Job ID = 10536498 sra ファイルのダウンロード中... Completed: 1469762K bytes transferred in 64 seconds (187427K 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 37992704 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3671194/SRR6696946.sra Written 37992704 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: 00:25:02 37992704 reads; of these: 37992704 (100.00%) were paired; of these: 6577632 (17.31%) aligned concordantly 0 times 27756865 (73.06%) aligned concordantly exactly 1 time 3658207 (9.63%) aligned concordantly >1 times ---- 6577632 pairs aligned concordantly 0 times; of these: 276980 (4.21%) aligned discordantly 1 time ---- 6300652 pairs aligned 0 times concordantly or discordantly; of these: 12601304 mates make up the pairs; of these: 12337590 (97.91%) aligned 0 times 131879 (1.05%) aligned exactly 1 time 131835 (1.05%) aligned >1 times 83.76% overall alignment rate Time searching: 00:25:02 Overall time: 00:25:02 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] 9704789 / 31607418 = 0.3070 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 10:29:15: # Command line: callpeak -t SRX3671194.bam -f BAM -g 12100000 -n SRX3671194.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3671194.10 # format = BAM # ChIP-seq file = ['SRX3671194.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 10:29:15: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:29:15: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:29:15: # Command line: callpeak -t SRX3671194.bam -f BAM -g 12100000 -n SRX3671194.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3671194.05 # format = BAM # ChIP-seq file = ['SRX3671194.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 10:29:15: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:29:15: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:29:15: # Command line: callpeak -t SRX3671194.bam -f BAM -g 12100000 -n SRX3671194.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3671194.20 # format = BAM # ChIP-seq file = ['SRX3671194.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 10:29:15: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:29:15: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:29:20: 1000000 INFO @ Thu, 05 Apr 2018 10:29:20: 1000000 INFO @ Thu, 05 Apr 2018 10:29:20: 1000000 INFO @ Thu, 05 Apr 2018 10:29:26: 2000000 INFO @ Thu, 05 Apr 2018 10:29:26: 2000000 INFO @ Thu, 05 Apr 2018 10:29:26: 2000000 INFO @ Thu, 05 Apr 2018 10:29:31: 3000000 INFO @ Thu, 05 Apr 2018 10:29:31: 3000000 INFO @ Thu, 05 Apr 2018 10:29:31: 3000000 INFO @ Thu, 05 Apr 2018 10:29:36: 4000000 INFO @ Thu, 05 Apr 2018 10:29:37: 4000000 INFO @ Thu, 05 Apr 2018 10:29:38: 4000000 INFO @ Thu, 05 Apr 2018 10:29:42: 5000000 INFO @ Thu, 05 Apr 2018 10:29:42: 5000000 INFO @ Thu, 05 Apr 2018 10:29:44: 5000000 INFO @ Thu, 05 Apr 2018 10:29:48: 6000000 INFO @ Thu, 05 Apr 2018 10:29:48: 6000000 INFO @ Thu, 05 Apr 2018 10:29:51: 6000000 INFO @ Thu, 05 Apr 2018 10:29:53: 7000000 INFO @ Thu, 05 Apr 2018 10:29:54: 7000000 INFO @ Thu, 05 Apr 2018 10:29:56: 7000000 INFO @ Thu, 05 Apr 2018 10:29:59: 8000000 INFO @ Thu, 05 Apr 2018 10:29:59: 8000000 INFO @ Thu, 05 Apr 2018 10:30:02: 8000000 INFO @ Thu, 05 Apr 2018 10:30:04: 9000000 INFO @ Thu, 05 Apr 2018 10:30:05: 9000000 INFO @ Thu, 05 Apr 2018 10:30:07: 9000000 INFO @ Thu, 05 Apr 2018 10:30:09: 10000000 INFO @ Thu, 05 Apr 2018 10:30:10: 10000000 INFO @ Thu, 05 Apr 2018 10:30:13: 10000000 INFO @ Thu, 05 Apr 2018 10:30:15: 11000000 INFO @ Thu, 05 Apr 2018 10:30:16: 11000000 INFO @ Thu, 05 Apr 2018 10:30:18: 11000000 INFO @ Thu, 05 Apr 2018 10:30:20: 12000000 INFO @ Thu, 05 Apr 2018 10:30:21: 12000000 INFO @ Thu, 05 Apr 2018 10:30:23: 12000000 INFO @ Thu, 05 Apr 2018 10:30:25: 13000000 INFO @ Thu, 05 Apr 2018 10:30:27: 13000000 INFO @ Thu, 05 Apr 2018 10:30:29: 13000000 INFO @ Thu, 05 Apr 2018 10:30:31: 14000000 INFO @ Thu, 05 Apr 2018 10:30:32: 14000000 INFO @ Thu, 05 Apr 2018 10:30:34: 14000000 INFO @ Thu, 05 Apr 2018 10:30:36: 15000000 INFO @ Thu, 05 Apr 2018 10:30:38: 15000000 INFO @ Thu, 05 Apr 2018 10:30:39: 15000000 INFO @ Thu, 05 Apr 2018 10:30:41: 16000000 INFO @ Thu, 05 Apr 2018 10:30:43: 16000000 INFO @ Thu, 05 Apr 2018 10:30:45: 16000000 INFO @ Thu, 05 Apr 2018 10:30:47: 17000000 INFO @ Thu, 05 Apr 2018 10:30:48: 17000000 INFO @ Thu, 05 Apr 2018 10:30:50: 17000000 INFO @ Thu, 05 Apr 2018 10:30:52: 18000000 INFO @ Thu, 05 Apr 2018 10:30:54: 18000000 INFO @ Thu, 05 Apr 2018 10:30:56: 18000000 INFO @ Thu, 05 Apr 2018 10:30:57: 19000000 INFO @ Thu, 05 Apr 2018 10:30:59: 19000000 INFO @ Thu, 05 Apr 2018 10:31:01: 19000000 INFO @ Thu, 05 Apr 2018 10:31:03: 20000000 INFO @ Thu, 05 Apr 2018 10:31:05: 20000000 INFO @ Thu, 05 Apr 2018 10:31:06: 20000000 INFO @ Thu, 05 Apr 2018 10:31:08: 21000000 INFO @ Thu, 05 Apr 2018 10:31:10: 21000000 INFO @ Thu, 05 Apr 2018 10:31:12: 21000000 INFO @ Thu, 05 Apr 2018 10:31:13: 22000000 INFO @ Thu, 05 Apr 2018 10:31:16: 22000000 INFO @ Thu, 05 Apr 2018 10:31:17: 22000000 INFO @ Thu, 05 Apr 2018 10:31:19: 23000000 INFO @ Thu, 05 Apr 2018 10:31:21: 23000000 INFO @ Thu, 05 Apr 2018 10:31:23: 23000000 INFO @ Thu, 05 Apr 2018 10:31:24: 24000000 INFO @ Thu, 05 Apr 2018 10:31:27: 24000000 INFO @ Thu, 05 Apr 2018 10:31:28: 24000000 INFO @ Thu, 05 Apr 2018 10:31:29: 25000000 INFO @ Thu, 05 Apr 2018 10:31:32: 25000000 INFO @ Thu, 05 Apr 2018 10:31:33: 25000000 INFO @ Thu, 05 Apr 2018 10:31:35: 26000000 INFO @ Thu, 05 Apr 2018 10:31:38: 26000000 INFO @ Thu, 05 Apr 2018 10:31:39: 26000000 INFO @ Thu, 05 Apr 2018 10:31:40: 27000000 INFO @ Thu, 05 Apr 2018 10:31:43: 27000000 INFO @ Thu, 05 Apr 2018 10:31:45: 27000000 INFO @ Thu, 05 Apr 2018 10:31:45: 28000000 INFO @ Thu, 05 Apr 2018 10:31:48: 28000000 INFO @ Thu, 05 Apr 2018 10:31:50: 28000000 INFO @ Thu, 05 Apr 2018 10:31:51: 29000000 INFO @ Thu, 05 Apr 2018 10:31:54: 29000000 INFO @ Thu, 05 Apr 2018 10:31:55: 29000000 INFO @ Thu, 05 Apr 2018 10:31:56: 30000000 INFO @ Thu, 05 Apr 2018 10:31:59: 30000000 INFO @ Thu, 05 Apr 2018 10:32:01: 30000000 INFO @ Thu, 05 Apr 2018 10:32:01: 31000000 INFO @ Thu, 05 Apr 2018 10:32:05: 31000000 INFO @ Thu, 05 Apr 2018 10:32:06: 31000000 INFO @ Thu, 05 Apr 2018 10:32:07: 32000000 INFO @ Thu, 05 Apr 2018 10:32:10: 32000000 INFO @ Thu, 05 Apr 2018 10:32:11: 32000000 INFO @ Thu, 05 Apr 2018 10:32:12: 33000000 INFO @ Thu, 05 Apr 2018 10:32:15: 33000000 INFO @ Thu, 05 Apr 2018 10:32:17: 33000000 INFO @ Thu, 05 Apr 2018 10:32:17: 34000000 INFO @ Thu, 05 Apr 2018 10:32:21: 34000000 INFO @ Thu, 05 Apr 2018 10:32:22: 34000000 INFO @ Thu, 05 Apr 2018 10:32:22: 35000000 INFO @ Thu, 05 Apr 2018 10:32:26: 35000000 INFO @ Thu, 05 Apr 2018 10:32:27: 35000000 INFO @ Thu, 05 Apr 2018 10:32:28: 36000000 INFO @ Thu, 05 Apr 2018 10:32:32: 36000000 INFO @ Thu, 05 Apr 2018 10:32:33: 36000000 INFO @ Thu, 05 Apr 2018 10:32:33: 37000000 INFO @ Thu, 05 Apr 2018 10:32:37: 37000000 INFO @ Thu, 05 Apr 2018 10:32:38: 37000000 INFO @ Thu, 05 Apr 2018 10:32:38: 38000000 INFO @ Thu, 05 Apr 2018 10:32:42: 38000000 INFO @ Thu, 05 Apr 2018 10:32:43: 38000000 INFO @ Thu, 05 Apr 2018 10:32:44: 39000000 INFO @ Thu, 05 Apr 2018 10:32:48: 39000000 INFO @ Thu, 05 Apr 2018 10:32:49: 39000000 INFO @ Thu, 05 Apr 2018 10:32:49: 40000000 INFO @ Thu, 05 Apr 2018 10:32:53: 40000000 INFO @ Thu, 05 Apr 2018 10:32:54: 40000000 INFO @ Thu, 05 Apr 2018 10:32:54: 41000000 INFO @ Thu, 05 Apr 2018 10:32:59: 41000000 INFO @ Thu, 05 Apr 2018 10:32:59: 41000000 INFO @ Thu, 05 Apr 2018 10:32:59: 42000000 INFO @ Thu, 05 Apr 2018 10:33:04: 42000000 INFO @ Thu, 05 Apr 2018 10:33:05: 42000000 INFO @ Thu, 05 Apr 2018 10:33:05: 43000000 INFO @ Thu, 05 Apr 2018 10:33:10: 43000000 INFO @ Thu, 05 Apr 2018 10:33:10: 44000000 INFO @ Thu, 05 Apr 2018 10:33:10: 43000000 INFO @ Thu, 05 Apr 2018 10:33:12: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:33:12: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:33:12: #1 total tags in treatment: 21794344 INFO @ Thu, 05 Apr 2018 10:33:12: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:33:12: #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 10:33:12: #1 tags after filtering in treatment: 7576841 INFO @ Thu, 05 Apr 2018 10:33:12: #1 Redundant rate of treatment: 0.65 INFO @ Thu, 05 Apr 2018 10:33:12: #1 finished! INFO @ Thu, 05 Apr 2018 10:33:12: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:33:12: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:33:13: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:33:13: 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 10:33:13: Process for pairing-model is terminated! cat: SRX3671194.10_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 `SRX3671194.10_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 `SRX3671194.10_*.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 `SRX3671194.10_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 10:33:15: 44000000 INFO @ Thu, 05 Apr 2018 10:33:15: 44000000 INFO @ Thu, 05 Apr 2018 10:33:16: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:33:16: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:33:16: #1 total tags in treatment: 21794344 INFO @ Thu, 05 Apr 2018 10:33:16: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:33:16: #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 10:33:17: #1 tags after filtering in treatment: 7576841 INFO @ Thu, 05 Apr 2018 10:33:17: #1 Redundant rate of treatment: 0.65 INFO @ Thu, 05 Apr 2018 10:33:17: #1 finished! INFO @ Thu, 05 Apr 2018 10:33:17: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:33:17: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:33:17: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:33:17: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:33:17: #1 total tags in treatment: 21794344 INFO @ Thu, 05 Apr 2018 10:33:17: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:33:17: #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 10:33:17: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:33:17: 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 10:33:17: Process for pairing-model is terminated! cat: SRX3671194.05_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 `SRX3671194.05_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 `SRX3671194.05_*.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 `SRX3671194.05_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 10:33:18: #1 tags after filtering in treatment: 7576841 INFO @ Thu, 05 Apr 2018 10:33:18: #1 Redundant rate of treatment: 0.65 INFO @ Thu, 05 Apr 2018 10:33:18: #1 finished! INFO @ Thu, 05 Apr 2018 10:33:18: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:33:18: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:33:18: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:33:18: 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 10:33:18: Process for pairing-model is terminated! cat: SRX3671194.20_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 `SRX3671194.20_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 `SRX3671194.20_*.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 `SRX3671194.20_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。