Thanks for the suggestion! I have tried running NASP with the example data, but am running into the same issue. This is the output in the runlog.txt file:
09/19/2018 11:34:24 INFO $PATH=/home/ubuntu/nasp/bin:/home/ubuntu/bin:/home/ubuntu/.local/bin:/home/linuxbrew/.linuxbrew/bin:/home/linuxbrew/.linuxbrew/sbin:/mnt/galaxy/tools/bin:/usr/lib/postgresql/9.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/usr/lib/jvm/java-8-oracle/bin:/usr/lib/jvm/java-8-oracle/db/bin:/usr/lib/jvm/java-8-oracle/jre/bin
09/19/2018 11:34:24 INFO $PYTHONPATH=
09/19/2018 11:34:24 INFO LOADEDMODULES=
09/19/2018 11:34:38 INFO Reference = ('reference', '/home/ubuntu/Analysis/NASP/example_1/reference.fasta')
09/19/2018 11:34:40 INFO FindDups = True
09/19/2018 11:34:42 INFO JobSubmitter = NONE
09/19/2018 11:34:42 INFO RunName = example_test1
09/19/2018 11:34:42 INFO Samtools = ('Samtools', '/home/linuxbrew/.linuxbrew/bin/samtools', '', {})
09/19/2018 11:34:42 INFO Index = ('Index', '/home/ubuntu/nasp/bin', '', {'name': 'nasp_index', 'num_cpus': '1', 'mem_requested': '2', 'walltime': '4', 'queue': '', 'args': ''})
09/19/2018 11:35:09 INFO Looking for external fastas in /home/ubuntu/Analysis/NASP/example_1...
09/19/2018 11:35:09 INFO ('reference', '/home/ubuntu/Analysis/NASP/example_1/reference.fasta')
09/19/2018 11:35:09 INFO ('example_1', '/home/ubuntu/Analysis/NASP/example_1/example_1.fasta')
09/19/2018 11:35:28 INFO AssemblyImporter = ('AssemblyImporter', '/home/linuxbrew/.linuxbrew/bin/delta-filter', '', {'num_cpus': '1', 'mem_requested': '4', 'walltime': '4', 'queue': '', 'args': ''})
09/19/2018 11:35:28 INFO DupFinder = ('DupFinder', '/home/linuxbrew/.linuxbrew/bin/nucmer', '', {'num_cpus': '1', 'mem_requested': '4', 'walltime': '4', 'queue': '', 'args': ''})
09/19/2018 11:35:39 INFO Looking for read files in /home/ubuntu/Analysis/NASP/example_1...
09/19/2018 11:35:39 INFO ('example_1_L001', '/home/ubuntu/Analysis/NASP/example_1/example_1_L001_R1_001.fastq.gz', '/home/ubuntu/Analysis/NASP/example_1/example_1_L001_R2_001.fastq.gz')
09/19/2018 11:35:47 INFO Getting Aligners...
09/19/2018 11:35:51 INFO ('BWA-mem', '/home/linuxbrew/.linuxbrew/bin/bwa', '', {'num_cpus': '4', 'mem_requested': '10', 'walltime': '36', 'queue': '', 'args': ''})
09/19/2018 11:35:55 INFO Getting SNP Callers...
09/19/2018 11:35:59 INFO ('GATK', '/home/ubuntu/programs/GenomeAnalysisTK.jar', '-stand_call_conf 100 -ploidy 1', {'num_cpus': '4', 'mem_requested': '10', 'walltime': '36', 'queue': '', 'args': ''})
09/19/2018 11:36:07 INFO ('SAMtools', '/home/linuxbrew/.linuxbrew/bin/bcftools', '', {'num_cpus': '4', 'mem_requested': '10', 'walltime': '36', 'queue': '', 'args': ''})
09/19/2018 11:36:08 INFO Picard = ('Picard', '/home/ubuntu/programs/picard.jar', '', {})
09/19/2018 11:36:12 INFO CoverageFilter = 10
09/19/2018 11:36:12 INFO ProportionFilter = 0.9
09/19/2018 11:36:14 INFO MatrixGenerator = ('MatrixGenerator', '/home/ubuntu/nasp/lib/python3.6/site-packages/nasp/nasptool_linux_64', '', {'name': 'nasp_matrix', 'num_cpus': '8', 'mem_requested': '8', 'walltime': '48', 'queue': '', 'args': ''})
09/19/2018 11:36:24 INFO command = format_fasta --inputfasta /home/ubuntu/Analysis/NASP/example_1/reference.fasta --outputfasta /home/ubuntu/Analysis/NASP/example_test1/reference/reference.fasta
/home/linuxbrew/.linuxbrew/bin/bwa index /home/ubuntu/Analysis/NASP/example_test1/reference/reference.fasta
java -Xmx2G -jar /home/ubuntu/programs/picard.jar CreateSequenceDictionary R=/home/ubuntu/Analysis/NASP/example_test1/reference/reference.fasta O=/home/ubuntu/Analysis/NASP/example_test1/reference/reference.dict
/home/linuxbrew/.linuxbrew/bin/samtools faidx /home/ubuntu/Analysis/NASP/example_test1/reference/reference.fasta
09/19/2018 11:36:24 DEBUG submit_command = while [ `free -m | grep cache: | awk '{ print $4 }'` -lt 1500 ]; do sleep 300; done; format_fasta --inputfasta /home/ubuntu/Analysis/NASP/example_1/reference.fasta --outputfasta /home/ubuntu/Analysis/NASP/example_test1/reference/reference.fasta; /home/linuxbrew/.linuxbrew/bin/bwa index /home/ubuntu/Analysis/NASP/example_test1/reference/reference.fasta; java -Xmx2G -jar /home/ubuntu/programs/picard.jar CreateSequenceDictionary R=/home/ubuntu/Analysis/NASP/example_test1/reference/reference.fasta O=/home/ubuntu/Analysis/NASP/example_test1/reference/reference.dict; /home/linuxbrew/.linuxbrew/bin/samtools faidx /home/ubuntu/Analysis/NASP/example_test1/reference/reference.fasta
09/19/2018 11:36:24 INFO jobid = 16352
09/19/2018 11:36:24 INFO command = find_duplicates --nucmerpath /home/linuxbrew/.linuxbrew/bin/nucmer --reference /home/ubuntu/Analysis/NASP/example_test1/reference/reference.fasta
09/19/2018 11:36:24 DEBUG submit_command = while kill -0 16352; do sleep 300; done; while [ `free -m | grep cache: | awk '{ print $4 }'` -lt 3000 ]; do sleep 300; done; find_duplicates --nucmerpath /home/linuxbrew/.linuxbrew/bin/nucmer --reference /home/ubuntu/Analysis/NASP/example_test1/reference/reference.fasta
09/19/2018 11:36:24 INFO jobid = 16362
09/19/2018 11:36:24 INFO command = format_fasta --inputfasta /home/ubuntu/Analysis/NASP/example_1/example_1.fasta --outputfasta /home/ubuntu/Analysis/NASP/example_test1/external/example_1.fasta
convert_external_genome --nucmerpath /home/linuxbrew/.linuxbrew/bin/nucmer --nucmerargs '' --deltafilterpath /home/linuxbrew/.linuxbrew/bin/delta-filter --deltafilterargs '' --reference /home/ubuntu/Analysis/NASP/example_test1/reference/reference.fasta --external /home/ubuntu/Analysis/NASP/example_test1/external/example_1.fasta --name example_1
09/19/2018 11:36:24 DEBUG submit_command = while kill -0 16352; do sleep 300; done; while [ `free -m | grep cache: | awk '{ print $4 }'` -lt 3000 ]; do sleep 300; done; format_fasta --inputfasta /home/ubuntu/Analysis/NASP/example_1/example_1.fasta --outputfasta /home/ubuntu/Analysis/NASP/example_test1/external/example_1.fasta; convert_external_genome --nucmerpath /home/linuxbrew/.linuxbrew/bin/nucmer --nucmerargs '' --deltafilterpath /home/linuxbrew/.linuxbrew/bin/delta-filter --deltafilterargs '' --reference /home/ubuntu/Analysis/NASP/example_test1/reference/reference.fasta --external /home/ubuntu/Analysis/NASP/example_test1/external/example_1.fasta --name example_1
09/19/2018 11:36:24 INFO jobid = 16368
09/19/2018 11:36:24 INFO command = /home/linuxbrew/.linuxbrew/bin/bwa mem -R '@RG\tID:example_1_L001\tSM:example_1_L001' -t 4 /home/ubuntu/Analysis/NASP/example_test1/reference/reference.fasta /home/ubuntu/Analysis/NASP/example_1/example_1_L001_R1_001.fastq.gz /home/ubuntu/Analysis/NASP/example_1/example_1_L001_R2_001.fastq.gz | /home/linuxbrew/.linuxbrew/bin/samtools view -S -b -h - | /home/linuxbrew/.linuxbrew/bin/samtools sort - example_1_L001-bwamem
/home/linuxbrew/.linuxbrew/bin/samtools index example_1_L001-bwamem.bam
09/19/2018 11:36:24 DEBUG submit_command = while kill -0 16352; do sleep 300; done; while [ `free -m | grep cache: | awk '{ print $4 }'` -lt 7500 ]; do sleep 300; done; /home/linuxbrew/.linuxbrew/bin/bwa mem -R '@RG\tID:example_1_L001\tSM:example_1_L001' -t 4 /home/ubuntu/Analysis/NASP/example_test1/reference/reference.fasta /home/ubuntu/Analysis/NASP/example_1/example_1_L001_R1_001.fastq.gz /home/ubuntu/Analysis/NASP/example_1/example_1_L001_R2_001.fastq.gz | /home/linuxbrew/.linuxbrew/bin/samtools view -S -b -h - | /home/linuxbrew/.linuxbrew/bin/samtools sort - example_1_L001-bwamem ; /home/linuxbrew/.linuxbrew/bin/samtools index example_1_L001-bwamem.bam
09/19/2018 11:36:24 INFO jobid = 16374
09/19/2018 11:36:24 INFO command = java -Xmx10G -jar /home/ubuntu/programs/GenomeAnalysisTK.jar -T UnifiedGenotyper -dt NONE -glm BOTH -I /home/ubuntu/Analysis/NASP/example_test1/bwamem/example_1_L001-bwamem.bam -R /home/ubuntu/Analysis/NASP/example_test1/reference/reference.fasta -nt 4 -o example_1_L001-bwamem-gatk.vcf -out_mode EMIT_ALL_CONFIDENT_SITES -baq RECALCULATE -stand_call_conf 100 -ploidy 1
09/19/2018 11:36:24 DEBUG submit_command = while kill -0 16374; do sleep 300; done; while [ `free -m | grep cache: | awk '{ print $4 }'` -lt 7500 ]; do sleep 300; done; java -Xmx10G -jar /home/ubuntu/programs/GenomeAnalysisTK.jar -T UnifiedGenotyper -dt NONE -glm BOTH -I /home/ubuntu/Analysis/NASP/example_test1/bwamem/example_1_L001-bwamem.bam -R /home/ubuntu/Analysis/NASP/example_test1/reference/reference.fasta -nt 4 -o example_1_L001-bwamem-gatk.vcf -out_mode EMIT_ALL_CONFIDENT_SITES -baq RECALCULATE -stand_call_conf 100 -ploidy 1
09/19/2018 11:36:24 INFO jobid = 16380
09/19/2018 11:36:24 INFO command = /home/linuxbrew/.linuxbrew/bin/samtools mpileup -uD -d 10000000 -f /home/ubuntu/Analysis/NASP/example_test1/reference/reference.fasta /home/ubuntu/Analysis/NASP/example_test1/bwamem/example_1_L001-bwamem.bam | /home/linuxbrew/.linuxbrew/bin/bcftools view -ceg - > /home/ubuntu/Analysis/NASP/example_test1/samtools/example_1_L001-bwamem-samtools.vcf
09/19/2018 11:36:24 DEBUG submit_command = while kill -0 16374; do sleep 300; done; while [ `free -m | grep cache: | awk '{ print $4 }'` -lt 7500 ]; do sleep 300; done; /home/linuxbrew/.linuxbrew/bin/samtools mpileup -uD -d 10000000 -f /home/ubuntu/Analysis/NASP/example_test1/reference/reference.fasta /home/ubuntu/Analysis/NASP/example_test1/bwamem/example_1_L001-bwamem.bam | /home/linuxbrew/.linuxbrew/bin/bcftools view -ceg - > /home/ubuntu/Analysis/NASP/example_test1/samtools/example_1_L001-bwamem-samtools.vcf
09/19/2018 11:36:24 INFO jobid = 16386
09/19/2018 11:36:24 INFO command = /home/ubuntu/nasp/lib/python3.6/site-packages/nasp/nasptool_linux_64 matrix --dto-file /home/ubuntu/Analysis/NASP/example_test1/matrix_dto.xml --num-threads 8
09/19/2018 11:36:24 DEBUG submit_command = while [ -s /home/ubuntu/Analysis/NASP/example_test1/nasp_matrix_dependent_pids ]; do sleep 600; for pid in `cat /home/ubuntu/Analysis/NASP/example_test1/nasp_matrix_dependent_pids`; do kill -0 "$pid" 2>/dev/null || sed -i "/^$pid$/d" /home/ubuntu/Analysis/NASP/example_test1/nasp_matrix_dependent_pids; done; done; rm /home/ubuntu/Analysis/NASP/example_test1/nasp_matrix_dependent_pids; while [ `free -m | grep cache: | awk '{ print $4 }'` -lt 46500 ]; do sleep 300; done; /home/ubuntu/nasp/lib/python3.6/site-packages/nasp/nasptool_linux_64 matrix --dto-file /home/ubuntu/Analysis/NASP/example_test1/matrix_dto.xml --num-threads 8
09/19/2018 11:36:24 INFO jobid = 16392
09/19/2018 11:36:24 INFO command = /home/ubuntu/nasp/lib/python3.6/site-packages/nasp/nasptool_linux_64 export --type vcf bestsnp.tsv > bestsnp.vcf & /home/ubuntu/nasp/lib/python3.6/site-packages/nasp/nasptool_linux_64 export --type vcf missingdata.tsv > missingdata.vcf & /home/ubuntu/nasp/lib/python3.6/site-packages/nasp/nasptool_linux_64 export --type fasta bestsnp.tsv > bestsnp.fasta & /home/ubuntu/nasp/lib/python3.6/site-packages/nasp/nasptool_linux_64 export --type fasta missingdata.tsv > missingdata.fasta & wait
09/19/2018 11:36:24 DEBUG submit_command = while kill -0 16392; do sleep 300; done; while [ `free -m | grep cache: | awk '{ print $4 }'` -lt 46500 ]; do sleep 300; done; /home/ubuntu/nasp/lib/python3.6/site-packages/nasp/nasptool_linux_64 export --type vcf bestsnp.tsv > bestsnp.vcf & /home/ubuntu/nasp/lib/python3.6/site-packages/nasp/nasptool_linux_64 export --type vcf missingdata.tsv > missingdata.vcf & /home/ubuntu/nasp/lib/python3.6/site-packages/nasp/nasptool_linux_64 export --type fasta bestsnp.tsv > bestsnp.fasta & /home/ubuntu/nasp/lib/python3.6/site-packages/nasp/nasptool_linux_64 export --type fasta missingdata.tsv > missingdata.fasta & wait
09/19/2018 11:36:24 INFO jobid = 16398