N E X T F L O W ~ version 23.10.1 Pulling adamd3/BactSeq ... Fast-forward Launching `https://github.com/adamd3/BactSeq` [deadly_varahamihira] DSL2 - revision: 0e927244b7 [main] [- ] process > MAKE_META_FILE - [- ] process > TRIMGALORE - [- ] process > MAKE_BWA_INDEX - [- ] process > BWA_ALIGN - [- ] process > MAKE_META_FILE - [- ] process > TRIMGALORE - [- ] process > MAKE_BWA_INDEX - [- ] process > BWA_ALIGN - [- ] process > COUNT_READS - [- ] process > NORMALISE_COUNTS - [- ] process > PCA_SAMPLES - [- ] process > DIFF_EXPRESSION - executor > slurm (1) [- ] process > MAKE_META_FILE [ 0%] 0 of 1 [- ] process > TRIMGALORE - [9f/d4e140] process > MAKE_BWA_INDEX (GCF_0001959... [ 0%] 0 of 1 [- ] process > BWA_ALIGN - [- ] process > COUNT_READS - [- ] process > NORMALISE_COUNTS - [- ] process > PCA_SAMPLES - [- ] process > DIFF_EXPRESSION - executor > slurm (2) [c4/fce7e1] process > MAKE_META_FILE (samplesheet... [ 0%] 0 of 1 [- ] process > TRIMGALORE - [9f/d4e140] process > MAKE_BWA_INDEX (GCF_0001959... [ 0%] 0 of 1 [- ] process > BWA_ALIGN - [- ] process > COUNT_READS - [- ] process > NORMALISE_COUNTS - [- ] process > PCA_SAMPLES - [- ] process > DIFF_EXPRESSION - executor > slurm (2) [c4/fce7e1] process > MAKE_META_FILE (samplesheet... [ 0%] 0 of 1 [- ] process > TRIMGALORE - [9f/d4e140] process > MAKE_BWA_INDEX (GCF_0001959... [ 0%] 0 of 1 [- ] process > BWA_ALIGN - [- ] process > COUNT_READS - [- ] process > NORMALISE_COUNTS - [- ] process > PCA_SAMPLES - [- ] process > DIFF_EXPRESSION - executor > slurm (4) [c4/fce7e1] process > MAKE_META_FILE (samplesheet... [100%] 1 of 1 ✔ [18/9350d4] process > TRIMGALORE (CAM-Eff) [ 0%] 0 of 7 [9f/d4e140] process > MAKE_BWA_INDEX (GCF_0001959... [ 0%] 0 of 1 [- ] process > BWA_ALIGN - [- ] process > COUNT_READS - [- ] process > NORMALISE_COUNTS - [- ] process > PCA_SAMPLES - [- ] process > DIFF_EXPRESSION - executor > slurm (4) [c4/fce7e1] process > MAKE_META_FILE (samplesheet... [100%] 1 of 1 ✔ [18/9350d4] process > TRIMGALORE (CAM-Eff) [ 0%] 0 of 12 [9f/d4e140] process > MAKE_BWA_INDEX (GCF_0001959... [ 0%] 0 of 1 [- ] process > BWA_ALIGN - [- ] process > COUNT_READS - [- ] process > NORMALISE_COUNTS - [- ] process > PCA_SAMPLES - [- ] process > DIFF_EXPRESSION - executor > slurm (5) [c4/fce7e1] process > MAKE_META_FILE (samplesheet... [100%] 1 of 1 ✔ [75/d9a34c] process > TRIMGALORE (GHA-Eff) [ 0%] 0 of 12 [9f/d4e140] process > MAKE_BWA_INDEX (GCF_0001959... [ 0%] 0 of 1 [- ] process > BWA_ALIGN - [- ] process > COUNT_READS - [- ] process > NORMALISE_COUNTS - [- ] process > PCA_SAMPLES - [- ] process > DIFF_EXPRESSION - executor > slurm (6) [c4/fce7e1] process > MAKE_META_FILE (samplesheet... [100%] 1 of 1 ✔ [09/3b0194] process > TRIMGALORE (GHA-Inf) [ 0%] 0 of 12 [9f/d4e140] process > MAKE_BWA_INDEX (GCF_0001959... [ 0%] 0 of 1 [- ] process > BWA_ALIGN - [- ] process > COUNT_READS - [- ] process > NORMALISE_COUNTS - [- ] process > PCA_SAMPLES - [- ] process > DIFF_EXPRESSION - executor > slurm (7) [c4/fce7e1] process > MAKE_META_FILE (samplesheet... [100%] 1 of 1 ✔ [5a/2fd5b0] process > TRIMGALORE (KEN-Eff) [ 0%] 0 of 12 [9f/d4e140] process > MAKE_BWA_INDEX (GCF_0001959... [ 0%] 0 of 1 [- ] process > BWA_ALIGN - [- ] process > COUNT_READS - [- ] process > NORMALISE_COUNTS - [- ] process > PCA_SAMPLES - [- ] process > DIFF_EXPRESSION - executor > slurm (8) [c4/fce7e1] process > MAKE_META_FILE (samplesheet... [100%] 1 of 1 ✔ [c8/fef432] process > TRIMGALORE (NIG-Eff) [ 0%] 0 of 12 [9f/d4e140] process > MAKE_BWA_INDEX (GCF_0001959... [ 0%] 0 of 1 [- ] process > BWA_ALIGN - [- ] process > COUNT_READS - [- ] process > NORMALISE_COUNTS - [- ] process > PCA_SAMPLES - [- ] process > DIFF_EXPRESSION - executor > slurm (9) [c4/fce7e1] process > MAKE_META_FILE (samplesheet... [100%] 1 of 1 ✔ [55/351be0] process > TRIMGALORE (KEN-Inf) [ 0%] 0 of 12 [9f/d4e140] process > MAKE_BWA_INDEX (GCF_0001959... [ 0%] 0 of 1 [- ] process > BWA_ALIGN - [- ] process > COUNT_READS - [- ] process > NORMALISE_COUNTS - [- ] process > PCA_SAMPLES - [- ] process > DIFF_EXPRESSION - executor > slurm (9) [c4/fce7e1] process > MAKE_META_FILE (samplesheet... [100%] 1 of 1 ✔ [55/351be0] process > TRIMGALORE (KEN-Inf) [ 0%] 0 of 12 [9f/d4e140] process > MAKE_BWA_INDEX (GCF_0001959... [ 0%] 0 of 1 [- ] process > BWA_ALIGN - [- ] process > COUNT_READS - [- ] process > NORMALISE_COUNTS - [- ] process > PCA_SAMPLES - [- ] process > DIFF_EXPRESSION - executor > slurm (10) [c4/fce7e1] process > MAKE_META_FILE (samplesheet... [100%] 1 of 1 ✔ [f0/f4c9c1] process > TRIMGALORE (UGA-Eff) [ 0%] 0 of 12 [9f/d4e140] process > MAKE_BWA_INDEX (GCF_0001959... [100%] 1 of 1 ✔ [- ] process > BWA_ALIGN - [- ] process > COUNT_READS - [- ] process > NORMALISE_COUNTS - [- ] process > PCA_SAMPLES - [- ] process > DIFF_EXPRESSION - executor > slurm (10) [c4/fce7e1] process > MAKE_META_FILE (samplesheet... [100%] 1 of 1 ✔ [f0/f4c9c1] process > TRIMGALORE (UGA-Eff) [ 0%] 0 of 12 [9f/d4e140] process > MAKE_BWA_INDEX (GCF_0001959... [100%] 1 of 1 ✔ [- ] process > BWA_ALIGN - [- ] process > COUNT_READS - [- ] process > NORMALISE_COUNTS - [- ] process > PCA_SAMPLES - [- ] process > DIFF_EXPRESSION - executor > slurm (10) [c4/fce7e1] process > MAKE_META_FILE (samplesheet... [100%] 1 of 1 ✔ [f0/f4c9c1] process > TRIMGALORE (UGA-Eff) [ 8%] 1 of 12 [9f/d4e140] process > MAKE_BWA_INDEX (GCF_0001959... [100%] 1 of 1 ✔ [- ] process > BWA_ALIGN [ 0%] 0 of 1 [- ] process > COUNT_READS - [- ] process > NORMALISE_COUNTS - [- ] process > PCA_SAMPLES - [- ] process > DIFF_EXPRESSION - executor > slurm (11) [c4/fce7e1] process > MAKE_META_FILE (samplesheet... [100%] 1 of 1 ✔ [34/69dfb1] process > TRIMGALORE (NIG-Inf) [ 8%] 1 of 12 [9f/d4e140] process > MAKE_BWA_INDEX (GCF_0001959... [100%] 1 of 1 ✔ [- ] process > BWA_ALIGN [ 0%] 0 of 1 [- ] process > COUNT_READS - [- ] process > NORMALISE_COUNTS - [- ] process > PCA_SAMPLES - [- ] process > DIFF_EXPRESSION - executor > slurm (11) [c4/fce7e1] process > MAKE_META_FILE (samplesheet... [100%] 1 of 1 ✔ [34/69dfb1] process > TRIMGALORE (NIG-Inf) [ 8%] 1 of 12 [9f/d4e140] process > MAKE_BWA_INDEX (GCF_0001959... [100%] 1 of 1 ✔ [- ] process > BWA_ALIGN [ 0%] 0 of 1 [- ] process > COUNT_READS - [- ] process > NORMALISE_COUNTS - [- ] process > PCA_SAMPLES - [- ] process > DIFF_EXPRESSION - executor > slurm (12) [c4/fce7e1] process > MAKE_META_FILE (samplesheet... [100%] 1 of 1 ✔ [18/9350d4] process > TRIMGALORE (CAM-Eff) [ 16%] 2 of 12 [9f/d4e140] process > MAKE_BWA_INDEX (GCF_0001959... [100%] 1 of 1 ✔ [08/a51ab6] process > BWA_ALIGN (UGA-Eff) [ 0%] 0 of 2 [- ] process > COUNT_READS - [- ] process > NORMALISE_COUNTS - [- ] process > PCA_SAMPLES - [- ] process > DIFF_EXPRESSION - executor > slurm (12) [c4/fce7e1] process > MAKE_META_FILE (samplesheet... [100%] 1 of 1 ✔ [18/9350d4] process > TRIMGALORE (CAM-Eff) [ 16%] 2 of 12 [9f/d4e140] process > MAKE_BWA_INDEX (GCF_0001959... [100%] 1 of 1 ✔ [08/a51ab6] process > BWA_ALIGN (UGA-Eff) [ 0%] 0 of 2 [- ] process > COUNT_READS - [- ] process > NORMALISE_COUNTS - [- ] process > PCA_SAMPLES - [- ] process > DIFF_EXPRESSION - executor > slurm (13) [c4/fce7e1] process > MAKE_META_FILE (samplesheet... [100%] 1 of 1 ✔ [c8/fef432] process > TRIMGALORE (NIG-Eff) [ 33%] 4 of 12 [9f/d4e140] process > MAKE_BWA_INDEX (GCF_0001959... [100%] 1 of 1 ✔ [a9/fdd3f6] process > BWA_ALIGN (CAM-Eff) [ 0%] 0 of 4 [- ] process > COUNT_READS - [- ] process > NORMALISE_COUNTS - [- ] process > PCA_SAMPLES - [- ] process > DIFF_EXPRESSION - executor > slurm (14) [c4/fce7e1] process > MAKE_META_FILE (samplesheet... [100%] 1 of 1 ✔ [73/0ac017] process > TRIMGALORE (SAF-Eff) [ 33%] 4 of 12 [9f/d4e140] process > MAKE_BWA_INDEX (GCF_0001959... [100%] 1 of 1 ✔ [a9/fdd3f6] process > BWA_ALIGN (CAM-Eff) [ 0%] 0 of 4 [- ] process > COUNT_READS - [- ] process > NORMALISE_COUNTS - [- ] process > PCA_SAMPLES - [- ] process > DIFF_EXPRESSION - executor > slurm (14) [c4/fce7e1] process > MAKE_META_FILE (samplesheet... [100%] 1 of 1 ✔ [73/0ac017] process > TRIMGALORE (SAF-Eff) [ 33%] 4 of 12 [9f/d4e140] process > MAKE_BWA_INDEX (GCF_0001959... [100%] 1 of 1 ✔ [a9/fdd3f6] process > BWA_ALIGN (CAM-Eff) [ 0%] 0 of 4 [- ] process > COUNT_READS - [- ] process > NORMALISE_COUNTS - [- ] process > PCA_SAMPLES - [- ] process > DIFF_EXPRESSION - executor > slurm (15) [c4/fce7e1] process > MAKE_META_FILE (samplesheet... [100%] 1 of 1 ✔ [55/351be0] process > TRIMGALORE (KEN-Inf) [ 41%] 5 of 12 [9f/d4e140] process > MAKE_BWA_INDEX (GCF_0001959... [100%] 1 of 1 ✔ [d5/6a73f7] process > BWA_ALIGN (KEN-Eff) [ 0%] 0 of 5 [- ] process > COUNT_READS - [- ] process > NORMALISE_COUNTS - [- ] process > PCA_SAMPLES - [- ] process > DIFF_EXPRESSION - executor > slurm (15) [c4/fce7e1] process > MAKE_META_FILE (samplesheet... [100%] 1 of 1 ✔ [55/351be0] process > TRIMGALORE (KEN-Inf) [ 41%] 5 of 12 [9f/d4e140] process > MAKE_BWA_INDEX (GCF_0001959... [100%] 1 of 1 ✔ [d5/6a73f7] process > BWA_ALIGN (KEN-Eff) [ 0%] 0 of 5 [- ] process > COUNT_READS - [- ] process > NORMALISE_COUNTS - [- ] process > PCA_SAMPLES - [- ] process > DIFF_EXPRESSION - executor > slurm (16) [c4/fce7e1] process > MAKE_META_FILE (samplesheet... [100%] 1 of 1 ✔ [28/a5ec93] process > TRIMGALORE (SAF-Inf) [ 41%] 5 of 12 [9f/d4e140] process > MAKE_BWA_INDEX (GCF_0001959... [100%] 1 of 1 ✔ [08/a51ab6] process > BWA_ALIGN (UGA-Eff) [ 20%] 1 of 5 [- ] process > COUNT_READS - [- ] process > NORMALISE_COUNTS - [- ] process > PCA_SAMPLES - [- ] process > DIFF_EXPRESSION - executor > slurm (16) [c4/fce7e1] process > MAKE_META_FILE (samplesheet... [100%] 1 of 1 ✔ [28/a5ec93] process > TRIMGALORE (SAF-Inf) [ 41%] 5 of 12 [9f/d4e140] process > MAKE_BWA_INDEX (GCF_0001959... [100%] 1 of 1 ✔ [08/a51ab6] process > BWA_ALIGN (UGA-Eff) [ 20%] 1 of 5 [- ] process > COUNT_READS - [- ] process > NORMALISE_COUNTS - [- ] process > PCA_SAMPLES - [- ] process > DIFF_EXPRESSION - executor > slurm (17) [c4/fce7e1] process > MAKE_META_FILE (samplesheet... [100%] 1 of 1 ✔ [63/9a9560] process > TRIMGALORE (UGA-Inf) [ 50%] 6 of 12 [9f/d4e140] process > MAKE_BWA_INDEX (GCF_0001959... [100%] 1 of 1 ✔ [08/a51ab6] process > BWA_ALIGN (UGA-Eff) [ 16%] 1 of 6 [- ] process > COUNT_READS - [- ] process > NORMALISE_COUNTS - [- ] process > PCA_SAMPLES - [- ] process > DIFF_EXPRESSION - executor > slurm (17) [c4/fce7e1] process > MAKE_META_FILE (samplesheet... [100%] 1 of 1 ✔ [63/9a9560] process > TRIMGALORE (UGA-Inf) [ 50%] 6 of 12 [9f/d4e140] process > MAKE_BWA_INDEX (GCF_0001959... [100%] 1 of 1 ✔ [08/a51ab6] process > BWA_ALIGN (UGA-Eff) [ 16%] 1 of 6 [- ] process > COUNT_READS - [- ] process > NORMALISE_COUNTS - [- ] process > PCA_SAMPLES - [- ] process > DIFF_EXPRESSION - executor > slurm (18) [c4/fce7e1] process > MAKE_META_FILE (samplesheet... [100%] 1 of 1 ✔ [75/d9a34c] process > TRIMGALORE (GHA-Eff) [ 58%] 7 of 12 [9f/d4e140] process > MAKE_BWA_INDEX (GCF_0001959... [100%] 1 of 1 ✔ [02/b6aca0] process > BWA_ALIGN (KEN-Inf) [ 14%] 1 of 7 [- ] process > COUNT_READS - [- ] process > NORMALISE_COUNTS - [- ] process > PCA_SAMPLES - [- ] process > DIFF_EXPRESSION - executor > slurm (18) [c4/fce7e1] process > MAKE_META_FILE (samplesheet... [100%] 1 of 1 ✔ [75/d9a34c] process > TRIMGALORE (GHA-Eff) [ 58%] 7 of 12 [9f/d4e140] process > MAKE_BWA_INDEX (GCF_0001959... [100%] 1 of 1 ✔ [02/b6aca0] process > BWA_ALIGN (KEN-Inf) [ 14%] 1 of 7 [- ] process > COUNT_READS - [- ] process > NORMALISE_COUNTS - [- ] process > PCA_SAMPLES - [- ] process > DIFF_EXPRESSION - executor > slurm (18) [c4/fce7e1] process > MAKE_META_FILE (samplesheet... [100%] 1 of 1 ✔ [09/3b0194] process > TRIMGALORE (GHA-Inf) [ 66%] 8 of 12 [9f/d4e140] process > MAKE_BWA_INDEX (GCF_0001959... [100%] 1 of 1 ✔ [02/b6aca0] process > BWA_ALIGN (KEN-Inf) [ 12%] 1 of 8 [- ] process > COUNT_READS - [- ] process > NORMALISE_COUNTS - [- ] process > PCA_SAMPLES - [- ] process > DIFF_EXPRESSION - executor > slurm (19) [c4/fce7e1] process > MAKE_META_FILE (samplesheet... [100%] 1 of 1 ✔ [09/3b0194] process > TRIMGALORE (GHA-Inf) [ 66%] 8 of 12 [9f/d4e140] process > MAKE_BWA_INDEX (GCF_0001959... [100%] 1 of 1 ✔ [97/fcb4e2] process > BWA_ALIGN (CAM-Inf) [ 12%] 1 of 8 [- ] process > COUNT_READS - [- ] process > NORMALISE_COUNTS - [- ] process > PCA_SAMPLES - [- ] process > DIFF_EXPRESSION - executor > slurm (19) [c4/fce7e1] process > MAKE_META_FILE (samplesheet... [100%] 1 of 1 ✔ [09/3b0194] process > TRIMGALORE (GHA-Inf) [ 66%] 8 of 12 [9f/d4e140] process > MAKE_BWA_INDEX (GCF_0001959... [100%] 1 of 1 ✔ [97/fcb4e2] process > BWA_ALIGN (CAM-Inf) [ 12%] 1 of 8 [- ] process > COUNT_READS - [- ] process > NORMALISE_COUNTS - [- ] process > PCA_SAMPLES - [- ] process > DIFF_EXPRESSION - executor > slurm (20) [c4/fce7e1] process > MAKE_META_FILE (samplesheet... [100%] 1 of 1 ✔ [34/69dfb1] process > TRIMGALORE (NIG-Inf) [ 75%] 9 of 12 [9f/d4e140] process > MAKE_BWA_INDEX (GCF_0001959... [100%] 1 of 1 ✔ [19/8200b2] process > BWA_ALIGN (GHA-Eff) [ 11%] 1 of 9 [- ] process > COUNT_READS - [- ] process > NORMALISE_COUNTS - [- ] process > PCA_SAMPLES - [- ] process > DIFF_EXPRESSION - executor > slurm (20) [c4/fce7e1] process > MAKE_META_FILE (samplesheet... [100%] 1 of 1 ✔ [34/69dfb1] process > TRIMGALORE (NIG-Inf) [ 75%] 9 of 12 [9f/d4e140] process > MAKE_BWA_INDEX (GCF_0001959... [100%] 1 of 1 ✔ [19/8200b2] process > BWA_ALIGN (GHA-Eff) [ 11%] 1 of 9 [- ] process > COUNT_READS - [- ] process > NORMALISE_COUNTS - [- ] process > PCA_SAMPLES - [- ] process > DIFF_EXPRESSION - executor > slurm (20) [c4/fce7e1] process > MAKE_META_FILE (samplesheet... [100%] 1 of 1 ✔ [34/69dfb1] process > TRIMGALORE (NIG-Inf) [ 75%] 9 of 12 [9f/d4e140] process > MAKE_BWA_INDEX (GCF_0001959... [100%] 1 of 1 ✔ [a9/fdd3f6] process > BWA_ALIGN (CAM-Eff) [ 22%] 2 of 9 [- ] process > COUNT_READS - [- ] process > NORMALISE_COUNTS - [- ] process > PCA_SAMPLES - [- ] process > DIFF_EXPRESSION - executor > slurm (21) [c4/fce7e1] process > MAKE_META_FILE (samplesheet... [100%] 1 of 1 ✔ [34/69dfb1] process > TRIMGALORE (NIG-Inf) [ 75%] 9 of 12 [9f/d4e140] process > MAKE_BWA_INDEX (GCF_0001959... [100%] 1 of 1 ✔ [26/757e74] process > BWA_ALIGN (NIG-Inf) [ 22%] 2 of 9 [- ] process > COUNT_READS - [- ] process > NORMALISE_COUNTS - [- ] process > PCA_SAMPLES - [- ] process > DIFF_EXPRESSION - executor > slurm (21) [c4/fce7e1] process > MAKE_META_FILE (samplesheet... [100%] 1 of 1 ✔ [34/69dfb1] process > TRIMGALORE (NIG-Inf) [ 75%] 9 of 12 [9f/d4e140] process > MAKE_BWA_INDEX (GCF_0001959... [100%] 1 of 1 ✔ [26/757e74] process > BWA_ALIGN (NIG-Inf) [ 22%] 2 of 9 [- ] process > COUNT_READS - [- ] process > NORMALISE_COUNTS - [- ] process > PCA_SAMPLES - [- ] process > DIFF_EXPRESSION - executor > slurm (22) [c4/fce7e1] process > MAKE_META_FILE (samplesheet... [100%] 1 of 1 ✔ [34/69dfb1] process > TRIMGALORE (NIG-Inf) [ 75%] 9 of 12 [9f/d4e140] process > MAKE_BWA_INDEX (GCF_0001959... [100%] 1 of 1 ✔ [98/f1d13b] process > BWA_ALIGN (GHA-Inf) [ 33%] 3 of 9 [- ] process > COUNT_READS - [- ] process > NORMALISE_COUNTS - [- ] process > PCA_SAMPLES - [- ] process > DIFF_EXPRESSION - executor > slurm (22) [c4/fce7e1] process > MAKE_META_FILE (samplesheet... [100%] 1 of 1 ✔ [34/69dfb1] process > TRIMGALORE (NIG-Inf) [ 75%] 9 of 12 [9f/d4e140] process > MAKE_BWA_INDEX (GCF_0001959... [100%] 1 of 1 ✔ [98/f1d13b] process > BWA_ALIGN (GHA-Inf) [ 33%] 3 of 9 [- ] process > COUNT_READS - [- ] process > NORMALISE_COUNTS - [- ] process > PCA_SAMPLES - [- ] process > DIFF_EXPRESSION - executor > slurm (23) [c4/fce7e1] process > MAKE_META_FILE (samplesheet... [100%] 1 of 1 ✔ [34/69dfb1] process > TRIMGALORE (NIG-Inf) [ 75%] 9 of 12 [9f/d4e140] process > MAKE_BWA_INDEX (GCF_0001959... [100%] 1 of 1 ✔ [09/d8386b] process > BWA_ALIGN (NIG-Eff) [ 44%] 4 of 9 [- ] process > COUNT_READS - [- ] process > NORMALISE_COUNTS - [- ] process > PCA_SAMPLES - [- ] process > DIFF_EXPRESSION - executor > slurm (23) [c4/fce7e1] process > MAKE_META_FILE (samplesheet... [100%] 1 of 1 ✔ [34/69dfb1] process > TRIMGALORE (NIG-Inf) [ 75%] 9 of 12 [9f/d4e140] process > MAKE_BWA_INDEX (GCF_0001959... [100%] 1 of 1 ✔ [09/d8386b] process > BWA_ALIGN (NIG-Eff) [ 44%] 4 of 9 [- ] process > COUNT_READS - [- ] process > NORMALISE_COUNTS - [- ] process > PCA_SAMPLES - [- ] process > DIFF_EXPRESSION - executor > slurm (24) [c4/fce7e1] process > MAKE_META_FILE (samplesheet... [100%] 1 of 1 ✔ [73/0ac017] process > TRIMGALORE (SAF-Eff) [ 83%] 10 of 12 [9f/d4e140] process > MAKE_BWA_INDEX (GCF_0001959... [100%] 1 of 1 ✔ [86/950519] process > BWA_ALIGN (SAF-Eff) [ 40%] 4 of 10 [- ] process > COUNT_READS - [- ] process > NORMALISE_COUNTS - [- ] process > PCA_SAMPLES - [- ] process > DIFF_EXPRESSION - executor > slurm (24) [c4/fce7e1] process > MAKE_META_FILE (samplesheet... [100%] 1 of 1 ✔ [73/0ac017] process > TRIMGALORE (SAF-Eff) [ 83%] 10 of 12 [9f/d4e140] process > MAKE_BWA_INDEX (GCF_0001959... [100%] 1 of 1 ✔ [86/950519] process > BWA_ALIGN (SAF-Eff) [ 40%] 4 of 10 [- ] process > COUNT_READS - [- ] process > NORMALISE_COUNTS - [- ] process > PCA_SAMPLES - [- ] process > DIFF_EXPRESSION - executor > slurm (24) [c4/fce7e1] process > MAKE_META_FILE (samplesheet... [100%] 1 of 1 ✔ [28/a5ec93] process > TRIMGALORE (SAF-Inf) [ 91%] 11 of 12 [9f/d4e140] process > MAKE_BWA_INDEX (GCF_0001959... [100%] 1 of 1 ✔ [86/950519] process > BWA_ALIGN (SAF-Eff) [ 36%] 4 of 11 [- ] process > COUNT_READS - [- ] process > NORMALISE_COUNTS - [- ] process > PCA_SAMPLES - [- ] process > DIFF_EXPRESSION - executor > slurm (25) [c4/fce7e1] process > MAKE_META_FILE (samplesheet... [100%] 1 of 1 ✔ [28/a5ec93] process > TRIMGALORE (SAF-Inf) [ 91%] 11 of 12 [9f/d4e140] process > MAKE_BWA_INDEX (GCF_0001959... [100%] 1 of 1 ✔ [9f/33edd4] process > BWA_ALIGN (SAF-Inf) [ 45%] 5 of 11 [- ] process > COUNT_READS - [- ] process > NORMALISE_COUNTS - [- ] process > PCA_SAMPLES - [- ] process > DIFF_EXPRESSION - executor > slurm (25) [c4/fce7e1] process > MAKE_META_FILE (samplesheet... [100%] 1 of 1 ✔ [28/a5ec93] process > TRIMGALORE (SAF-Inf) [ 91%] 11 of 12 [9f/d4e140] process > MAKE_BWA_INDEX (GCF_0001959... [100%] 1 of 1 ✔ [9f/33edd4] process > BWA_ALIGN (SAF-Inf) [ 45%] 5 of 11 [- ] process > COUNT_READS - [- ] process > NORMALISE_COUNTS - [- ] process > PCA_SAMPLES - [- ] process > DIFF_EXPRESSION - executor > slurm (25) [c4/fce7e1] process > MAKE_META_FILE (samplesheet... [100%] 1 of 1 ✔ [28/a5ec93] process > TRIMGALORE (SAF-Inf) [ 91%] 11 of 12 [9f/d4e140] process > MAKE_BWA_INDEX (GCF_0001959... [100%] 1 of 1 ✔ [97/fcb4e2] process > BWA_ALIGN (CAM-Inf) [ 54%] 6 of 11 [- ] process > COUNT_READS - [- ] process > NORMALISE_COUNTS - [- ] process > PCA_SAMPLES - [- ] process > DIFF_EXPRESSION - executor > slurm (26) [c4/fce7e1] process > MAKE_META_FILE (samplesheet... [100%] 1 of 1 ✔ [63/9a9560] process > TRIMGALORE (UGA-Inf) [100%] 12 of 12 ✔ [9f/d4e140] process > MAKE_BWA_INDEX (GCF_0001959... [100%] 1 of 1 ✔ [45/71b624] process > BWA_ALIGN (UGA-Inf) [ 50%] 6 of 12 [- ] process > COUNT_READS - [- ] process > NORMALISE_COUNTS - [- ] process > PCA_SAMPLES - [- ] process > DIFF_EXPRESSION - executor > slurm (26) [c4/fce7e1] process > MAKE_META_FILE (samplesheet... [100%] 1 of 1 ✔ [63/9a9560] process > TRIMGALORE (UGA-Inf) [100%] 12 of 12 ✔ [9f/d4e140] process > MAKE_BWA_INDEX (GCF_0001959... [100%] 1 of 1 ✔ [45/71b624] process > BWA_ALIGN (UGA-Inf) [ 50%] 6 of 12 [- ] process > COUNT_READS - [- ] process > NORMALISE_COUNTS - [- ] process > PCA_SAMPLES - [- ] process > DIFF_EXPRESSION - executor > slurm (26) [c4/fce7e1] process > MAKE_META_FILE (samplesheet... [100%] 1 of 1 ✔ [63/9a9560] process > TRIMGALORE (UGA-Inf) [100%] 12 of 12 ✔ [9f/d4e140] process > MAKE_BWA_INDEX (GCF_0001959... [100%] 1 of 1 ✔ [19/8200b2] process > BWA_ALIGN (GHA-Eff) [ 58%] 7 of 12 [- ] process > COUNT_READS - [- ] process > NORMALISE_COUNTS - [- ] process > PCA_SAMPLES - [- ] process > DIFF_EXPRESSION - executor > slurm (26) [c4/fce7e1] process > MAKE_META_FILE (samplesheet... [100%] 1 of 1 ✔ [63/9a9560] process > TRIMGALORE (UGA-Inf) [100%] 12 of 12 ✔ [9f/d4e140] process > MAKE_BWA_INDEX (GCF_0001959... [100%] 1 of 1 ✔ [98/f1d13b] process > BWA_ALIGN (GHA-Inf) [ 66%] 8 of 12 [- ] process > COUNT_READS - [- ] process > NORMALISE_COUNTS - [- ] process > PCA_SAMPLES - [- ] process > DIFF_EXPRESSION - executor > slurm (26) [c4/fce7e1] process > MAKE_META_FILE (samplesheet... [100%] 1 of 1 ✔ [63/9a9560] process > TRIMGALORE (UGA-Inf) [100%] 12 of 12 ✔ [9f/d4e140] process > MAKE_BWA_INDEX (GCF_0001959... [100%] 1 of 1 ✔ [09/d8386b] process > BWA_ALIGN (NIG-Eff) [ 75%] 9 of 12 [- ] process > COUNT_READS - [- ] process > NORMALISE_COUNTS - [- ] process > PCA_SAMPLES - [- ] process > DIFF_EXPRESSION - executor > slurm (26) [c4/fce7e1] process > MAKE_META_FILE (samplesheet... [100%] 1 of 1 ✔ [63/9a9560] process > TRIMGALORE (UGA-Inf) [100%] 12 of 12 ✔ [9f/d4e140] process > MAKE_BWA_INDEX (GCF_0001959... [100%] 1 of 1 ✔ [86/950519] process > BWA_ALIGN (SAF-Eff) [ 83%] 10 of 12 [- ] process > COUNT_READS - [- ] process > NORMALISE_COUNTS - [- ] process > PCA_SAMPLES - [- ] process > DIFF_EXPRESSION - executor > slurm (26) [c4/fce7e1] process > MAKE_META_FILE (samplesheet... [100%] 1 of 1 ✔ [63/9a9560] process > TRIMGALORE (UGA-Inf) [100%] 12 of 12 ✔ [9f/d4e140] process > MAKE_BWA_INDEX (GCF_0001959... [100%] 1 of 1 ✔ [9f/33edd4] process > BWA_ALIGN (SAF-Inf) [ 91%] 11 of 12 [- ] process > COUNT_READS - [- ] process > NORMALISE_COUNTS - [- ] process > PCA_SAMPLES - [- ] process > DIFF_EXPRESSION - executor > slurm (26) [c4/fce7e1] process > MAKE_META_FILE (samplesheet... [100%] 1 of 1 ✔ [63/9a9560] process > TRIMGALORE (UGA-Inf) [100%] 12 of 12 ✔ [9f/d4e140] process > MAKE_BWA_INDEX (GCF_0001959... [100%] 1 of 1 ✔ [45/71b624] process > BWA_ALIGN (UGA-Inf) [100%] 12 of 12 ✔ [- ] process > COUNT_READS [ 0%] 0 of 1 [- ] process > NORMALISE_COUNTS - [- ] process > PCA_SAMPLES - [- ] process > DIFF_EXPRESSION - executor > slurm (27) [c4/fce7e1] process > MAKE_META_FILE (samplesheet... [100%] 1 of 1 ✔ [63/9a9560] process > TRIMGALORE (UGA-Inf) [100%] 12 of 12 ✔ [9f/d4e140] process > MAKE_BWA_INDEX (GCF_0001959... [100%] 1 of 1 ✔ [45/71b624] process > BWA_ALIGN (UGA-Inf) [100%] 12 of 12 ✔ [74/7c7305] process > COUNT_READS (genomic.gff) [ 0%] 0 of 1 [- ] process > NORMALISE_COUNTS - [- ] process > PCA_SAMPLES - [- ] process > DIFF_EXPRESSION - executor > slurm (27) [c4/fce7e1] process > MAKE_META_FILE (samplesheet... [100%] 1 of 1 ✔ [63/9a9560] process > TRIMGALORE (UGA-Inf) [100%] 12 of 12 ✔ [9f/d4e140] process > MAKE_BWA_INDEX (GCF_0001959... [100%] 1 of 1 ✔ [45/71b624] process > BWA_ALIGN (UGA-Inf) [100%] 12 of 12 ✔ [74/7c7305] process > COUNT_READS (genomic.gff) [ 0%] 0 of 1 [- ] process > NORMALISE_COUNTS - [- ] process > PCA_SAMPLES - [- ] process > DIFF_EXPRESSION - executor > slurm (29) [c4/fce7e1] process > MAKE_META_FILE (samplesheet... [100%] 1 of 1 ✔ [63/9a9560] process > TRIMGALORE (UGA-Inf) [100%] 12 of 12 ✔ [9f/d4e140] process > MAKE_BWA_INDEX (GCF_0001959... [100%] 1 of 1 ✔ [45/71b624] process > BWA_ALIGN (UGA-Inf) [100%] 12 of 12 ✔ [74/7c7305] process > COUNT_READS (genomic.gff) [100%] 1 of 1 ✔ [26/94bb6b] process > NORMALISE_COUNTS (gene_coun... [ 0%] 0 of 1 [- ] process > PCA_SAMPLES - [85/3c2a07] process > DIFF_EXPRESSION (gene_count... [ 0%] 0 of 1 executor > slurm (29) [c4/fce7e1] process > MAKE_META_FILE (samplesheet... [100%] 1 of 1 ✔ [63/9a9560] process > TRIMGALORE (UGA-Inf) [100%] 12 of 12 ✔ [9f/d4e140] process > MAKE_BWA_INDEX (GCF_0001959... [100%] 1 of 1 ✔ [45/71b624] process > BWA_ALIGN (UGA-Inf) [100%] 12 of 12 ✔ [74/7c7305] process > COUNT_READS (genomic.gff) [100%] 1 of 1 ✔ [26/94bb6b] process > NORMALISE_COUNTS (gene_coun... [ 0%] 0 of 1 [- ] process > PCA_SAMPLES - [85/3c2a07] process > DIFF_EXPRESSION (gene_count... [ 0%] 0 of 1 executor > slurm (30) [c4/fce7e1] process > MAKE_META_FILE (samplesheet... [100%] 1 of 1 ✔ [63/9a9560] process > TRIMGALORE (UGA-Inf) [100%] 12 of 12 ✔ [9f/d4e140] process > MAKE_BWA_INDEX (GCF_0001959... [100%] 1 of 1 ✔ [45/71b624] process > BWA_ALIGN (UGA-Inf) [100%] 12 of 12 ✔ [74/7c7305] process > COUNT_READS (genomic.gff) [100%] 1 of 1 ✔ [26/94bb6b] process > NORMALISE_COUNTS (gene_coun... [100%] 1 of 1 ✔ [11/0b7ad0] process > PCA_SAMPLES (cpm_counts.tsv) [ 0%] 0 of 1 [85/3c2a07] process > DIFF_EXPRESSION (gene_count... [ 0%] 0 of 1 ERROR ~ Error executing process > 'DIFF_EXPRESSION (gene_counts_pc.tsv)' Caused by: Process `DIFF_EXPRESSION (gene_counts_pc.tsv)` terminated with an error exit status (1) Command executed: [ ! -f contrast_table.tsv ] && ln -s contrasts.tsv contrast_table.tsv diffexpr.R -p 0.05 -l 1 -o ./ Command exit status: 1 Command output: (empty) Command error: rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'Biobase' The following object is masked from 'package:MatrixGenerics': rowMedians The following objects are masked from 'package:matrixStats': anyMissing, rowMedians Attaching package: 'plyr' The following object is masked from 'package:matrixStats': count The following object is masked from 'package:IRanges': desc The following object is masked from 'package:S4Vectors': rename Loading required package: EnhancedVolcano Loading required package: ggrepel converting counts to integer mode estimating size factors estimating dispersions gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates fitting model and testing Error in cleanContrast(object, contrast, expanded = isExpanded, listValues = listValues, : as EFF is the reference level, was expecting group_Inf_vs_EFF to be present in 'resultsNames(object)' Calls: lapply ... lapply -> FUN -> lfcShrink -> results -> cleanContrast Execution halted INFO: Cleaning up image... Work dir: /scratch/sysuser/jonathan/ops/MRC/DE_RNA/work/85/3c2a07bb96c5c2d9a9477c010c3efd Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh` -- Check '.nextflow.log' file for details Execution status: failed Results are reported here: ./results  WARN: Killing running tasks (1) executor > slurm (30) [c4/fce7e1] process > MAKE_META_FILE (samplesheet... [100%] 1 of 1 ✔ [63/9a9560] process > TRIMGALORE (UGA-Inf) [100%] 12 of 12 ✔ [9f/d4e140] process > MAKE_BWA_INDEX (GCF_0001959... [100%] 1 of 1 ✔ [45/71b624] process > BWA_ALIGN (UGA-Inf) [100%] 12 of 12 ✔ [74/7c7305] process > COUNT_READS (genomic.gff) [100%] 1 of 1 ✔ [26/94bb6b] process > NORMALISE_COUNTS (gene_coun... [100%] 1 of 1 ✔ [- ] process > PCA_SAMPLES (cpm_counts.tsv) - [85/3c2a07] process > DIFF_EXPRESSION (gene_count... [100%] 1 of 1, failed: 1 ✘ ERROR ~ Error executing process > 'DIFF_EXPRESSION (gene_counts_pc.tsv)' Caused by: Process `DIFF_EXPRESSION (gene_counts_pc.tsv)` terminated with an error exit status (1) Command executed: [ ! -f contrast_table.tsv ] && ln -s contrasts.tsv contrast_table.tsv diffexpr.R -p 0.05 -l 1 -o ./ Command exit status: 1 Command output: (empty) Command error: rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'Biobase' The following object is masked from 'package:MatrixGenerics': rowMedians The following objects are masked from 'package:matrixStats': anyMissing, rowMedians Attaching package: 'plyr' The following object is masked from 'package:matrixStats': count The following object is masked from 'package:IRanges': desc The following object is masked from 'package:S4Vectors': rename Loading required package: EnhancedVolcano Loading required package: ggrepel converting counts to integer mode estimating size factors estimating dispersions gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates fitting model and testing Error in cleanContrast(object, contrast, expanded = isExpanded, listValues = listValues, : as EFF is the reference level, was expecting group_Inf_vs_EFF to be present in 'resultsNames(object)' Calls: lapply ... lapply -> FUN -> lfcShrink -> results -> cleanContrast Execution halted INFO: Cleaning up image... Work dir: /scratch/sysuser/jonathan/ops/MRC/DE_RNA/work/85/3c2a07bb96c5c2d9a9477c010c3efd Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh` -- Check '.nextflow.log' file for details