Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/1104c/< Genome directory: >/gscratch/srlab/sr320/data/geoduck/v074/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 1-based (default) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v074/ chr PGA_scaffold1__77_contigs__length_89643857 (89643857 bp) chr PGA_scaffold2__36_contigs__length_69596280 (69596280 bp) chr PGA_scaffold3__111_contigs__length_57743597 (57743597 bp) chr PGA_scaffold4__129_contigs__length_65288255 (65288255 bp) chr PGA_scaffold5__109_contigs__length_67248332 (67248332 bp) chr PGA_scaffold6__104_contigs__length_61759565 (61759565 bp) chr PGA_scaffold7__69_contigs__length_43120122 (43120122 bp) chr PGA_scaffold8__63_contigs__length_61151155 (61151155 bp) chr PGA_scaffold9__45_contigs__length_38581958 (38581958 bp) chr PGA_scaffold10__49_contigs__length_53961475 (53961475 bp) chr PGA_scaffold11__79_contigs__length_51449921 (51449921 bp) chr PGA_scaffold12__71_contigs__length_50438331 (50438331 bp) chr PGA_scaffold13__52_contigs__length_44396874 (44396874 bp) chr PGA_scaffold14__91_contigs__length_45393038 (45393038 bp) chr PGA_scaffold15__101_contigs__length_47938513 (47938513 bp) chr PGA_scaffold16__33_contigs__length_31980953 (31980953 bp) chr PGA_scaffold17__51_contigs__length_34923512 (34923512 bp) chr PGA_scaffold18__69_contigs__length_27737463 (27737463 bp) Stored sequence information of 18 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: EPI-103_S27_L005_.CpG_report.txt <<< gzip: EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz: No such file or directory No last chromosome was defined, something must have gone wrong while reading the data in (e.g. specified wrong file path for a gzipped coverage file?). Please check your command! xargs: /gscratch/srlab/programs/Bismark-0.21.0/coverage2cytosine: exited with status 255; aborting