Job ID = 10536506 sra ファイルのダウンロード中... Completed: 1153407K bytes transferred in 31 seconds (303187K 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... Written 29733373 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3671201/SRR6696953.sra Written 29733373 spots total 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: 00:20:59 29733373 reads; of these: 29733373 (100.00%) were paired; of these: 4865006 (16.36%) aligned concordantly 0 times 21877218 (73.58%) aligned concordantly exactly 1 time 2991149 (10.06%) aligned concordantly >1 times ---- 4865006 pairs aligned concordantly 0 times; of these: 146371 (3.01%) aligned discordantly 1 time ---- 4718635 pairs aligned 0 times concordantly or discordantly; of these: 9437270 mates make up the pairs; of these: 9253130 (98.05%) aligned 0 times 100284 (1.06%) aligned exactly 1 time 83856 (0.89%) aligned >1 times 84.44% overall alignment rate Time searching: 00:20:59 Overall time: 00:20:59 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 24 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] 6371888 / 24968060 = 0.2552 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, 05 Apr 2018 10:31:22: # Command line: callpeak -t SRX3671201.bam -f BAM -g 12100000 -n SRX3671201.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3671201.05 # format = BAM # ChIP-seq file = ['SRX3671201.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, 05 Apr 2018 10:31:22: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:31:22: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:31:22: # Command line: callpeak -t SRX3671201.bam -f BAM -g 12100000 -n SRX3671201.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3671201.10 # format = BAM # ChIP-seq file = ['SRX3671201.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, 05 Apr 2018 10:31:22: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:31:22: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:31:22: # Command line: callpeak -t SRX3671201.bam -f BAM -g 12100000 -n SRX3671201.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3671201.20 # format = BAM # ChIP-seq file = ['SRX3671201.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, 05 Apr 2018 10:31:22: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:31:22: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:31:27: 1000000 INFO @ Thu, 05 Apr 2018 10:31:27: 1000000 INFO @ Thu, 05 Apr 2018 10:31:27: 1000000 INFO @ Thu, 05 Apr 2018 10:31:32: 2000000 INFO @ Thu, 05 Apr 2018 10:31:32: 2000000 INFO @ Thu, 05 Apr 2018 10:31:32: 2000000 INFO @ Thu, 05 Apr 2018 10:31:38: 3000000 INFO @ Thu, 05 Apr 2018 10:31:38: 3000000 INFO @ Thu, 05 Apr 2018 10:31:38: 3000000 INFO @ Thu, 05 Apr 2018 10:31:43: 4000000 INFO @ Thu, 05 Apr 2018 10:31:43: 4000000 INFO @ Thu, 05 Apr 2018 10:31:43: 4000000 INFO @ Thu, 05 Apr 2018 10:31:48: 5000000 INFO @ Thu, 05 Apr 2018 10:31:48: 5000000 INFO @ Thu, 05 Apr 2018 10:31:48: 5000000 INFO @ Thu, 05 Apr 2018 10:31:54: 6000000 INFO @ Thu, 05 Apr 2018 10:31:54: 6000000 INFO @ Thu, 05 Apr 2018 10:31:54: 6000000 INFO @ Thu, 05 Apr 2018 10:31:59: 7000000 INFO @ Thu, 05 Apr 2018 10:31:59: 7000000 INFO @ Thu, 05 Apr 2018 10:31:59: 7000000 INFO @ Thu, 05 Apr 2018 10:32:04: 8000000 INFO @ Thu, 05 Apr 2018 10:32:04: 8000000 INFO @ Thu, 05 Apr 2018 10:32:04: 8000000 INFO @ Thu, 05 Apr 2018 10:32:09: 9000000 INFO @ Thu, 05 Apr 2018 10:32:10: 9000000 INFO @ Thu, 05 Apr 2018 10:32:10: 9000000 INFO @ Thu, 05 Apr 2018 10:32:14: 10000000 INFO @ Thu, 05 Apr 2018 10:32:15: 10000000 INFO @ Thu, 05 Apr 2018 10:32:15: 10000000 INFO @ Thu, 05 Apr 2018 10:32:20: 11000000 INFO @ Thu, 05 Apr 2018 10:32:20: 11000000 INFO @ Thu, 05 Apr 2018 10:32:20: 11000000 INFO @ Thu, 05 Apr 2018 10:32:25: 12000000 INFO @ Thu, 05 Apr 2018 10:32:25: 12000000 INFO @ Thu, 05 Apr 2018 10:32:25: 12000000 INFO @ Thu, 05 Apr 2018 10:32:30: 13000000 INFO @ Thu, 05 Apr 2018 10:32:31: 13000000 INFO @ Thu, 05 Apr 2018 10:32:31: 13000000 INFO @ Thu, 05 Apr 2018 10:32:35: 14000000 INFO @ Thu, 05 Apr 2018 10:32:36: 14000000 INFO @ Thu, 05 Apr 2018 10:32:36: 14000000 INFO @ Thu, 05 Apr 2018 10:32:40: 15000000 INFO @ Thu, 05 Apr 2018 10:32:41: 15000000 INFO @ Thu, 05 Apr 2018 10:32:41: 15000000 INFO @ Thu, 05 Apr 2018 10:32:45: 16000000 INFO @ Thu, 05 Apr 2018 10:32:46: 16000000 INFO @ Thu, 05 Apr 2018 10:32:46: 16000000 INFO @ Thu, 05 Apr 2018 10:32:50: 17000000 INFO @ Thu, 05 Apr 2018 10:32:52: 17000000 INFO @ Thu, 05 Apr 2018 10:32:52: 17000000 INFO @ Thu, 05 Apr 2018 10:32:55: 18000000 INFO @ Thu, 05 Apr 2018 10:32:57: 18000000 INFO @ Thu, 05 Apr 2018 10:32:57: 18000000 INFO @ Thu, 05 Apr 2018 10:33:00: 19000000 INFO @ Thu, 05 Apr 2018 10:33:02: 19000000 INFO @ Thu, 05 Apr 2018 10:33:02: 19000000 INFO @ Thu, 05 Apr 2018 10:33:06: 20000000 INFO @ Thu, 05 Apr 2018 10:33:08: 20000000 INFO @ Thu, 05 Apr 2018 10:33:08: 20000000 INFO @ Thu, 05 Apr 2018 10:33:12: 21000000 INFO @ Thu, 05 Apr 2018 10:33:13: 21000000 INFO @ Thu, 05 Apr 2018 10:33:13: 21000000 INFO @ Thu, 05 Apr 2018 10:33:18: 22000000 INFO @ Thu, 05 Apr 2018 10:33:19: 22000000 INFO @ Thu, 05 Apr 2018 10:33:19: 22000000 INFO @ Thu, 05 Apr 2018 10:33:24: 23000000 INFO @ Thu, 05 Apr 2018 10:33:24: 23000000 INFO @ Thu, 05 Apr 2018 10:33:24: 23000000 INFO @ Thu, 05 Apr 2018 10:33:29: 24000000 INFO @ Thu, 05 Apr 2018 10:33:29: 24000000 INFO @ Thu, 05 Apr 2018 10:33:29: 24000000 INFO @ Thu, 05 Apr 2018 10:33:34: 25000000 INFO @ Thu, 05 Apr 2018 10:33:35: 25000000 INFO @ Thu, 05 Apr 2018 10:33:35: 25000000 INFO @ Thu, 05 Apr 2018 10:33:40: 26000000 INFO @ Thu, 05 Apr 2018 10:33:40: 26000000 INFO @ Thu, 05 Apr 2018 10:33:40: 26000000 INFO @ Thu, 05 Apr 2018 10:33:45: 27000000 INFO @ Thu, 05 Apr 2018 10:33:45: 27000000 INFO @ Thu, 05 Apr 2018 10:33:46: 27000000 INFO @ Thu, 05 Apr 2018 10:33:51: 28000000 INFO @ Thu, 05 Apr 2018 10:33:51: 28000000 INFO @ Thu, 05 Apr 2018 10:33:52: 28000000 INFO @ Thu, 05 Apr 2018 10:33:56: 29000000 INFO @ Thu, 05 Apr 2018 10:33:56: 29000000 INFO @ Thu, 05 Apr 2018 10:33:58: 29000000 INFO @ Thu, 05 Apr 2018 10:34:02: 30000000 INFO @ Thu, 05 Apr 2018 10:34:02: 30000000 INFO @ Thu, 05 Apr 2018 10:34:04: 30000000 INFO @ Thu, 05 Apr 2018 10:34:07: 31000000 INFO @ Thu, 05 Apr 2018 10:34:07: 31000000 INFO @ Thu, 05 Apr 2018 10:34:10: 31000000 INFO @ Thu, 05 Apr 2018 10:34:13: 32000000 INFO @ Thu, 05 Apr 2018 10:34:13: 32000000 INFO @ Thu, 05 Apr 2018 10:34:16: 32000000 INFO @ Thu, 05 Apr 2018 10:34:18: 33000000 INFO @ Thu, 05 Apr 2018 10:34:18: 33000000 INFO @ Thu, 05 Apr 2018 10:34:22: 33000000 INFO @ Thu, 05 Apr 2018 10:34:24: 34000000 INFO @ Thu, 05 Apr 2018 10:34:24: 34000000 INFO @ Thu, 05 Apr 2018 10:34:28: 34000000 INFO @ Thu, 05 Apr 2018 10:34:29: 35000000 INFO @ Thu, 05 Apr 2018 10:34:30: 35000000 INFO @ Thu, 05 Apr 2018 10:34:34: 35000000 INFO @ Thu, 05 Apr 2018 10:34:35: 36000000 INFO @ Thu, 05 Apr 2018 10:34:35: 36000000 INFO @ Thu, 05 Apr 2018 10:34:40: 36000000 INFO @ Thu, 05 Apr 2018 10:34:40: 37000000 INFO @ Thu, 05 Apr 2018 10:34:41: 37000000 INFO @ Thu, 05 Apr 2018 10:34:43: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:34:43: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:34:43: #1 total tags in treatment: 18530349 INFO @ Thu, 05 Apr 2018 10:34:43: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:34:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Apr 2018 10:34:44: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:34:44: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:34:44: #1 total tags in treatment: 18530349 INFO @ Thu, 05 Apr 2018 10:34:44: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:34:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Apr 2018 10:34:44: #1 tags after filtering in treatment: 6903683 INFO @ Thu, 05 Apr 2018 10:34:44: #1 Redundant rate of treatment: 0.63 INFO @ Thu, 05 Apr 2018 10:34:44: #1 finished! INFO @ Thu, 05 Apr 2018 10:34:44: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:34:44: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:34:44: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:34:44: 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, 05 Apr 2018 10:34:44: Process for pairing-model is terminated! cat: SRX3671201.05_peaks.narrowPeak: そのようなファイルやディレクトリはありません INFO @ Thu, 05 Apr 2018 10:34:44: #1 tags after filtering in treatment: 6903683 INFO @ Thu, 05 Apr 2018 10:34:44: #1 Redundant rate of treatment: 0.63 INFO @ Thu, 05 Apr 2018 10:34:44: #1 finished! INFO @ Thu, 05 Apr 2018 10:34:44: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:34:44: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3671201.05_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 `SRX3671201.05_*.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 `SRX3671201.05_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 @ Thu, 05 Apr 2018 10:34:45: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:34:45: 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, 05 Apr 2018 10:34:45: Process for pairing-model is terminated! cat: SRX3671201.10_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 `SRX3671201.10_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 `SRX3671201.10_*.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 `SRX3671201.10_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, 05 Apr 2018 10:34:46: 37000000 INFO @ Thu, 05 Apr 2018 10:34:48: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:34:48: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:34:48: #1 total tags in treatment: 18530349 INFO @ Thu, 05 Apr 2018 10:34:48: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:34:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Apr 2018 10:34:49: #1 tags after filtering in treatment: 6903683 INFO @ Thu, 05 Apr 2018 10:34:49: #1 Redundant rate of treatment: 0.63 INFO @ Thu, 05 Apr 2018 10:34:49: #1 finished! INFO @ Thu, 05 Apr 2018 10:34:49: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:34:49: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:34:49: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:34:49: 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, 05 Apr 2018 10:34:49: Process for pairing-model is terminated! cat: SRX3671201.20_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 `SRX3671201.20_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 `SRX3671201.20_*.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 `SRX3671201.20_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。