/var/spool/slurm/d/job1292353/slurm_script: line 28: fg: no job control Begin flipping the strand of read 2 Sat Sep 7 13:57:09 2019 Input not indexed. Indexing... Sat Sep 7 14:10:33 2019 [mpileup] 1 samples in 1 input files Reference fasta not indexed. Indexing. Begin flipping the strand of read 2 Sat Sep 7 14:34:46 2019 Input not indexed. Indexing... Sat Sep 7 14:46:50 2019 [mpileup] 1 samples in 1 input files Begin flipping the strand of read 2 Sat Sep 7 15:06:11 2019 Input not indexed. Indexing... Sat Sep 7 15:15:35 2019 [mpileup] 1 samples in 1 input files Begin flipping the strand of read 2 Sat Sep 7 15:32:16 2019 Input not indexed. Indexing... Sat Sep 7 15:43:21 2019 [mpileup] 1 samples in 1 input files Begin flipping the strand of read 2 Sat Sep 7 16:03:21 2019 Input not indexed. Indexing... Sat Sep 7 16:15:14 2019 [mpileup] 1 samples in 1 input files Begin flipping the strand of read 2 Sat Sep 7 16:34:08 2019 Input not indexed. Indexing... Sat Sep 7 16:46:05 2019 [mpileup] 1 samples in 1 input files Begin flipping the strand of read 2 Sat Sep 7 17:06:30 2019 Input not indexed. Indexing... Sat Sep 7 17:15:12 2019 [mpileup] 1 samples in 1 input files Begin flipping the strand of read 2 Sat Sep 7 17:30:57 2019 Input not indexed. Indexing... Sat Sep 7 17:42:42 2019 [mpileup] 1 samples in 1 input files Begin flipping the strand of read 2 Sat Sep 7 18:03:42 2019 Input not indexed. Indexing... Sat Sep 7 18:16:14 2019 [mpileup] 1 samples in 1 input files Begin flipping the strand of read 2 Sat Sep 7 18:37:49 2019 Input not indexed. Indexing... Sat Sep 7 18:50:07 2019 [mpileup] 1 samples in 1 input files Begin flipping the strand of read 2 Sat Sep 7 19:12:32 2019 Input not indexed. Indexing... Sat Sep 7 19:23:07 2019 [mpileup] 1 samples in 1 input files Begin flipping the strand of read 2 Sat Sep 7 19:40:25 2019 Input not indexed. Indexing... Sat Sep 7 19:49:06 2019 [mpileup] 1 samples in 1 input files Begin flipping the strand of read 2 Sat Sep 7 20:02:39 2019 Input not indexed. Indexing... Sat Sep 7 20:11:10 2019 [mpileup] 1 samples in 1 input files Begin flipping the strand of read 2 Sat Sep 7 20:24:18 2019 Input not indexed. Indexing... Sat Sep 7 20:32:52 2019 [mpileup] 1 samples in 1 input files Begin flipping the strand of read 2 Sat Sep 7 20:49:21 2019 Input not indexed. Indexing... Sat Sep 7 20:58:57 2019 [mpileup] 1 samples in 1 input files Begin flipping the strand of read 2 Sat Sep 7 21:14:23 2019 Input not indexed. Indexing... Sat Sep 7 21:24:26 2019 [mpileup] 1 samples in 1 input files Begin flipping the strand of read 2 Sat Sep 7 21:41:01 2019 Input not indexed. Indexing... Sat Sep 7 21:53:04 2019 [mpileup] 1 samples in 1 input files Begin flipping the strand of read 2 Sat Sep 7 22:10:28 2019 Input not indexed. Indexing... Sat Sep 7 22:18:24 2019 [mpileup] 1 samples in 1 input files Begin flipping the strand of read 2 Sat Sep 7 22:29:38 2019 Input not indexed. Indexing... Sat Sep 7 22:39:20 2019 [mpileup] 1 samples in 1 input files Begin flipping the strand of read 2 Sat Sep 7 22:57:32 2019 Input not indexed. Indexing... Sat Sep 7 23:06:58 2019 [mpileup] 1 samples in 1 input files /var/spool/slurm/d/job1292353/slurm_script: line 67: fg: no job control /var/spool/slurm/d/job1292353/slurm_script: line 76: /gscratch/scrubbed/strigg/analyses/20190907/destrand_allc_files/allc_16C_26psu_1_S13.tsv.gz: No such file or directory /var/spool/slurm/d/job1292353/slurm_script: line 76: /gscratch/scrubbed/strigg/analyses/20190907/destrand_allc_files/allc_16C_26psu_2_S14.tsv.gz: No such file or directory /var/spool/slurm/d/job1292353/slurm_script: line 76: /gscratch/scrubbed/strigg/analyses/20190907/destrand_allc_files/allc_16C_26psu_3_S15.tsv.gz: No such file or directory /var/spool/slurm/d/job1292353/slurm_script: line 76: /gscratch/scrubbed/strigg/analyses/20190907/destrand_allc_files/allc_16C_26psu_4_S16.tsv.gz: No such file or directory /var/spool/slurm/d/job1292353/slurm_script: line 76: /gscratch/scrubbed/strigg/analyses/20190907/destrand_allc_files/allc_16C_32psu_1_S1.tsv.gz: No such file or directory /var/spool/slurm/d/job1292353/slurm_script: line 76: /gscratch/scrubbed/strigg/analyses/20190907/destrand_allc_files/allc_16C_32psu_2_S2.tsv.gz: No such file or directory /var/spool/slurm/d/job1292353/slurm_script: line 76: /gscratch/scrubbed/strigg/analyses/20190907/destrand_allc_files/allc_16C_32psu_3_S3.tsv.gz: No such file or directory /var/spool/slurm/d/job1292353/slurm_script: line 76: /gscratch/scrubbed/strigg/analyses/20190907/destrand_allc_files/allc_16C_32psu_4_S4.tsv.gz: No such file or directory /var/spool/slurm/d/job1292353/slurm_script: line 76: /gscratch/scrubbed/strigg/analyses/20190907/destrand_allc_files/allc_8C_26psu_1_S9.tsv.gz: No such file or directory /var/spool/slurm/d/job1292353/slurm_script: line 76: /gscratch/scrubbed/strigg/analyses/20190907/destrand_allc_files/allc_8C_26psu_2_S10.tsv.gz: No such file or directory /var/spool/slurm/d/job1292353/slurm_script: line 76: /gscratch/scrubbed/strigg/analyses/20190907/destrand_allc_files/allc_8C_26psu_3_S11.tsv.gz: No such file or directory /var/spool/slurm/d/job1292353/slurm_script: line 76: /gscratch/scrubbed/strigg/analyses/20190907/destrand_allc_files/allc_8C_26psu_4_S12.tsv.gz: No such file or directory /var/spool/slurm/d/job1292353/slurm_script: line 76: /gscratch/scrubbed/strigg/analyses/20190907/destrand_allc_files/allc_8C_32psu_1_S5.tsv.gz: No such file or directory /var/spool/slurm/d/job1292353/slurm_script: line 76: /gscratch/scrubbed/strigg/analyses/20190907/destrand_allc_files/allc_8C_32psu_2_S6.tsv.gz: No such file or directory /var/spool/slurm/d/job1292353/slurm_script: line 76: /gscratch/scrubbed/strigg/analyses/20190907/destrand_allc_files/allc_8C_32psu_3_S7.tsv.gz: No such file or directory /var/spool/slurm/d/job1292353/slurm_script: line 76: /gscratch/scrubbed/strigg/analyses/20190907/destrand_allc_files/allc_8C_32psu_4_S8.tsv.gz: No such file or directory /var/spool/slurm/d/job1292353/slurm_script: line 76: /gscratch/scrubbed/strigg/analyses/20190907/destrand_allc_files/allc_CTRL_16C_26psu_1_S19.tsv.gz: No such file or directory /var/spool/slurm/d/job1292353/slurm_script: line 76: /gscratch/scrubbed/strigg/analyses/20190907/destrand_allc_files/allc_CTRL_16C_26psu_2_S21.tsv.gz: No such file or directory /var/spool/slurm/d/job1292353/slurm_script: line 76: /gscratch/scrubbed/strigg/analyses/20190907/destrand_allc_files/allc_CTRL_8C_26psu_1_S17.tsv.gz: No such file or directory /var/spool/slurm/d/job1292353/slurm_script: line 76: /gscratch/scrubbed/strigg/analyses/20190907/destrand_allc_files/allc_CTRL_8C_26psu_2_S18.tsv.gz: No such file or directory /var/spool/slurm/d/job1292353/slurm_script: line 85: 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/job1292353/slurm_script: line 109: --samples: command not found