Job ID = 9161694 sra ファイルのダウンロード中... Completed: 858348K bytes transferred in 13 seconds (535236K 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 23837846 spots for /home/okishinya/chipatlas/results/sacCer3/SRX079677/SRR292348.sra Written 23837846 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: 00:14:41 23837846 reads; of these: 23837846 (100.00%) were paired; of these: 10230981 (42.92%) aligned concordantly 0 times 10725090 (44.99%) aligned concordantly exactly 1 time 2881775 (12.09%) aligned concordantly >1 times ---- 10230981 pairs aligned concordantly 0 times; of these: 1748821 (17.09%) aligned discordantly 1 time ---- 8482160 pairs aligned 0 times concordantly or discordantly; of these: 16964320 mates make up the pairs; of these: 13266916 (78.20%) aligned 0 times 985888 (5.81%) aligned exactly 1 time 2711516 (15.98%) aligned >1 times 72.17% overall alignment rate Time searching: 00:14:41 Overall time: 00:14:41 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 12 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] 4051058 / 14980813 = 0.2704 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 04:44:15: # Command line: callpeak -t SRX079677.bam -f BAM -g 12100000 -n SRX079677.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX079677.10 # format = BAM # ChIP-seq file = ['SRX079677.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 04:44:15: #1 read tag files... INFO @ Wed, 28 Jun 2017 04:44:15: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 04:44:15: # Command line: callpeak -t SRX079677.bam -f BAM -g 12100000 -n SRX079677.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX079677.05 # format = BAM # ChIP-seq file = ['SRX079677.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 04:44:15: #1 read tag files... INFO @ Wed, 28 Jun 2017 04:44:15: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 04:44:15: # Command line: callpeak -t SRX079677.bam -f BAM -g 12100000 -n SRX079677.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX079677.20 # format = BAM # ChIP-seq file = ['SRX079677.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 04:44:15: #1 read tag files... INFO @ Wed, 28 Jun 2017 04:44:15: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 04:44:22: 1000000 INFO @ Wed, 28 Jun 2017 04:44:23: 1000000 INFO @ Wed, 28 Jun 2017 04:44:23: 1000000 INFO @ Wed, 28 Jun 2017 04:44:29: 2000000 INFO @ Wed, 28 Jun 2017 04:44:30: 2000000 INFO @ Wed, 28 Jun 2017 04:44:30: 2000000 INFO @ Wed, 28 Jun 2017 04:44:36: 3000000 INFO @ Wed, 28 Jun 2017 04:44:38: 3000000 INFO @ Wed, 28 Jun 2017 04:44:38: 3000000 INFO @ Wed, 28 Jun 2017 04:44:44: 4000000 INFO @ Wed, 28 Jun 2017 04:44:46: 4000000 INFO @ Wed, 28 Jun 2017 04:44:46: 4000000 INFO @ Wed, 28 Jun 2017 04:44:51: 5000000 INFO @ Wed, 28 Jun 2017 04:44:54: 5000000 INFO @ Wed, 28 Jun 2017 04:44:54: 5000000 INFO @ Wed, 28 Jun 2017 04:44:59: 6000000 INFO @ Wed, 28 Jun 2017 04:45:01: 6000000 INFO @ Wed, 28 Jun 2017 04:45:03: 6000000 INFO @ Wed, 28 Jun 2017 04:45:06: 7000000 INFO @ Wed, 28 Jun 2017 04:45:09: 7000000 INFO @ Wed, 28 Jun 2017 04:45:11: 7000000 INFO @ Wed, 28 Jun 2017 04:45:14: 8000000 INFO @ Wed, 28 Jun 2017 04:45:16: 8000000 INFO @ Wed, 28 Jun 2017 04:45:20: 8000000 INFO @ Wed, 28 Jun 2017 04:45:22: 9000000 INFO @ Wed, 28 Jun 2017 04:45:23: 9000000 INFO @ Wed, 28 Jun 2017 04:45:29: 9000000 INFO @ Wed, 28 Jun 2017 04:45:29: 10000000 INFO @ Wed, 28 Jun 2017 04:45:30: 10000000 INFO @ Wed, 28 Jun 2017 04:45:37: 11000000 INFO @ Wed, 28 Jun 2017 04:45:37: 11000000 INFO @ Wed, 28 Jun 2017 04:45:38: 10000000 INFO @ Wed, 28 Jun 2017 04:45:44: 12000000 INFO @ Wed, 28 Jun 2017 04:45:45: 12000000 INFO @ Wed, 28 Jun 2017 04:45:46: 11000000 INFO @ Wed, 28 Jun 2017 04:45:52: 13000000 INFO @ Wed, 28 Jun 2017 04:45:52: 13000000 INFO @ Wed, 28 Jun 2017 04:45:54: 12000000 INFO @ Wed, 28 Jun 2017 04:45:59: 14000000 INFO @ Wed, 28 Jun 2017 04:45:59: 14000000 INFO @ Wed, 28 Jun 2017 04:46:01: 13000000 INFO @ Wed, 28 Jun 2017 04:46:06: 15000000 INFO @ Wed, 28 Jun 2017 04:46:06: 15000000 INFO @ Wed, 28 Jun 2017 04:46:09: 14000000 INFO @ Wed, 28 Jun 2017 04:46:12: 16000000 INFO @ Wed, 28 Jun 2017 04:46:13: 16000000 INFO @ Wed, 28 Jun 2017 04:46:16: 15000000 INFO @ Wed, 28 Jun 2017 04:46:19: 17000000 INFO @ Wed, 28 Jun 2017 04:46:20: 17000000 INFO @ Wed, 28 Jun 2017 04:46:23: 16000000 INFO @ Wed, 28 Jun 2017 04:46:26: 18000000 INFO @ Wed, 28 Jun 2017 04:46:27: 18000000 INFO @ Wed, 28 Jun 2017 04:46:31: 17000000 INFO @ Wed, 28 Jun 2017 04:46:33: 19000000 INFO @ Wed, 28 Jun 2017 04:46:35: 19000000 INFO @ Wed, 28 Jun 2017 04:46:38: 18000000 INFO @ Wed, 28 Jun 2017 04:46:40: 20000000 INFO @ Wed, 28 Jun 2017 04:46:42: 20000000 INFO @ Wed, 28 Jun 2017 04:46:46: 19000000 INFO @ Wed, 28 Jun 2017 04:46:47: 21000000 INFO @ Wed, 28 Jun 2017 04:46:48: 21000000 INFO @ Wed, 28 Jun 2017 04:46:53: 20000000 INFO @ Wed, 28 Jun 2017 04:46:54: 22000000 INFO @ Wed, 28 Jun 2017 04:46:54: 22000000 INFO @ Wed, 28 Jun 2017 04:47:00: 23000000 INFO @ Wed, 28 Jun 2017 04:47:00: 21000000 INFO @ Wed, 28 Jun 2017 04:47:01: 23000000 INFO @ Wed, 28 Jun 2017 04:47:06: 24000000 INFO @ Wed, 28 Jun 2017 04:47:07: 22000000 INFO @ Wed, 28 Jun 2017 04:47:08: 24000000 INFO @ Wed, 28 Jun 2017 04:47:11: 25000000 INFO @ Wed, 28 Jun 2017 04:47:15: 23000000 INFO @ Wed, 28 Jun 2017 04:47:15: 25000000 INFO @ Wed, 28 Jun 2017 04:47:18: 26000000 INFO @ Wed, 28 Jun 2017 04:47:20: #1 tag size is determined as 36 bps INFO @ Wed, 28 Jun 2017 04:47:20: #1 tag size = 36 INFO @ Wed, 28 Jun 2017 04:47:20: #1 total tags in treatment: 10331147 INFO @ Wed, 28 Jun 2017 04:47:20: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 04:47:20: #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 04:47:20: #1 tags after filtering in treatment: 5349112 INFO @ Wed, 28 Jun 2017 04:47:20: #1 Redundant rate of treatment: 0.48 INFO @ Wed, 28 Jun 2017 04:47:20: #1 finished! INFO @ Wed, 28 Jun 2017 04:47:20: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 04:47:20: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 04:47:21: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 04:47:21: 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 04:47:21: Process for pairing-model is terminated! cat: SRX079677.20_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 `SRX079677.20_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 `SRX079677.20_*.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 `SRX079677.20_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 04:47:23: 26000000 INFO @ Wed, 28 Jun 2017 04:47:23: 24000000 INFO @ Wed, 28 Jun 2017 04:47:25: #1 tag size is determined as 36 bps INFO @ Wed, 28 Jun 2017 04:47:25: #1 tag size = 36 INFO @ Wed, 28 Jun 2017 04:47:25: #1 total tags in treatment: 10331147 INFO @ Wed, 28 Jun 2017 04:47:25: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 04:47:25: #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 04:47:25: #1 tags after filtering in treatment: 5349112 INFO @ Wed, 28 Jun 2017 04:47:25: #1 Redundant rate of treatment: 0.48 INFO @ Wed, 28 Jun 2017 04:47:25: #1 finished! INFO @ Wed, 28 Jun 2017 04:47:25: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 04:47:25: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 04:47:25: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 04:47:25: 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 04:47:25: Process for pairing-model is terminated! cat: SRX079677.10_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 `SRX079677.10_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 `SRX079677.10_*.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 `SRX079677.10_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... INFO @ Wed, 28 Jun 2017 04:47:31: 25000000 INFO @ Wed, 28 Jun 2017 04:47:39: 26000000 INFO @ Wed, 28 Jun 2017 04:47:41: #1 tag size is determined as 36 bps INFO @ Wed, 28 Jun 2017 04:47:41: #1 tag size = 36 INFO @ Wed, 28 Jun 2017 04:47:41: #1 total tags in treatment: 10331147 INFO @ Wed, 28 Jun 2017 04:47:41: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 04:47:41: #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 04:47:41: #1 tags after filtering in treatment: 5349112 INFO @ Wed, 28 Jun 2017 04:47:41: #1 Redundant rate of treatment: 0.48 INFO @ Wed, 28 Jun 2017 04:47:41: #1 finished! INFO @ Wed, 28 Jun 2017 04:47:41: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 04:47:41: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 04:47:42: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 04:47:42: 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 04:47:42: Process for pairing-model is terminated! cat: SRX079677.05_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 `SRX079677.05_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 `SRX079677.05_*.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 `SRX079677.05_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。