/var/spool/slurm/d/job1465421/slurm_script: line 31: fg: no job control
usage: methylpy DMRfind [-h] --allc-files ALLC_FILES [ALLC_FILES ...]
                        --output-prefix OUTPUT_PREFIX
                        [--samples SAMPLES [SAMPLES ...]]
                        [--chroms CHROMS [CHROMS ...]]
                        [--mc-type MC_TYPE [MC_TYPE ...]]
                        [--num-procs NUM_PROCS] [--min-cov MIN_COV]
                        [--dmr-max-dist DMR_MAX_DIST]
                        [--sig-cutoff SIG_CUTOFF] [--num-sims NUM_SIMS]
                        [--min-tests MIN_TESTS] [--min-num-dms MIN_NUM_DMS]
                        [--sample-category SAMPLE_CATEGORY [SAMPLE_CATEGORY ...]]
                        [--mc-max-dist MC_MAX_DIST]
                        [--resid-cutoff RESID_CUTOFF]
                        [--keep-temp-files KEEP_TEMP_FILES]
                        [--min-cluster MIN_CLUSTER] [--seed SEED]
methylpy DMRfind: error: the following arguments are required: --output-prefix
/var/spool/slurm/d/job1465421/slurm_script: line 55: --samples: command not found
/var/spool/slurm/d/job1465421/slurm_script: line 70: fg: no job control
Processing /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_1_S13.sorted.bam file methylpy bam-quality-filter --input-file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_1_S13.sorted.bam --output-file 16C_26psu_1_S13.sorted.bam.sorted.bam.MQ20.filtered.bam --ref-fasta /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/GCF_000233375.1_ICSASG_v2_genomic.fa --min-mapq 20 --buffer-line-number 100
Processing /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_2_S14.sorted.bam file methylpy bam-quality-filter --input-file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_2_S14.sorted.bam --output-file 16C_26psu_2_S14.sorted.bam.sorted.bam.MQ20.filtered.bam --ref-fasta /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/GCF_000233375.1_ICSASG_v2_genomic.fa --min-mapq 20 --buffer-line-number 100
Processing /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_3_S15.sorted.bam file methylpy bam-quality-filter --input-file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_3_S15.sorted.bam --output-file 16C_26psu_3_S15.sorted.bam.sorted.bam.MQ20.filtered.bam --ref-fasta /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/GCF_000233375.1_ICSASG_v2_genomic.fa --min-mapq 20 --buffer-line-number 100
Processing /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_4_S16.sorted.bam file methylpy bam-quality-filter --input-file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_4_S16.sorted.bam --output-file 16C_26psu_4_S16.sorted.bam.sorted.bam.MQ20.filtered.bam --ref-fasta /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/GCF_000233375.1_ICSASG_v2_genomic.fa --min-mapq 20 --buffer-line-number 100
Processing /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_1_S1.sorted.bam file methylpy bam-quality-filter --input-file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_1_S1.sorted.bam --output-file 16C_32psu_1_S1.sorted.bam.sorted.bam.MQ20.filtered.bam --ref-fasta /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/GCF_000233375.1_ICSASG_v2_genomic.fa --min-mapq 20 --buffer-line-number 100
Processing /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_2_S2.sorted.bam file methylpy bam-quality-filter --input-file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_2_S2.sorted.bam --output-file 16C_32psu_2_S2.sorted.bam.sorted.bam.MQ20.filtered.bam --ref-fasta /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/GCF_000233375.1_ICSASG_v2_genomic.fa --min-mapq 20 --buffer-line-number 100
Processing /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_3_S3.sorted.bam file methylpy bam-quality-filter --input-file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_3_S3.sorted.bam --output-file 16C_32psu_3_S3.sorted.bam.sorted.bam.MQ20.filtered.bam --ref-fasta /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/GCF_000233375.1_ICSASG_v2_genomic.fa --min-mapq 20 --buffer-line-number 100
Processing /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_4_S4.sorted.bam file methylpy bam-quality-filter --input-file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_4_S4.sorted.bam --output-file 16C_32psu_4_S4.sorted.bam.sorted.bam.MQ20.filtered.bam --ref-fasta /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/GCF_000233375.1_ICSASG_v2_genomic.fa --min-mapq 20 --buffer-line-number 100
Processing /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_1_S9.sorted.bam file methylpy bam-quality-filter --input-file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_1_S9.sorted.bam --output-file 8C_26psu_1_S9.sorted.bam.sorted.bam.MQ20.filtered.bam --ref-fasta /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/GCF_000233375.1_ICSASG_v2_genomic.fa --min-mapq 20 --buffer-line-number 100
Processing /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_2_S10.sorted.bam file methylpy bam-quality-filter --input-file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_2_S10.sorted.bam --output-file 8C_26psu_2_S10.sorted.bam.sorted.bam.MQ20.filtered.bam --ref-fasta /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/GCF_000233375.1_ICSASG_v2_genomic.fa --min-mapq 20 --buffer-line-number 100
Processing /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_3_S11.sorted.bam file methylpy bam-quality-filter --input-file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_3_S11.sorted.bam --output-file 8C_26psu_3_S11.sorted.bam.sorted.bam.MQ20.filtered.bam --ref-fasta /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/GCF_000233375.1_ICSASG_v2_genomic.fa --min-mapq 20 --buffer-line-number 100
Processing /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_4_S12.sorted.bam file methylpy bam-quality-filter --input-file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_4_S12.sorted.bam --output-file 8C_26psu_4_S12.sorted.bam.sorted.bam.MQ20.filtered.bam --ref-fasta /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/GCF_000233375.1_ICSASG_v2_genomic.fa --min-mapq 20 --buffer-line-number 100
Processing /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_1_S5.sorted.bam file methylpy bam-quality-filter --input-file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_1_S5.sorted.bam --output-file 8C_32psu_1_S5.sorted.bam.sorted.bam.MQ20.filtered.bam --ref-fasta /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/GCF_000233375.1_ICSASG_v2_genomic.fa --min-mapq 20 --buffer-line-number 100
Processing /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_2_S6.sorted.bam file methylpy bam-quality-filter --input-file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_2_S6.sorted.bam --output-file 8C_32psu_2_S6.sorted.bam.sorted.bam.MQ20.filtered.bam --ref-fasta /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/GCF_000233375.1_ICSASG_v2_genomic.fa --min-mapq 20 --buffer-line-number 100
Processing /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_3_S7.sorted.bam file methylpy bam-quality-filter --input-file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_3_S7.sorted.bam --output-file 8C_32psu_3_S7.sorted.bam.sorted.bam.MQ20.filtered.bam --ref-fasta /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/GCF_000233375.1_ICSASG_v2_genomic.fa --min-mapq 20 --buffer-line-number 100
Processing /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_4_S8.sorted.bam file methylpy bam-quality-filter --input-file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_4_S8.sorted.bam --output-file 8C_32psu_4_S8.sorted.bam.sorted.bam.MQ20.filtered.bam --ref-fasta /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/GCF_000233375.1_ICSASG_v2_genomic.fa --min-mapq 20 --buffer-line-number 100
Processing /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_16C_26psu_1_S19.sorted.bam file methylpy bam-quality-filter --input-file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_16C_26psu_1_S19.sorted.bam --output-file CTRL_16C_26psu_1_S19.sorted.bam.sorted.bam.MQ20.filtered.bam --ref-fasta /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/GCF_000233375.1_ICSASG_v2_genomic.fa --min-mapq 20 --buffer-line-number 100
Processing /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_16C_26psu_2_S21.sorted.bam file methylpy bam-quality-filter --input-file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_16C_26psu_2_S21.sorted.bam --output-file CTRL_16C_26psu_2_S21.sorted.bam.sorted.bam.MQ20.filtered.bam --ref-fasta /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/GCF_000233375.1_ICSASG_v2_genomic.fa --min-mapq 20 --buffer-line-number 100
Processing /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_8C_26psu_1_S17.sorted.bam file methylpy bam-quality-filter --input-file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_8C_26psu_1_S17.sorted.bam --output-file CTRL_8C_26psu_1_S17.sorted.bam.sorted.bam.MQ20.filtered.bam --ref-fasta /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/GCF_000233375.1_ICSASG_v2_genomic.fa --min-mapq 20 --buffer-line-number 100
Processing /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_8C_26psu_2_S18.sorted.bam file methylpy bam-quality-filter --input-file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_8C_26psu_2_S18.sorted.bam --output-file CTRL_8C_26psu_2_S18.sorted.bam.sorted.bam.MQ20.filtered.bam --ref-fasta /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/GCF_000233375.1_ICSASG_v2_genomic.fa --min-mapq 20 --buffer-line-number 100
[E::hts_open_format] Failed to open file *.MQ20.filtered.bam
samtools index: failed to open "*.MQ20.filtered.bam": No such file or directory