Job ID = 10714540 sra ファイルのダウンロード中... Completed: 1944305K bytes transferred in 23 seconds (678712K 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 32351775 spots for /home/okishinya/chipatlas/results/dm3/SRX1704845/SRR3383179.sra Written 32351775 spots for /home/okishinya/chipatlas/results/dm3/SRX1704845/SRR3383179.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: 01:04:44 32351775 reads; of these: 32351775 (100.00%) were paired; of these: 5612417 (17.35%) aligned concordantly 0 times 22308590 (68.96%) aligned concordantly exactly 1 time 4430768 (13.70%) aligned concordantly >1 times ---- 5612417 pairs aligned concordantly 0 times; of these: 2758018 (49.14%) aligned discordantly 1 time ---- 2854399 pairs aligned 0 times concordantly or discordantly; of these: 5708798 mates make up the pairs; of these: 2624968 (45.98%) aligned 0 times 1605066 (28.12%) aligned exactly 1 time 1478764 (25.90%) aligned >1 times 95.94% overall alignment rate Time searching: 01:04:44 Overall time: 01:04:44 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 28 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 2301691 / 29234142 = 0.0787 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 @ Sun, 03 Jun 2018 14:41:54: # Command line: callpeak -t SRX1704845.bam -f BAM -g dm -n SRX1704845.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1704845.20 # format = BAM # ChIP-seq file = ['SRX1704845.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 03 Jun 2018 14:41:54: #1 read tag files... INFO @ Sun, 03 Jun 2018 14:41:54: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 14:41:54: # Command line: callpeak -t SRX1704845.bam -f BAM -g dm -n SRX1704845.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1704845.10 # format = BAM # ChIP-seq file = ['SRX1704845.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 03 Jun 2018 14:41:54: #1 read tag files... INFO @ Sun, 03 Jun 2018 14:41:54: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 14:41:54: # Command line: callpeak -t SRX1704845.bam -f BAM -g dm -n SRX1704845.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1704845.05 # format = BAM # ChIP-seq file = ['SRX1704845.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 03 Jun 2018 14:41:54: #1 read tag files... INFO @ Sun, 03 Jun 2018 14:41:54: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 14:42:00: 1000000 INFO @ Sun, 03 Jun 2018 14:42:01: 1000000 INFO @ Sun, 03 Jun 2018 14:42:01: 1000000 INFO @ Sun, 03 Jun 2018 14:42:07: 2000000 INFO @ Sun, 03 Jun 2018 14:42:07: 2000000 INFO @ Sun, 03 Jun 2018 14:42:07: 2000000 INFO @ Sun, 03 Jun 2018 14:42:13: 3000000 INFO @ Sun, 03 Jun 2018 14:42:14: 3000000 INFO @ Sun, 03 Jun 2018 14:42:14: 3000000 INFO @ Sun, 03 Jun 2018 14:42:19: 4000000 INFO @ Sun, 03 Jun 2018 14:42:20: 4000000 INFO @ Sun, 03 Jun 2018 14:42:20: 4000000 INFO @ Sun, 03 Jun 2018 14:42:25: 5000000 INFO @ Sun, 03 Jun 2018 14:42:27: 5000000 INFO @ Sun, 03 Jun 2018 14:42:27: 5000000 INFO @ Sun, 03 Jun 2018 14:42:31: 6000000 INFO @ Sun, 03 Jun 2018 14:42:33: 6000000 INFO @ Sun, 03 Jun 2018 14:42:33: 6000000 INFO @ Sun, 03 Jun 2018 14:42:37: 7000000 INFO @ Sun, 03 Jun 2018 14:42:40: 7000000 INFO @ Sun, 03 Jun 2018 14:42:40: 7000000 INFO @ Sun, 03 Jun 2018 14:42:44: 8000000 INFO @ Sun, 03 Jun 2018 14:42:46: 8000000 INFO @ Sun, 03 Jun 2018 14:42:46: 8000000 INFO @ Sun, 03 Jun 2018 14:42:50: 9000000 INFO @ Sun, 03 Jun 2018 14:42:53: 9000000 INFO @ Sun, 03 Jun 2018 14:42:53: 9000000 INFO @ Sun, 03 Jun 2018 14:42:56: 10000000 INFO @ Sun, 03 Jun 2018 14:43:00: 10000000 INFO @ Sun, 03 Jun 2018 14:43:00: 10000000 INFO @ Sun, 03 Jun 2018 14:43:03: 11000000 INFO @ Sun, 03 Jun 2018 14:43:06: 11000000 INFO @ Sun, 03 Jun 2018 14:43:06: 11000000 INFO @ Sun, 03 Jun 2018 14:43:09: 12000000 INFO @ Sun, 03 Jun 2018 14:43:13: 12000000 INFO @ Sun, 03 Jun 2018 14:43:13: 12000000 INFO @ Sun, 03 Jun 2018 14:43:15: 13000000 INFO @ Sun, 03 Jun 2018 14:43:19: 13000000 INFO @ Sun, 03 Jun 2018 14:43:19: 13000000 INFO @ Sun, 03 Jun 2018 14:43:22: 14000000 INFO @ Sun, 03 Jun 2018 14:43:26: 14000000 INFO @ Sun, 03 Jun 2018 14:43:26: 14000000 INFO @ Sun, 03 Jun 2018 14:43:28: 15000000 INFO @ Sun, 03 Jun 2018 14:43:33: 15000000 INFO @ Sun, 03 Jun 2018 14:43:33: 15000000 INFO @ Sun, 03 Jun 2018 14:43:34: 16000000 INFO @ Sun, 03 Jun 2018 14:43:40: 16000000 INFO @ Sun, 03 Jun 2018 14:43:40: 16000000 INFO @ Sun, 03 Jun 2018 14:43:42: 17000000 INFO @ Sun, 03 Jun 2018 14:43:48: 17000000 INFO @ Sun, 03 Jun 2018 14:43:48: 17000000 INFO @ Sun, 03 Jun 2018 14:43:50: 18000000 INFO @ Sun, 03 Jun 2018 14:43:56: 18000000 INFO @ Sun, 03 Jun 2018 14:43:57: 18000000 INFO @ Sun, 03 Jun 2018 14:43:58: 19000000 INFO @ Sun, 03 Jun 2018 14:44:05: 19000000 INFO @ Sun, 03 Jun 2018 14:44:06: 20000000 INFO @ Sun, 03 Jun 2018 14:44:06: 19000000 INFO @ Sun, 03 Jun 2018 14:44:13: 20000000 INFO @ Sun, 03 Jun 2018 14:44:14: 21000000 INFO @ Sun, 03 Jun 2018 14:44:15: 20000000 INFO @ Sun, 03 Jun 2018 14:44:21: 21000000 INFO @ Sun, 03 Jun 2018 14:44:22: 22000000 INFO @ Sun, 03 Jun 2018 14:44:25: 21000000 INFO @ Sun, 03 Jun 2018 14:44:29: 22000000 INFO @ Sun, 03 Jun 2018 14:44:30: 23000000 INFO @ Sun, 03 Jun 2018 14:44:34: 22000000 INFO @ Sun, 03 Jun 2018 14:44:37: 23000000 INFO @ Sun, 03 Jun 2018 14:44:38: 24000000 INFO @ Sun, 03 Jun 2018 14:44:43: 23000000 INFO @ Sun, 03 Jun 2018 14:44:45: 24000000 INFO @ Sun, 03 Jun 2018 14:44:46: 25000000 INFO @ Sun, 03 Jun 2018 14:44:52: 24000000 INFO @ Sun, 03 Jun 2018 14:44:53: 25000000 INFO @ Sun, 03 Jun 2018 14:44:54: 26000000 INFO @ Sun, 03 Jun 2018 14:45:01: 25000000 INFO @ Sun, 03 Jun 2018 14:45:01: 26000000 INFO @ Sun, 03 Jun 2018 14:45:02: 27000000 INFO @ Sun, 03 Jun 2018 14:45:09: 27000000 INFO @ Sun, 03 Jun 2018 14:45:10: 26000000 INFO @ Sun, 03 Jun 2018 14:45:10: 28000000 INFO @ Sun, 03 Jun 2018 14:45:17: 28000000 INFO @ Sun, 03 Jun 2018 14:45:18: 29000000 INFO @ Sun, 03 Jun 2018 14:45:19: 27000000 INFO @ Sun, 03 Jun 2018 14:45:25: 29000000 INFO @ Sun, 03 Jun 2018 14:45:26: 30000000 INFO @ Sun, 03 Jun 2018 14:45:28: 28000000 INFO @ Sun, 03 Jun 2018 14:45:33: 30000000 INFO @ Sun, 03 Jun 2018 14:45:34: 31000000 INFO @ Sun, 03 Jun 2018 14:45:37: 29000000 INFO @ Sun, 03 Jun 2018 14:45:41: 31000000 INFO @ Sun, 03 Jun 2018 14:45:41: 32000000 INFO @ Sun, 03 Jun 2018 14:45:44: 30000000 INFO @ Sun, 03 Jun 2018 14:45:48: 33000000 INFO @ Sun, 03 Jun 2018 14:45:48: 32000000 INFO @ Sun, 03 Jun 2018 14:45:52: 31000000 INFO @ Sun, 03 Jun 2018 14:45:54: 34000000 INFO @ Sun, 03 Jun 2018 14:45:55: 33000000 INFO @ Sun, 03 Jun 2018 14:45:59: 32000000 INFO @ Sun, 03 Jun 2018 14:46:00: 35000000 INFO @ Sun, 03 Jun 2018 14:46:02: 34000000 INFO @ Sun, 03 Jun 2018 14:46:06: 33000000 INFO @ Sun, 03 Jun 2018 14:46:07: 36000000 INFO @ Sun, 03 Jun 2018 14:46:09: 35000000 INFO @ Sun, 03 Jun 2018 14:46:13: 37000000 INFO @ Sun, 03 Jun 2018 14:46:13: 34000000 INFO @ Sun, 03 Jun 2018 14:46:16: 36000000 INFO @ Sun, 03 Jun 2018 14:46:19: 38000000 INFO @ Sun, 03 Jun 2018 14:46:20: 35000000 INFO @ Sun, 03 Jun 2018 14:46:23: 37000000 INFO @ Sun, 03 Jun 2018 14:46:26: 39000000 INFO @ Sun, 03 Jun 2018 14:46:27: 36000000 INFO @ Sun, 03 Jun 2018 14:46:30: 38000000 INFO @ Sun, 03 Jun 2018 14:46:32: 40000000 INFO @ Sun, 03 Jun 2018 14:46:35: 37000000 INFO @ Sun, 03 Jun 2018 14:46:37: 39000000 INFO @ Sun, 03 Jun 2018 14:46:39: 41000000 INFO @ Sun, 03 Jun 2018 14:46:42: 38000000 INFO @ Sun, 03 Jun 2018 14:46:44: 40000000 INFO @ Sun, 03 Jun 2018 14:46:45: 42000000 INFO @ Sun, 03 Jun 2018 14:46:49: 39000000 INFO @ Sun, 03 Jun 2018 14:46:51: 41000000 INFO @ Sun, 03 Jun 2018 14:46:51: 43000000 INFO @ Sun, 03 Jun 2018 14:46:55: 40000000 INFO @ Sun, 03 Jun 2018 14:46:58: 44000000 INFO @ Sun, 03 Jun 2018 14:46:58: 42000000 INFO @ Sun, 03 Jun 2018 14:47:02: 41000000 INFO @ Sun, 03 Jun 2018 14:47:04: 45000000 INFO @ Sun, 03 Jun 2018 14:47:05: 43000000 INFO @ Sun, 03 Jun 2018 14:47:09: 42000000 INFO @ Sun, 03 Jun 2018 14:47:10: 46000000 INFO @ Sun, 03 Jun 2018 14:47:12: 44000000 INFO @ Sun, 03 Jun 2018 14:47:16: 43000000 INFO @ Sun, 03 Jun 2018 14:47:17: 47000000 INFO @ Sun, 03 Jun 2018 14:47:19: 45000000 INFO @ Sun, 03 Jun 2018 14:47:23: 48000000 INFO @ Sun, 03 Jun 2018 14:47:23: 44000000 INFO @ Sun, 03 Jun 2018 14:47:25: 46000000 INFO @ Sun, 03 Jun 2018 14:47:30: 49000000 INFO @ Sun, 03 Jun 2018 14:47:31: 45000000 INFO @ Sun, 03 Jun 2018 14:47:32: 47000000 INFO @ Sun, 03 Jun 2018 14:47:36: 50000000 INFO @ Sun, 03 Jun 2018 14:47:38: 46000000 INFO @ Sun, 03 Jun 2018 14:47:39: 48000000 INFO @ Sun, 03 Jun 2018 14:47:43: 51000000 INFO @ Sun, 03 Jun 2018 14:47:45: 47000000 INFO @ Sun, 03 Jun 2018 14:47:47: 49000000 INFO @ Sun, 03 Jun 2018 14:47:49: 52000000 INFO @ Sun, 03 Jun 2018 14:47:52: 48000000 INFO @ Sun, 03 Jun 2018 14:47:54: 50000000 INFO @ Sun, 03 Jun 2018 14:47:55: 53000000 INFO @ Sun, 03 Jun 2018 14:47:59: 49000000 INFO @ Sun, 03 Jun 2018 14:48:01: 51000000 INFO @ Sun, 03 Jun 2018 14:48:02: 54000000 INFO @ Sun, 03 Jun 2018 14:48:06: 50000000 INFO @ Sun, 03 Jun 2018 14:48:08: 52000000 INFO @ Sun, 03 Jun 2018 14:48:08: 55000000 INFO @ Sun, 03 Jun 2018 14:48:13: 51000000 INFO @ Sun, 03 Jun 2018 14:48:15: 56000000 INFO @ Sun, 03 Jun 2018 14:48:15: 53000000 INFO @ Sun, 03 Jun 2018 14:48:21: 52000000 INFO @ Sun, 03 Jun 2018 14:48:21: 57000000 INFO @ Sun, 03 Jun 2018 14:48:22: 54000000 INFO @ Sun, 03 Jun 2018 14:48:24: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 14:48:24: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 14:48:24: #1 total tags in treatment: 24522494 INFO @ Sun, 03 Jun 2018 14:48:24: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 14:48:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 14:48:25: #1 tags after filtering in treatment: 17851835 INFO @ Sun, 03 Jun 2018 14:48:25: #1 Redundant rate of treatment: 0.27 INFO @ Sun, 03 Jun 2018 14:48:25: #1 finished! INFO @ Sun, 03 Jun 2018 14:48:25: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 14:48:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 14:48:26: #2 number of paired peaks: 9 WARNING @ Sun, 03 Jun 2018 14:48:26: Too few paired peaks (9) 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 @ Sun, 03 Jun 2018 14:48:26: Process for pairing-model is terminated! cat: SRX1704845.10_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 `SRX1704845.10_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 `SRX1704845.10_*.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 `SRX1704845.10_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 @ Sun, 03 Jun 2018 14:48:28: 53000000 INFO @ Sun, 03 Jun 2018 14:48:29: 55000000 INFO @ Sun, 03 Jun 2018 14:48:35: 54000000 INFO @ Sun, 03 Jun 2018 14:48:36: 56000000 INFO @ Sun, 03 Jun 2018 14:48:42: 55000000 INFO @ Sun, 03 Jun 2018 14:48:42: 57000000 INFO @ Sun, 03 Jun 2018 14:48:46: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 14:48:46: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 14:48:46: #1 total tags in treatment: 24522494 INFO @ Sun, 03 Jun 2018 14:48:46: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 14:48:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 14:48:46: #1 tags after filtering in treatment: 17851835 INFO @ Sun, 03 Jun 2018 14:48:46: #1 Redundant rate of treatment: 0.27 INFO @ Sun, 03 Jun 2018 14:48:46: #1 finished! INFO @ Sun, 03 Jun 2018 14:48:46: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 14:48:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 14:48:48: #2 number of paired peaks: 9 WARNING @ Sun, 03 Jun 2018 14:48:48: Too few paired peaks (9) 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 @ Sun, 03 Jun 2018 14:48:48: Process for pairing-model is terminated! cat: SRX1704845.05_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 `SRX1704845.05_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 `SRX1704845.05_*.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 `SRX1704845.05_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 @ Sun, 03 Jun 2018 14:48:48: 56000000 INFO @ Sun, 03 Jun 2018 14:48:54: 57000000 INFO @ Sun, 03 Jun 2018 14:48:57: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 14:48:57: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 14:48:57: #1 total tags in treatment: 24522494 INFO @ Sun, 03 Jun 2018 14:48:57: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 14:48:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 14:48:58: #1 tags after filtering in treatment: 17851835 INFO @ Sun, 03 Jun 2018 14:48:58: #1 Redundant rate of treatment: 0.27 INFO @ Sun, 03 Jun 2018 14:48:58: #1 finished! INFO @ Sun, 03 Jun 2018 14:48:58: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 14:48:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 14:48:59: #2 number of paired peaks: 9 WARNING @ Sun, 03 Jun 2018 14:48:59: Too few paired peaks (9) 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 @ Sun, 03 Jun 2018 14:48:59: Process for pairing-model is terminated! cat: SRX1704845.20_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 `SRX1704845.20_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 `SRX1704845.20_*.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 `SRX1704845.20_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。