[stdout]
Loading index
Loading index
Checking sample info...
Checking FASTQ folder...
Checking reference...
Checking reference_path (/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/mm10_premrna_usethis) on scc-wj2...
detect_chemistry get-transcripts /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/mm10_premrna_usethis/fasta/genome.fa /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/mm10_premrna_usethis/genes/genes.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_premRNA_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/CHEMISTRY_DETECTOR/DETECT_CHEMISTRY/fork0/chnk0-u0b157e3faf/files/transcriptome.fa
detect_chemistry index-transcripts --skip=2 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_premRNA_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/CHEMISTRY_DETECTOR/DETECT_CHEMISTRY/fork0/chnk0-u0b157e3faf/files/transcriptome.fa /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_premRNA_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/CHEMISTRY_DETECTOR/DETECT_CHEMISTRY/fork0/chnk0-u0b157e3faf/files/kmers.idx
detect_chemistry map-reads /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_premRNA_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/CHEMISTRY_DETECTOR/DETECT_CHEMISTRY/fork0/chnk0-u0b157e3faf/files/kmers.idx /dev/null /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_premRNA_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/CHEMISTRY_DETECTOR/DETECT_CHEMISTRY/fork0/chnk0-u0b157e3faf/files/R1_out.json --initial-reads 10000 --fastqs /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_premRNA_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/CHEMISTRY_DETECTOR/DETECT_CHEMISTRY/fork0/chnk0-u0b157e3faf/files/R1_in.json
detect_chemistry map-reads /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_premRNA_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/CHEMISTRY_DETECTOR/DETECT_CHEMISTRY/fork0/chnk0-u0b157e3faf/files/kmers.idx /dev/null /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_premRNA_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/CHEMISTRY_DETECTOR/DETECT_CHEMISTRY/fork0/chnk0-u0b157e3faf/files/R2_out.json --initial-reads 10000 --fastqs /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_premRNA_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/CHEMISTRY_DETECTOR/DETECT_CHEMISTRY/fork0/chnk0-u0b157e3faf/files/R2_in.json
