Job ID = 9162521 sra ファイルのダウンロード中... Completed: 969561K bytes transferred in 10 seconds (733405K 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 15716723 spots for /home/okishinya/chipatlas/results/sacCer3/SRX362242/SRR1005862.sra Written 15716723 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: 00:12:47 15716723 reads; of these: 15716723 (100.00%) were paired; of these: 1382239 (8.79%) aligned concordantly 0 times 11750164 (74.76%) aligned concordantly exactly 1 time 2584320 (16.44%) aligned concordantly >1 times ---- 1382239 pairs aligned concordantly 0 times; of these: 17983 (1.30%) aligned discordantly 1 time ---- 1364256 pairs aligned 0 times concordantly or discordantly; of these: 2728512 mates make up the pairs; of these: 2222116 (81.44%) aligned 0 times 344837 (12.64%) aligned exactly 1 time 161559 (5.92%) aligned >1 times 92.93% overall alignment rate Time searching: 00:12:47 Overall time: 00:12:47 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] 396927 / 14343849 = 0.0277 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 08:25:08: # Command line: callpeak -t SRX362242.bam -f BAM -g 12100000 -n SRX362242.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX362242.10 # format = BAM # ChIP-seq file = ['SRX362242.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 08:25:08: #1 read tag files... INFO @ Wed, 28 Jun 2017 08:25:08: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 08:25:08: # Command line: callpeak -t SRX362242.bam -f BAM -g 12100000 -n SRX362242.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX362242.05 # format = BAM # ChIP-seq file = ['SRX362242.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 08:25:08: #1 read tag files... INFO @ Wed, 28 Jun 2017 08:25:08: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 08:25:08: # Command line: callpeak -t SRX362242.bam -f BAM -g 12100000 -n SRX362242.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX362242.20 # format = BAM # ChIP-seq file = ['SRX362242.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 08:25:08: #1 read tag files... INFO @ Wed, 28 Jun 2017 08:25:08: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 08:25:13: 1000000 INFO @ Wed, 28 Jun 2017 08:25:15: 1000000 INFO @ Wed, 28 Jun 2017 08:25:15: 1000000 INFO @ Wed, 28 Jun 2017 08:25:19: 2000000 INFO @ Wed, 28 Jun 2017 08:25:21: 2000000 INFO @ Wed, 28 Jun 2017 08:25:21: 2000000 INFO @ Wed, 28 Jun 2017 08:25:25: 3000000 INFO @ Wed, 28 Jun 2017 08:25:28: 3000000 INFO @ Wed, 28 Jun 2017 08:25:28: 3000000 INFO @ Wed, 28 Jun 2017 08:25:30: 4000000 INFO @ Wed, 28 Jun 2017 08:25:35: 4000000 INFO @ Wed, 28 Jun 2017 08:25:35: 4000000 INFO @ Wed, 28 Jun 2017 08:25:36: 5000000 INFO @ Wed, 28 Jun 2017 08:25:41: 5000000 INFO @ Wed, 28 Jun 2017 08:25:41: 5000000 INFO @ Wed, 28 Jun 2017 08:25:42: 6000000 INFO @ Wed, 28 Jun 2017 08:25:47: 6000000 INFO @ Wed, 28 Jun 2017 08:25:47: 6000000 INFO @ Wed, 28 Jun 2017 08:25:48: 7000000 INFO @ Wed, 28 Jun 2017 08:25:53: 8000000 INFO @ Wed, 28 Jun 2017 08:25:54: 7000000 INFO @ Wed, 28 Jun 2017 08:25:54: 7000000 INFO @ Wed, 28 Jun 2017 08:25:59: 9000000 INFO @ Wed, 28 Jun 2017 08:26:00: 8000000 INFO @ Wed, 28 Jun 2017 08:26:00: 8000000 INFO @ Wed, 28 Jun 2017 08:26:05: 10000000 INFO @ Wed, 28 Jun 2017 08:26:07: 9000000 INFO @ Wed, 28 Jun 2017 08:26:07: 9000000 INFO @ Wed, 28 Jun 2017 08:26:10: 11000000 INFO @ Wed, 28 Jun 2017 08:26:13: 10000000 INFO @ Wed, 28 Jun 2017 08:26:13: 10000000 INFO @ Wed, 28 Jun 2017 08:26:16: 12000000 INFO @ Wed, 28 Jun 2017 08:26:19: 11000000 INFO @ Wed, 28 Jun 2017 08:26:19: 11000000 INFO @ Wed, 28 Jun 2017 08:26:21: 13000000 INFO @ Wed, 28 Jun 2017 08:26:25: 12000000 INFO @ Wed, 28 Jun 2017 08:26:25: 12000000 INFO @ Wed, 28 Jun 2017 08:26:27: 14000000 INFO @ Wed, 28 Jun 2017 08:26:31: 13000000 INFO @ Wed, 28 Jun 2017 08:26:31: 13000000 INFO @ Wed, 28 Jun 2017 08:26:33: 15000000 INFO @ Wed, 28 Jun 2017 08:26:37: 14000000 INFO @ Wed, 28 Jun 2017 08:26:37: 14000000 INFO @ Wed, 28 Jun 2017 08:26:39: 16000000 INFO @ Wed, 28 Jun 2017 08:26:42: 15000000 INFO @ Wed, 28 Jun 2017 08:26:42: 15000000 INFO @ Wed, 28 Jun 2017 08:26:44: 17000000 INFO @ Wed, 28 Jun 2017 08:26:48: 16000000 INFO @ Wed, 28 Jun 2017 08:26:48: 16000000 INFO @ Wed, 28 Jun 2017 08:26:50: 18000000 INFO @ Wed, 28 Jun 2017 08:26:55: 17000000 INFO @ Wed, 28 Jun 2017 08:26:55: 17000000 INFO @ Wed, 28 Jun 2017 08:26:56: 19000000 INFO @ Wed, 28 Jun 2017 08:27:00: 18000000 INFO @ Wed, 28 Jun 2017 08:27:00: 18000000 INFO @ Wed, 28 Jun 2017 08:27:01: 20000000 INFO @ Wed, 28 Jun 2017 08:27:06: 19000000 INFO @ Wed, 28 Jun 2017 08:27:06: 19000000 INFO @ Wed, 28 Jun 2017 08:27:07: 21000000 INFO @ Wed, 28 Jun 2017 08:27:12: 20000000 INFO @ Wed, 28 Jun 2017 08:27:12: 20000000 INFO @ Wed, 28 Jun 2017 08:27:12: 22000000 INFO @ Wed, 28 Jun 2017 08:27:18: 21000000 INFO @ Wed, 28 Jun 2017 08:27:18: 21000000 INFO @ Wed, 28 Jun 2017 08:27:18: 23000000 INFO @ Wed, 28 Jun 2017 08:27:24: 24000000 INFO @ Wed, 28 Jun 2017 08:27:25: 22000000 INFO @ Wed, 28 Jun 2017 08:27:25: 22000000 INFO @ Wed, 28 Jun 2017 08:27:31: 25000000 INFO @ Wed, 28 Jun 2017 08:27:33: 23000000 INFO @ Wed, 28 Jun 2017 08:27:33: 23000000 INFO @ Wed, 28 Jun 2017 08:27:39: 26000000 INFO @ Wed, 28 Jun 2017 08:27:41: 24000000 INFO @ Wed, 28 Jun 2017 08:27:41: 24000000 INFO @ Wed, 28 Jun 2017 08:27:45: 27000000 INFO @ Wed, 28 Jun 2017 08:27:47: 25000000 INFO @ Wed, 28 Jun 2017 08:27:47: 25000000 INFO @ Wed, 28 Jun 2017 08:27:50: 28000000 INFO @ Wed, 28 Jun 2017 08:27:53: #1 tag size is determined as 45 bps INFO @ Wed, 28 Jun 2017 08:27:53: #1 tag size = 45 INFO @ Wed, 28 Jun 2017 08:27:53: #1 total tags in treatment: 13937895 INFO @ Wed, 28 Jun 2017 08:27:53: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 08:27:53: #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 08:27:53: 26000000 INFO @ Wed, 28 Jun 2017 08:27:53: 26000000 INFO @ Wed, 28 Jun 2017 08:27:53: #1 tags after filtering in treatment: 8216563 INFO @ Wed, 28 Jun 2017 08:27:53: #1 Redundant rate of treatment: 0.41 INFO @ Wed, 28 Jun 2017 08:27:53: #1 finished! INFO @ Wed, 28 Jun 2017 08:27:53: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 08:27:53: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 08:27:54: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 08:27:54: 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 @ Wed, 28 Jun 2017 08:27:54: Process for pairing-model is terminated! cat: SRX362242.10_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 `SRX362242.10_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 `SRX362242.10_*.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 `SRX362242.10_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 @ Wed, 28 Jun 2017 08:27:59: 27000000 INFO @ Wed, 28 Jun 2017 08:27:59: 27000000 INFO @ Wed, 28 Jun 2017 08:28:04: 28000000 INFO @ Wed, 28 Jun 2017 08:28:04: 28000000 INFO @ Wed, 28 Jun 2017 08:28:07: #1 tag size is determined as 45 bps INFO @ Wed, 28 Jun 2017 08:28:07: #1 tag size is determined as 45 bps INFO @ Wed, 28 Jun 2017 08:28:07: #1 tag size = 45 INFO @ Wed, 28 Jun 2017 08:28:07: #1 tag size = 45 INFO @ Wed, 28 Jun 2017 08:28:07: #1 total tags in treatment: 13937895 INFO @ Wed, 28 Jun 2017 08:28:07: #1 total tags in treatment: 13937895 INFO @ Wed, 28 Jun 2017 08:28:07: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 08:28:07: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 08:28:07: #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 08:28:07: #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 08:28:07: #1 tags after filtering in treatment: 8216563 INFO @ Wed, 28 Jun 2017 08:28:07: #1 tags after filtering in treatment: 8216563 INFO @ Wed, 28 Jun 2017 08:28:07: #1 Redundant rate of treatment: 0.41 INFO @ Wed, 28 Jun 2017 08:28:07: #1 Redundant rate of treatment: 0.41 INFO @ Wed, 28 Jun 2017 08:28:07: #1 finished! INFO @ Wed, 28 Jun 2017 08:28:07: #1 finished! INFO @ Wed, 28 Jun 2017 08:28:07: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 08:28:07: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 08:28:07: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 08:28:07: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 08:28:07: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 08:28:07: 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 08:28:07: Process for pairing-model is terminated! cat: SRX362242.05_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) INFO @ Wed, 28 Jun 2017 08:28:07: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 08:28:07: 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 08:28:07: Process for pairing-model is terminated! rm: cannot remove `SRX362242.05_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 `SRX362242.05_*.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 `SRX362242.05_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 cat: SRX362242.20_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 `SRX362242.20_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 `SRX362242.20_*.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 `SRX362242.20_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。