squid running errors about squid HOT 2 OPEN

The error indicates that no edges are constructed. It shouldn't be because of memory. Can you make sure that your BAM alignments are sorted? And can you check that chimeric alignments exist in the BAM by selecting sam flag not to be 14 and count alignments:

samtools view -F14 <bam file> | wc -l

If the BAM is sorted and contains chimeric alignments, is it possible for you to share the BAM file for us to further look into the error?

from squid.

Hi,
I know that this issue is 1 year old but I had the same problem and I found a/the solution. It may help some people coming here with the same problem.
Based on @Congm12 answer, I saw that no chimera were found in my alignment where I was supposed to (experimental control).
I changed my bwa algorithm command from bwa aln to bwa mem and it worked. (Based on : http://bio-bwa.sourceforge.net/bwa.shtml )
NB: I have Illumina reads

from squid.