Malabady

Thanks! here is it reads_to_ctg_map.py --threads 2 \ /home/malabady/Projects/Ab10/Ab10Only_reads/reads/passQC_corr/mp6k75_good_1.cor.fastq.gz \ /home/malabady/Projects/Ab10/Ab10Only_reads/reads/passQC_corr/mp6k75_good_2.cor.fastq.gz \ /home/malabady/Projects/Ab10/Ab10Only_reads/assembly/spades/scaffolds.min0.5k.fasta \ mp6k75.bwa.bam \

theres is no back slash are the end of the last line.

Just got a clone of BESST using git clone and rerun the script again but it produced the same error (see below.) earlier I was looking up this error online...

But mp6k75.bwa.bam dir is generated by the script during the run. I didn't make it. I think the script the need to be modified not to produce this folder!!

this part: pysam.sort("-o", bwa_output + ".bam", output_path)