Job ID = 10714536 sra ファイルのダウンロード中... Completed: 2006718K bytes transferred in 27 seconds (602773K 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 34381483 spots for /home/okishinya/chipatlas/results/dm3/SRX1619259/SRR3211635.sra Written 34381483 spots for /home/okishinya/chipatlas/results/dm3/SRX1619259/SRR3211635.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: 01:21:58 34381483 reads; of these: 34381483 (100.00%) were paired; of these: 4654993 (13.54%) aligned concordantly 0 times 22901354 (66.61%) aligned concordantly exactly 1 time 6825136 (19.85%) aligned concordantly >1 times ---- 4654993 pairs aligned concordantly 0 times; of these: 2299602 (49.40%) aligned discordantly 1 time ---- 2355391 pairs aligned 0 times concordantly or discordantly; of these: 4710782 mates make up the pairs; of these: 2030836 (43.11%) aligned 0 times 1331120 (28.26%) aligned exactly 1 time 1348826 (28.63%) aligned >1 times 97.05% overall alignment rate Time searching: 01:21:58 Overall time: 01:21:58 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] 3993349 / 31936075 = 0.1250 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 14:58:13: # Command line: callpeak -t SRX1619259.bam -f BAM -g dm -n SRX1619259.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1619259.20 # format = BAM # ChIP-seq file = ['SRX1619259.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 14:58:13: #1 read tag files... INFO @ Sun, 03 Jun 2018 14:58:13: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 14:58:13: # Command line: callpeak -t SRX1619259.bam -f BAM -g dm -n SRX1619259.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1619259.05 # format = BAM # ChIP-seq file = ['SRX1619259.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 14:58:13: #1 read tag files... INFO @ Sun, 03 Jun 2018 14:58:13: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 14:58:13: # Command line: callpeak -t SRX1619259.bam -f BAM -g dm -n SRX1619259.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1619259.10 # format = BAM # ChIP-seq file = ['SRX1619259.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 14:58:13: #1 read tag files... INFO @ Sun, 03 Jun 2018 14:58:13: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 14:58:18: 1000000 INFO @ Sun, 03 Jun 2018 14:58:18: 1000000 INFO @ Sun, 03 Jun 2018 14:58:18: 1000000 INFO @ Sun, 03 Jun 2018 14:58:23: 2000000 INFO @ Sun, 03 Jun 2018 14:58:23: 2000000 INFO @ Sun, 03 Jun 2018 14:58:24: 2000000 INFO @ Sun, 03 Jun 2018 14:58:29: 3000000 INFO @ Sun, 03 Jun 2018 14:58:29: 3000000 INFO @ Sun, 03 Jun 2018 14:58:30: 3000000 INFO @ Sun, 03 Jun 2018 14:58:34: 4000000 INFO @ Sun, 03 Jun 2018 14:58:34: 4000000 INFO @ Sun, 03 Jun 2018 14:58:35: 4000000 INFO @ Sun, 03 Jun 2018 14:58:39: 5000000 INFO @ Sun, 03 Jun 2018 14:58:39: 5000000 INFO @ Sun, 03 Jun 2018 14:58:41: 5000000 INFO @ Sun, 03 Jun 2018 14:58:44: 6000000 INFO @ Sun, 03 Jun 2018 14:58:45: 6000000 INFO @ Sun, 03 Jun 2018 14:58:46: 6000000 INFO @ Sun, 03 Jun 2018 14:58:50: 7000000 INFO @ Sun, 03 Jun 2018 14:58:50: 7000000 INFO @ Sun, 03 Jun 2018 14:58:52: 7000000 INFO @ Sun, 03 Jun 2018 14:58:55: 8000000 INFO @ Sun, 03 Jun 2018 14:58:55: 8000000 INFO @ Sun, 03 Jun 2018 14:58:57: 8000000 INFO @ Sun, 03 Jun 2018 14:59:00: 9000000 INFO @ Sun, 03 Jun 2018 14:59:00: 9000000 INFO @ Sun, 03 Jun 2018 14:59:03: 9000000 INFO @ Sun, 03 Jun 2018 14:59:05: 10000000 INFO @ Sun, 03 Jun 2018 14:59:06: 10000000 INFO @ Sun, 03 Jun 2018 14:59:08: 10000000 INFO @ Sun, 03 Jun 2018 14:59:10: 11000000 INFO @ Sun, 03 Jun 2018 14:59:11: 11000000 INFO @ Sun, 03 Jun 2018 14:59:14: 11000000 INFO @ Sun, 03 Jun 2018 14:59:15: 12000000 INFO @ Sun, 03 Jun 2018 14:59:16: 12000000 INFO @ Sun, 03 Jun 2018 14:59:19: 12000000 INFO @ Sun, 03 Jun 2018 14:59:20: 13000000 INFO @ Sun, 03 Jun 2018 14:59:22: 13000000 INFO @ Sun, 03 Jun 2018 14:59:25: 13000000 INFO @ Sun, 03 Jun 2018 14:59:25: 14000000 INFO @ Sun, 03 Jun 2018 14:59:27: 14000000 INFO @ Sun, 03 Jun 2018 14:59:30: 14000000 INFO @ Sun, 03 Jun 2018 14:59:30: 15000000 INFO @ Sun, 03 Jun 2018 14:59:32: 15000000 INFO @ Sun, 03 Jun 2018 14:59:36: 16000000 INFO @ Sun, 03 Jun 2018 14:59:36: 15000000 INFO @ Sun, 03 Jun 2018 14:59:38: 16000000 INFO @ Sun, 03 Jun 2018 14:59:41: 17000000 INFO @ Sun, 03 Jun 2018 14:59:41: 16000000 INFO @ Sun, 03 Jun 2018 14:59:43: 17000000 INFO @ Sun, 03 Jun 2018 14:59:46: 18000000 INFO @ Sun, 03 Jun 2018 14:59:47: 17000000 INFO @ Sun, 03 Jun 2018 14:59:48: 18000000 INFO @ Sun, 03 Jun 2018 14:59:51: 19000000 INFO @ Sun, 03 Jun 2018 14:59:52: 18000000 INFO @ Sun, 03 Jun 2018 14:59:53: 19000000 INFO @ Sun, 03 Jun 2018 14:59:56: 20000000 INFO @ Sun, 03 Jun 2018 14:59:58: 19000000 INFO @ Sun, 03 Jun 2018 14:59:59: 20000000 INFO @ Sun, 03 Jun 2018 15:00:01: 21000000 INFO @ Sun, 03 Jun 2018 15:00:03: 20000000 INFO @ Sun, 03 Jun 2018 15:00:04: 21000000 INFO @ Sun, 03 Jun 2018 15:00:06: 22000000 INFO @ Sun, 03 Jun 2018 15:00:09: 21000000 INFO @ Sun, 03 Jun 2018 15:00:10: 22000000 INFO @ Sun, 03 Jun 2018 15:00:11: 23000000 INFO @ Sun, 03 Jun 2018 15:00:15: 22000000 INFO @ Sun, 03 Jun 2018 15:00:15: 23000000 INFO @ Sun, 03 Jun 2018 15:00:16: 24000000 INFO @ Sun, 03 Jun 2018 15:00:20: 24000000 INFO @ Sun, 03 Jun 2018 15:00:20: 23000000 INFO @ Sun, 03 Jun 2018 15:00:21: 25000000 INFO @ Sun, 03 Jun 2018 15:00:25: 25000000 INFO @ Sun, 03 Jun 2018 15:00:26: 24000000 INFO @ Sun, 03 Jun 2018 15:00:27: 26000000 INFO @ Sun, 03 Jun 2018 15:00:30: 26000000 INFO @ Sun, 03 Jun 2018 15:00:32: 25000000 INFO @ Sun, 03 Jun 2018 15:00:32: 27000000 INFO @ Sun, 03 Jun 2018 15:00:36: 27000000 INFO @ Sun, 03 Jun 2018 15:00:37: 28000000 INFO @ Sun, 03 Jun 2018 15:00:37: 26000000 INFO @ Sun, 03 Jun 2018 15:00:41: 28000000 INFO @ Sun, 03 Jun 2018 15:00:42: 29000000 INFO @ Sun, 03 Jun 2018 15:00:43: 27000000 INFO @ Sun, 03 Jun 2018 15:00:46: 29000000 INFO @ Sun, 03 Jun 2018 15:00:48: 30000000 INFO @ Sun, 03 Jun 2018 15:00:48: 28000000 INFO @ Sun, 03 Jun 2018 15:00:51: 30000000 INFO @ Sun, 03 Jun 2018 15:00:53: 31000000 INFO @ Sun, 03 Jun 2018 15:00:54: 29000000 INFO @ Sun, 03 Jun 2018 15:00:57: 31000000 INFO @ Sun, 03 Jun 2018 15:00:58: 32000000 INFO @ Sun, 03 Jun 2018 15:01:00: 30000000 INFO @ Sun, 03 Jun 2018 15:01:02: 32000000 INFO @ Sun, 03 Jun 2018 15:01:03: 33000000 INFO @ Sun, 03 Jun 2018 15:01:05: 31000000 INFO @ Sun, 03 Jun 2018 15:01:07: 33000000 INFO @ Sun, 03 Jun 2018 15:01:08: 34000000 INFO @ Sun, 03 Jun 2018 15:01:11: 32000000 INFO @ Sun, 03 Jun 2018 15:01:13: 34000000 INFO @ Sun, 03 Jun 2018 15:01:13: 35000000 INFO @ Sun, 03 Jun 2018 15:01:17: 33000000 INFO @ Sun, 03 Jun 2018 15:01:18: 36000000 INFO @ Sun, 03 Jun 2018 15:01:18: 35000000 INFO @ Sun, 03 Jun 2018 15:01:22: 34000000 INFO @ Sun, 03 Jun 2018 15:01:23: 37000000 INFO @ Sun, 03 Jun 2018 15:01:24: 36000000 INFO @ Sun, 03 Jun 2018 15:01:28: 35000000 INFO @ Sun, 03 Jun 2018 15:01:28: 38000000 INFO @ Sun, 03 Jun 2018 15:01:29: 37000000 INFO @ Sun, 03 Jun 2018 15:01:33: 39000000 INFO @ Sun, 03 Jun 2018 15:01:34: 36000000 INFO @ Sun, 03 Jun 2018 15:01:34: 38000000 INFO @ Sun, 03 Jun 2018 15:01:38: 40000000 INFO @ Sun, 03 Jun 2018 15:01:39: 37000000 INFO @ Sun, 03 Jun 2018 15:01:40: 39000000 INFO @ Sun, 03 Jun 2018 15:01:43: 41000000 INFO @ Sun, 03 Jun 2018 15:01:45: 38000000 INFO @ Sun, 03 Jun 2018 15:01:45: 40000000 INFO @ Sun, 03 Jun 2018 15:01:48: 42000000 INFO @ Sun, 03 Jun 2018 15:01:50: 41000000 INFO @ Sun, 03 Jun 2018 15:01:51: 39000000 INFO @ Sun, 03 Jun 2018 15:01:53: 43000000 INFO @ Sun, 03 Jun 2018 15:01:56: 42000000 INFO @ Sun, 03 Jun 2018 15:01:56: 40000000 INFO @ Sun, 03 Jun 2018 15:01:58: 44000000 INFO @ Sun, 03 Jun 2018 15:02:01: 43000000 INFO @ Sun, 03 Jun 2018 15:02:02: 41000000 INFO @ Sun, 03 Jun 2018 15:02:03: 45000000 INFO @ Sun, 03 Jun 2018 15:02:06: 44000000 INFO @ Sun, 03 Jun 2018 15:02:07: 42000000 INFO @ Sun, 03 Jun 2018 15:02:08: 46000000 INFO @ Sun, 03 Jun 2018 15:02:12: 45000000 INFO @ Sun, 03 Jun 2018 15:02:13: 43000000 INFO @ Sun, 03 Jun 2018 15:02:13: 47000000 INFO @ Sun, 03 Jun 2018 15:02:17: 46000000 INFO @ Sun, 03 Jun 2018 15:02:18: 48000000 INFO @ Sun, 03 Jun 2018 15:02:18: 44000000 INFO @ Sun, 03 Jun 2018 15:02:22: 47000000 INFO @ Sun, 03 Jun 2018 15:02:23: 49000000 INFO @ Sun, 03 Jun 2018 15:02:24: 45000000 INFO @ Sun, 03 Jun 2018 15:02:28: 48000000 INFO @ Sun, 03 Jun 2018 15:02:29: 50000000 INFO @ Sun, 03 Jun 2018 15:02:30: 46000000 INFO @ Sun, 03 Jun 2018 15:02:33: 49000000 INFO @ Sun, 03 Jun 2018 15:02:34: 51000000 INFO @ Sun, 03 Jun 2018 15:02:35: 47000000 INFO @ Sun, 03 Jun 2018 15:02:39: 52000000 INFO @ Sun, 03 Jun 2018 15:02:39: 50000000 INFO @ Sun, 03 Jun 2018 15:02:41: 48000000 INFO @ Sun, 03 Jun 2018 15:02:44: 53000000 INFO @ Sun, 03 Jun 2018 15:02:44: 51000000 INFO @ Sun, 03 Jun 2018 15:02:46: 49000000 INFO @ Sun, 03 Jun 2018 15:02:49: 54000000 INFO @ Sun, 03 Jun 2018 15:02:49: 52000000 INFO @ Sun, 03 Jun 2018 15:02:52: 50000000 INFO @ Sun, 03 Jun 2018 15:02:54: 55000000 INFO @ Sun, 03 Jun 2018 15:02:55: 53000000 INFO @ Sun, 03 Jun 2018 15:02:58: 51000000 INFO @ Sun, 03 Jun 2018 15:02:59: 56000000 INFO @ Sun, 03 Jun 2018 15:03:00: 54000000 INFO @ Sun, 03 Jun 2018 15:03:03: 52000000 INFO @ Sun, 03 Jun 2018 15:03:04: 57000000 INFO @ Sun, 03 Jun 2018 15:03:05: 55000000 INFO @ Sun, 03 Jun 2018 15:03:09: 53000000 INFO @ Sun, 03 Jun 2018 15:03:09: 58000000 INFO @ Sun, 03 Jun 2018 15:03:10: 56000000 INFO @ Sun, 03 Jun 2018 15:03:13: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 15:03:13: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 15:03:13: #1 total tags in treatment: 25813091 INFO @ Sun, 03 Jun 2018 15:03:13: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 15:03:13: #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 15:03:14: #1 tags after filtering in treatment: 18512683 INFO @ Sun, 03 Jun 2018 15:03:14: #1 Redundant rate of treatment: 0.28 INFO @ Sun, 03 Jun 2018 15:03:14: #1 finished! INFO @ Sun, 03 Jun 2018 15:03:14: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 15:03:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 15:03:14: 54000000 INFO @ Sun, 03 Jun 2018 15:03:15: #2 number of paired peaks: 10 WARNING @ Sun, 03 Jun 2018 15:03:15: Too few paired peaks (10) 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 15:03:15: Process for pairing-model is terminated! cat: SRX1619259.05_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): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX1619259.05_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 `SRX1619259.05_*.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 `SRX1619259.05_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 15:03:15: 57000000 INFO @ Sun, 03 Jun 2018 15:03:20: 55000000 INFO @ Sun, 03 Jun 2018 15:03:21: 58000000 INFO @ Sun, 03 Jun 2018 15:03:25: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 15:03:25: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 15:03:25: #1 total tags in treatment: 25813091 INFO @ Sun, 03 Jun 2018 15:03:25: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 15:03:25: #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 15:03:25: 56000000 INFO @ Sun, 03 Jun 2018 15:03:25: #1 tags after filtering in treatment: 18512683 INFO @ Sun, 03 Jun 2018 15:03:25: #1 Redundant rate of treatment: 0.28 INFO @ Sun, 03 Jun 2018 15:03:25: #1 finished! INFO @ Sun, 03 Jun 2018 15:03:25: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 15:03:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 15:03:27: #2 number of paired peaks: 10 WARNING @ Sun, 03 Jun 2018 15:03:27: Too few paired peaks (10) 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 15:03:27: Process for pairing-model is terminated! cat: SRX1619259.10_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 `SRX1619259.10_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 `SRX1619259.10_*.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 `SRX1619259.10_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 15:03:30: 57000000 INFO @ Sun, 03 Jun 2018 15:03:36: 58000000 INFO @ Sun, 03 Jun 2018 15:03:40: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 15:03:40: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 15:03:40: #1 total tags in treatment: 25813091 INFO @ Sun, 03 Jun 2018 15:03:40: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 15:03:40: #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 15:03:41: #1 tags after filtering in treatment: 18512683 INFO @ Sun, 03 Jun 2018 15:03:41: #1 Redundant rate of treatment: 0.28 INFO @ Sun, 03 Jun 2018 15:03:41: #1 finished! INFO @ Sun, 03 Jun 2018 15:03:41: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 15:03:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 15:03:42: #2 number of paired peaks: 10 WARNING @ Sun, 03 Jun 2018 15:03:42: Too few paired peaks (10) 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 15:03:42: Process for pairing-model is terminated! cat: SRX1619259.20_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): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX1619259.20_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 `SRX1619259.20_*.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 `SRX1619259.20_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。