[stdout]
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Error fetching io for 49347: permission deniedChecking sample info...
Checking FASTQ folder...
Checking reference...
Checking reference_path (/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/updated-usethis-mm10plus-pcg-ercc-lnc-nodups-mcherry) on scc-wk2...
detect_chemistry get-transcripts /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/updated-usethis-mm10plus-pcg-ercc-lnc-nodups-mcherry/fasta/genome.fa /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/updated-usethis-mm10plus-pcg-ercc-lnc-nodups-mcherry/genes/genes.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/CHEMISTRY_DETECTOR/DETECT_CHEMISTRY/fork0/chnk0-ubebf71c328/files/transcriptome.fa
detect_chemistry index-transcripts /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/CHEMISTRY_DETECTOR/DETECT_CHEMISTRY/fork0/chnk0-ubebf71c328/files/transcriptome.fa /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/CHEMISTRY_DETECTOR/DETECT_CHEMISTRY/fork0/chnk0-ubebf71c328/files/kmers.idx
detect_chemistry map-reads /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/CHEMISTRY_DETECTOR/DETECT_CHEMISTRY/fork0/chnk0-ubebf71c328/files/kmers.idx /dev/null /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/CHEMISTRY_DETECTOR/DETECT_CHEMISTRY/fork0/chnk0-ubebf71c328/files/R1_out.json --initial-reads 10000 --fastqs /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/CHEMISTRY_DETECTOR/DETECT_CHEMISTRY/fork0/chnk0-ubebf71c328/files/R1_in.json
detect_chemistry map-reads /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/CHEMISTRY_DETECTOR/DETECT_CHEMISTRY/fork0/chnk0-ubebf71c328/files/kmers.idx /dev/null /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/CHEMISTRY_DETECTOR/DETECT_CHEMISTRY/fork0/chnk0-ubebf71c328/files/R2_out.json --initial-reads 10000 --fastqs /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/CHEMISTRY_DETECTOR/DETECT_CHEMISTRY/fork0/chnk0-ubebf71c328/files/R2_in.json
