Job ID = 9163665 sra ファイルのダウンロード中... Completed: 3135137K bytes transferred in 28 seconds (915190K 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 30210042 spots for /home/okishinya/chipatlas/results/sacCer3/SRX997489/SRR1976521.sra Written 30210042 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: 00:25:07 30210042 reads; of these: 30210042 (100.00%) were paired; of these: 8029509 (26.58%) aligned concordantly 0 times 20276854 (67.12%) aligned concordantly exactly 1 time 1903679 (6.30%) aligned concordantly >1 times ---- 8029509 pairs aligned concordantly 0 times; of these: 448864 (5.59%) aligned discordantly 1 time ---- 7580645 pairs aligned 0 times concordantly or discordantly; of these: 15161290 mates make up the pairs; of these: 13887862 (91.60%) aligned 0 times 1006758 (6.64%) aligned exactly 1 time 266670 (1.76%) aligned >1 times 77.01% overall alignment rate Time searching: 00:25:07 Overall time: 00:25:07 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] 900973 / 22529423 = 0.0400 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 12:00:07: # Command line: callpeak -t SRX997489.bam -f BAM -g 12100000 -n SRX997489.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX997489.20 # format = BAM # ChIP-seq file = ['SRX997489.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 12:00:07: #1 read tag files... INFO @ Wed, 28 Jun 2017 12:00:07: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 12:00:07: # Command line: callpeak -t SRX997489.bam -f BAM -g 12100000 -n SRX997489.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX997489.10 # format = BAM # ChIP-seq file = ['SRX997489.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 12:00:07: #1 read tag files... INFO @ Wed, 28 Jun 2017 12:00:07: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 12:00:07: # Command line: callpeak -t SRX997489.bam -f BAM -g 12100000 -n SRX997489.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX997489.05 # format = BAM # ChIP-seq file = ['SRX997489.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 12:00:07: #1 read tag files... INFO @ Wed, 28 Jun 2017 12:00:07: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 12:00:15: 1000000 INFO @ Wed, 28 Jun 2017 12:00:15: 1000000 INFO @ Wed, 28 Jun 2017 12:00:15: 1000000 INFO @ Wed, 28 Jun 2017 12:00:22: 2000000 INFO @ Wed, 28 Jun 2017 12:00:23: 2000000 INFO @ Wed, 28 Jun 2017 12:00:23: 2000000 INFO @ Wed, 28 Jun 2017 12:00:30: 3000000 INFO @ Wed, 28 Jun 2017 12:00:31: 3000000 INFO @ Wed, 28 Jun 2017 12:00:32: 3000000 INFO @ Wed, 28 Jun 2017 12:00:37: 4000000 INFO @ Wed, 28 Jun 2017 12:00:40: 4000000 INFO @ Wed, 28 Jun 2017 12:00:40: 4000000 INFO @ Wed, 28 Jun 2017 12:00:45: 5000000 INFO @ Wed, 28 Jun 2017 12:00:48: 5000000 INFO @ Wed, 28 Jun 2017 12:00:49: 5000000 INFO @ Wed, 28 Jun 2017 12:00:52: 6000000 INFO @ Wed, 28 Jun 2017 12:00:56: 6000000 INFO @ Wed, 28 Jun 2017 12:00:57: 6000000 INFO @ Wed, 28 Jun 2017 12:00:59: 7000000 INFO @ Wed, 28 Jun 2017 12:01:05: 7000000 INFO @ Wed, 28 Jun 2017 12:01:06: 7000000 INFO @ Wed, 28 Jun 2017 12:01:07: 8000000 INFO @ Wed, 28 Jun 2017 12:01:13: 8000000 INFO @ Wed, 28 Jun 2017 12:01:14: 9000000 INFO @ Wed, 28 Jun 2017 12:01:14: 8000000 INFO @ Wed, 28 Jun 2017 12:01:21: 10000000 INFO @ Wed, 28 Jun 2017 12:01:21: 9000000 INFO @ Wed, 28 Jun 2017 12:01:23: 9000000 INFO @ Wed, 28 Jun 2017 12:01:29: 11000000 INFO @ Wed, 28 Jun 2017 12:01:30: 10000000 INFO @ Wed, 28 Jun 2017 12:01:31: 10000000 INFO @ Wed, 28 Jun 2017 12:01:36: 12000000 INFO @ Wed, 28 Jun 2017 12:01:38: 11000000 INFO @ Wed, 28 Jun 2017 12:01:40: 11000000 INFO @ Wed, 28 Jun 2017 12:01:42: 13000000 INFO @ Wed, 28 Jun 2017 12:01:46: 12000000 INFO @ Wed, 28 Jun 2017 12:01:48: 12000000 INFO @ Wed, 28 Jun 2017 12:01:49: 14000000 INFO @ Wed, 28 Jun 2017 12:01:54: 13000000 INFO @ Wed, 28 Jun 2017 12:01:56: 15000000 INFO @ Wed, 28 Jun 2017 12:01:56: 13000000 INFO @ Wed, 28 Jun 2017 12:02:02: 14000000 INFO @ Wed, 28 Jun 2017 12:02:03: 16000000 INFO @ Wed, 28 Jun 2017 12:02:05: 14000000 INFO @ Wed, 28 Jun 2017 12:02:10: 15000000 INFO @ Wed, 28 Jun 2017 12:02:11: 17000000 INFO @ Wed, 28 Jun 2017 12:02:13: 15000000 INFO @ Wed, 28 Jun 2017 12:02:18: 18000000 INFO @ Wed, 28 Jun 2017 12:02:18: 16000000 INFO @ Wed, 28 Jun 2017 12:02:21: 16000000 INFO @ Wed, 28 Jun 2017 12:02:25: 19000000 INFO @ Wed, 28 Jun 2017 12:02:26: 17000000 INFO @ Wed, 28 Jun 2017 12:02:30: 17000000 INFO @ Wed, 28 Jun 2017 12:02:32: 20000000 INFO @ Wed, 28 Jun 2017 12:02:35: 18000000 INFO @ Wed, 28 Jun 2017 12:02:38: 18000000 INFO @ Wed, 28 Jun 2017 12:02:39: 21000000 INFO @ Wed, 28 Jun 2017 12:02:43: 19000000 INFO @ Wed, 28 Jun 2017 12:02:47: 22000000 INFO @ Wed, 28 Jun 2017 12:02:47: 19000000 INFO @ Wed, 28 Jun 2017 12:02:51: 20000000 INFO @ Wed, 28 Jun 2017 12:02:54: 23000000 INFO @ Wed, 28 Jun 2017 12:02:56: 20000000 INFO @ Wed, 28 Jun 2017 12:02:59: 21000000 INFO @ Wed, 28 Jun 2017 12:03:01: 24000000 INFO @ Wed, 28 Jun 2017 12:03:04: 21000000 INFO @ Wed, 28 Jun 2017 12:03:08: 22000000 INFO @ Wed, 28 Jun 2017 12:03:08: 25000000 INFO @ Wed, 28 Jun 2017 12:03:13: 22000000 INFO @ Wed, 28 Jun 2017 12:03:15: 26000000 INFO @ Wed, 28 Jun 2017 12:03:16: 23000000 INFO @ Wed, 28 Jun 2017 12:03:21: 23000000 INFO @ Wed, 28 Jun 2017 12:03:22: 27000000 INFO @ Wed, 28 Jun 2017 12:03:24: 24000000 INFO @ Wed, 28 Jun 2017 12:03:29: 28000000 INFO @ Wed, 28 Jun 2017 12:03:30: 24000000 INFO @ Wed, 28 Jun 2017 12:03:32: 25000000 INFO @ Wed, 28 Jun 2017 12:03:37: 29000000 INFO @ Wed, 28 Jun 2017 12:03:38: 25000000 INFO @ Wed, 28 Jun 2017 12:03:40: 26000000 INFO @ Wed, 28 Jun 2017 12:03:44: 30000000 INFO @ Wed, 28 Jun 2017 12:03:47: 26000000 INFO @ Wed, 28 Jun 2017 12:03:49: 27000000 INFO @ Wed, 28 Jun 2017 12:03:51: 31000000 INFO @ Wed, 28 Jun 2017 12:03:55: 27000000 INFO @ Wed, 28 Jun 2017 12:03:57: 28000000 INFO @ Wed, 28 Jun 2017 12:03:58: 32000000 INFO @ Wed, 28 Jun 2017 12:04:04: 28000000 INFO @ Wed, 28 Jun 2017 12:04:05: 29000000 INFO @ Wed, 28 Jun 2017 12:04:05: 33000000 INFO @ Wed, 28 Jun 2017 12:04:12: 29000000 INFO @ Wed, 28 Jun 2017 12:04:12: 34000000 INFO @ Wed, 28 Jun 2017 12:04:13: 30000000 INFO @ Wed, 28 Jun 2017 12:04:20: 35000000 INFO @ Wed, 28 Jun 2017 12:04:20: 30000000 INFO @ Wed, 28 Jun 2017 12:04:20: 31000000 INFO @ Wed, 28 Jun 2017 12:04:27: 36000000 INFO @ Wed, 28 Jun 2017 12:04:28: 32000000 INFO @ Wed, 28 Jun 2017 12:04:28: 31000000 INFO @ Wed, 28 Jun 2017 12:04:34: 37000000 INFO @ Wed, 28 Jun 2017 12:04:36: 33000000 INFO @ Wed, 28 Jun 2017 12:04:36: 32000000 INFO @ Wed, 28 Jun 2017 12:04:41: 38000000 INFO @ Wed, 28 Jun 2017 12:04:44: 34000000 INFO @ Wed, 28 Jun 2017 12:04:45: 33000000 INFO @ Wed, 28 Jun 2017 12:04:48: 39000000 INFO @ Wed, 28 Jun 2017 12:04:52: 35000000 INFO @ Wed, 28 Jun 2017 12:04:53: 34000000 INFO @ Wed, 28 Jun 2017 12:04:56: 40000000 INFO @ Wed, 28 Jun 2017 12:04:59: 36000000 INFO @ Wed, 28 Jun 2017 12:05:01: 35000000 INFO @ Wed, 28 Jun 2017 12:05:03: 41000000 INFO @ Wed, 28 Jun 2017 12:05:07: 37000000 INFO @ Wed, 28 Jun 2017 12:05:09: 36000000 INFO @ Wed, 28 Jun 2017 12:05:10: 42000000 INFO @ Wed, 28 Jun 2017 12:05:15: 38000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 28 Jun 2017 12:05:17: 37000000 INFO @ Wed, 28 Jun 2017 12:05:17: 43000000 INFO @ Wed, 28 Jun 2017 12:05:22: 39000000 INFO @ Wed, 28 Jun 2017 12:05:24: 44000000 INFO @ Wed, 28 Jun 2017 12:05:25: 38000000 INFO @ Wed, 28 Jun 2017 12:05:30: #1 tag size is determined as 75 bps INFO @ Wed, 28 Jun 2017 12:05:30: #1 tag size = 75 INFO @ Wed, 28 Jun 2017 12:05:30: #1 total tags in treatment: 21291430 INFO @ Wed, 28 Jun 2017 12:05:30: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 12:05:30: #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 12:05:30: 40000000 INFO @ Wed, 28 Jun 2017 12:05:30: #1 tags after filtering in treatment: 13012154 INFO @ Wed, 28 Jun 2017 12:05:30: #1 Redundant rate of treatment: 0.39 INFO @ Wed, 28 Jun 2017 12:05:30: #1 finished! INFO @ Wed, 28 Jun 2017 12:05:30: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 12:05:30: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 12:05:31: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 12:05:31: 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 12:05:31: Process for pairing-model is terminated! cat: SRX997489.05_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 `SRX997489.05_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 `SRX997489.05_*.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 `SRX997489.05_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 12:05:33: 39000000 INFO @ Wed, 28 Jun 2017 12:05:38: 41000000 BigWig に変換しました。 INFO @ Wed, 28 Jun 2017 12:05:41: 40000000 INFO @ Wed, 28 Jun 2017 12:05:46: 42000000 INFO @ Wed, 28 Jun 2017 12:05:49: 41000000 INFO @ Wed, 28 Jun 2017 12:05:53: 43000000 INFO @ Wed, 28 Jun 2017 12:05:58: 42000000 INFO @ Wed, 28 Jun 2017 12:06:01: 44000000 INFO @ Wed, 28 Jun 2017 12:06:06: 43000000 INFO @ Wed, 28 Jun 2017 12:06:07: #1 tag size is determined as 75 bps INFO @ Wed, 28 Jun 2017 12:06:07: #1 tag size = 75 INFO @ Wed, 28 Jun 2017 12:06:07: #1 total tags in treatment: 21291430 INFO @ Wed, 28 Jun 2017 12:06:07: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 12:06:07: #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 12:06:07: #1 tags after filtering in treatment: 13012154 INFO @ Wed, 28 Jun 2017 12:06:07: #1 Redundant rate of treatment: 0.39 INFO @ Wed, 28 Jun 2017 12:06:07: #1 finished! INFO @ Wed, 28 Jun 2017 12:06:07: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 12:06:07: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 12:06:08: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 12:06:08: 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 12:06:08: Process for pairing-model is terminated! cat: SRX997489.20_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 `SRX997489.20_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 `SRX997489.20_*.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 `SRX997489.20_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 @ Wed, 28 Jun 2017 12:06:13: 44000000 INFO @ Wed, 28 Jun 2017 12:06:18: #1 tag size is determined as 75 bps INFO @ Wed, 28 Jun 2017 12:06:18: #1 tag size = 75 INFO @ Wed, 28 Jun 2017 12:06:18: #1 total tags in treatment: 21291430 INFO @ Wed, 28 Jun 2017 12:06:18: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 12:06:18: #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 12:06:19: #1 tags after filtering in treatment: 13012154 INFO @ Wed, 28 Jun 2017 12:06:19: #1 Redundant rate of treatment: 0.39 INFO @ Wed, 28 Jun 2017 12:06:19: #1 finished! INFO @ Wed, 28 Jun 2017 12:06:19: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 12:06:19: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 12:06:20: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 12:06:20: 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 12:06:20: Process for pairing-model is terminated! cat: SRX997489.10_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 `SRX997489.10_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 `SRX997489.10_*.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 `SRX997489.10_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