In NF 4 Science, Genomics, Part 1: Method overview, step 1.2.3:
The command given:
gatk HaplotypeCaller \
-R /data/ref/ref.fasta \
-I /data/bam/reads_mother.bam \
-O /data/vcf/reads_mother.vcf \
-L /data/ref/intervals.bed
fails because the /data/vcf directory does not exist yet, and GATK will not create it. It will work if the directory is created in advance, but the command output given has this option as just -O reads_mother.vcf:
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /opt/conda/share/gatk4-4.5.0.0-0/gatk-package-4.5.0.0-local.jar HaplotypeCaller -R /data/ref/ref.fasta -I /data/bam/reads_mother.bam -O reads_mother.vcf -L /data/ref/intervals.bed
And step 1.2.4 has directions to create /data/vcf and move the files there, so it seems the intention was to have the files initially generate in the container's /tmp space (also as shown in the Directory contents box).
In NF 4 Science, Genomics, Part 1: Method overview, step 1.2.3:
The command given:
fails because the /data/vcf directory does not exist yet, and GATK will not create it. It will work if the directory is created in advance, but the command output given has this option as just -O reads_mother.vcf:
And step 1.2.4 has directions to create /data/vcf and move the files there, so it seems the intention was to have the files initially generate in the container's /tmp space (also as shown in the Directory contents box).