Job ID = 9162097 sra ファイルのダウンロード中... Completed: 1010636K bytes transferred in 9 seconds (903620K 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 23302719 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1631831/SRR3225759.sra Written 23302719 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: 00:21:42 23302719 reads; of these: 23302719 (100.00%) were paired; of these: 920043 (3.95%) aligned concordantly 0 times 18306081 (78.56%) aligned concordantly exactly 1 time 4076595 (17.49%) aligned concordantly >1 times ---- 920043 pairs aligned concordantly 0 times; of these: 449767 (48.89%) aligned discordantly 1 time ---- 470276 pairs aligned 0 times concordantly or discordantly; of these: 940552 mates make up the pairs; of these: 515584 (54.82%) aligned 0 times 151156 (16.07%) aligned exactly 1 time 273812 (29.11%) aligned >1 times 98.89% overall alignment rate Time searching: 00:21:42 Overall time: 00:21:42 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 20 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] 1170042 / 22727995 = 0.0515 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 06:24:32: # Command line: callpeak -t SRX1631831.bam -f BAM -g 12100000 -n SRX1631831.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1631831.10 # format = BAM # ChIP-seq file = ['SRX1631831.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 06:24:32: #1 read tag files... INFO @ Wed, 28 Jun 2017 06:24:32: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 06:24:32: # Command line: callpeak -t SRX1631831.bam -f BAM -g 12100000 -n SRX1631831.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1631831.20 # format = BAM # ChIP-seq file = ['SRX1631831.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 06:24:32: #1 read tag files... INFO @ Wed, 28 Jun 2017 06:24:32: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 06:24:32: # Command line: callpeak -t SRX1631831.bam -f BAM -g 12100000 -n SRX1631831.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1631831.05 # format = BAM # ChIP-seq file = ['SRX1631831.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 06:24:32: #1 read tag files... INFO @ Wed, 28 Jun 2017 06:24:32: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 06:24:38: 1000000 INFO @ Wed, 28 Jun 2017 06:24:38: 1000000 INFO @ Wed, 28 Jun 2017 06:24:38: 1000000 INFO @ Wed, 28 Jun 2017 06:24:43: 2000000 INFO @ Wed, 28 Jun 2017 06:24:44: 2000000 INFO @ Wed, 28 Jun 2017 06:24:44: 2000000 INFO @ Wed, 28 Jun 2017 06:24:49: 3000000 INFO @ Wed, 28 Jun 2017 06:24:50: 3000000 INFO @ Wed, 28 Jun 2017 06:24:50: 3000000 INFO @ Wed, 28 Jun 2017 06:24:54: 4000000 INFO @ Wed, 28 Jun 2017 06:24:56: 4000000 INFO @ Wed, 28 Jun 2017 06:24:56: 4000000 INFO @ Wed, 28 Jun 2017 06:24:59: 5000000 INFO @ Wed, 28 Jun 2017 06:25:02: 5000000 INFO @ Wed, 28 Jun 2017 06:25:02: 5000000 INFO @ Wed, 28 Jun 2017 06:25:05: 6000000 INFO @ Wed, 28 Jun 2017 06:25:08: 6000000 INFO @ Wed, 28 Jun 2017 06:25:08: 6000000 INFO @ Wed, 28 Jun 2017 06:25:10: 7000000 INFO @ Wed, 28 Jun 2017 06:25:14: 7000000 INFO @ Wed, 28 Jun 2017 06:25:14: 7000000 INFO @ Wed, 28 Jun 2017 06:25:16: 8000000 INFO @ Wed, 28 Jun 2017 06:25:20: 8000000 INFO @ Wed, 28 Jun 2017 06:25:21: 8000000 INFO @ Wed, 28 Jun 2017 06:25:22: 9000000 INFO @ Wed, 28 Jun 2017 06:25:26: 9000000 INFO @ Wed, 28 Jun 2017 06:25:27: 9000000 INFO @ Wed, 28 Jun 2017 06:25:27: 10000000 INFO @ Wed, 28 Jun 2017 06:25:32: 10000000 INFO @ Wed, 28 Jun 2017 06:25:33: 11000000 INFO @ Wed, 28 Jun 2017 06:25:34: 10000000 INFO @ Wed, 28 Jun 2017 06:25:37: 11000000 INFO @ Wed, 28 Jun 2017 06:25:39: 12000000 INFO @ Wed, 28 Jun 2017 06:25:41: 11000000 INFO @ Wed, 28 Jun 2017 06:25:43: 12000000 INFO @ Wed, 28 Jun 2017 06:25:45: 13000000 INFO @ Wed, 28 Jun 2017 06:25:47: 12000000 INFO @ Wed, 28 Jun 2017 06:25:49: 13000000 INFO @ Wed, 28 Jun 2017 06:25:51: 14000000 INFO @ Wed, 28 Jun 2017 06:25:54: 13000000 INFO @ Wed, 28 Jun 2017 06:25:55: 14000000 INFO @ Wed, 28 Jun 2017 06:25:58: 15000000 INFO @ Wed, 28 Jun 2017 06:26:00: 14000000 INFO @ Wed, 28 Jun 2017 06:26:01: 15000000 INFO @ Wed, 28 Jun 2017 06:26:04: 16000000 INFO @ Wed, 28 Jun 2017 06:26:05: 15000000 INFO @ Wed, 28 Jun 2017 06:26:07: 16000000 INFO @ Wed, 28 Jun 2017 06:26:11: 16000000 INFO @ Wed, 28 Jun 2017 06:26:11: 17000000 INFO @ Wed, 28 Jun 2017 06:26:14: 17000000 INFO @ Wed, 28 Jun 2017 06:26:17: 17000000 INFO @ Wed, 28 Jun 2017 06:26:18: 18000000 INFO @ Wed, 28 Jun 2017 06:26:20: 18000000 INFO @ Wed, 28 Jun 2017 06:26:22: 18000000 INFO @ Wed, 28 Jun 2017 06:26:24: 19000000 INFO @ Wed, 28 Jun 2017 06:26:26: 19000000 INFO @ Wed, 28 Jun 2017 06:26:28: 19000000 INFO @ Wed, 28 Jun 2017 06:26:31: 20000000 INFO @ Wed, 28 Jun 2017 06:26:33: 20000000 INFO @ Wed, 28 Jun 2017 06:26:34: 20000000 INFO @ Wed, 28 Jun 2017 06:26:37: 21000000 INFO @ Wed, 28 Jun 2017 06:26:39: 21000000 INFO @ Wed, 28 Jun 2017 06:26:41: 21000000 INFO @ Wed, 28 Jun 2017 06:26:42: 22000000 INFO @ Wed, 28 Jun 2017 06:26:45: 22000000 INFO @ Wed, 28 Jun 2017 06:26:47: 22000000 INFO @ Wed, 28 Jun 2017 06:26:48: 23000000 INFO @ Wed, 28 Jun 2017 06:26:52: 23000000 INFO @ Wed, 28 Jun 2017 06:26:53: 24000000 INFO @ Wed, 28 Jun 2017 06:26:54: 23000000 INFO @ Wed, 28 Jun 2017 06:26:58: 24000000 INFO @ Wed, 28 Jun 2017 06:26:59: 25000000 INFO @ Wed, 28 Jun 2017 06:27:00: 24000000 INFO @ Wed, 28 Jun 2017 06:27:04: 25000000 INFO @ Wed, 28 Jun 2017 06:27:05: 26000000 INFO @ Wed, 28 Jun 2017 06:27:07: 25000000 INFO @ Wed, 28 Jun 2017 06:27:10: 27000000 INFO @ Wed, 28 Jun 2017 06:27:11: 26000000 INFO @ Wed, 28 Jun 2017 06:27:13: 26000000 INFO @ Wed, 28 Jun 2017 06:27:15: 28000000 INFO @ Wed, 28 Jun 2017 06:27:17: 27000000 INFO @ Wed, 28 Jun 2017 06:27:20: 27000000 INFO @ Wed, 28 Jun 2017 06:27:21: 29000000 INFO @ Wed, 28 Jun 2017 06:27:23: 28000000 INFO @ Wed, 28 Jun 2017 06:27:26: 28000000 INFO @ Wed, 28 Jun 2017 06:27:27: 30000000 INFO @ Wed, 28 Jun 2017 06:27:30: 29000000 INFO @ Wed, 28 Jun 2017 06:27:32: 31000000 INFO @ Wed, 28 Jun 2017 06:27:32: 29000000 INFO @ Wed, 28 Jun 2017 06:27:36: 30000000 INFO @ Wed, 28 Jun 2017 06:27:37: 32000000 INFO @ Wed, 28 Jun 2017 06:27:39: 30000000 INFO @ Wed, 28 Jun 2017 06:27:42: 31000000 INFO @ Wed, 28 Jun 2017 06:27:43: 33000000 INFO @ Wed, 28 Jun 2017 06:27:45: 31000000 INFO @ Wed, 28 Jun 2017 06:27:48: 32000000 INFO @ Wed, 28 Jun 2017 06:27:48: 34000000 INFO @ Wed, 28 Jun 2017 06:27:51: 32000000 INFO @ Wed, 28 Jun 2017 06:27:54: 35000000 INFO @ Wed, 28 Jun 2017 06:27:55: 33000000 INFO @ Wed, 28 Jun 2017 06:27:58: 33000000 INFO @ Wed, 28 Jun 2017 06:27:59: 36000000 INFO @ Wed, 28 Jun 2017 06:28:01: 34000000 INFO @ Wed, 28 Jun 2017 06:28:04: 34000000 INFO @ Wed, 28 Jun 2017 06:28:05: 37000000 INFO @ Wed, 28 Jun 2017 06:28:07: 35000000 INFO @ Wed, 28 Jun 2017 06:28:10: 38000000 INFO @ Wed, 28 Jun 2017 06:28:10: 35000000 INFO @ Wed, 28 Jun 2017 06:28:13: 36000000 INFO @ Wed, 28 Jun 2017 06:28:16: 39000000 INFO @ Wed, 28 Jun 2017 06:28:17: 36000000 INFO @ Wed, 28 Jun 2017 06:28:19: 37000000 INFO @ Wed, 28 Jun 2017 06:28:21: 40000000 INFO @ Wed, 28 Jun 2017 06:28:23: 37000000 INFO @ Wed, 28 Jun 2017 06:28:26: 38000000 INFO @ Wed, 28 Jun 2017 06:28:27: 41000000 INFO @ Wed, 28 Jun 2017 06:28:29: 38000000 INFO @ Wed, 28 Jun 2017 06:28:32: 39000000 INFO @ Wed, 28 Jun 2017 06:28:32: 42000000 INFO @ Wed, 28 Jun 2017 06:28:36: 39000000 INFO @ Wed, 28 Jun 2017 06:28:37: 43000000 INFO @ Wed, 28 Jun 2017 06:28:38: 40000000 INFO @ Wed, 28 Jun 2017 06:28:42: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 06:28:42: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 06:28:42: #1 total tags in treatment: 21214707 INFO @ Wed, 28 Jun 2017 06:28:42: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 06:28:42: #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 06:28:42: 40000000 INFO @ Wed, 28 Jun 2017 06:28:42: #1 tags after filtering in treatment: 10424924 INFO @ Wed, 28 Jun 2017 06:28:42: #1 Redundant rate of treatment: 0.51 INFO @ Wed, 28 Jun 2017 06:28:42: #1 finished! INFO @ Wed, 28 Jun 2017 06:28:42: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 06:28:42: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 06:28:43: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 06:28:43: 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 06:28:43: Process for pairing-model is terminated! cat: SRX1631831.05_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 `SRX1631831.05_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 `SRX1631831.05_*.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 `SRX1631831.05_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 06:28:44: 41000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 28 Jun 2017 06:28:48: 41000000 INFO @ Wed, 28 Jun 2017 06:28:50: 42000000 INFO @ Wed, 28 Jun 2017 06:28:54: 42000000 INFO @ Wed, 28 Jun 2017 06:28:56: 43000000 INFO @ Wed, 28 Jun 2017 06:29:00: 43000000 INFO @ Wed, 28 Jun 2017 06:29:01: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 06:29:01: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 06:29:01: #1 total tags in treatment: 21214707 INFO @ Wed, 28 Jun 2017 06:29:01: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 06:29:01: #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 06:29:01: #1 tags after filtering in treatment: 10424924 INFO @ Wed, 28 Jun 2017 06:29:01: #1 Redundant rate of treatment: 0.51 INFO @ Wed, 28 Jun 2017 06:29:01: #1 finished! INFO @ Wed, 28 Jun 2017 06:29:01: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 06:29:01: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 06:29:02: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 06:29:02: 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 06:29:02: Process for pairing-model is terminated! cat: SRX1631831.20_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 `SRX1631831.20_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 `SRX1631831.20_*.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 `SRX1631831.20_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 06:29:05: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 06:29:05: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 06:29:05: #1 total tags in treatment: 21214707 INFO @ Wed, 28 Jun 2017 06:29:05: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 06:29:05: #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 06:29:05: #1 tags after filtering in treatment: 10424924 INFO @ Wed, 28 Jun 2017 06:29:05: #1 Redundant rate of treatment: 0.51 INFO @ Wed, 28 Jun 2017 06:29:05: #1 finished! INFO @ Wed, 28 Jun 2017 06:29:05: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 06:29:05: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 06:29:06: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 06:29:06: 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 06:29:06: Process for pairing-model is terminated! cat: SRX1631831.10_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 `SRX1631831.10_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 `SRX1631831.10_*.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 `SRX1631831.10_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 BigWig に変換しました。