[stdout]
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Checking FASTQ folder...
Checking reference...
Checking reference_path (/restricted/projectnb/waxmanlab/kkarri/tabula_muris/drop-seq/mm10_ref/updated-usethis-mm10plus-pcg-ercc-lnc-nodups) on scc-wj2...
samtools faidx /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH3/Nash_3_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/CHEMISTRY_DETECTOR/DETECT_CHEMISTRY/fork0/chnk0-u9daea754d0/files/ref.fa
detect_chemistry get-transcripts /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH3/Nash_3_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/CHEMISTRY_DETECTOR/DETECT_CHEMISTRY/fork0/chnk0-u9daea754d0/files/ref.fa /restricted/projectnb/waxmanlab/kkarri/tabula_muris/drop-seq/mm10_ref/updated-usethis-mm10plus-pcg-ercc-lnc-nodups/genes/genes.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH3/Nash_3_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/CHEMISTRY_DETECTOR/DETECT_CHEMISTRY/fork0/chnk0-u9daea754d0/files/transcriptome.fa
detect_chemistry index-transcripts /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH3/Nash_3_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/CHEMISTRY_DETECTOR/DETECT_CHEMISTRY/fork0/chnk0-u9daea754d0/files/transcriptome.fa /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH3/Nash_3_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/CHEMISTRY_DETECTOR/DETECT_CHEMISTRY/fork0/chnk0-u9daea754d0/files/kmers.idx
detect_chemistry map-reads /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH3/Nash_3_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/CHEMISTRY_DETECTOR/DETECT_CHEMISTRY/fork0/chnk0-u9daea754d0/files/kmers.idx /dev/null /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH3/Nash_3_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/CHEMISTRY_DETECTOR/DETECT_CHEMISTRY/fork0/chnk0-u9daea754d0/files/R1_out.json --initial-reads 10000 --fastqs /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH3/Nash_3_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/CHEMISTRY_DETECTOR/DETECT_CHEMISTRY/fork0/chnk0-u9daea754d0/files/R1_in.json
detect_chemistry map-reads /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH3/Nash_3_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/CHEMISTRY_DETECTOR/DETECT_CHEMISTRY/fork0/chnk0-u9daea754d0/files/kmers.idx /dev/null /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH3/Nash_3_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/CHEMISTRY_DETECTOR/DETECT_CHEMISTRY/fork0/chnk0-u9daea754d0/files/R2_out.json --initial-reads 10000 --fastqs /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH3/Nash_3_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/CHEMISTRY_DETECTOR/DETECT_CHEMISTRY/fork0/chnk0-u9daea754d0/files/R2_in.json
