Job ID = 11388933 sra ファイルのダウンロード中... Completed: 1744839K bytes transferred in 31 seconds (451708K 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 31596181 spots for /home/okishinya/chipatlas/results/sacCer3/SRX5017452/SRR8198075.sra Written 31596181 spots for /home/okishinya/chipatlas/results/sacCer3/SRX5017452/SRR8198075.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: 01:02:09 31596181 reads; of these: 31596181 (100.00%) were paired; of these: 1977958 (6.26%) aligned concordantly 0 times 26556245 (84.05%) aligned concordantly exactly 1 time 3061978 (9.69%) aligned concordantly >1 times ---- 1977958 pairs aligned concordantly 0 times; of these: 367734 (18.59%) aligned discordantly 1 time ---- 1610224 pairs aligned 0 times concordantly or discordantly; of these: 3220448 mates make up the pairs; of these: 2809710 (87.25%) aligned 0 times 257439 (7.99%) aligned exactly 1 time 153299 (4.76%) aligned >1 times 95.55% overall alignment rate Time searching: 01:02:09 Overall time: 01:02:09 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 28 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] 4150768 / 29838635 = 0.1391 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 @ Thu, 13 Dec 2018 01:46:29: # Command line: callpeak -t SRX5017452.bam -f BAM -g 12100000 -n SRX5017452.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX5017452.20 # format = BAM # ChIP-seq file = ['SRX5017452.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 @ Thu, 13 Dec 2018 01:46:29: #1 read tag files... INFO @ Thu, 13 Dec 2018 01:46:29: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 01:46:29: # Command line: callpeak -t SRX5017452.bam -f BAM -g 12100000 -n SRX5017452.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX5017452.05 # format = BAM # ChIP-seq file = ['SRX5017452.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 @ Thu, 13 Dec 2018 01:46:29: #1 read tag files... INFO @ Thu, 13 Dec 2018 01:46:29: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 01:46:29: # Command line: callpeak -t SRX5017452.bam -f BAM -g 12100000 -n SRX5017452.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX5017452.10 # format = BAM # ChIP-seq file = ['SRX5017452.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 @ Thu, 13 Dec 2018 01:46:29: #1 read tag files... INFO @ Thu, 13 Dec 2018 01:46:29: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 01:46:40: 1000000 INFO @ Thu, 13 Dec 2018 01:46:42: 1000000 INFO @ Thu, 13 Dec 2018 01:46:42: 1000000 INFO @ Thu, 13 Dec 2018 01:46:50: 2000000 INFO @ Thu, 13 Dec 2018 01:46:51: 2000000 INFO @ Thu, 13 Dec 2018 01:46:55: 2000000 INFO @ Thu, 13 Dec 2018 01:46:59: 3000000 INFO @ Thu, 13 Dec 2018 01:46:59: 3000000 INFO @ Thu, 13 Dec 2018 01:47:07: 3000000 INFO @ Thu, 13 Dec 2018 01:47:07: 4000000 INFO @ Thu, 13 Dec 2018 01:47:10: 4000000 INFO @ Thu, 13 Dec 2018 01:47:15: 5000000 INFO @ Thu, 13 Dec 2018 01:47:19: 4000000 INFO @ Thu, 13 Dec 2018 01:47:19: 5000000 INFO @ Thu, 13 Dec 2018 01:47:23: 6000000 INFO @ Thu, 13 Dec 2018 01:47:28: 6000000 INFO @ Thu, 13 Dec 2018 01:47:30: 5000000 INFO @ Thu, 13 Dec 2018 01:47:31: 7000000 INFO @ Thu, 13 Dec 2018 01:47:38: 7000000 INFO @ Thu, 13 Dec 2018 01:47:39: 8000000 INFO @ Thu, 13 Dec 2018 01:47:43: 6000000 INFO @ Thu, 13 Dec 2018 01:47:47: 9000000 INFO @ Thu, 13 Dec 2018 01:47:51: 8000000 INFO @ Thu, 13 Dec 2018 01:47:55: 7000000 INFO @ Thu, 13 Dec 2018 01:47:57: 10000000 INFO @ Thu, 13 Dec 2018 01:48:03: 9000000 INFO @ Thu, 13 Dec 2018 01:48:05: 11000000 INFO @ Thu, 13 Dec 2018 01:48:08: 8000000 INFO @ Thu, 13 Dec 2018 01:48:13: 12000000 INFO @ Thu, 13 Dec 2018 01:48:13: 10000000 INFO @ Thu, 13 Dec 2018 01:48:21: 9000000 INFO @ Thu, 13 Dec 2018 01:48:21: 13000000 INFO @ Thu, 13 Dec 2018 01:48:24: 11000000 INFO @ Thu, 13 Dec 2018 01:48:28: 14000000 INFO @ Thu, 13 Dec 2018 01:48:32: 10000000 INFO @ Thu, 13 Dec 2018 01:48:35: 12000000 INFO @ Thu, 13 Dec 2018 01:48:36: 15000000 INFO @ Thu, 13 Dec 2018 01:48:43: 11000000 INFO @ Thu, 13 Dec 2018 01:48:44: 16000000 INFO @ Thu, 13 Dec 2018 01:48:46: 13000000 INFO @ Thu, 13 Dec 2018 01:48:52: 17000000 INFO @ Thu, 13 Dec 2018 01:48:54: 12000000 INFO @ Thu, 13 Dec 2018 01:48:55: 14000000 INFO @ Thu, 13 Dec 2018 01:49:00: 18000000 INFO @ Thu, 13 Dec 2018 01:49:05: 15000000 INFO @ Thu, 13 Dec 2018 01:49:06: 13000000 INFO @ Thu, 13 Dec 2018 01:49:07: 19000000 INFO @ Thu, 13 Dec 2018 01:49:14: 16000000 INFO @ Thu, 13 Dec 2018 01:49:15: 20000000 INFO @ Thu, 13 Dec 2018 01:49:18: 14000000 INFO @ Thu, 13 Dec 2018 01:49:22: 21000000 INFO @ Thu, 13 Dec 2018 01:49:23: 17000000 INFO @ Thu, 13 Dec 2018 01:49:30: 15000000 INFO @ Thu, 13 Dec 2018 01:49:31: 18000000 INFO @ Thu, 13 Dec 2018 01:49:33: 22000000 INFO @ Thu, 13 Dec 2018 01:49:42: 19000000 INFO @ Thu, 13 Dec 2018 01:49:44: 23000000 INFO @ Thu, 13 Dec 2018 01:49:46: 16000000 INFO @ Thu, 13 Dec 2018 01:49:53: 20000000 INFO @ Thu, 13 Dec 2018 01:49:57: 24000000 INFO @ Thu, 13 Dec 2018 01:50:00: 17000000 INFO @ Thu, 13 Dec 2018 01:50:06: 21000000 INFO @ Thu, 13 Dec 2018 01:50:08: 25000000 INFO @ Thu, 13 Dec 2018 01:50:14: 18000000 INFO @ Thu, 13 Dec 2018 01:50:18: 22000000 INFO @ Thu, 13 Dec 2018 01:50:19: 26000000 INFO @ Thu, 13 Dec 2018 01:50:27: 19000000 INFO @ Thu, 13 Dec 2018 01:50:28: 23000000 INFO @ Thu, 13 Dec 2018 01:50:32: 27000000 INFO @ Thu, 13 Dec 2018 01:50:38: 24000000 INFO @ Thu, 13 Dec 2018 01:50:40: 20000000 INFO @ Thu, 13 Dec 2018 01:50:48: 28000000 INFO @ Thu, 13 Dec 2018 01:50:49: 25000000 INFO @ Thu, 13 Dec 2018 01:50:54: 21000000 INFO @ Thu, 13 Dec 2018 01:51:04: 29000000 INFO @ Thu, 13 Dec 2018 01:51:08: 26000000 INFO @ Thu, 13 Dec 2018 01:51:10: 22000000 INFO @ Thu, 13 Dec 2018 01:51:19: 30000000 INFO @ Thu, 13 Dec 2018 01:51:19: 27000000 INFO @ Thu, 13 Dec 2018 01:51:25: 23000000 INFO @ Thu, 13 Dec 2018 01:51:28: 28000000 INFO @ Thu, 13 Dec 2018 01:51:30: 31000000 INFO @ Thu, 13 Dec 2018 01:51:36: 29000000 INFO @ Thu, 13 Dec 2018 01:51:39: 32000000 INFO @ Thu, 13 Dec 2018 01:51:42: 24000000 INFO @ Thu, 13 Dec 2018 01:51:47: 33000000 INFO @ Thu, 13 Dec 2018 01:51:50: 30000000 INFO @ Thu, 13 Dec 2018 01:51:57: 34000000 INFO @ Thu, 13 Dec 2018 01:51:57: 25000000 INFO @ Thu, 13 Dec 2018 01:52:05: 35000000 INFO @ Thu, 13 Dec 2018 01:52:06: 31000000 INFO @ Thu, 13 Dec 2018 01:52:12: 26000000 INFO @ Thu, 13 Dec 2018 01:52:14: 36000000 INFO @ Thu, 13 Dec 2018 01:52:22: 32000000 INFO @ Thu, 13 Dec 2018 01:52:23: 37000000 INFO @ Thu, 13 Dec 2018 01:52:33: 27000000 INFO @ Thu, 13 Dec 2018 01:52:41: 38000000 INFO @ Thu, 13 Dec 2018 01:52:42: 33000000 INFO @ Thu, 13 Dec 2018 01:52:55: 39000000 INFO @ Thu, 13 Dec 2018 01:52:55: 28000000 INFO @ Thu, 13 Dec 2018 01:52:57: 34000000 INFO @ Thu, 13 Dec 2018 01:53:06: 40000000 INFO @ Thu, 13 Dec 2018 01:53:06: 35000000 INFO @ Thu, 13 Dec 2018 01:53:16: 36000000 INFO @ Thu, 13 Dec 2018 01:53:17: 29000000 INFO @ Thu, 13 Dec 2018 01:53:17: 41000000 INFO @ Thu, 13 Dec 2018 01:53:25: 37000000 INFO @ Thu, 13 Dec 2018 01:53:29: 42000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 13 Dec 2018 01:53:34: 38000000 INFO @ Thu, 13 Dec 2018 01:53:38: 30000000 INFO @ Thu, 13 Dec 2018 01:53:43: 43000000 INFO @ Thu, 13 Dec 2018 01:53:44: 39000000 INFO @ Thu, 13 Dec 2018 01:53:54: 40000000 INFO @ Thu, 13 Dec 2018 01:53:56: 44000000 INFO @ Thu, 13 Dec 2018 01:54:00: 31000000 BigWig に変換しました。 INFO @ Thu, 13 Dec 2018 01:54:04: 41000000 INFO @ Thu, 13 Dec 2018 01:54:10: 45000000 INFO @ Thu, 13 Dec 2018 01:54:14: 42000000 INFO @ Thu, 13 Dec 2018 01:54:22: 32000000 INFO @ Thu, 13 Dec 2018 01:54:24: 43000000 INFO @ Thu, 13 Dec 2018 01:54:24: 46000000 INFO @ Thu, 13 Dec 2018 01:54:35: 44000000 INFO @ Thu, 13 Dec 2018 01:54:38: 47000000 INFO @ Thu, 13 Dec 2018 01:54:44: 45000000 INFO @ Thu, 13 Dec 2018 01:54:45: 33000000 INFO @ Thu, 13 Dec 2018 01:54:52: 48000000 INFO @ Thu, 13 Dec 2018 01:54:53: 46000000 INFO @ Thu, 13 Dec 2018 01:55:03: 47000000 INFO @ Thu, 13 Dec 2018 01:55:07: 49000000 INFO @ Thu, 13 Dec 2018 01:55:08: 34000000 INFO @ Thu, 13 Dec 2018 01:55:12: 48000000 INFO @ Thu, 13 Dec 2018 01:55:21: 50000000 INFO @ Thu, 13 Dec 2018 01:55:22: 49000000 INFO @ Thu, 13 Dec 2018 01:55:29: 35000000 INFO @ Thu, 13 Dec 2018 01:55:32: 50000000 INFO @ Thu, 13 Dec 2018 01:55:36: 51000000 INFO @ Thu, 13 Dec 2018 01:55:41: 51000000 INFO @ Thu, 13 Dec 2018 01:55:48: 36000000 INFO @ Thu, 13 Dec 2018 01:55:50: 52000000 INFO @ Thu, 13 Dec 2018 01:55:51: #1 tag size is determined as 75 bps INFO @ Thu, 13 Dec 2018 01:55:51: #1 tag size = 75 INFO @ Thu, 13 Dec 2018 01:55:51: #1 total tags in treatment: 25486689 INFO @ Thu, 13 Dec 2018 01:55:51: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 01:55:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 13 Dec 2018 01:55:52: #1 tags after filtering in treatment: 13585012 INFO @ Thu, 13 Dec 2018 01:55:52: #1 Redundant rate of treatment: 0.47 INFO @ Thu, 13 Dec 2018 01:55:52: #1 finished! INFO @ Thu, 13 Dec 2018 01:55:52: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 01:55:52: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 01:55:53: #2 number of paired peaks: 0 WARNING @ Thu, 13 Dec 2018 01:55:53: 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 @ Thu, 13 Dec 2018 01:55:53: Process for pairing-model is terminated! cat: SRX5017452.20_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): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX5017452.20_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 `SRX5017452.20_*.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 `SRX5017452.20_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 @ Thu, 13 Dec 2018 01:55:56: 52000000 INFO @ Thu, 13 Dec 2018 01:55:58: #1 tag size is determined as 75 bps INFO @ Thu, 13 Dec 2018 01:55:58: #1 tag size = 75 INFO @ Thu, 13 Dec 2018 01:55:58: #1 total tags in treatment: 25486689 INFO @ Thu, 13 Dec 2018 01:55:58: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 01:55:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 13 Dec 2018 01:55:59: #1 tags after filtering in treatment: 13585012 INFO @ Thu, 13 Dec 2018 01:55:59: #1 Redundant rate of treatment: 0.47 INFO @ Thu, 13 Dec 2018 01:55:59: #1 finished! INFO @ Thu, 13 Dec 2018 01:55:59: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 01:55:59: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 01:56:00: #2 number of paired peaks: 0 WARNING @ Thu, 13 Dec 2018 01:56:00: 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 @ Thu, 13 Dec 2018 01:56:00: Process for pairing-model is terminated! cat: SRX5017452.10_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): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX5017452.10_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 `SRX5017452.10_*.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 `SRX5017452.10_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 @ Thu, 13 Dec 2018 01:56:05: 37000000 INFO @ Thu, 13 Dec 2018 01:56:25: 38000000 INFO @ Thu, 13 Dec 2018 01:56:43: 39000000 INFO @ Thu, 13 Dec 2018 01:57:03: 40000000 INFO @ Thu, 13 Dec 2018 01:57:21: 41000000 INFO @ Thu, 13 Dec 2018 01:57:41: 42000000 INFO @ Thu, 13 Dec 2018 01:57:56: 43000000 INFO @ Thu, 13 Dec 2018 01:58:10: 44000000 INFO @ Thu, 13 Dec 2018 01:58:26: 45000000 INFO @ Thu, 13 Dec 2018 01:58:42: 46000000 INFO @ Thu, 13 Dec 2018 01:58:56: 47000000 INFO @ Thu, 13 Dec 2018 01:59:08: 48000000 INFO @ Thu, 13 Dec 2018 01:59:20: 49000000 INFO @ Thu, 13 Dec 2018 01:59:31: 50000000 INFO @ Thu, 13 Dec 2018 01:59:44: 51000000 INFO @ Thu, 13 Dec 2018 01:59:57: 52000000 INFO @ Thu, 13 Dec 2018 01:59:58: #1 tag size is determined as 75 bps INFO @ Thu, 13 Dec 2018 01:59:58: #1 tag size = 75 INFO @ Thu, 13 Dec 2018 01:59:58: #1 total tags in treatment: 25486689 INFO @ Thu, 13 Dec 2018 01:59:58: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 01:59:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 13 Dec 2018 01:59:59: #1 tags after filtering in treatment: 13585012 INFO @ Thu, 13 Dec 2018 01:59:59: #1 Redundant rate of treatment: 0.47 INFO @ Thu, 13 Dec 2018 01:59:59: #1 finished! INFO @ Thu, 13 Dec 2018 01:59:59: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 01:59:59: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 02:00:00: #2 number of paired peaks: 0 WARNING @ Thu, 13 Dec 2018 02:00:00: 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 @ Thu, 13 Dec 2018 02:00:00: Process for pairing-model is terminated! cat: SRX5017452.05_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): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX5017452.05_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 `SRX5017452.05_*.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 `SRX5017452.05_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