Error - report not written and empty samples

Hi, We are running Nullarbor on a mixture of samples we sequenced ourselves, and some downloaded from ENA. When we run, we don't get a final report. Looking more closely, it looks like, for the samples we downlaoded from ENA, the assembled contigs (fasta) and snps (vcf) are empty (fasta all gaps and vcf is just the header). The nohup.out says there has been some error with java - I've compressed it and added it below.

I ran the offending samples through a workflow I use for mapping/snp calling (bwa mem, samtools, freebayes) and I found that there is a problem with bwa mem throwing an error due to orphan reads in the split paired read files generated by using the ena toolkit 'fastq-dump' command. When I download the .fastq files as a single interleaved file seems to work fine. Not sure if this is contributing to the problem or not.

The command we ran was: Command 1: nullarbor2.pl --name ancientA --ref /home/ubuntu/volume_sdb/Anthrax/AncientA/CZC5_NZ_AP018443.1.fasta --input ./ancientA.tab --outdir ancientA Command 2: nohup nice make -j 2 -C /home/ubuntu/volume_sdb/Nullarbor/AncientA/ancientA &

Any assistance would be greatly appreciated, thank you so much!

nohup.out.gz