Job ID = 10536519 sra ファイルのダウンロード中... Completed: 1434727K bytes transferred in 37 seconds (310844K 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 36759752 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3671212/SRR6696964.sra Written 36759752 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: 00:24:08 36759752 reads; of these: 36759752 (100.00%) were paired; of these: 8715299 (23.71%) aligned concordantly 0 times 24231337 (65.92%) aligned concordantly exactly 1 time 3813116 (10.37%) aligned concordantly >1 times ---- 8715299 pairs aligned concordantly 0 times; of these: 243012 (2.79%) aligned discordantly 1 time ---- 8472287 pairs aligned 0 times concordantly or discordantly; of these: 16944574 mates make up the pairs; of these: 16659247 (98.32%) aligned 0 times 135747 (0.80%) aligned exactly 1 time 149580 (0.88%) aligned >1 times 77.34% overall alignment rate Time searching: 00:24:08 Overall time: 00:24:08 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] 7908115 / 28217924 = 0.2803 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 10:40:51: # Command line: callpeak -t SRX3671212.bam -f BAM -g 12100000 -n SRX3671212.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3671212.05 # format = BAM # ChIP-seq file = ['SRX3671212.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 10:40:51: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:40:51: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:40:51: # Command line: callpeak -t SRX3671212.bam -f BAM -g 12100000 -n SRX3671212.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3671212.10 # format = BAM # ChIP-seq file = ['SRX3671212.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 10:40:51: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:40:51: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:40:51: # Command line: callpeak -t SRX3671212.bam -f BAM -g 12100000 -n SRX3671212.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3671212.20 # format = BAM # ChIP-seq file = ['SRX3671212.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 10:40:51: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:40:51: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:40:57: 1000000 INFO @ Thu, 05 Apr 2018 10:40:58: 1000000 INFO @ Thu, 05 Apr 2018 10:40:58: 1000000 INFO @ Thu, 05 Apr 2018 10:41:03: 2000000 INFO @ Thu, 05 Apr 2018 10:41:03: 2000000 INFO @ Thu, 05 Apr 2018 10:41:03: 2000000 INFO @ Thu, 05 Apr 2018 10:41:08: 3000000 INFO @ Thu, 05 Apr 2018 10:41:09: 3000000 INFO @ Thu, 05 Apr 2018 10:41:09: 3000000 INFO @ Thu, 05 Apr 2018 10:41:17: 4000000 INFO @ Thu, 05 Apr 2018 10:41:18: 4000000 INFO @ Thu, 05 Apr 2018 10:41:18: 4000000 INFO @ Thu, 05 Apr 2018 10:41:23: 5000000 INFO @ Thu, 05 Apr 2018 10:41:23: 5000000 INFO @ Thu, 05 Apr 2018 10:41:24: 5000000 INFO @ Thu, 05 Apr 2018 10:41:29: 6000000 INFO @ Thu, 05 Apr 2018 10:41:29: 6000000 INFO @ Thu, 05 Apr 2018 10:41:29: 6000000 INFO @ Thu, 05 Apr 2018 10:41:35: 7000000 INFO @ Thu, 05 Apr 2018 10:41:35: 7000000 INFO @ Thu, 05 Apr 2018 10:41:35: 7000000 INFO @ Thu, 05 Apr 2018 10:41:40: 8000000 INFO @ Thu, 05 Apr 2018 10:41:41: 8000000 INFO @ Thu, 05 Apr 2018 10:41:42: 8000000 INFO @ Thu, 05 Apr 2018 10:41:47: 9000000 INFO @ Thu, 05 Apr 2018 10:41:47: 9000000 INFO @ Thu, 05 Apr 2018 10:41:48: 9000000 INFO @ Thu, 05 Apr 2018 10:41:53: 10000000 INFO @ Thu, 05 Apr 2018 10:41:53: 10000000 INFO @ Thu, 05 Apr 2018 10:41:54: 10000000 INFO @ Thu, 05 Apr 2018 10:41:58: 11000000 INFO @ Thu, 05 Apr 2018 10:41:59: 11000000 INFO @ Thu, 05 Apr 2018 10:42:00: 11000000 INFO @ Thu, 05 Apr 2018 10:42:03: 12000000 INFO @ Thu, 05 Apr 2018 10:42:05: 12000000 INFO @ Thu, 05 Apr 2018 10:42:06: 12000000 INFO @ Thu, 05 Apr 2018 10:42:09: 13000000 INFO @ Thu, 05 Apr 2018 10:42:11: 13000000 INFO @ Thu, 05 Apr 2018 10:42:12: 13000000 INFO @ Thu, 05 Apr 2018 10:42:14: 14000000 INFO @ Thu, 05 Apr 2018 10:42:17: 14000000 INFO @ Thu, 05 Apr 2018 10:42:17: 14000000 INFO @ Thu, 05 Apr 2018 10:42:21: 15000000 INFO @ Thu, 05 Apr 2018 10:42:23: 15000000 INFO @ Thu, 05 Apr 2018 10:42:23: 15000000 INFO @ Thu, 05 Apr 2018 10:42:27: 16000000 INFO @ Thu, 05 Apr 2018 10:42:29: 16000000 INFO @ Thu, 05 Apr 2018 10:42:30: 16000000 INFO @ Thu, 05 Apr 2018 10:42:33: 17000000 INFO @ Thu, 05 Apr 2018 10:42:35: 17000000 INFO @ Thu, 05 Apr 2018 10:42:36: 17000000 INFO @ Thu, 05 Apr 2018 10:42:39: 18000000 INFO @ Thu, 05 Apr 2018 10:42:41: 18000000 INFO @ Thu, 05 Apr 2018 10:42:42: 18000000 INFO @ Thu, 05 Apr 2018 10:42:44: 19000000 INFO @ Thu, 05 Apr 2018 10:42:47: 19000000 INFO @ Thu, 05 Apr 2018 10:42:48: 19000000 INFO @ Thu, 05 Apr 2018 10:42:50: 20000000 INFO @ Thu, 05 Apr 2018 10:42:54: 20000000 INFO @ Thu, 05 Apr 2018 10:42:55: 20000000 INFO @ Thu, 05 Apr 2018 10:42:56: 21000000 INFO @ Thu, 05 Apr 2018 10:43:00: 21000000 INFO @ Thu, 05 Apr 2018 10:43:00: 21000000 INFO @ Thu, 05 Apr 2018 10:43:02: 22000000 INFO @ Thu, 05 Apr 2018 10:43:06: 22000000 INFO @ Thu, 05 Apr 2018 10:43:06: 22000000 INFO @ Thu, 05 Apr 2018 10:43:08: 23000000 INFO @ Thu, 05 Apr 2018 10:43:12: 23000000 INFO @ Thu, 05 Apr 2018 10:43:12: 23000000 INFO @ Thu, 05 Apr 2018 10:43:14: 24000000 INFO @ Thu, 05 Apr 2018 10:43:17: 24000000 INFO @ Thu, 05 Apr 2018 10:43:17: 24000000 INFO @ Thu, 05 Apr 2018 10:43:20: 25000000 INFO @ Thu, 05 Apr 2018 10:43:23: 25000000 INFO @ Thu, 05 Apr 2018 10:43:23: 25000000 INFO @ Thu, 05 Apr 2018 10:43:26: 26000000 INFO @ Thu, 05 Apr 2018 10:43:28: 26000000 INFO @ Thu, 05 Apr 2018 10:43:29: 26000000 INFO @ Thu, 05 Apr 2018 10:43:31: 27000000 INFO @ Thu, 05 Apr 2018 10:43:34: 27000000 INFO @ Thu, 05 Apr 2018 10:43:34: 27000000 INFO @ Thu, 05 Apr 2018 10:43:37: 28000000 INFO @ Thu, 05 Apr 2018 10:43:39: 28000000 INFO @ Thu, 05 Apr 2018 10:43:40: 28000000 INFO @ Thu, 05 Apr 2018 10:43:43: 29000000 INFO @ Thu, 05 Apr 2018 10:43:45: 29000000 INFO @ Thu, 05 Apr 2018 10:43:46: 29000000 INFO @ Thu, 05 Apr 2018 10:43:49: 30000000 INFO @ Thu, 05 Apr 2018 10:43:51: 30000000 INFO @ Thu, 05 Apr 2018 10:43:51: 30000000 INFO @ Thu, 05 Apr 2018 10:43:56: 31000000 INFO @ Thu, 05 Apr 2018 10:43:57: 31000000 INFO @ Thu, 05 Apr 2018 10:43:58: 31000000 INFO @ Thu, 05 Apr 2018 10:44:02: 32000000 INFO @ Thu, 05 Apr 2018 10:44:03: 32000000 INFO @ Thu, 05 Apr 2018 10:44:03: 32000000 INFO @ Thu, 05 Apr 2018 10:44:07: 33000000 INFO @ Thu, 05 Apr 2018 10:44:08: 33000000 INFO @ Thu, 05 Apr 2018 10:44:09: 33000000 INFO @ Thu, 05 Apr 2018 10:44:13: 34000000 INFO @ Thu, 05 Apr 2018 10:44:14: 34000000 INFO @ Thu, 05 Apr 2018 10:44:14: 34000000 INFO @ Thu, 05 Apr 2018 10:44:19: 35000000 INFO @ Thu, 05 Apr 2018 10:44:19: 35000000 INFO @ Thu, 05 Apr 2018 10:44:20: 35000000 INFO @ Thu, 05 Apr 2018 10:44:25: 36000000 INFO @ Thu, 05 Apr 2018 10:44:25: 36000000 INFO @ Thu, 05 Apr 2018 10:44:26: 36000000 INFO @ Thu, 05 Apr 2018 10:44:30: 37000000 INFO @ Thu, 05 Apr 2018 10:44:31: 37000000 INFO @ Thu, 05 Apr 2018 10:44:32: 37000000 INFO @ Thu, 05 Apr 2018 10:44:36: 38000000 INFO @ Thu, 05 Apr 2018 10:44:37: 38000000 INFO @ Thu, 05 Apr 2018 10:44:38: 38000000 INFO @ Thu, 05 Apr 2018 10:44:42: 39000000 INFO @ Thu, 05 Apr 2018 10:44:43: 39000000 INFO @ Thu, 05 Apr 2018 10:44:44: 39000000 INFO @ Thu, 05 Apr 2018 10:44:48: 40000000 INFO @ Thu, 05 Apr 2018 10:44:48: 40000000 INFO @ Thu, 05 Apr 2018 10:44:50: 40000000 INFO @ Thu, 05 Apr 2018 10:44:53: 41000000 INFO @ Thu, 05 Apr 2018 10:44:54: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:44:54: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:44:54: #1 total tags in treatment: 20206484 INFO @ Thu, 05 Apr 2018 10:44:54: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:44:54: #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 10:44:54: 41000000 INFO @ Thu, 05 Apr 2018 10:44:54: #1 tags after filtering in treatment: 7326113 INFO @ Thu, 05 Apr 2018 10:44:54: #1 Redundant rate of treatment: 0.64 INFO @ Thu, 05 Apr 2018 10:44:54: #1 finished! INFO @ Thu, 05 Apr 2018 10:44:54: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:44:54: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 05 Apr 2018 10:44:54: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:44:54: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:44:54: #1 total tags in treatment: 20206484 INFO @ Thu, 05 Apr 2018 10:44:54: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:44:54: #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 10:44:54: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:44:54: 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 10:44:54: Process for pairing-model is terminated! cat: SRX3671212.10_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 `SRX3671212.10_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 `SRX3671212.10_*.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 `SRX3671212.10_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 10:44:55: #1 tags after filtering in treatment: 7326113 INFO @ Thu, 05 Apr 2018 10:44:55: #1 Redundant rate of treatment: 0.64 INFO @ Thu, 05 Apr 2018 10:44:55: #1 finished! INFO @ Thu, 05 Apr 2018 10:44:55: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:44:55: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:44:55: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:44:55: 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 10:44:55: Process for pairing-model is terminated! cat: SRX3671212.20_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 `SRX3671212.20_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 `SRX3671212.20_*.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 `SRX3671212.20_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 10:44:55: 41000000 INFO @ Thu, 05 Apr 2018 10:44:56: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:44:56: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:44:56: #1 total tags in treatment: 20206484 INFO @ Thu, 05 Apr 2018 10:44:56: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:44:56: #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 10:44:56: #1 tags after filtering in treatment: 7326113 INFO @ Thu, 05 Apr 2018 10:44:56: #1 Redundant rate of treatment: 0.64 INFO @ Thu, 05 Apr 2018 10:44:56: #1 finished! INFO @ Thu, 05 Apr 2018 10:44:56: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:44:56: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:44:57: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:44:57: 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 10:44:57: Process for pairing-model is terminated! cat: SRX3671212.05_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 `SRX3671212.05_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 `SRX3671212.05_*.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 `SRX3671212.05_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 BigWig に変換しました。