Job ID = 9162109 sra ファイルのダウンロード中... Completed: 863134K bytes transferred in 8 seconds (846434K bits/sec), in 1 file, 2 directories. 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 17232813 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1631850/SRR3225789.sra Written 17232813 spots total 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: 00:15:17 17232813 reads; of these: 17232813 (100.00%) were paired; of these: 865846 (5.02%) aligned concordantly 0 times 12365918 (71.76%) aligned concordantly exactly 1 time 4001049 (23.22%) aligned concordantly >1 times ---- 865846 pairs aligned concordantly 0 times; of these: 280620 (32.41%) aligned discordantly 1 time ---- 585226 pairs aligned 0 times concordantly or discordantly; of these: 1170452 mates make up the pairs; of these: 687908 (58.77%) aligned 0 times 163065 (13.93%) aligned exactly 1 time 319479 (27.30%) aligned >1 times 98.00% overall alignment rate Time searching: 00:15:17 Overall time: 00:15:17 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 16 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] 1464172 / 16593750 = 0.0882 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 @ Wed, 28 Jun 2017 06:18:30: # Command line: callpeak -t SRX1631850.bam -f BAM -g 12100000 -n SRX1631850.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1631850.05 # format = BAM # ChIP-seq file = ['SRX1631850.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 @ Wed, 28 Jun 2017 06:18:30: #1 read tag files... INFO @ Wed, 28 Jun 2017 06:18:30: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 06:18:30: # Command line: callpeak -t SRX1631850.bam -f BAM -g 12100000 -n SRX1631850.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1631850.20 # format = BAM # ChIP-seq file = ['SRX1631850.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 @ Wed, 28 Jun 2017 06:18:30: #1 read tag files... INFO @ Wed, 28 Jun 2017 06:18:30: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 06:18:30: # Command line: callpeak -t SRX1631850.bam -f BAM -g 12100000 -n SRX1631850.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1631850.10 # format = BAM # ChIP-seq file = ['SRX1631850.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 @ Wed, 28 Jun 2017 06:18:30: #1 read tag files... INFO @ Wed, 28 Jun 2017 06:18:30: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 06:18:36: 1000000 INFO @ Wed, 28 Jun 2017 06:18:37: 1000000 INFO @ Wed, 28 Jun 2017 06:18:37: 1000000 INFO @ Wed, 28 Jun 2017 06:18:43: 2000000 INFO @ Wed, 28 Jun 2017 06:18:45: 2000000 INFO @ Wed, 28 Jun 2017 06:18:45: 2000000 INFO @ Wed, 28 Jun 2017 06:18:49: 3000000 INFO @ Wed, 28 Jun 2017 06:18:52: 3000000 INFO @ Wed, 28 Jun 2017 06:18:52: 3000000 INFO @ Wed, 28 Jun 2017 06:18:56: 4000000 INFO @ Wed, 28 Jun 2017 06:19:00: 4000000 INFO @ Wed, 28 Jun 2017 06:19:00: 4000000 INFO @ Wed, 28 Jun 2017 06:19:03: 5000000 INFO @ Wed, 28 Jun 2017 06:19:07: 5000000 INFO @ Wed, 28 Jun 2017 06:19:07: 5000000 INFO @ Wed, 28 Jun 2017 06:19:09: 6000000 INFO @ Wed, 28 Jun 2017 06:19:14: 6000000 INFO @ Wed, 28 Jun 2017 06:19:14: 6000000 INFO @ Wed, 28 Jun 2017 06:19:16: 7000000 INFO @ Wed, 28 Jun 2017 06:19:21: 7000000 INFO @ Wed, 28 Jun 2017 06:19:21: 7000000 INFO @ Wed, 28 Jun 2017 06:19:22: 8000000 INFO @ Wed, 28 Jun 2017 06:19:28: 8000000 INFO @ Wed, 28 Jun 2017 06:19:29: 8000000 INFO @ Wed, 28 Jun 2017 06:19:29: 9000000 INFO @ Wed, 28 Jun 2017 06:19:35: 9000000 INFO @ Wed, 28 Jun 2017 06:19:35: 10000000 INFO @ Wed, 28 Jun 2017 06:19:36: 9000000 INFO @ Wed, 28 Jun 2017 06:19:42: 11000000 INFO @ Wed, 28 Jun 2017 06:19:42: 10000000 INFO @ Wed, 28 Jun 2017 06:19:43: 10000000 INFO @ Wed, 28 Jun 2017 06:19:48: 12000000 INFO @ Wed, 28 Jun 2017 06:19:50: 11000000 INFO @ Wed, 28 Jun 2017 06:19:51: 11000000 INFO @ Wed, 28 Jun 2017 06:19:55: 13000000 INFO @ Wed, 28 Jun 2017 06:19:57: 12000000 INFO @ Wed, 28 Jun 2017 06:19:59: 12000000 INFO @ Wed, 28 Jun 2017 06:20:01: 14000000 INFO @ Wed, 28 Jun 2017 06:20:04: 13000000 INFO @ Wed, 28 Jun 2017 06:20:06: 13000000 INFO @ Wed, 28 Jun 2017 06:20:07: 15000000 INFO @ Wed, 28 Jun 2017 06:20:12: 14000000 INFO @ Wed, 28 Jun 2017 06:20:15: 16000000 INFO @ Wed, 28 Jun 2017 06:20:15: 14000000 INFO @ Wed, 28 Jun 2017 06:20:20: 15000000 INFO @ Wed, 28 Jun 2017 06:20:21: 17000000 INFO @ Wed, 28 Jun 2017 06:20:23: 15000000 INFO @ Wed, 28 Jun 2017 06:20:27: 16000000 INFO @ Wed, 28 Jun 2017 06:20:27: 18000000 INFO @ Wed, 28 Jun 2017 06:20:30: 16000000 INFO @ Wed, 28 Jun 2017 06:20:34: 19000000 INFO @ Wed, 28 Jun 2017 06:20:34: 17000000 INFO @ Wed, 28 Jun 2017 06:20:38: 17000000 INFO @ Wed, 28 Jun 2017 06:20:41: 20000000 INFO @ Wed, 28 Jun 2017 06:20:42: 18000000 INFO @ Wed, 28 Jun 2017 06:20:46: 18000000 INFO @ Wed, 28 Jun 2017 06:20:48: 21000000 INFO @ Wed, 28 Jun 2017 06:20:50: 19000000 INFO @ Wed, 28 Jun 2017 06:20:54: 19000000 INFO @ Wed, 28 Jun 2017 06:20:54: 22000000 INFO @ Wed, 28 Jun 2017 06:20:57: 20000000 INFO @ Wed, 28 Jun 2017 06:21:01: 23000000 INFO @ Wed, 28 Jun 2017 06:21:01: 20000000 INFO @ Wed, 28 Jun 2017 06:21:04: 21000000 INFO @ Wed, 28 Jun 2017 06:21:08: 24000000 INFO @ Wed, 28 Jun 2017 06:21:09: 21000000 INFO @ Wed, 28 Jun 2017 06:21:12: 22000000 INFO @ Wed, 28 Jun 2017 06:21:15: 25000000 INFO @ Wed, 28 Jun 2017 06:21:17: 22000000 INFO @ Wed, 28 Jun 2017 06:21:19: 23000000 INFO @ Wed, 28 Jun 2017 06:21:21: 26000000 INFO @ Wed, 28 Jun 2017 06:21:25: 23000000 INFO @ Wed, 28 Jun 2017 06:21:27: 24000000 INFO @ Wed, 28 Jun 2017 06:21:28: 27000000 INFO @ Wed, 28 Jun 2017 06:21:32: 24000000 INFO @ Wed, 28 Jun 2017 06:21:34: 25000000 INFO @ Wed, 28 Jun 2017 06:21:35: 28000000 INFO @ Wed, 28 Jun 2017 06:21:40: 25000000 INFO @ Wed, 28 Jun 2017 06:21:42: 29000000 INFO @ Wed, 28 Jun 2017 06:21:42: 26000000 INFO @ Wed, 28 Jun 2017 06:21:48: 30000000 INFO @ Wed, 28 Jun 2017 06:21:48: 26000000 INFO @ Wed, 28 Jun 2017 06:21:49: 27000000 INFO @ Wed, 28 Jun 2017 06:21:53: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 06:21:53: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 06:21:53: #1 total tags in treatment: 14905047 INFO @ Wed, 28 Jun 2017 06:21:53: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 06:21:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 06:21:54: #1 tags after filtering in treatment: 7776262 INFO @ Wed, 28 Jun 2017 06:21:54: #1 Redundant rate of treatment: 0.48 INFO @ Wed, 28 Jun 2017 06:21:54: #1 finished! INFO @ Wed, 28 Jun 2017 06:21:54: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 06:21:54: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 06:21:54: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 06:21:54: 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 @ Wed, 28 Jun 2017 06:21:54: Process for pairing-model is terminated! cat: SRX1631850.05_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 `SRX1631850.05_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 `SRX1631850.05_*.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 `SRX1631850.05_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 @ Wed, 28 Jun 2017 06:21:56: 27000000 INFO @ Wed, 28 Jun 2017 06:21:57: 28000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 28 Jun 2017 06:22:04: 28000000 INFO @ Wed, 28 Jun 2017 06:22:05: 29000000 INFO @ Wed, 28 Jun 2017 06:22:12: 29000000 INFO @ Wed, 28 Jun 2017 06:22:12: 30000000 BigWig に変換しました。 INFO @ Wed, 28 Jun 2017 06:22:18: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 06:22:18: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 06:22:18: #1 total tags in treatment: 14905047 INFO @ Wed, 28 Jun 2017 06:22:18: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 06:22:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 06:22:19: #1 tags after filtering in treatment: 7776262 INFO @ Wed, 28 Jun 2017 06:22:19: #1 Redundant rate of treatment: 0.48 INFO @ Wed, 28 Jun 2017 06:22:19: #1 finished! INFO @ Wed, 28 Jun 2017 06:22:19: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 06:22:19: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 06:22:19: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 06:22:19: 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 @ Wed, 28 Jun 2017 06:22:19: Process for pairing-model is terminated! cat: SRX1631850.20_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 `SRX1631850.20_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 `SRX1631850.20_*.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 `SRX1631850.20_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 INFO @ Wed, 28 Jun 2017 06:22:19: 30000000 INFO @ Wed, 28 Jun 2017 06:22:25: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 06:22:25: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 06:22:25: #1 total tags in treatment: 14905047 INFO @ Wed, 28 Jun 2017 06:22:25: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 06:22:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 06:22:26: #1 tags after filtering in treatment: 7776262 INFO @ Wed, 28 Jun 2017 06:22:26: #1 Redundant rate of treatment: 0.48 INFO @ Wed, 28 Jun 2017 06:22:26: #1 finished! INFO @ Wed, 28 Jun 2017 06:22:26: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 06:22:26: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 06:22:26: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 06:22:26: 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 @ Wed, 28 Jun 2017 06:22:26: Process for pairing-model is terminated! cat: SRX1631850.10_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 `SRX1631850.10_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 `SRX1631850.10_*.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 `SRX1631850.10_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