Job ID = 9162103 sra ファイルのダウンロード中... Completed: 999712K bytes transferred in 9 seconds (853558K 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 23626254 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1631839/SRR3225772.sra Written 23626254 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: 00:20:10 23626254 reads; of these: 23626254 (100.00%) were paired; of these: 767916 (3.25%) aligned concordantly 0 times 20454263 (86.57%) aligned concordantly exactly 1 time 2404075 (10.18%) aligned concordantly >1 times ---- 767916 pairs aligned concordantly 0 times; of these: 229064 (29.83%) aligned discordantly 1 time ---- 538852 pairs aligned 0 times concordantly or discordantly; of these: 1077704 mates make up the pairs; of these: 893502 (82.91%) aligned 0 times 98966 (9.18%) aligned exactly 1 time 85236 (7.91%) aligned >1 times 98.11% overall alignment rate Time searching: 00:20:10 Overall time: 00:20:10 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] 1029709 / 22987855 = 0.0448 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 06:26:11: # Command line: callpeak -t SRX1631839.bam -f BAM -g 12100000 -n SRX1631839.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1631839.10 # format = BAM # ChIP-seq file = ['SRX1631839.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 06:26:11: #1 read tag files... INFO @ Wed, 28 Jun 2017 06:26:11: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 06:26:11: # Command line: callpeak -t SRX1631839.bam -f BAM -g 12100000 -n SRX1631839.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1631839.05 # format = BAM # ChIP-seq file = ['SRX1631839.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 06:26:11: #1 read tag files... INFO @ Wed, 28 Jun 2017 06:26:11: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 06:26:11: # Command line: callpeak -t SRX1631839.bam -f BAM -g 12100000 -n SRX1631839.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1631839.20 # format = BAM # ChIP-seq file = ['SRX1631839.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 06:26:11: #1 read tag files... INFO @ Wed, 28 Jun 2017 06:26:11: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 06:26:17: 1000000 INFO @ Wed, 28 Jun 2017 06:26:17: 1000000 INFO @ Wed, 28 Jun 2017 06:26:17: 1000000 INFO @ Wed, 28 Jun 2017 06:26:23: 2000000 INFO @ Wed, 28 Jun 2017 06:26:23: 2000000 INFO @ Wed, 28 Jun 2017 06:26:23: 2000000 INFO @ Wed, 28 Jun 2017 06:26:29: 3000000 INFO @ Wed, 28 Jun 2017 06:26:29: 3000000 INFO @ Wed, 28 Jun 2017 06:26:29: 3000000 INFO @ Wed, 28 Jun 2017 06:26:35: 4000000 INFO @ Wed, 28 Jun 2017 06:26:35: 4000000 INFO @ Wed, 28 Jun 2017 06:26:35: 4000000 INFO @ Wed, 28 Jun 2017 06:26:41: 5000000 INFO @ Wed, 28 Jun 2017 06:26:42: 5000000 INFO @ Wed, 28 Jun 2017 06:26:42: 5000000 INFO @ Wed, 28 Jun 2017 06:26:47: 6000000 INFO @ Wed, 28 Jun 2017 06:26:48: 6000000 INFO @ Wed, 28 Jun 2017 06:26:48: 6000000 INFO @ Wed, 28 Jun 2017 06:26:52: 7000000 INFO @ Wed, 28 Jun 2017 06:26:54: 7000000 INFO @ Wed, 28 Jun 2017 06:26:54: 7000000 INFO @ Wed, 28 Jun 2017 06:26:58: 8000000 INFO @ Wed, 28 Jun 2017 06:27:00: 8000000 INFO @ Wed, 28 Jun 2017 06:27:00: 8000000 INFO @ Wed, 28 Jun 2017 06:27:04: 9000000 INFO @ Wed, 28 Jun 2017 06:27:06: 9000000 INFO @ Wed, 28 Jun 2017 06:27:06: 9000000 INFO @ Wed, 28 Jun 2017 06:27:10: 10000000 INFO @ Wed, 28 Jun 2017 06:27:12: 10000000 INFO @ Wed, 28 Jun 2017 06:27:12: 10000000 INFO @ Wed, 28 Jun 2017 06:27:16: 11000000 INFO @ Wed, 28 Jun 2017 06:27:18: 11000000 INFO @ Wed, 28 Jun 2017 06:27:18: 11000000 INFO @ Wed, 28 Jun 2017 06:27:24: 12000000 INFO @ Wed, 28 Jun 2017 06:27:26: 12000000 INFO @ Wed, 28 Jun 2017 06:27:26: 12000000 INFO @ Wed, 28 Jun 2017 06:27:32: 13000000 INFO @ Wed, 28 Jun 2017 06:27:34: 13000000 INFO @ Wed, 28 Jun 2017 06:27:34: 13000000 INFO @ Wed, 28 Jun 2017 06:27:40: 14000000 INFO @ Wed, 28 Jun 2017 06:27:42: 14000000 INFO @ Wed, 28 Jun 2017 06:27:42: 14000000 INFO @ Wed, 28 Jun 2017 06:27:48: 15000000 INFO @ Wed, 28 Jun 2017 06:27:50: 15000000 INFO @ Wed, 28 Jun 2017 06:27:50: 15000000 INFO @ Wed, 28 Jun 2017 06:27:56: 16000000 INFO @ Wed, 28 Jun 2017 06:27:57: 16000000 INFO @ Wed, 28 Jun 2017 06:27:57: 16000000 INFO @ Wed, 28 Jun 2017 06:28:04: 17000000 INFO @ Wed, 28 Jun 2017 06:28:05: 17000000 INFO @ Wed, 28 Jun 2017 06:28:05: 17000000 INFO @ Wed, 28 Jun 2017 06:28:12: 18000000 INFO @ Wed, 28 Jun 2017 06:28:13: 18000000 INFO @ Wed, 28 Jun 2017 06:28:13: 18000000 INFO @ Wed, 28 Jun 2017 06:28:20: 19000000 INFO @ Wed, 28 Jun 2017 06:28:21: 19000000 INFO @ Wed, 28 Jun 2017 06:28:21: 19000000 INFO @ Wed, 28 Jun 2017 06:28:28: 20000000 INFO @ Wed, 28 Jun 2017 06:28:29: 20000000 INFO @ Wed, 28 Jun 2017 06:28:29: 20000000 INFO @ Wed, 28 Jun 2017 06:28:37: 21000000 INFO @ Wed, 28 Jun 2017 06:28:37: 21000000 INFO @ Wed, 28 Jun 2017 06:28:37: 21000000 INFO @ Wed, 28 Jun 2017 06:28:45: 22000000 INFO @ Wed, 28 Jun 2017 06:28:45: 22000000 INFO @ Wed, 28 Jun 2017 06:28:45: 22000000 INFO @ Wed, 28 Jun 2017 06:28:53: 23000000 INFO @ Wed, 28 Jun 2017 06:28:54: 23000000 INFO @ Wed, 28 Jun 2017 06:28:55: 23000000 INFO @ Wed, 28 Jun 2017 06:29:01: 24000000 INFO @ Wed, 28 Jun 2017 06:29:03: 24000000 INFO @ Wed, 28 Jun 2017 06:29:04: 24000000 INFO @ Wed, 28 Jun 2017 06:29:09: 25000000 INFO @ Wed, 28 Jun 2017 06:29:12: 25000000 INFO @ Wed, 28 Jun 2017 06:29:14: 25000000 INFO @ Wed, 28 Jun 2017 06:29:18: 26000000 INFO @ Wed, 28 Jun 2017 06:29:20: 26000000 INFO @ Wed, 28 Jun 2017 06:29:24: 26000000 INFO @ Wed, 28 Jun 2017 06:29:28: 27000000 INFO @ Wed, 28 Jun 2017 06:29:28: 27000000 INFO @ Wed, 28 Jun 2017 06:29:33: 27000000 INFO @ Wed, 28 Jun 2017 06:29:36: 28000000 INFO @ Wed, 28 Jun 2017 06:29:37: 28000000 INFO @ Wed, 28 Jun 2017 06:29:42: 28000000 INFO @ Wed, 28 Jun 2017 06:29:44: 29000000 INFO @ Wed, 28 Jun 2017 06:29:47: 29000000 INFO @ Wed, 28 Jun 2017 06:29:52: 29000000 INFO @ Wed, 28 Jun 2017 06:29:54: 30000000 INFO @ Wed, 28 Jun 2017 06:29:56: 30000000 INFO @ Wed, 28 Jun 2017 06:30:01: 30000000 INFO @ Wed, 28 Jun 2017 06:30:03: 31000000 INFO @ Wed, 28 Jun 2017 06:30:05: 31000000 INFO @ Wed, 28 Jun 2017 06:30:10: 31000000 INFO @ Wed, 28 Jun 2017 06:30:12: 32000000 INFO @ Wed, 28 Jun 2017 06:30:14: 32000000 INFO @ Wed, 28 Jun 2017 06:30:18: 32000000 INFO @ Wed, 28 Jun 2017 06:30:21: 33000000 INFO @ Wed, 28 Jun 2017 06:30:22: 33000000 INFO @ Wed, 28 Jun 2017 06:30:27: 33000000 INFO @ Wed, 28 Jun 2017 06:30:29: 34000000 INFO @ Wed, 28 Jun 2017 06:30:31: 34000000 INFO @ Wed, 28 Jun 2017 06:30:36: 34000000 INFO @ Wed, 28 Jun 2017 06:30:38: 35000000 INFO @ Wed, 28 Jun 2017 06:30:40: 35000000 INFO @ Wed, 28 Jun 2017 06:30:44: 35000000 INFO @ Wed, 28 Jun 2017 06:30:47: 36000000 INFO @ Wed, 28 Jun 2017 06:30:48: 36000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 28 Jun 2017 06:30:53: 36000000 INFO @ Wed, 28 Jun 2017 06:30:56: 37000000 INFO @ Wed, 28 Jun 2017 06:30:57: 37000000 INFO @ Wed, 28 Jun 2017 06:31:02: 37000000 INFO @ Wed, 28 Jun 2017 06:31:04: 38000000 INFO @ Wed, 28 Jun 2017 06:31:06: 38000000 INFO @ Wed, 28 Jun 2017 06:31:11: 38000000 BigWig に変換しました。 INFO @ Wed, 28 Jun 2017 06:31:13: 39000000 INFO @ Wed, 28 Jun 2017 06:31:15: 39000000 INFO @ Wed, 28 Jun 2017 06:31:20: 39000000 INFO @ Wed, 28 Jun 2017 06:31:22: 40000000 INFO @ Wed, 28 Jun 2017 06:31:24: 40000000 INFO @ Wed, 28 Jun 2017 06:31:29: 40000000 INFO @ Wed, 28 Jun 2017 06:31:31: 41000000 INFO @ Wed, 28 Jun 2017 06:31:33: 41000000 INFO @ Wed, 28 Jun 2017 06:31:38: 41000000 INFO @ Wed, 28 Jun 2017 06:31:40: 42000000 INFO @ Wed, 28 Jun 2017 06:31:42: 42000000 INFO @ Wed, 28 Jun 2017 06:31:47: 42000000 INFO @ Wed, 28 Jun 2017 06:31:49: 43000000 INFO @ Wed, 28 Jun 2017 06:31:51: 43000000 INFO @ Wed, 28 Jun 2017 06:31:56: 43000000 INFO @ Wed, 28 Jun 2017 06:31:58: 44000000 INFO @ Wed, 28 Jun 2017 06:32:00: 44000000 INFO @ Wed, 28 Jun 2017 06:32:00: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 06:32:00: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 06:32:00: #1 total tags in treatment: 21831038 INFO @ Wed, 28 Jun 2017 06:32:00: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 06:32:00: #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 06:32:01: #1 tags after filtering in treatment: 13427589 INFO @ Wed, 28 Jun 2017 06:32:01: #1 Redundant rate of treatment: 0.38 INFO @ Wed, 28 Jun 2017 06:32:01: #1 finished! INFO @ Wed, 28 Jun 2017 06:32:01: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 06:32:01: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 06:32:02: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 06:32:02: 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 06:32:02: Process for pairing-model is terminated! cat: SRX1631839.10_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 `SRX1631839.10_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 `SRX1631839.10_*.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 `SRX1631839.10_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 06:32:02: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 06:32:02: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 06:32:02: #1 total tags in treatment: 21831038 INFO @ Wed, 28 Jun 2017 06:32:02: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 06:32:02: #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 06:32:02: #1 tags after filtering in treatment: 13427589 INFO @ Wed, 28 Jun 2017 06:32:02: #1 Redundant rate of treatment: 0.38 INFO @ Wed, 28 Jun 2017 06:32:02: #1 finished! INFO @ Wed, 28 Jun 2017 06:32:02: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 06:32:02: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 06:32:03: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 06:32:03: 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 06:32:03: Process for pairing-model is terminated! cat: SRX1631839.05_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 `SRX1631839.05_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 `SRX1631839.05_*.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 `SRX1631839.05_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 06:32:03: 44000000 INFO @ Wed, 28 Jun 2017 06:32:05: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 06:32:05: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 06:32:05: #1 total tags in treatment: 21831038 INFO @ Wed, 28 Jun 2017 06:32:05: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 06:32:05: #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 06:32:06: #1 tags after filtering in treatment: 13427589 INFO @ Wed, 28 Jun 2017 06:32:06: #1 Redundant rate of treatment: 0.38 INFO @ Wed, 28 Jun 2017 06:32:06: #1 finished! INFO @ Wed, 28 Jun 2017 06:32:06: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 06:32:06: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 06:32:07: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 06:32:07: 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 06:32:07: Process for pairing-model is terminated! cat: SRX1631839.20_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 `SRX1631839.20_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 `SRX1631839.20_*.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 `SRX1631839.20_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