Job ID = 10536391 sra ファイルのダウンロード中... Completed: 1267519K bytes transferred in 22 seconds (452321K 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... Written 31792681 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3671147/SRR6696899.sra Written 31792681 spots total 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: 00:20:20 31792681 reads; of these: 31792681 (100.00%) were paired; of these: 5824198 (18.32%) aligned concordantly 0 times 23017478 (72.40%) aligned concordantly exactly 1 time 2951005 (9.28%) aligned concordantly >1 times ---- 5824198 pairs aligned concordantly 0 times; of these: 61006 (1.05%) aligned discordantly 1 time ---- 5763192 pairs aligned 0 times concordantly or discordantly; of these: 11526384 mates make up the pairs; of these: 11069850 (96.04%) aligned 0 times 383706 (3.33%) aligned exactly 1 time 72828 (0.63%) aligned >1 times 82.59% overall alignment rate Time searching: 00:20:20 Overall time: 00:20:20 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 24 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] 10044756 / 25980014 = 0.3866 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 @ Thu, 05 Apr 2018 09:47:15: # Command line: callpeak -t SRX3671147.bam -f BAM -g 12100000 -n SRX3671147.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3671147.10 # format = BAM # ChIP-seq file = ['SRX3671147.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 @ Thu, 05 Apr 2018 09:47:15: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:47:15: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:47:15: # Command line: callpeak -t SRX3671147.bam -f BAM -g 12100000 -n SRX3671147.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3671147.05 # format = BAM # ChIP-seq file = ['SRX3671147.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 @ Thu, 05 Apr 2018 09:47:15: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:47:15: # Command line: callpeak -t SRX3671147.bam -f BAM -g 12100000 -n SRX3671147.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3671147.20 # format = BAM # ChIP-seq file = ['SRX3671147.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 @ Thu, 05 Apr 2018 09:47:15: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:47:15: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:47:15: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:47:22: 1000000 INFO @ Thu, 05 Apr 2018 09:47:22: 1000000 INFO @ Thu, 05 Apr 2018 09:47:22: 1000000 INFO @ Thu, 05 Apr 2018 09:47:28: 2000000 INFO @ Thu, 05 Apr 2018 09:47:28: 2000000 INFO @ Thu, 05 Apr 2018 09:47:28: 2000000 INFO @ Thu, 05 Apr 2018 09:47:33: 3000000 INFO @ Thu, 05 Apr 2018 09:47:34: 3000000 INFO @ Thu, 05 Apr 2018 09:47:34: 3000000 INFO @ Thu, 05 Apr 2018 09:47:39: 4000000 INFO @ Thu, 05 Apr 2018 09:47:40: 4000000 INFO @ Thu, 05 Apr 2018 09:47:40: 4000000 INFO @ Thu, 05 Apr 2018 09:47:45: 5000000 INFO @ Thu, 05 Apr 2018 09:47:46: 5000000 INFO @ Thu, 05 Apr 2018 09:47:47: 5000000 INFO @ Thu, 05 Apr 2018 09:47:51: 6000000 INFO @ Thu, 05 Apr 2018 09:47:53: 6000000 INFO @ Thu, 05 Apr 2018 09:47:53: 6000000 INFO @ Thu, 05 Apr 2018 09:47:57: 7000000 INFO @ Thu, 05 Apr 2018 09:47:59: 7000000 INFO @ Thu, 05 Apr 2018 09:47:59: 7000000 INFO @ Thu, 05 Apr 2018 09:48:03: 8000000 INFO @ Thu, 05 Apr 2018 09:48:05: 8000000 INFO @ Thu, 05 Apr 2018 09:48:05: 8000000 INFO @ Thu, 05 Apr 2018 09:48:09: 9000000 INFO @ Thu, 05 Apr 2018 09:48:11: 9000000 INFO @ Thu, 05 Apr 2018 09:48:11: 9000000 INFO @ Thu, 05 Apr 2018 09:48:15: 10000000 INFO @ Thu, 05 Apr 2018 09:48:17: 10000000 INFO @ Thu, 05 Apr 2018 09:48:17: 10000000 INFO @ Thu, 05 Apr 2018 09:48:21: 11000000 INFO @ Thu, 05 Apr 2018 09:48:24: 11000000 INFO @ Thu, 05 Apr 2018 09:48:24: 11000000 INFO @ Thu, 05 Apr 2018 09:48:27: 12000000 INFO @ Thu, 05 Apr 2018 09:48:30: 12000000 INFO @ Thu, 05 Apr 2018 09:48:30: 12000000 INFO @ Thu, 05 Apr 2018 09:48:32: 13000000 INFO @ Thu, 05 Apr 2018 09:48:36: 13000000 INFO @ Thu, 05 Apr 2018 09:48:36: 13000000 INFO @ Thu, 05 Apr 2018 09:48:38: 14000000 INFO @ Thu, 05 Apr 2018 09:48:42: 14000000 INFO @ Thu, 05 Apr 2018 09:48:42: 14000000 INFO @ Thu, 05 Apr 2018 09:48:44: 15000000 INFO @ Thu, 05 Apr 2018 09:48:48: 15000000 INFO @ Thu, 05 Apr 2018 09:48:48: 15000000 INFO @ Thu, 05 Apr 2018 09:48:50: 16000000 INFO @ Thu, 05 Apr 2018 09:48:54: 16000000 INFO @ Thu, 05 Apr 2018 09:48:54: 16000000 INFO @ Thu, 05 Apr 2018 09:48:56: 17000000 INFO @ Thu, 05 Apr 2018 09:49:01: 17000000 INFO @ Thu, 05 Apr 2018 09:49:01: 17000000 INFO @ Thu, 05 Apr 2018 09:49:02: 18000000 INFO @ Thu, 05 Apr 2018 09:49:07: 18000000 INFO @ Thu, 05 Apr 2018 09:49:07: 18000000 INFO @ Thu, 05 Apr 2018 09:49:08: 19000000 INFO @ Thu, 05 Apr 2018 09:49:13: 19000000 INFO @ Thu, 05 Apr 2018 09:49:13: 19000000 INFO @ Thu, 05 Apr 2018 09:49:14: 20000000 INFO @ Thu, 05 Apr 2018 09:49:19: 20000000 INFO @ Thu, 05 Apr 2018 09:49:19: 20000000 INFO @ Thu, 05 Apr 2018 09:49:20: 21000000 INFO @ Thu, 05 Apr 2018 09:49:25: 21000000 INFO @ Thu, 05 Apr 2018 09:49:25: 21000000 INFO @ Thu, 05 Apr 2018 09:49:26: 22000000 INFO @ Thu, 05 Apr 2018 09:49:31: 22000000 INFO @ Thu, 05 Apr 2018 09:49:31: 22000000 INFO @ Thu, 05 Apr 2018 09:49:32: 23000000 INFO @ Thu, 05 Apr 2018 09:49:37: 23000000 INFO @ Thu, 05 Apr 2018 09:49:37: 23000000 INFO @ Thu, 05 Apr 2018 09:49:38: 24000000 INFO @ Thu, 05 Apr 2018 09:49:44: 24000000 INFO @ Thu, 05 Apr 2018 09:49:44: 25000000 INFO @ Thu, 05 Apr 2018 09:49:44: 24000000 INFO @ Thu, 05 Apr 2018 09:49:50: 25000000 INFO @ Thu, 05 Apr 2018 09:49:50: 26000000 INFO @ Thu, 05 Apr 2018 09:49:50: 25000000 INFO @ Thu, 05 Apr 2018 09:49:55: 26000000 INFO @ Thu, 05 Apr 2018 09:49:56: 27000000 INFO @ Thu, 05 Apr 2018 09:49:57: 26000000 INFO @ Thu, 05 Apr 2018 09:50:01: 27000000 INFO @ Thu, 05 Apr 2018 09:50:03: 28000000 INFO @ Thu, 05 Apr 2018 09:50:03: 27000000 INFO @ Thu, 05 Apr 2018 09:50:07: 28000000 INFO @ Thu, 05 Apr 2018 09:50:09: 29000000 INFO @ Thu, 05 Apr 2018 09:50:10: 28000000 INFO @ Thu, 05 Apr 2018 09:50:13: 29000000 INFO @ Thu, 05 Apr 2018 09:50:15: 30000000 INFO @ Thu, 05 Apr 2018 09:50:16: 29000000 INFO @ Thu, 05 Apr 2018 09:50:19: 30000000 INFO @ Thu, 05 Apr 2018 09:50:22: 31000000 INFO @ Thu, 05 Apr 2018 09:50:23: 30000000 INFO @ Thu, 05 Apr 2018 09:50:25: 31000000 INFO @ Thu, 05 Apr 2018 09:50:28: 32000000 INFO @ Thu, 05 Apr 2018 09:50:29: 31000000 INFO @ Thu, 05 Apr 2018 09:50:30: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:50:30: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:50:30: #1 total tags in treatment: 15926607 INFO @ Thu, 05 Apr 2018 09:50:30: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:50:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Apr 2018 09:50:31: #1 tags after filtering in treatment: 10651641 INFO @ Thu, 05 Apr 2018 09:50:31: #1 Redundant rate of treatment: 0.33 INFO @ Thu, 05 Apr 2018 09:50:31: #1 finished! INFO @ Thu, 05 Apr 2018 09:50:31: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:50:31: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:50:31: 32000000 INFO @ Thu, 05 Apr 2018 09:50:31: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 09:50:31: 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 @ Thu, 05 Apr 2018 09:50:31: Process for pairing-model is terminated! cat: SRX3671147.10_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 `SRX3671147.10_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 `SRX3671147.10_*.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 `SRX3671147.10_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 @ Thu, 05 Apr 2018 09:50:34: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:50:34: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:50:34: #1 total tags in treatment: 15926607 INFO @ Thu, 05 Apr 2018 09:50:34: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:50:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Apr 2018 09:50:34: #1 tags after filtering in treatment: 10651641 INFO @ Thu, 05 Apr 2018 09:50:34: #1 Redundant rate of treatment: 0.33 INFO @ Thu, 05 Apr 2018 09:50:34: #1 finished! INFO @ Thu, 05 Apr 2018 09:50:34: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:50:34: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:50:35: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 09:50:35: 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 @ Thu, 05 Apr 2018 09:50:35: Process for pairing-model is terminated! cat: SRX3671147.05_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 `SRX3671147.05_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 `SRX3671147.05_*.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 `SRX3671147.05_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 @ Thu, 05 Apr 2018 09:50:35: 32000000 INFO @ Thu, 05 Apr 2018 09:50:37: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:50:37: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:50:37: #1 total tags in treatment: 15926607 INFO @ Thu, 05 Apr 2018 09:50:37: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:50:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Apr 2018 09:50:38: #1 tags after filtering in treatment: 10651641 INFO @ Thu, 05 Apr 2018 09:50:38: #1 Redundant rate of treatment: 0.33 INFO @ Thu, 05 Apr 2018 09:50:38: #1 finished! INFO @ Thu, 05 Apr 2018 09:50:38: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:50:38: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:50:39: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 09:50:39: 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 @ Thu, 05 Apr 2018 09:50:39: Process for pairing-model is terminated! cat: SRX3671147.20_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 `SRX3671147.20_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 `SRX3671147.20_*.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 `SRX3671147.20_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。