/var/spool/slurm/d/job2667042/slurm_script: line 24: fg: no job control + source /gscratch/srlab/strigg/bin/paths.sh ++ export PATH=/gscratch/srlab/programs/fastqc_v0.11.8:/gscratch/srlab/programs:/gscratch/strigg/bin:/gscratch/srlab/strigg/bin/anaconda3/bin:/gscratch/srlab/strigg/bin/anaconda3/condabin:/sw/local/bin:/usr/lib64/qt-3.3/bin:/sw/modules-1.775/bin:/usr/lpp/mmfs/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lusers/strigg/bin:/gscratch/srlab/programs/Bismark-0.22.3/:/gscratch/srlab/programs/bedtools-2.27.1/bin/:/gscratch/srlab/programs/bowtie2-2.3.5.1-linux-x86_64/:/gscratch/srlab/programs/snap:/gscratch/srlab/programs/scripts/:/gscratch/srlab/programs/SSPACE-LongRead_V1-1:/gscratch/srlab/programs/SSPACE-STANDARD-3.0_linux-x86_64:/gscratch/srlab/programs/gapclosr-1.12:/gscratch/srlab/programs/pyScaf:/gscratch/srlab/programs/FastaIndex:/gscratch/srlab/programs/last-852/src/:/gscratch/srlab/programs/PBSuite/bin/:/gscratch/srlab/programs/bwa-0.7.15:/gscratch/srlab/programs/GATK:/gscratch/srlab/programs/hmmer-3.1b2:/gscratch/srlab/programs/networkx-1.11:/gscratch/srlab/programs/pecan:/gscratch/srlab/programs/pitchfork:/gscratch/srlab/programs/samtools-1.9/:/gscratch/srlab/programs/sqlite:/gscratch/srlab/programs/transdecoder:/gscratch/srlab/programs/trinity:/gscratch/srlab/programs/decorator-4.0.11:/gscratch/srlab/programs/gcc:/gscratch/srlab/programs/ncbi-blast-2.6.0+:/gscratch/srlab/programs/picard-2.9.1:/signalp-4.1:/gscratch/srlab/programs/tmhmm-2.0c:/gscratch/srlab/programs/Trimmomatic-0.36:/gscratch/srlab/programs/trinotate ++ PATH=/gscratch/srlab/programs/fastqc_v0.11.8:/gscratch/srlab/programs:/gscratch/strigg/bin:/gscratch/srlab/strigg/bin/anaconda3/bin:/gscratch/srlab/strigg/bin/anaconda3/condabin:/sw/local/bin:/usr/lib64/qt-3.3/bin:/sw/modules-1.775/bin:/usr/lpp/mmfs/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lusers/strigg/bin:/gscratch/srlab/programs/Bismark-0.22.3/:/gscratch/srlab/programs/bedtools-2.27.1/bin/:/gscratch/srlab/programs/bowtie2-2.3.5.1-linux-x86_64/:/gscratch/srlab/programs/snap:/gscratch/srlab/programs/scripts/:/gscratch/srlab/programs/SSPACE-LongRead_V1-1:/gscratch/srlab/programs/SSPACE-STANDARD-3.0_linux-x86_64:/gscratch/srlab/programs/gapclosr-1.12:/gscratch/srlab/programs/pyScaf:/gscratch/srlab/programs/FastaIndex:/gscratch/srlab/programs/last-852/src/:/gscratch/srlab/programs/PBSuite/bin/:/gscratch/srlab/programs/bwa-0.7.15:/gscratch/srlab/programs/GATK:/gscratch/srlab/programs/hmmer-3.1b2:/gscratch/srlab/programs/networkx-1.11:/gscratch/srlab/programs/pecan:/gscratch/srlab/programs/pitchfork:/gscratch/srlab/programs/samtools-1.9/:/gscratch/srlab/programs/sqlite:/gscratch/srlab/programs/transdecoder:/gscratch/srlab/programs/trinity:/gscratch/srlab/programs/decorator-4.0.11:/gscratch/srlab/programs/gcc:/gscratch/srlab/programs/ncbi-blast-2.6.0+:/gscratch/srlab/programs/picard-2.9.1:/signalp-4.1:/gscratch/srlab/programs/tmhmm-2.0c:/gscratch/srlab/programs/Trimmomatic-0.36:/gscratch/srlab/programs/trinotate ++ LD_LIBRARY_PATH=/usr/lusers/seanb80/.cpan/build/Perl4-CoreLibs-0.003-UyQUvH/lib/:/usr/lusers/seanb80/gcc-6.3.0/lib64/: ++ export LD_LIBRARY_PATH + cat Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.CX_report.txt + awk '-F\t' '{if($6=="CG") print $0}' + cat Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.CX_report.txt + awk '-F\t' '{if($6=="CG") print $0}' + awk '-F\t' '{if($6=="CHG") print $0}' + cat Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.CX_report.txt + cat Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.CX_report.txt + awk '-F\t' '{if($6=="CHG") print $0}' + cat Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.CX_report.txt + awk '-F\t' '{if($6=="CHH") print $0}' + cat Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.CX_report.txt + awk '-F\t' '{if($6=="CHH") print $0}' + FILES='split_reports/*_report.txt' + for f in '$FILES' + awk '-F\t' '{if($4>0)print $0}' split_reports/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.CHG_report.txt + wc -l 1296446 + for f in '$FILES' + awk '-F\t' '{if($4>0)print $0}' split_reports/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.CHH_report.txt + wc -l 7071631 + for f in '$FILES' + awk '-F\t' '{if($4>0)print $0}' split_reports/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.CpG_report.txt + wc -l 1311934 + for f in '$FILES' + awk '-F\t' '{if($4>0)print $0}' split_reports/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.CHG_report.txt + wc -l 745915 + for f in '$FILES' + awk '-F\t' '{if($4>0)print $0}' split_reports/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.CHH_report.txt + wc -l 4665375 + for f in '$FILES' + awk '-F\t' '{if($4>0)print $0}' split_reports/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.CpG_report.txt + wc -l 773398 + for f in '$FILES' + awk '-F\t' '{if($4+$5>0)print $0}' split_reports/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.CHG_report.txt + wc -l 17399976 + for f in '$FILES' + awk '-F\t' '{if($4+$5>0)print $0}' split_reports/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.CHH_report.txt + wc -l 89520602 + for f in '$FILES' + awk '-F\t' '{if($4+$5>0)print $0}' split_reports/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.CpG_report.txt + wc -l 17252061 + for f in '$FILES' + awk '-F\t' '{if($4+$5>0)print $0}' split_reports/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.CHG_report.txt + wc -l 14732219 + for f in '$FILES' + awk '-F\t' '{if($4+$5>0)print $0}' split_reports/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.CHH_report.txt + wc -l 72075670 + for f in '$FILES' + awk '-F\t' '{if($4+$5>0)print $0}' split_reports/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.CpG_report.txt + wc -l 14609395 + for f in '$FILES' + awk '-F\t' '{if($4>=2)print $0}' split_reports/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.CHG_report.txt + wc -l 154271 + for f in '$FILES' + awk '-F\t' '{if($4>=2)print $0}' split_reports/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.CHH_report.txt + wc -l 925811 + for f in '$FILES' + awk '-F\t' '{if($4>=2)print $0}' split_reports/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.CpG_report.txt + wc -l 162200 + for f in '$FILES' + awk '-F\t' '{if($4>=2)print $0}' split_reports/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.CHG_report.txt + wc -l 67444 + for f in '$FILES' + awk '-F\t' '{if($4>=2)print $0}' split_reports/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.CHH_report.txt + wc -l 548859 + for f in '$FILES' + awk '-F\t' '{if($4>=2)print $0}' split_reports/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.CpG_report.txt + wc -l 78707 + for f in '$FILES' + awk '-F\t' '{if($4+$5>=2)print $0}' split_reports/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.CHG_report.txt + wc -l 14567060 + for f in '$FILES' + awk '-F\t' '{if($4+$5>=2)print $0}' split_reports/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.CHH_report.txt + wc -l 72011648 + for f in '$FILES' + wc -l + awk '-F\t' '{if($4+$5>=2)print $0}' split_reports/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.CpG_report.txt 14379375 + for f in '$FILES' + awk '-F\t' '{if($4+$5>=2)print $0}' split_reports/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.CHG_report.txt + wc -l 11326915 + for f in '$FILES' + awk '-F\t' '{if($4+$5>=2)print $0}' split_reports/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.CHH_report.txt + wc -l 51886534 + for f in '$FILES' + awk '-F\t' '{if($4+$5>=2)print $0}' split_reports/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.CpG_report.txt + wc -l 11177902 + for f in '$FILES' + awk '-F\t' '{if($4>=5)print $0}' split_reports/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.CHG_report.txt + wc -l 8512 + for f in '$FILES' + awk '-F\t' '{if($4>=5)print $0}' split_reports/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.CHH_report.txt + wc -l 66617 + for f in '$FILES' + awk '-F\t' '{if($4>=5)print $0}' split_reports/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.CpG_report.txt + wc -l 9857 + for f in '$FILES' + wc -l + awk '-F\t' '{if($4>=5)print $0}' split_reports/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.CHG_report.txt 4583 + for f in '$FILES' + awk '-F\t' '{if($4>=5)print $0}' split_reports/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.CHH_report.txt + wc -l 43956 + for f in '$FILES' + awk '-F\t' '{if($4>=5)print $0}' split_reports/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.CpG_report.txt + wc -l 6557 + for f in '$FILES' + awk '-F\t' '{if($4+$5>=5)print $0}' split_reports/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.CHG_report.txt + wc -l 9512947 + for f in '$FILES' + awk '-F\t' '{if($4+$5>=5)print $0}' split_reports/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.CHH_report.txt + wc -l 43428793 + for f in '$FILES' + awk '-F\t' '{if($4+$5>=5)print $0}' split_reports/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.CpG_report.txt + wc -l 9297453 + for f in '$FILES' + awk '-F\t' '{if($4+$5>=5)print $0}' split_reports/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.CHG_report.txt + wc -l 6490531 + for f in '$FILES' + awk '-F\t' '{if($4+$5>=5)print $0}' split_reports/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.CHH_report.txt + wc -l 26823827 + for f in '$FILES' + awk '-F\t' '{if($4+$5>=5)print $0}' split_reports/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.CpG_report.txt + wc -l 6353452 + for f in '$FILES' + wc -l + awk '-F\t' '{if($4>=7)print $0}' split_reports/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.CHG_report.txt 4199 + for f in '$FILES' + awk '-F\t' '{if($4>=7)print $0}' split_reports/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.CHH_report.txt + wc -l 34777 + for f in '$FILES' + awk '-F\t' '{if($4>=7)print $0}' split_reports/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.CpG_report.txt + wc -l 5018 + for f in '$FILES' + awk '-F\t' '{if($4>=7)print $0}' split_reports/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.CHG_report.txt + wc -l 2360 + for f in '$FILES' + awk '-F\t' '{if($4>=7)print $0}' split_reports/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.CHH_report.txt + wc -l 23363 + for f in '$FILES' + awk '-F\t' '{if($4>=7)print $0}' split_reports/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.CpG_report.txt + wc -l 3550 + for f in '$FILES' + awk '-F\t' '{if($4+$5>=7)print $0}' split_reports/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.CHG_report.txt + wc -l 7391187 + for f in '$FILES' + wc -l + awk '-F\t' '{if($4+$5>=7)print $0}' split_reports/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.CHH_report.txt 32605819 + for f in '$FILES' + awk '-F\t' '{if($4+$5>=7)print $0}' split_reports/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.CpG_report.txt + wc -l 7180134 + for f in '$FILES' + awk '-F\t' '{if($4+$5>=7)print $0}' split_reports/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.CHG_report.txt + wc -l 4786604 + for f in '$FILES' + awk '-F\t' '{if($4+$5>=7)print $0}' split_reports/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.CHH_report.txt + wc -l 19036662 + for f in '$FILES' + awk '-F\t' '{if($4+$5>=7)print $0}' split_reports/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.CpG_report.txt + wc -l 4669420 + for f in '$FILES' + awk '-F\t' '{if($4>=10)print $0}' split_reports/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.CHG_report.txt + wc -l 2264 + for f in '$FILES' + awk '-F\t' '{if($4>=10)print $0}' split_reports/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.CHH_report.txt + wc -l 19153 + for f in '$FILES' + awk '-F\t' '{if($4>=10)print $0}' split_reports/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.CpG_report.txt + wc -l 2822 + for f in '$FILES' + awk '-F\t' '{if($4>=10)print $0}' split_reports/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.CHG_report.txt + wc -l 1229 + for f in '$FILES' + awk '-F\t' '{if($4>=10)print $0}' split_reports/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.CHH_report.txt + wc -l 12900 + for f in '$FILES' + awk '-F\t' '{if($4>=10)print $0}' split_reports/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.CpG_report.txt + wc -l 2032 + for f in '$FILES' + awk '-F\t' '{if($4+$5>=10)print $0}' split_reports/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.CHG_report.txt + wc -l 5119888 + for f in '$FILES' + awk '-F\t' '{if($4+$5>=10)print $0}' split_reports/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.CHH_report.txt + wc -l 21800230 + for f in '$FILES' + awk '-F\t' '{if($4+$5>=10)print $0}' split_reports/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.CpG_report.txt + wc -l 4933708 + for f in '$FILES' + awk '-F\t' '{if($4+$5>=10)print $0}' split_reports/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.CHG_report.txt + wc -l 3129925 + for f in '$FILES' + awk '-F\t' '{if($4+$5>=10)print $0}' split_reports/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.CHH_report.txt + wc -l 11978342 + for f in '$FILES' + awk '-F\t' '{if($4+$5>=10)print $0}' split_reports/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.CpG_report.txt + wc -l 3040276 + for f in '$FILES' + awk '-F\t' '{if($4>=15)print $0}' split_reports/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.CHG_report.txt + wc -l 1196 + for f in '$FILES' + awk '-F\t' '{if($4>=15)print $0}' split_reports/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.CHH_report.txt + wc -l 10294 + for f in '$FILES' + awk '-F\t' '{if($4>=15)print $0}' split_reports/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.CpG_report.txt + wc -l 1688 + for f in '$FILES' + awk '-F\t' '{if($4>=15)print $0}' split_reports/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.CHG_report.txt + wc -l 623 + for f in '$FILES' + awk '-F\t' '{if($4>=15)print $0}' split_reports/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.CHH_report.txt + wc -l 7007 + for f in '$FILES' + awk '-F\t' '{if($4>=15)print $0}' split_reports/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.CpG_report.txt + wc -l 1212 + for f in '$FILES' + awk '-F\t' '{if($4+$5>=15)print $0}' split_reports/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.CHG_report.txt + wc -l 2784905 + for f in '$FILES' + awk '-F\t' '{if($4+$5>=15)print $0}' split_reports/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.CHH_report.txt + wc -l 11474268 + for f in '$FILES' + awk '-F\t' '{if($4+$5>=15)print $0}' split_reports/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.CpG_report.txt + wc -l 2645098 + for f in '$FILES' + awk '-F\t' '{if($4+$5>=15)print $0}' split_reports/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.CHG_report.txt + wc -l 1590680 + for f in '$FILES' + awk '-F\t' '{if($4+$5>=15)print $0}' split_reports/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.CHH_report.txt + wc -l 5882144 + for f in '$FILES' + awk '-F\t' '{if($4+$5>=15)print $0}' split_reports/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.CpG_report.txt + wc -l 1532705 + for f in '$FILES' + awk '-F\t' '{if($4>=20)print $0}' split_reports/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.CHG_report.txt + wc -l 750 + for f in '$FILES' + awk '-F\t' '{if($4>=20)print $0}' split_reports/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.CHH_report.txt + wc -l 6804 + for f in '$FILES' + awk '-F\t' '{if($4>=20)print $0}' split_reports/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.CpG_report.txt + wc -l 1259 + for f in '$FILES' + awk '-F\t' '{if($4>=20)print $0}' split_reports/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.CHG_report.txt + wc -l 391 + for f in '$FILES' + awk '-F\t' '{if($4>=20)print $0}' split_reports/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.CHH_report.txt + wc -l 4692 + for f in '$FILES' + awk '-F\t' '{if($4>=20)print $0}' split_reports/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.CpG_report.txt + wc -l 897 + for f in '$FILES' + awk '-F\t' '{if($4+$5>=20)print $0}' split_reports/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.CHG_report.txt + wc -l 1535816 + for f in '$FILES' + awk '-F\t' '{if($4+$5>=20)print $0}' split_reports/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.CHH_report.txt + wc -l 6239570 + for f in '$FILES' + awk '-F\t' '{if($4+$5>=20)print $0}' split_reports/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.CpG_report.txt + wc -l 1435437 + for f in '$FILES' + awk '-F\t' '{if($4+$5>=20)print $0}' split_reports/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.CHG_report.txt + wc -l 847890 + for f in '$FILES' + awk '-F\t' '{if($4+$5>=20)print $0}' split_reports/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.CHH_report.txt + wc -l 3100637 + for f in '$FILES' + awk '-F\t' '{if($4+$5>=20)print $0}' split_reports/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.CpG_report.txt + wc -l 808144