Dec 08 22:02:27 ..... started STAR run Dec 08 22:02:27 ... starting to generate Genome files Dec 08 22:02:35 ..... processing annotations GTF Dec 08 22:02:45 ... starting to sort Suffix Array. This may take a long time... Dec 08 22:02:51 ... sorting Suffix Array chunks and saving them to disk... Dec 08 22:03:38 ... loading chunks from disk, packing SA... Dec 08 22:03:53 ... finished generating suffix array Dec 08 22:03:53 ... generating Suffix Array index Dec 08 22:04:28 ... completed Suffix Array index Dec 08 22:04:29 ..... inserting junctions into the genome indices Dec 08 22:05:17 ... writing Genome to disk ... Dec 08 22:05:18 ... writing Suffix Array to disk ... Dec 08 22:05:21 ... writing SAindex to disk Dec 08 22:05:22 ..... finished successfully Dec 08 22:05:22 ..... started STAR run Dec 08 22:05:22 ..... loading genome Dec 08 22:05:25 ..... started mapping Dec 08 22:16:24 ..... finished mapping Dec 08 22:16:26 ..... started sorting BAM Dec 08 22:18:37 ..... finished successfully Generating MD5 checksum for /gscratch/srlab/sam/data/C_gigas/RNAseq/2M_AGTCAA_L001_R1_001.fastq. Completed: MD5 checksum for /gscratch/srlab/sam/data/C_gigas/RNAseq/2M_AGTCAA_L001_R1_001.fastq. Generating MD5 checksum for /gscratch/srlab/sam/data/C_gigas/RNAseq/2M-HS_CCGTCC_L001_R1_001.fastq. Completed: MD5 checksum for /gscratch/srlab/sam/data/C_gigas/RNAseq/2M-HS_CCGTCC_L001_R1_001.fastq. Generating MD5 checksum for /gscratch/srlab/sam/data/C_gigas/RNAseq/4M_AGTTCC_L001_R1_001.fastq. Completed: MD5 checksum for /gscratch/srlab/sam/data/C_gigas/RNAseq/4M_AGTTCC_L001_R1_001.fastq. Generating MD5 checksum for /gscratch/srlab/sam/data/C_gigas/RNAseq/4M-HS_GTCCGC_L001_R1_001.fastq. Completed: MD5 checksum for /gscratch/srlab/sam/data/C_gigas/RNAseq/4M-HS_GTCCGC_L001_R1_001.fastq. Generating MD5 checksum for /gscratch/srlab/sam/data/C_gigas/RNAseq/6M_ATGTCA_L001_R1_001.fastq. Completed: MD5 checksum for /gscratch/srlab/sam/data/C_gigas/RNAseq/6M_ATGTCA_L001_R1_001.fastq. Generating MD5 checksum for /gscratch/srlab/sam/data/C_gigas/RNAseq/6M-HS_GTGAAA_L001_R1_001.fastq. Completed: MD5 checksum for /gscratch/srlab/sam/data/C_gigas/RNAseq/6M-HS_GTGAAA_L001_R1_001.fastq. [INFO ] multiqc : This is MultiQC v1.8 [INFO ] multiqc : Template : default [INFO ] multiqc : Searching : /gscratch/scrubbed/samwhite/outputs/20201208_cgig_STAR_RNAseq-to-NCBI-GCF_000297895.1_oyster_v9 [INFO ] star : Found 1 reports [INFO ] multiqc : Compressing plot data [INFO ] multiqc : Report : multiqc_report.html [INFO ] multiqc : Data : multiqc_data [INFO ] multiqc : MultiQC complete Generating MD5 checksum for /gscratch/srlab/sam/data/C_gigas/genomes/GCF_000297895.1_oyster_v9_genomic.fasta. Completed: MD5 checksum for /gscratch/srlab/sam/data/C_gigas/genomes/GCF_000297895.1_oyster_v9_genomic.fasta. Generating MD5 hecksum for /gscratch/srlab/sam/data/C_gigas/transcriptomes/GCF_000297895.1_oyster_v9_genomic.gtf.wl_keep_mito_v7.sorted.gtf. Completed: MD5 checksum for /gscratch/srlab/sam/data/C_gigas/transcriptomes/GCF_000297895.1_oyster_v9_genomic.gtf.wl_keep_mito_v7.sorted.gtf. Logging program options... Finished logging program options. Logging system PATH. Finished logging system PATH