Job ID = 11244920 sra ファイルのダウンロード中... Completed: 561192K bytes transferred in 9 seconds (498997K bits/sec), in 1 file. sra ファイルのダウンロードが完了しました。 Read layout: PAIRED fastq に変換中... Read 17323613 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554663/SRR7696336.sra Written 17323613 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554663/SRR7696336.sra rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません rm: cannot remove `[DSE]RR*.fastq': そのようなファイルやディレクトリはありません 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: 00:11:23 17323613 reads; of these: 17323613 (100.00%) were paired; of these: 3381307 (19.52%) aligned concordantly 0 times 11697205 (67.52%) aligned concordantly exactly 1 time 2245101 (12.96%) aligned concordantly >1 times ---- 3381307 pairs aligned concordantly 0 times; of these: 392173 (11.60%) aligned discordantly 1 time ---- 2989134 pairs aligned 0 times concordantly or discordantly; of these: 5978268 mates make up the pairs; of these: 5352379 (89.53%) aligned 0 times 375084 (6.27%) aligned exactly 1 time 250805 (4.20%) aligned >1 times 84.55% overall alignment rate Time searching: 00:11:23 Overall time: 00:11:23 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_sort_core] merging from 8 files... [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] 681380 / 14255155 = 0.0478 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 @ Tue, 09 Oct 2018 23:10:50: # Command line: callpeak -t SRX4554663.bam -f BAM -g 12100000 -n SRX4554663.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4554663.10 # format = BAM # ChIP-seq file = ['SRX4554663.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 @ Tue, 09 Oct 2018 23:10:50: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:10:50: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:10:50: # Command line: callpeak -t SRX4554663.bam -f BAM -g 12100000 -n SRX4554663.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4554663.05 # format = BAM # ChIP-seq file = ['SRX4554663.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 @ Tue, 09 Oct 2018 23:10:50: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:10:50: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:10:50: # Command line: callpeak -t SRX4554663.bam -f BAM -g 12100000 -n SRX4554663.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4554663.20 # format = BAM # ChIP-seq file = ['SRX4554663.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 @ Tue, 09 Oct 2018 23:10:50: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:10:50: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:10:56: 1000000 INFO @ Tue, 09 Oct 2018 23:10:56: 1000000 INFO @ Tue, 09 Oct 2018 23:10:56: 1000000 INFO @ Tue, 09 Oct 2018 23:11:02: 2000000 INFO @ Tue, 09 Oct 2018 23:11:03: 2000000 INFO @ Tue, 09 Oct 2018 23:11:03: 2000000 INFO @ Tue, 09 Oct 2018 23:11:09: 3000000 INFO @ Tue, 09 Oct 2018 23:11:09: 3000000 INFO @ Tue, 09 Oct 2018 23:11:09: 3000000 INFO @ Tue, 09 Oct 2018 23:11:15: 4000000 INFO @ Tue, 09 Oct 2018 23:11:15: 4000000 INFO @ Tue, 09 Oct 2018 23:11:16: 4000000 INFO @ Tue, 09 Oct 2018 23:11:21: 5000000 INFO @ Tue, 09 Oct 2018 23:11:22: 5000000 INFO @ Tue, 09 Oct 2018 23:11:23: 5000000 INFO @ Tue, 09 Oct 2018 23:11:28: 6000000 INFO @ Tue, 09 Oct 2018 23:11:28: 6000000 INFO @ Tue, 09 Oct 2018 23:11:29: 6000000 INFO @ Tue, 09 Oct 2018 23:11:33: 7000000 INFO @ Tue, 09 Oct 2018 23:11:34: 7000000 INFO @ Tue, 09 Oct 2018 23:11:35: 7000000 INFO @ Tue, 09 Oct 2018 23:11:39: 8000000 INFO @ Tue, 09 Oct 2018 23:11:40: 8000000 INFO @ Tue, 09 Oct 2018 23:11:41: 8000000 INFO @ Tue, 09 Oct 2018 23:11:46: 9000000 INFO @ Tue, 09 Oct 2018 23:11:46: 9000000 INFO @ Tue, 09 Oct 2018 23:11:48: 9000000 INFO @ Tue, 09 Oct 2018 23:11:52: 10000000 INFO @ Tue, 09 Oct 2018 23:11:52: 10000000 INFO @ Tue, 09 Oct 2018 23:11:54: 10000000 INFO @ Tue, 09 Oct 2018 23:11:58: 11000000 INFO @ Tue, 09 Oct 2018 23:11:59: 11000000 INFO @ Tue, 09 Oct 2018 23:12:00: 11000000 INFO @ Tue, 09 Oct 2018 23:12:04: 12000000 INFO @ Tue, 09 Oct 2018 23:12:05: 12000000 INFO @ Tue, 09 Oct 2018 23:12:06: 12000000 INFO @ Tue, 09 Oct 2018 23:12:10: 13000000 INFO @ Tue, 09 Oct 2018 23:12:12: 13000000 INFO @ Tue, 09 Oct 2018 23:12:13: 13000000 INFO @ Tue, 09 Oct 2018 23:12:17: 14000000 INFO @ Tue, 09 Oct 2018 23:12:18: 14000000 INFO @ Tue, 09 Oct 2018 23:12:19: 14000000 INFO @ Tue, 09 Oct 2018 23:12:23: 15000000 INFO @ Tue, 09 Oct 2018 23:12:25: 15000000 INFO @ Tue, 09 Oct 2018 23:12:25: 15000000 INFO @ Tue, 09 Oct 2018 23:12:30: 16000000 INFO @ Tue, 09 Oct 2018 23:12:31: 16000000 INFO @ Tue, 09 Oct 2018 23:12:31: 16000000 INFO @ Tue, 09 Oct 2018 23:12:36: 17000000 INFO @ Tue, 09 Oct 2018 23:12:38: 17000000 INFO @ Tue, 09 Oct 2018 23:12:38: 17000000 INFO @ Tue, 09 Oct 2018 23:12:43: 18000000 INFO @ Tue, 09 Oct 2018 23:12:44: 18000000 INFO @ Tue, 09 Oct 2018 23:12:45: 18000000 INFO @ Tue, 09 Oct 2018 23:12:49: 19000000 INFO @ Tue, 09 Oct 2018 23:12:51: 19000000 INFO @ Tue, 09 Oct 2018 23:12:53: 19000000 INFO @ Tue, 09 Oct 2018 23:12:56: 20000000 INFO @ Tue, 09 Oct 2018 23:12:58: 20000000 INFO @ Tue, 09 Oct 2018 23:13:01: 20000000 INFO @ Tue, 09 Oct 2018 23:13:03: 21000000 INFO @ Tue, 09 Oct 2018 23:13:05: 21000000 INFO @ Tue, 09 Oct 2018 23:13:08: 21000000 INFO @ Tue, 09 Oct 2018 23:13:09: 22000000 INFO @ Tue, 09 Oct 2018 23:13:12: 22000000 INFO @ Tue, 09 Oct 2018 23:13:16: 22000000 INFO @ Tue, 09 Oct 2018 23:13:16: 23000000 INFO @ Tue, 09 Oct 2018 23:13:18: 23000000 INFO @ Tue, 09 Oct 2018 23:13:23: 24000000 INFO @ Tue, 09 Oct 2018 23:13:23: 23000000 INFO @ Tue, 09 Oct 2018 23:13:25: 24000000 INFO @ Tue, 09 Oct 2018 23:13:29: 25000000 INFO @ Tue, 09 Oct 2018 23:13:31: 24000000 INFO @ Tue, 09 Oct 2018 23:13:32: 25000000 INFO @ Tue, 09 Oct 2018 23:13:36: 26000000 INFO @ Tue, 09 Oct 2018 23:13:38: 25000000 INFO @ Tue, 09 Oct 2018 23:13:39: 26000000 INFO @ Tue, 09 Oct 2018 23:13:42: 27000000 INFO @ Tue, 09 Oct 2018 23:13:46: 26000000 INFO @ Tue, 09 Oct 2018 23:13:46: 27000000 INFO @ Tue, 09 Oct 2018 23:13:49: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:13:49: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:13:49: #1 total tags in treatment: 13274943 INFO @ Tue, 09 Oct 2018 23:13:49: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:13:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 23:13:49: #1 tags after filtering in treatment: 8162800 INFO @ Tue, 09 Oct 2018 23:13:49: #1 Redundant rate of treatment: 0.39 INFO @ Tue, 09 Oct 2018 23:13:49: #1 finished! INFO @ Tue, 09 Oct 2018 23:13:49: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:13:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:13:49: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 23:13:49: Too few paired peaks (0) 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 @ Tue, 09 Oct 2018 23:13:49: Process for pairing-model is terminated! cat: SRX4554663.10_peaks.narrowPeak: そのようなファイルやディレクトリはありません pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4554663.10_model.r': そのようなファイルやディレクトリはありません rm: cannot remove `SRX4554663.10_*.xls': そのようなファイルやディレクトリはありません rm: cannot remove `SRX4554663.10_peaks.narrowPeak': そのようなファイルやディレクトリはありません CompletedMACS2peakCalling INFO @ Tue, 09 Oct 2018 23:13:52: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:13:52: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:13:52: #1 total tags in treatment: 13274943 INFO @ Tue, 09 Oct 2018 23:13:52: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:13:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 23:13:52: #1 tags after filtering in treatment: 8162800 INFO @ Tue, 09 Oct 2018 23:13:52: #1 Redundant rate of treatment: 0.39 INFO @ Tue, 09 Oct 2018 23:13:52: #1 finished! INFO @ Tue, 09 Oct 2018 23:13:52: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:13:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:13:52: 27000000 INFO @ Tue, 09 Oct 2018 23:13:53: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 23:13:53: Too few paired peaks (0) 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 @ Tue, 09 Oct 2018 23:13:53: Process for pairing-model is terminated! cat: SRX4554663.05_peaks.narrowPeak: そのようなファイルやディレクトリはありません pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4554663.05_model.r': そのようなファイルやディレクトリはありません rm: cannot remove `SRX4554663.05_*.xls': そのようなファイルやディレクトリはありません rm: cannot remove `SRX4554663.05_peaks.narrowPeak': そのようなファイルやディレクトリはありません CompletedMACS2peakCalling INFO @ Tue, 09 Oct 2018 23:13:58: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:13:58: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:13:58: #1 total tags in treatment: 13274943 INFO @ Tue, 09 Oct 2018 23:13:58: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:13:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 23:13:58: #1 tags after filtering in treatment: 8162800 INFO @ Tue, 09 Oct 2018 23:13:58: #1 Redundant rate of treatment: 0.39 INFO @ Tue, 09 Oct 2018 23:13:58: #1 finished! INFO @ Tue, 09 Oct 2018 23:13:58: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:13:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:13:59: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 23:13:59: Too few paired peaks (0) 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 @ Tue, 09 Oct 2018 23:13:59: Process for pairing-model is terminated! cat: SRX4554663.20_peaks.narrowPeak: そのようなファイルやディレクトリはありません pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4554663.20_model.r': そのようなファイルやディレクトリはありません rm: cannot remove `SRX4554663.20_*.xls': そのようなファイルやディレクトリはありません rm: cannot remove `SRX4554663.20_peaks.narrowPeak': そのようなファイルやディレクトリはありません CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。