Job ID = 2010684 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 8,759,288 reads read : 17,518,576 reads written : 17,518,576 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: 00:04:35 8759288 reads; of these: 8759288 (100.00%) were paired; of these: 3086982 (35.24%) aligned concordantly 0 times 5356515 (61.15%) aligned concordantly exactly 1 time 315791 (3.61%) aligned concordantly >1 times ---- 3086982 pairs aligned concordantly 0 times; of these: 8560 (0.28%) aligned discordantly 1 time ---- 3078422 pairs aligned 0 times concordantly or discordantly; of these: 6156844 mates make up the pairs; of these: 3864531 (62.77%) aligned 0 times 2149632 (34.91%) aligned exactly 1 time 142681 (2.32%) aligned >1 times 77.94% overall alignment rate Time searching: 00:04:35 Overall time: 00:04:35 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] 330171 / 5680456 = 0.0581 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 @ Sat, 06 Jul 2019 00:03:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3865906/SRX3865906.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3865906/SRX3865906.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3865906/SRX3865906.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3865906/SRX3865906.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 @ Sat, 06 Jul 2019 00:03:05: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:03:05: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:03:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3865906/SRX3865906.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3865906/SRX3865906.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3865906/SRX3865906.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3865906/SRX3865906.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 @ Sat, 06 Jul 2019 00:03:06: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:03:06: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:03:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3865906/SRX3865906.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3865906/SRX3865906.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3865906/SRX3865906.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3865906/SRX3865906.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 @ Sat, 06 Jul 2019 00:03:07: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:03:07: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:03:12: 1000000 INFO @ Sat, 06 Jul 2019 00:03:15: 1000000 INFO @ Sat, 06 Jul 2019 00:03:17: 1000000 INFO @ Sat, 06 Jul 2019 00:03:19: 2000000 INFO @ Sat, 06 Jul 2019 00:03:23: 2000000 INFO @ Sat, 06 Jul 2019 00:03:26: 3000000 INFO @ Sat, 06 Jul 2019 00:03:27: 2000000 INFO @ Sat, 06 Jul 2019 00:03:31: 3000000 INFO @ Sat, 06 Jul 2019 00:03:33: 4000000 INFO @ Sat, 06 Jul 2019 00:03:37: 3000000 INFO @ Sat, 06 Jul 2019 00:03:39: 4000000 INFO @ Sat, 06 Jul 2019 00:03:40: 5000000 INFO @ Sat, 06 Jul 2019 00:03:47: 6000000 INFO @ Sat, 06 Jul 2019 00:03:47: 5000000 INFO @ Sat, 06 Jul 2019 00:03:47: 4000000 INFO @ Sat, 06 Jul 2019 00:03:53: 7000000 INFO @ Sat, 06 Jul 2019 00:03:55: 6000000 INFO @ Sat, 06 Jul 2019 00:03:57: 5000000 INFO @ Sat, 06 Jul 2019 00:04:00: 8000000 INFO @ Sat, 06 Jul 2019 00:04:03: 7000000 INFO @ Sat, 06 Jul 2019 00:04:07: 9000000 INFO @ Sat, 06 Jul 2019 00:04:07: 6000000 INFO @ Sat, 06 Jul 2019 00:04:11: 8000000 INFO @ Sat, 06 Jul 2019 00:04:14: 10000000 INFO @ Sat, 06 Jul 2019 00:04:17: 7000000 INFO @ Sat, 06 Jul 2019 00:04:18: 9000000 INFO @ Sat, 06 Jul 2019 00:04:21: 11000000 INFO @ Sat, 06 Jul 2019 00:04:26: 10000000 INFO @ Sat, 06 Jul 2019 00:04:27: 8000000 INFO @ Sat, 06 Jul 2019 00:04:28: 12000000 INFO @ Sat, 06 Jul 2019 00:04:34: 11000000 INFO @ Sat, 06 Jul 2019 00:04:34: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 00:04:34: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 00:04:34: #1 total tags in treatment: 5342232 INFO @ Sat, 06 Jul 2019 00:04:34: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:04:34: #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 00:04:35: #1 tags after filtering in treatment: 2900526 INFO @ Sat, 06 Jul 2019 00:04:35: #1 Redundant rate of treatment: 0.46 INFO @ Sat, 06 Jul 2019 00:04:35: #1 finished! INFO @ Sat, 06 Jul 2019 00:04:35: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:04:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:04:35: #2 number of paired peaks: 1 WARNING @ Sat, 06 Jul 2019 00:04:35: Too few paired peaks (1) 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 00:04:35: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3865906/SRX3865906.05_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/SRX3865906/SRX3865906.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865906/SRX3865906.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865906/SRX3865906.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 00:04:37: 9000000 INFO @ Sat, 06 Jul 2019 00:04:42: 12000000 INFO @ Sat, 06 Jul 2019 00:04:47: 10000000 INFO @ Sat, 06 Jul 2019 00:04:49: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 00:04:49: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 00:04:49: #1 total tags in treatment: 5342232 INFO @ Sat, 06 Jul 2019 00:04:49: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:04:49: #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 00:04:50: #1 tags after filtering in treatment: 2900526 INFO @ Sat, 06 Jul 2019 00:04:50: #1 Redundant rate of treatment: 0.46 INFO @ Sat, 06 Jul 2019 00:04:50: #1 finished! INFO @ Sat, 06 Jul 2019 00:04:50: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:04:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:04:50: #2 number of paired peaks: 1 WARNING @ Sat, 06 Jul 2019 00:04:50: Too few paired peaks (1) 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 00:04:50: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3865906/SRX3865906.20_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/SRX3865906/SRX3865906.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865906/SRX3865906.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865906/SRX3865906.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 00:04:57: 11000000 INFO @ Sat, 06 Jul 2019 00:05:06: 12000000 BigWig に変換しました。 INFO @ Sat, 06 Jul 2019 00:05:15: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 00:05:15: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 00:05:15: #1 total tags in treatment: 5342232 INFO @ Sat, 06 Jul 2019 00:05:15: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:05:15: #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 00:05:15: #1 tags after filtering in treatment: 2900526 INFO @ Sat, 06 Jul 2019 00:05:15: #1 Redundant rate of treatment: 0.46 INFO @ Sat, 06 Jul 2019 00:05:15: #1 finished! INFO @ Sat, 06 Jul 2019 00:05:15: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:05:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:05:15: #2 number of paired peaks: 1 WARNING @ Sat, 06 Jul 2019 00:05:15: Too few paired peaks (1) 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 00:05:15: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3865906/SRX3865906.10_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/SRX3865906/SRX3865906.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865906/SRX3865906.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865906/SRX3865906.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling