Issue with finding sPCR products

[Deco313]

HI, I am testing Sharkmer's sPCR function on a library that I have previously retrieved a full mitogenome from using the standard primers for this group

sequence I am trying to recover GCTGCTAGTTGGTATTGGCATTTTGTAGATGTGGTTTGGTTGTTTTTATATGTATGTATTTACTGGTGGGGTTCTTAGCCCGGGCCATGGTTACATAATGCTTAGCTAAGCTTGTAGAGTCAACTAACGGTAAGTTTTCAGACTCATAATCTGATTATGCAGGTTCAACTCCTGCCTCTACCTATAGAATCGCCATGGGGAACTTATTCGCTCTGTATGCCCTTAGCAAGGGCCAAATACCTGTACAGTATTTTAACTTAATGGAGGAGAATTATTCTAAGTATGGGCTATCAGTAATCCAGCTTATCCAGATTGGTAAGTTCTATGAACTTTGGCAGAAGCCTGATGTTCCTAGTATCCAACAAGCATACTCTCAAGCTGAGTTATTAGTTGAGTCGTCCATACGAAGTAGGTCTTTAGGGGTAACACCTCCCATTGAACAAGTTGCTTCGTTACTTGATATGAGAATAACATCACCCGGTAAAAGATCCTTGCTTCAAATGGGGTTTCCTATTTATTCCCTAACTACTTATCTAAGCACCTTGTTGGATAAAGGTTGGACTATTATAGTTATTGATGAATTAGCCACTGATAAATCGGGGCCGAAACAACGCGCAGTATCTCAGGTTTATTCTCCTAGTTGTAATTTAGAAGATTGTCCGGAATTATCTTATGTGATATCAATCTATTTTAAAGATGACTTACTAGGTATTACTTTATTTTCTGCCATGAATGGGCACAGTATAATGTTTCCTGTCTATTGGGCCGACAGAGATAAAGTGGCTCGACTACTAATCAGTTATCGTATTAAAGAGGTAGTAATTAGGGCGGACTCGGAGGCCAATTATAGGGCACTAAATAAGATATATGATTTATTAATTGGTTGGAATTTATTCCCCTCTGAACCTAATGCCATAATTGAAGTTATGGAGGACCCGTGTTATTTATCTTATAGGTACGAAAATGATAATAAGGAGTGGCTTTTGCTTCA

Forward GCTGCTAGTTGGTATTGGCAT Reverse TSGAGCAAAAGCCACTCC

code:

zcat BAM_R*_P.fastq.gz | sharkmer -s BAM --max-reads 1000000 --pcr "GCTGCTAGTTGGTATTGGCAT,TSGAGCAAAAGCCACTCC,1200,mtMutS"

For gene mtMutS, no path was found from a forward primer binding site to a reverse binding site. Abandoning PCR. Suggested actions:

• The max_length for the PCR product of 1200 my be too short. Consider increasing it.
• The primers may have non-specific binding and are not close enough to generate a product. Consider increasing the primer TRIM length from the default to create a more specific primer.

Is there any reason why this isn't working?