Job ID = 10536366 sra ファイルのダウンロード中... Completed: 1142086K bytes transferred in 26 seconds (357499K 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 32358686 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3433228/SRR6333869.sra Written 32358686 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: 00:26:00 32358686 reads; of these: 32358686 (100.00%) were paired; of these: 5308077 (16.40%) aligned concordantly 0 times 24778576 (76.57%) aligned concordantly exactly 1 time 2272033 (7.02%) aligned concordantly >1 times ---- 5308077 pairs aligned concordantly 0 times; of these: 2154056 (40.58%) aligned discordantly 1 time ---- 3154021 pairs aligned 0 times concordantly or discordantly; of these: 6308042 mates make up the pairs; of these: 3816626 (60.50%) aligned 0 times 1962711 (31.11%) aligned exactly 1 time 528705 (8.38%) aligned >1 times 94.10% overall alignment rate Time searching: 00:26:00 Overall time: 00:26:01 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] 6563987 / 27225199 = 0.2411 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 09:40:16: # Command line: callpeak -t SRX3433228.bam -f BAM -g 12100000 -n SRX3433228.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3433228.05 # format = BAM # ChIP-seq file = ['SRX3433228.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 09:40:16: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:40:16: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:40:16: # Command line: callpeak -t SRX3433228.bam -f BAM -g 12100000 -n SRX3433228.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3433228.10 # format = BAM # ChIP-seq file = ['SRX3433228.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 09:40:16: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:40:16: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:40:16: # Command line: callpeak -t SRX3433228.bam -f BAM -g 12100000 -n SRX3433228.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3433228.20 # format = BAM # ChIP-seq file = ['SRX3433228.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 09:40:16: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:40:16: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:40:22: 1000000 INFO @ Thu, 05 Apr 2018 09:40:22: 1000000 INFO @ Thu, 05 Apr 2018 09:40:22: 1000000 INFO @ Thu, 05 Apr 2018 09:40:27: 2000000 INFO @ Thu, 05 Apr 2018 09:40:27: 2000000 INFO @ Thu, 05 Apr 2018 09:40:28: 2000000 INFO @ Thu, 05 Apr 2018 09:40:33: 3000000 INFO @ Thu, 05 Apr 2018 09:40:34: 3000000 INFO @ Thu, 05 Apr 2018 09:40:35: 3000000 INFO @ Thu, 05 Apr 2018 09:40:39: 4000000 INFO @ Thu, 05 Apr 2018 09:40:40: 4000000 INFO @ Thu, 05 Apr 2018 09:40:41: 4000000 INFO @ Thu, 05 Apr 2018 09:40:45: 5000000 INFO @ Thu, 05 Apr 2018 09:40:46: 5000000 INFO @ Thu, 05 Apr 2018 09:40:47: 5000000 INFO @ Thu, 05 Apr 2018 09:40:51: 6000000 INFO @ Thu, 05 Apr 2018 09:40:51: 6000000 INFO @ Thu, 05 Apr 2018 09:40:53: 6000000 INFO @ Thu, 05 Apr 2018 09:40:57: 7000000 INFO @ Thu, 05 Apr 2018 09:40:57: 7000000 INFO @ Thu, 05 Apr 2018 09:40:59: 7000000 INFO @ Thu, 05 Apr 2018 09:41:02: 8000000 INFO @ Thu, 05 Apr 2018 09:41:02: 8000000 INFO @ Thu, 05 Apr 2018 09:41:05: 8000000 INFO @ Thu, 05 Apr 2018 09:41:07: 9000000 INFO @ Thu, 05 Apr 2018 09:41:08: 9000000 INFO @ Thu, 05 Apr 2018 09:41:11: 9000000 INFO @ Thu, 05 Apr 2018 09:41:13: 10000000 INFO @ Thu, 05 Apr 2018 09:41:14: 10000000 INFO @ Thu, 05 Apr 2018 09:41:17: 10000000 INFO @ Thu, 05 Apr 2018 09:41:18: 11000000 INFO @ Thu, 05 Apr 2018 09:41:19: 11000000 INFO @ Thu, 05 Apr 2018 09:41:23: 11000000 INFO @ Thu, 05 Apr 2018 09:41:23: 12000000 INFO @ Thu, 05 Apr 2018 09:41:25: 12000000 INFO @ Thu, 05 Apr 2018 09:41:28: 13000000 INFO @ Thu, 05 Apr 2018 09:41:28: 12000000 INFO @ Thu, 05 Apr 2018 09:41:30: 13000000 INFO @ Thu, 05 Apr 2018 09:41:33: 14000000 INFO @ Thu, 05 Apr 2018 09:41:34: 13000000 INFO @ Thu, 05 Apr 2018 09:41:36: 14000000 INFO @ Thu, 05 Apr 2018 09:41:38: 15000000 INFO @ Thu, 05 Apr 2018 09:41:40: 14000000 INFO @ Thu, 05 Apr 2018 09:41:41: 15000000 INFO @ Thu, 05 Apr 2018 09:41:44: 16000000 INFO @ Thu, 05 Apr 2018 09:41:46: 15000000 INFO @ Thu, 05 Apr 2018 09:41:47: 16000000 INFO @ Thu, 05 Apr 2018 09:41:49: 17000000 INFO @ Thu, 05 Apr 2018 09:41:51: 16000000 INFO @ Thu, 05 Apr 2018 09:41:52: 17000000 INFO @ Thu, 05 Apr 2018 09:41:54: 18000000 INFO @ Thu, 05 Apr 2018 09:41:57: 17000000 INFO @ Thu, 05 Apr 2018 09:41:58: 18000000 INFO @ Thu, 05 Apr 2018 09:41:59: 19000000 INFO @ Thu, 05 Apr 2018 09:42:03: 18000000 INFO @ Thu, 05 Apr 2018 09:42:03: 19000000 INFO @ Thu, 05 Apr 2018 09:42:04: 20000000 INFO @ Thu, 05 Apr 2018 09:42:09: 19000000 INFO @ Thu, 05 Apr 2018 09:42:09: 20000000 INFO @ Thu, 05 Apr 2018 09:42:10: 21000000 INFO @ Thu, 05 Apr 2018 09:42:14: 20000000 INFO @ Thu, 05 Apr 2018 09:42:14: 21000000 INFO @ Thu, 05 Apr 2018 09:42:15: 22000000 INFO @ Thu, 05 Apr 2018 09:42:20: 23000000 INFO @ Thu, 05 Apr 2018 09:42:20: 22000000 INFO @ Thu, 05 Apr 2018 09:42:20: 21000000 INFO @ Thu, 05 Apr 2018 09:42:25: 24000000 INFO @ Thu, 05 Apr 2018 09:42:25: 23000000 INFO @ Thu, 05 Apr 2018 09:42:26: 22000000 INFO @ Thu, 05 Apr 2018 09:42:30: 25000000 INFO @ Thu, 05 Apr 2018 09:42:31: 24000000 INFO @ Thu, 05 Apr 2018 09:42:31: 23000000 INFO @ Thu, 05 Apr 2018 09:42:35: 26000000 INFO @ Thu, 05 Apr 2018 09:42:37: 25000000 INFO @ Thu, 05 Apr 2018 09:42:37: 24000000 INFO @ Thu, 05 Apr 2018 09:42:41: 27000000 INFO @ Thu, 05 Apr 2018 09:42:42: 26000000 INFO @ Thu, 05 Apr 2018 09:42:43: 25000000 INFO @ Thu, 05 Apr 2018 09:42:46: 28000000 INFO @ Thu, 05 Apr 2018 09:42:48: 27000000 INFO @ Thu, 05 Apr 2018 09:42:49: 26000000 INFO @ Thu, 05 Apr 2018 09:42:51: 29000000 INFO @ Thu, 05 Apr 2018 09:42:53: 28000000 INFO @ Thu, 05 Apr 2018 09:42:55: 27000000 INFO @ Thu, 05 Apr 2018 09:42:56: 30000000 INFO @ Thu, 05 Apr 2018 09:42:59: 29000000 INFO @ Thu, 05 Apr 2018 09:43:00: 28000000 INFO @ Thu, 05 Apr 2018 09:43:01: 31000000 INFO @ Thu, 05 Apr 2018 09:43:04: 30000000 INFO @ Thu, 05 Apr 2018 09:43:06: 29000000 INFO @ Thu, 05 Apr 2018 09:43:07: 32000000 INFO @ Thu, 05 Apr 2018 09:43:09: 31000000 INFO @ Thu, 05 Apr 2018 09:43:11: 30000000 INFO @ Thu, 05 Apr 2018 09:43:12: 33000000 INFO @ Thu, 05 Apr 2018 09:43:15: 32000000 INFO @ Thu, 05 Apr 2018 09:43:16: 31000000 INFO @ Thu, 05 Apr 2018 09:43:18: 34000000 INFO @ Thu, 05 Apr 2018 09:43:20: 33000000 INFO @ Thu, 05 Apr 2018 09:43:22: 32000000 INFO @ Thu, 05 Apr 2018 09:43:23: 35000000 INFO @ Thu, 05 Apr 2018 09:43:25: 34000000 INFO @ Thu, 05 Apr 2018 09:43:27: 33000000 INFO @ Thu, 05 Apr 2018 09:43:28: 36000000 INFO @ Thu, 05 Apr 2018 09:43:31: 35000000 INFO @ Thu, 05 Apr 2018 09:43:33: 34000000 INFO @ Thu, 05 Apr 2018 09:43:34: 37000000 INFO @ Thu, 05 Apr 2018 09:43:36: 36000000 INFO @ Thu, 05 Apr 2018 09:43:38: 35000000 INFO @ Thu, 05 Apr 2018 09:43:39: 38000000 INFO @ Thu, 05 Apr 2018 09:43:42: 37000000 INFO @ Thu, 05 Apr 2018 09:43:44: 39000000 INFO @ Thu, 05 Apr 2018 09:43:44: 36000000 INFO @ Thu, 05 Apr 2018 09:43:47: 38000000 INFO @ Thu, 05 Apr 2018 09:43:49: 40000000 INFO @ Thu, 05 Apr 2018 09:43:50: 37000000 INFO @ Thu, 05 Apr 2018 09:43:53: 39000000 INFO @ Thu, 05 Apr 2018 09:43:54: 41000000 INFO @ Thu, 05 Apr 2018 09:43:55: 38000000 INFO @ Thu, 05 Apr 2018 09:43:58: 40000000 INFO @ Thu, 05 Apr 2018 09:43:59: 42000000 INFO @ Thu, 05 Apr 2018 09:44:01: 39000000 INFO @ Thu, 05 Apr 2018 09:44:04: 41000000 INFO @ Thu, 05 Apr 2018 09:44:05: 43000000 INFO @ Thu, 05 Apr 2018 09:44:07: 40000000 INFO @ Thu, 05 Apr 2018 09:44:09: 42000000 INFO @ Thu, 05 Apr 2018 09:44:10: 44000000 INFO @ Thu, 05 Apr 2018 09:44:12: 41000000 INFO @ Thu, 05 Apr 2018 09:44:14: 43000000 INFO @ Thu, 05 Apr 2018 09:44:15: 45000000 INFO @ Thu, 05 Apr 2018 09:44:18: 42000000 INFO @ Thu, 05 Apr 2018 09:44:20: 44000000 INFO @ Thu, 05 Apr 2018 09:44:20: 46000000 INFO @ Thu, 05 Apr 2018 09:44:23: 43000000 INFO @ Thu, 05 Apr 2018 09:44:25: 45000000 INFO @ Thu, 05 Apr 2018 09:44:25: 47000000 INFO @ Thu, 05 Apr 2018 09:44:29: 44000000 INFO @ Thu, 05 Apr 2018 09:44:30: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:44:30: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:44:30: #1 total tags in treatment: 20528681 INFO @ Thu, 05 Apr 2018 09:44:30: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:44:30: #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 09:44:30: #1 tags after filtering in treatment: 11147826 INFO @ Thu, 05 Apr 2018 09:44:30: #1 Redundant rate of treatment: 0.46 INFO @ Thu, 05 Apr 2018 09:44:30: #1 finished! INFO @ Thu, 05 Apr 2018 09:44:30: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:44:30: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:44:30: 46000000 INFO @ Thu, 05 Apr 2018 09:44:31: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 09:44:31: 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 @ Thu, 05 Apr 2018 09:44:31: Process for pairing-model is terminated! cat: SRX3433228.20_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 `SRX3433228.20_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 `SRX3433228.20_*.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 `SRX3433228.20_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, 05 Apr 2018 09:44:34: 45000000 INFO @ Thu, 05 Apr 2018 09:44:36: 47000000 INFO @ Thu, 05 Apr 2018 09:44:40: 46000000 INFO @ Thu, 05 Apr 2018 09:44:40: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:44:40: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:44:40: #1 total tags in treatment: 20528681 INFO @ Thu, 05 Apr 2018 09:44:40: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:44:40: #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 09:44:40: #1 tags after filtering in treatment: 11147826 INFO @ Thu, 05 Apr 2018 09:44:40: #1 Redundant rate of treatment: 0.46 INFO @ Thu, 05 Apr 2018 09:44:40: #1 finished! INFO @ Thu, 05 Apr 2018 09:44:40: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:44:40: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:44:41: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 09:44:41: 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 09:44:41: Process for pairing-model is terminated! cat: SRX3433228.05_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 `SRX3433228.05_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 `SRX3433228.05_*.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 `SRX3433228.05_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 09:44:45: 47000000 INFO @ Thu, 05 Apr 2018 09:44:49: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:44:49: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:44:49: #1 total tags in treatment: 20528681 INFO @ Thu, 05 Apr 2018 09:44:49: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:44:49: #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 09:44:50: #1 tags after filtering in treatment: 11147826 INFO @ Thu, 05 Apr 2018 09:44:50: #1 Redundant rate of treatment: 0.46 INFO @ Thu, 05 Apr 2018 09:44:50: #1 finished! INFO @ Thu, 05 Apr 2018 09:44:50: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:44:50: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:44:50: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 09:44:50: 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 09:44:50: Process for pairing-model is terminated! cat: SRX3433228.10_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 `SRX3433228.10_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 `SRX3433228.10_*.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 `SRX3433228.10_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 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。