Description
Hi, I do not know if it is a silly error... but I am trying to run pyScaf to do scaffolding in my Canu (Pabio) assembly with my nanopore reads.
this is my .sh
pyScaf -f /dataX/sami/genomes/p_ulei_polished.fasta -o p_ulei_scaf_nano --dotplot pdf -n /data1/sami/rawdata/nanopore/nanopore_all.fastq
the less slurm-XX.out is
Options: Namespace(dotplot='pdf', fasta='/dataX/sami/genomes/p_ulei_polished.fasta', fastq=None, identity=0.33, joins=5, linkratio=0.7, load=0.2, log=<open file '', mode 'w' at 0x7f1660bc61e0>, longreads=['/data1/sami/rawdata/nanopore/nanopore_all.fastq'], mapq=10, maxgap=0, norearrangements=False, output=<open file 'p_ulei_scaf_nano', mode 'w' at 0x7f165a43f6f0>, overlap=0.66, ref='', threads=4)
maxgap cut-off of 936958 bp
##################################################
[Tue Oct 8 17:05:21 2019][ 7 Mb] Aligning long reads on contigs...
File "/home/sami/anaconda2/bin/maf-convert", line 136
print(line, end="")
^
SyntaxError: invalid syntax
0 0
##################################################
[Tue Oct 8 17:05:21 2019][ 7 Mb] Reporting scaffolds...
93695813 bp in 230 scaffolds. Details in p_ulei_scaf_nano.tsv
Scaffolds saved to: p_ulei_scaf_nano
##################################################
[Tue Oct 8 17:05:21 2019][ 56 Mb] Saving dotplots to: p_ulei_scaf_nano.pdf
[WARNING] Unsupported sequence format p_ulei_scaf_nano in /data1/sami/rawdata/nanopore/nanopore_all.fastq
The program is not running. Can you advise me something? my nanopore reads are not compressed. We install both pyScaf and Dependencies with bioconda.
Thanks a miilion