[stdout]
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Checking FASTQ folder...
Checking reference...
Checking reference_path (/ufrc/ewang/lancetdenes/refdata-cellranger-mm10-3.0.0) on c2a-s12.ufhpc...
detect_chemistry get-transcripts /ufrc/ewang/lancetdenes/refdata-cellranger-mm10-3.0.0/fasta/genome.fa /ufrc/ewang/lancetdenes/refdata-cellranger-mm10-3.0.0/genes/genes.gtf /ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/CHEMISTRY_DETECTOR/DETECT_CHEMISTRY/fork0/chnk0-u85e8936e6d/files/transcriptome.fa
detect_chemistry index-transcripts /ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/CHEMISTRY_DETECTOR/DETECT_CHEMISTRY/fork0/chnk0-u85e8936e6d/files/transcriptome.fa /ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/CHEMISTRY_DETECTOR/DETECT_CHEMISTRY/fork0/chnk0-u85e8936e6d/files/kmers.idx
detect_chemistry map-reads /ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/CHEMISTRY_DETECTOR/DETECT_CHEMISTRY/fork0/chnk0-u85e8936e6d/files/kmers.idx /dev/null /ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/CHEMISTRY_DETECTOR/DETECT_CHEMISTRY/fork0/chnk0-u85e8936e6d/files/R1_out.json --initial-reads 10000 --fastqs /ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/CHEMISTRY_DETECTOR/DETECT_CHEMISTRY/fork0/chnk0-u85e8936e6d/files/R1_in.json
detect_chemistry map-reads /ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/CHEMISTRY_DETECTOR/DETECT_CHEMISTRY/fork0/chnk0-u85e8936e6d/files/kmers.idx /dev/null /ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/CHEMISTRY_DETECTOR/DETECT_CHEMISTRY/fork0/chnk0-u85e8936e6d/files/R2_out.json --initial-reads 10000 --fastqs /ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/CHEMISTRY_DETECTOR/DETECT_CHEMISTRY/fork0/chnk0-u85e8936e6d/files/R2_in.json
