Job ID = 2010686 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 4,883,113 reads read : 9,766,226 reads written : 9,766,226 rm: cannot remove ‘[DSE]RR*’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:02 4883113 reads; of these: 4883113 (100.00%) were paired; of these: 1737864 (35.59%) aligned concordantly 0 times 2649168 (54.25%) aligned concordantly exactly 1 time 496081 (10.16%) aligned concordantly >1 times ---- 1737864 pairs aligned concordantly 0 times; of these: 3009 (0.17%) aligned discordantly 1 time ---- 1734855 pairs aligned 0 times concordantly or discordantly; of these: 3469710 mates make up the pairs; of these: 2198455 (63.36%) aligned 0 times 1058575 (30.51%) aligned exactly 1 time 212680 (6.13%) aligned >1 times 77.49% overall alignment rate Time searching: 00:03:02 Overall time: 00:03:02 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 244556 / 3147816 = 0.0777 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Fri, 05 Jul 2019 23:59:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3865907/SRX3865907.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3865907/SRX3865907.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3865907/SRX3865907.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3865907/SRX3865907.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 05 Jul 2019 23:59:08: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:59:08: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:59:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3865907/SRX3865907.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3865907/SRX3865907.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3865907/SRX3865907.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3865907/SRX3865907.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 05 Jul 2019 23:59:09: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:59:09: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:59:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3865907/SRX3865907.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3865907/SRX3865907.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3865907/SRX3865907.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3865907/SRX3865907.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 05 Jul 2019 23:59:10: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:59:10: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:59:15: 1000000 INFO @ Fri, 05 Jul 2019 23:59:17: 1000000 INFO @ Fri, 05 Jul 2019 23:59:19: 1000000 INFO @ Fri, 05 Jul 2019 23:59:22: 2000000 INFO @ Fri, 05 Jul 2019 23:59:25: 2000000 INFO @ Fri, 05 Jul 2019 23:59:27: 2000000 INFO @ Fri, 05 Jul 2019 23:59:28: 3000000 INFO @ Fri, 05 Jul 2019 23:59:32: 3000000 INFO @ Fri, 05 Jul 2019 23:59:35: 3000000 INFO @ Fri, 05 Jul 2019 23:59:35: 4000000 INFO @ Fri, 05 Jul 2019 23:59:39: 4000000 INFO @ Fri, 05 Jul 2019 23:59:41: 5000000 INFO @ Fri, 05 Jul 2019 23:59:42: 4000000 INFO @ Fri, 05 Jul 2019 23:59:47: 5000000 INFO @ Fri, 05 Jul 2019 23:59:48: 6000000 INFO @ Fri, 05 Jul 2019 23:59:49: 5000000 INFO @ Fri, 05 Jul 2019 23:59:54: 6000000 INFO @ Fri, 05 Jul 2019 23:59:54: 7000000 INFO @ Fri, 05 Jul 2019 23:59:55: #1 tag size is determined as 37 bps INFO @ Fri, 05 Jul 2019 23:59:55: #1 tag size = 37 INFO @ Fri, 05 Jul 2019 23:59:55: #1 total tags in treatment: 2900737 INFO @ Fri, 05 Jul 2019 23:59:55: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:59:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 23:59:55: #1 tags after filtering in treatment: 2115685 INFO @ Fri, 05 Jul 2019 23:59:55: #1 Redundant rate of treatment: 0.27 INFO @ Fri, 05 Jul 2019 23:59:55: #1 finished! INFO @ Fri, 05 Jul 2019 23:59:55: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:59:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:59:55: #2 number of paired peaks: 26 WARNING @ Fri, 05 Jul 2019 23:59:55: Too few paired peaks (26) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Fri, 05 Jul 2019 23:59:55: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3865907/SRX3865907.05_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865907/SRX3865907.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865907/SRX3865907.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865907/SRX3865907.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 23:59:56: 6000000 INFO @ Sat, 06 Jul 2019 00:00:01: 7000000 INFO @ Sat, 06 Jul 2019 00:00:02: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 00:00:02: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 00:00:02: #1 total tags in treatment: 2900737 INFO @ Sat, 06 Jul 2019 00:00:02: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:00:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 00:00:02: #1 tags after filtering in treatment: 2115685 INFO @ Sat, 06 Jul 2019 00:00:02: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 06 Jul 2019 00:00:02: #1 finished! INFO @ Sat, 06 Jul 2019 00:00:02: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:00:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:00:02: #2 number of paired peaks: 26 WARNING @ Sat, 06 Jul 2019 00:00:02: Too few paired peaks (26) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Sat, 06 Jul 2019 00:00:02: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3865907/SRX3865907.10_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865907/SRX3865907.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865907/SRX3865907.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865907/SRX3865907.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 00:00:04: 7000000 INFO @ Sat, 06 Jul 2019 00:00:04: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 00:00:04: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 00:00:04: #1 total tags in treatment: 2900737 INFO @ Sat, 06 Jul 2019 00:00:04: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:00:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 00:00:04: #1 tags after filtering in treatment: 2115685 INFO @ Sat, 06 Jul 2019 00:00:04: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 06 Jul 2019 00:00:04: #1 finished! INFO @ Sat, 06 Jul 2019 00:00:04: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:00:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:00:04: #2 number of paired peaks: 26 WARNING @ Sat, 06 Jul 2019 00:00:04: Too few paired peaks (26) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Sat, 06 Jul 2019 00:00:04: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3865907/SRX3865907.20_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865907/SRX3865907.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865907/SRX3865907.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865907/SRX3865907.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。