Job ID = 9161697 sra ファイルのダウンロード中... Completed: 1128456K bytes transferred in 11 seconds (815490K 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 28539995 spots for /home/okishinya/chipatlas/results/sacCer3/SRX079680/SRR292351.sra Written 28539995 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: 00:18:12 28539995 reads; of these: 28539995 (100.00%) were paired; of these: 6161992 (21.59%) aligned concordantly 0 times 16967103 (59.45%) aligned concordantly exactly 1 time 5410900 (18.96%) aligned concordantly >1 times ---- 6161992 pairs aligned concordantly 0 times; of these: 981887 (15.93%) aligned discordantly 1 time ---- 5180105 pairs aligned 0 times concordantly or discordantly; of these: 10360210 mates make up the pairs; of these: 7982739 (77.05%) aligned 0 times 900924 (8.70%) aligned exactly 1 time 1476547 (14.25%) aligned >1 times 86.01% overall alignment rate Time searching: 00:18:12 Overall time: 00:18:12 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] 4880382 / 23013193 = 0.2121 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 04:51:58: # Command line: callpeak -t SRX079680.bam -f BAM -g 12100000 -n SRX079680.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX079680.05 # format = BAM # ChIP-seq file = ['SRX079680.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 04:51:58: #1 read tag files... INFO @ Wed, 28 Jun 2017 04:51:58: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 04:51:58: # Command line: callpeak -t SRX079680.bam -f BAM -g 12100000 -n SRX079680.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX079680.10 # format = BAM # ChIP-seq file = ['SRX079680.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 04:51:58: #1 read tag files... INFO @ Wed, 28 Jun 2017 04:51:58: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 04:51:58: # Command line: callpeak -t SRX079680.bam -f BAM -g 12100000 -n SRX079680.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX079680.20 # format = BAM # ChIP-seq file = ['SRX079680.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 04:51:58: #1 read tag files... INFO @ Wed, 28 Jun 2017 04:51:58: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 04:52:03: 1000000 INFO @ Wed, 28 Jun 2017 04:52:04: 1000000 INFO @ Wed, 28 Jun 2017 04:52:04: 1000000 INFO @ Wed, 28 Jun 2017 04:52:09: 2000000 INFO @ Wed, 28 Jun 2017 04:52:10: 2000000 INFO @ Wed, 28 Jun 2017 04:52:10: 2000000 INFO @ Wed, 28 Jun 2017 04:52:14: 3000000 INFO @ Wed, 28 Jun 2017 04:52:16: 3000000 INFO @ Wed, 28 Jun 2017 04:52:16: 3000000 INFO @ Wed, 28 Jun 2017 04:52:20: 4000000 INFO @ Wed, 28 Jun 2017 04:52:22: 4000000 INFO @ Wed, 28 Jun 2017 04:52:22: 4000000 INFO @ Wed, 28 Jun 2017 04:52:25: 5000000 INFO @ Wed, 28 Jun 2017 04:52:28: 5000000 INFO @ Wed, 28 Jun 2017 04:52:28: 5000000 INFO @ Wed, 28 Jun 2017 04:52:31: 6000000 INFO @ Wed, 28 Jun 2017 04:52:34: 6000000 INFO @ Wed, 28 Jun 2017 04:52:34: 6000000 INFO @ Wed, 28 Jun 2017 04:52:37: 7000000 INFO @ Wed, 28 Jun 2017 04:52:40: 7000000 INFO @ Wed, 28 Jun 2017 04:52:40: 7000000 INFO @ Wed, 28 Jun 2017 04:52:43: 8000000 INFO @ Wed, 28 Jun 2017 04:52:46: 8000000 INFO @ Wed, 28 Jun 2017 04:52:46: 8000000 INFO @ Wed, 28 Jun 2017 04:52:49: 9000000 INFO @ Wed, 28 Jun 2017 04:52:52: 9000000 INFO @ Wed, 28 Jun 2017 04:52:52: 9000000 INFO @ Wed, 28 Jun 2017 04:52:55: 10000000 INFO @ Wed, 28 Jun 2017 04:52:57: 10000000 INFO @ Wed, 28 Jun 2017 04:52:58: 10000000 INFO @ Wed, 28 Jun 2017 04:53:00: 11000000 INFO @ Wed, 28 Jun 2017 04:53:03: 11000000 INFO @ Wed, 28 Jun 2017 04:53:03: 11000000 INFO @ Wed, 28 Jun 2017 04:53:06: 12000000 INFO @ Wed, 28 Jun 2017 04:53:08: 12000000 INFO @ Wed, 28 Jun 2017 04:53:09: 12000000 INFO @ Wed, 28 Jun 2017 04:53:11: 13000000 INFO @ Wed, 28 Jun 2017 04:53:14: 13000000 INFO @ Wed, 28 Jun 2017 04:53:15: 13000000 INFO @ Wed, 28 Jun 2017 04:53:17: 14000000 INFO @ Wed, 28 Jun 2017 04:53:20: 14000000 INFO @ Wed, 28 Jun 2017 04:53:22: 14000000 INFO @ Wed, 28 Jun 2017 04:53:23: 15000000 INFO @ Wed, 28 Jun 2017 04:53:27: 15000000 INFO @ Wed, 28 Jun 2017 04:53:28: 16000000 INFO @ Wed, 28 Jun 2017 04:53:28: 15000000 INFO @ Wed, 28 Jun 2017 04:53:33: 16000000 INFO @ Wed, 28 Jun 2017 04:53:33: 17000000 INFO @ Wed, 28 Jun 2017 04:53:35: 16000000 INFO @ Wed, 28 Jun 2017 04:53:39: 18000000 INFO @ Wed, 28 Jun 2017 04:53:39: 17000000 INFO @ Wed, 28 Jun 2017 04:53:42: 17000000 INFO @ Wed, 28 Jun 2017 04:53:44: 19000000 INFO @ Wed, 28 Jun 2017 04:53:46: 18000000 INFO @ Wed, 28 Jun 2017 04:53:48: 18000000 INFO @ Wed, 28 Jun 2017 04:53:49: 20000000 INFO @ Wed, 28 Jun 2017 04:53:52: 19000000 INFO @ Wed, 28 Jun 2017 04:53:55: 21000000 INFO @ Wed, 28 Jun 2017 04:53:55: 19000000 INFO @ Wed, 28 Jun 2017 04:53:58: 20000000 INFO @ Wed, 28 Jun 2017 04:54:00: 22000000 INFO @ Wed, 28 Jun 2017 04:54:02: 20000000 INFO @ Wed, 28 Jun 2017 04:54:05: 21000000 INFO @ Wed, 28 Jun 2017 04:54:06: 23000000 INFO @ Wed, 28 Jun 2017 04:54:09: 21000000 INFO @ Wed, 28 Jun 2017 04:54:11: 24000000 INFO @ Wed, 28 Jun 2017 04:54:11: 22000000 INFO @ Wed, 28 Jun 2017 04:54:15: 22000000 INFO @ Wed, 28 Jun 2017 04:54:16: 25000000 INFO @ Wed, 28 Jun 2017 04:54:18: 23000000 INFO @ Wed, 28 Jun 2017 04:54:22: 26000000 INFO @ Wed, 28 Jun 2017 04:54:23: 23000000 INFO @ Wed, 28 Jun 2017 04:54:25: 24000000 INFO @ Wed, 28 Jun 2017 04:54:28: 27000000 INFO @ Wed, 28 Jun 2017 04:54:31: 25000000 INFO @ Wed, 28 Jun 2017 04:54:31: 24000000 INFO @ Wed, 28 Jun 2017 04:54:35: 28000000 INFO @ Wed, 28 Jun 2017 04:54:38: 26000000 INFO @ Wed, 28 Jun 2017 04:54:39: 25000000 INFO @ Wed, 28 Jun 2017 04:54:41: 29000000 INFO @ Wed, 28 Jun 2017 04:54:45: 27000000 INFO @ Wed, 28 Jun 2017 04:54:47: 26000000 INFO @ Wed, 28 Jun 2017 04:54:47: 30000000 INFO @ Wed, 28 Jun 2017 04:54:52: 28000000 INFO @ Wed, 28 Jun 2017 04:54:54: 31000000 INFO @ Wed, 28 Jun 2017 04:54:54: 27000000 INFO @ Wed, 28 Jun 2017 04:54:59: 29000000 INFO @ Wed, 28 Jun 2017 04:54:59: 32000000 INFO @ Wed, 28 Jun 2017 04:55:02: 28000000 INFO @ Wed, 28 Jun 2017 04:55:05: 33000000 INFO @ Wed, 28 Jun 2017 04:55:05: 30000000 INFO @ Wed, 28 Jun 2017 04:55:08: 29000000 INFO @ Wed, 28 Jun 2017 04:55:10: 34000000 INFO @ Wed, 28 Jun 2017 04:55:11: 31000000 INFO @ Wed, 28 Jun 2017 04:55:13: 30000000 INFO @ Wed, 28 Jun 2017 04:55:16: 35000000 INFO @ Wed, 28 Jun 2017 04:55:17: 32000000 INFO @ Wed, 28 Jun 2017 04:55:19: 31000000 INFO @ Wed, 28 Jun 2017 04:55:21: 36000000 INFO @ Wed, 28 Jun 2017 04:55:22: 33000000 INFO @ Wed, 28 Jun 2017 04:55:25: 32000000 INFO @ Wed, 28 Jun 2017 04:55:27: 37000000 INFO @ Wed, 28 Jun 2017 04:55:28: 34000000 INFO @ Wed, 28 Jun 2017 04:55:31: 33000000 INFO @ Wed, 28 Jun 2017 04:55:32: 38000000 INFO @ Wed, 28 Jun 2017 04:55:34: 35000000 INFO @ Wed, 28 Jun 2017 04:55:37: 34000000 INFO @ Wed, 28 Jun 2017 04:55:38: 39000000 INFO @ Wed, 28 Jun 2017 04:55:40: #1 tag size is determined as 36 bps INFO @ Wed, 28 Jun 2017 04:55:40: #1 tag size = 36 INFO @ Wed, 28 Jun 2017 04:55:40: #1 total tags in treatment: 17791639 INFO @ Wed, 28 Jun 2017 04:55:40: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 04:55:40: #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 04:55:40: 36000000 INFO @ Wed, 28 Jun 2017 04:55:40: #1 tags after filtering in treatment: 9011166 INFO @ Wed, 28 Jun 2017 04:55:40: #1 Redundant rate of treatment: 0.49 INFO @ Wed, 28 Jun 2017 04:55:40: #1 finished! INFO @ Wed, 28 Jun 2017 04:55:40: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 04:55:40: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 04:55:40: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 04:55:40: 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 04:55:40: Process for pairing-model is terminated! cat: SRX079680.05_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 `SRX079680.05_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 `SRX079680.05_*.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 `SRX079680.05_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 04:55:43: 35000000 INFO @ Wed, 28 Jun 2017 04:55:45: 37000000 INFO @ Wed, 28 Jun 2017 04:55:49: 36000000 INFO @ Wed, 28 Jun 2017 04:55:51: 38000000 INFO @ Wed, 28 Jun 2017 04:55:55: 37000000 INFO @ Wed, 28 Jun 2017 04:55:57: 39000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 28 Jun 2017 04:55:59: #1 tag size is determined as 36 bps INFO @ Wed, 28 Jun 2017 04:55:59: #1 tag size = 36 INFO @ Wed, 28 Jun 2017 04:55:59: #1 total tags in treatment: 17791639 INFO @ Wed, 28 Jun 2017 04:55:59: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 04:55:59: #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 04:55:59: #1 tags after filtering in treatment: 9011166 INFO @ Wed, 28 Jun 2017 04:55:59: #1 Redundant rate of treatment: 0.49 INFO @ Wed, 28 Jun 2017 04:55:59: #1 finished! INFO @ Wed, 28 Jun 2017 04:55:59: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 04:55:59: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 04:56:00: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 04:56:00: 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 04:56:00: Process for pairing-model is terminated! cat: SRX079680.10_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 `SRX079680.10_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 `SRX079680.10_*.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 `SRX079680.10_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 @ Wed, 28 Jun 2017 04:56:00: 38000000 INFO @ Wed, 28 Jun 2017 04:56:06: 39000000 INFO @ Wed, 28 Jun 2017 04:56:08: #1 tag size is determined as 36 bps INFO @ Wed, 28 Jun 2017 04:56:08: #1 tag size = 36 INFO @ Wed, 28 Jun 2017 04:56:08: #1 total tags in treatment: 17791639 INFO @ Wed, 28 Jun 2017 04:56:08: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 04:56:08: #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 04:56:08: #1 tags after filtering in treatment: 9011166 INFO @ Wed, 28 Jun 2017 04:56:08: #1 Redundant rate of treatment: 0.49 INFO @ Wed, 28 Jun 2017 04:56:08: #1 finished! INFO @ Wed, 28 Jun 2017 04:56:08: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 04:56:08: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 04:56:08: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 04:56:08: 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 04:56:08: Process for pairing-model is terminated! cat: SRX079680.20_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): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX079680.20_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 `SRX079680.20_*.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 `SRX079680.20_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 BigWig に変換しました。