suggestion.

- Marco.

[Ben Vandervalk]

Hi Marco,

On the line:

$ PathConsensus -v -k$k -p1 -s ${contigs}2 -g ${contigs}2.adj -o ${contigs}2.path $contigs $contigs $contigs.path 

Replace the second occurrence of $contigs with '$contigs.path.dot'.

- Ben


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[marcovth]

Thanks a lot for the reply.

Do you mean? ...

PathConsensus -v -k 25 -p1 -s Cgriseus17AGY.seq2 -g Cgriseus17AGY.seq2.adj -o Cgriseus17AGY.seq2.path Cgriseus17AGY.seq Cgriseus17AGY.seq.path.dot Cgriseus17AGY.seq.path 

Reading `Cgriseus17AGY.seq.path.dot'...

Reading `Cgriseus17AGY.seq'...

error: unexpected ID: `gi|530169401|gb|APMK01000002.1|'

I also tried without success ...

PathConsensus -v -k 25 -p1 -s Cgriseus17AGY.seq2 -g Cgriseus17AGY.seq2.adj -o Cgriseus17AGY.seq2.path Cgriseus17AGY.seq.path.dot Cgriseus17AGY.seq Cgriseus17AGY.seq.path 

[Ben Vandervalk]

Hi Marco,

The first command line is the right one, I think (based on PathConsensus --help).

Sorry to hear you are getting another error, though. 

I notice that 'gi|530169401|gb|APMK01000002.1|' is only the second sequence in your list of input FASTA sequences.   That leads me to suspect that the problem is due to using multiline FASTA as input.

Could you try converting to single-line fasta and running your script again?  I think you can do the conversion with:

$ abyss-tofastq Cgriseus17AGY.seq > single-line.fasta

Another thing to try would be replacing the FASTA IDs with integers (to see if the problem is related to parsing the FASTA headers.)

- Ben

[marcovth]

Unfortunately, abyss-tofastq didn't make a difference.

Do you know of a tools that could delete the "Cricetulus griseus strain 17A/GY chromosome 1 chr1_contig_64483, whole genome shotgun sequence" in each of the fasta ID's? 

The fasta file is too big for a text editor.

e.g. 

>gi|529499428|gb|APMK01319215.1| Cricetulus griseus strain 17A/GY chromosome 1 chr1_contig_64483, whole genome shotgun sequence

[Ka Ming Nip]

Hi Marco,

You can use the unix `cut` command, ie.

$ cut -f1 -d ' ' input_reads.fa | abyss-tofastq > output_reads.fa

Note:
-d ' ' to set space character as delimiter
-f1 to extract the first column

Hope that helps!

Ka Ming