Job ID = 9161989 sra ファイルのダウンロード中... Completed: 1089772K bytes transferred in 12 seconds (715315K 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 17401885 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1423721/SRR2931010.sra Written 17401885 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: 00:11:00 17401885 reads; of these: 17401885 (100.00%) were paired; of these: 3381326 (19.43%) aligned concordantly 0 times 12168571 (69.93%) aligned concordantly exactly 1 time 1851988 (10.64%) aligned concordantly >1 times ---- 3381326 pairs aligned concordantly 0 times; of these: 36428 (1.08%) aligned discordantly 1 time ---- 3344898 pairs aligned 0 times concordantly or discordantly; of these: 6689796 mates make up the pairs; of these: 6580841 (98.37%) aligned 0 times 77827 (1.16%) aligned exactly 1 time 31128 (0.47%) aligned >1 times 81.09% overall alignment rate Time searching: 00:11:00 Overall time: 00:11:00 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] 5159800 / 14039031 = 0.3675 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 05:29:24: # Command line: callpeak -t SRX1423721.bam -f BAM -g 12100000 -n SRX1423721.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1423721.05 # format = BAM # ChIP-seq file = ['SRX1423721.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 05:29:24: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:29:24: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:29:24: # Command line: callpeak -t SRX1423721.bam -f BAM -g 12100000 -n SRX1423721.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1423721.10 # format = BAM # ChIP-seq file = ['SRX1423721.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 05:29:24: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:29:24: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:29:24: # Command line: callpeak -t SRX1423721.bam -f BAM -g 12100000 -n SRX1423721.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1423721.20 # format = BAM # ChIP-seq file = ['SRX1423721.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 05:29:24: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:29:24: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:29:30: 1000000 INFO @ Wed, 28 Jun 2017 05:29:30: 1000000 INFO @ Wed, 28 Jun 2017 05:29:30: 1000000 INFO @ Wed, 28 Jun 2017 05:29:36: 2000000 INFO @ Wed, 28 Jun 2017 05:29:36: 2000000 INFO @ Wed, 28 Jun 2017 05:29:36: 2000000 INFO @ Wed, 28 Jun 2017 05:29:43: 3000000 INFO @ Wed, 28 Jun 2017 05:29:43: 3000000 INFO @ Wed, 28 Jun 2017 05:29:44: 3000000 INFO @ Wed, 28 Jun 2017 05:29:50: 4000000 INFO @ Wed, 28 Jun 2017 05:29:51: 4000000 INFO @ Wed, 28 Jun 2017 05:29:51: 4000000 INFO @ Wed, 28 Jun 2017 05:29:57: 5000000 INFO @ Wed, 28 Jun 2017 05:29:58: 5000000 INFO @ Wed, 28 Jun 2017 05:29:59: 5000000 INFO @ Wed, 28 Jun 2017 05:30:05: 6000000 INFO @ Wed, 28 Jun 2017 05:30:05: 6000000 INFO @ Wed, 28 Jun 2017 05:30:08: 6000000 INFO @ Wed, 28 Jun 2017 05:30:12: 7000000 INFO @ Wed, 28 Jun 2017 05:30:12: 7000000 INFO @ Wed, 28 Jun 2017 05:30:16: 7000000 INFO @ Wed, 28 Jun 2017 05:30:19: 8000000 INFO @ Wed, 28 Jun 2017 05:30:20: 8000000 INFO @ Wed, 28 Jun 2017 05:30:24: 8000000 INFO @ Wed, 28 Jun 2017 05:30:26: 9000000 INFO @ Wed, 28 Jun 2017 05:30:27: 9000000 INFO @ Wed, 28 Jun 2017 05:30:33: 9000000 INFO @ Wed, 28 Jun 2017 05:30:33: 10000000 INFO @ Wed, 28 Jun 2017 05:30:35: 10000000 INFO @ Wed, 28 Jun 2017 05:30:40: 11000000 INFO @ Wed, 28 Jun 2017 05:30:41: 10000000 INFO @ Wed, 28 Jun 2017 05:30:42: 11000000 INFO @ Wed, 28 Jun 2017 05:30:47: 12000000 INFO @ Wed, 28 Jun 2017 05:30:49: 12000000 INFO @ Wed, 28 Jun 2017 05:30:50: 11000000 INFO @ Wed, 28 Jun 2017 05:30:53: 13000000 INFO @ Wed, 28 Jun 2017 05:30:57: 13000000 INFO @ Wed, 28 Jun 2017 05:30:58: 12000000 INFO @ Wed, 28 Jun 2017 05:31:00: 14000000 INFO @ Wed, 28 Jun 2017 05:31:04: 14000000 INFO @ Wed, 28 Jun 2017 05:31:07: 13000000 INFO @ Wed, 28 Jun 2017 05:31:07: 15000000 INFO @ Wed, 28 Jun 2017 05:31:12: 15000000 INFO @ Wed, 28 Jun 2017 05:31:14: 16000000 INFO @ Wed, 28 Jun 2017 05:31:15: 14000000 INFO @ Wed, 28 Jun 2017 05:31:19: 16000000 INFO @ Wed, 28 Jun 2017 05:31:21: 17000000 INFO @ Wed, 28 Jun 2017 05:31:23: 15000000 INFO @ Wed, 28 Jun 2017 05:31:26: 17000000 INFO @ Wed, 28 Jun 2017 05:31:28: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:31:28: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:31:28: #1 total tags in treatment: 8874128 INFO @ Wed, 28 Jun 2017 05:31:28: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:31:28: #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 05:31:28: #1 tags after filtering in treatment: 6071965 INFO @ Wed, 28 Jun 2017 05:31:28: #1 Redundant rate of treatment: 0.32 INFO @ Wed, 28 Jun 2017 05:31:28: #1 finished! INFO @ Wed, 28 Jun 2017 05:31:28: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:31:28: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:31:28: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 05:31:28: 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 05:31:28: Process for pairing-model is terminated! cat: SRX1423721.05_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 `SRX1423721.05_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 `SRX1423721.05_*.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 `SRX1423721.05_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 @ Wed, 28 Jun 2017 05:31:31: 16000000 INFO @ Wed, 28 Jun 2017 05:31:32: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:31:32: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:31:32: #1 total tags in treatment: 8874128 INFO @ Wed, 28 Jun 2017 05:31:32: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:31:32: #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 05:31:32: #1 tags after filtering in treatment: 6071965 INFO @ Wed, 28 Jun 2017 05:31:32: #1 Redundant rate of treatment: 0.32 INFO @ Wed, 28 Jun 2017 05:31:32: #1 finished! INFO @ Wed, 28 Jun 2017 05:31:32: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:31:32: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:31:33: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 05:31:33: 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 05:31:33: Process for pairing-model is terminated! cat: SRX1423721.20_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 `SRX1423721.20_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 `SRX1423721.20_*.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 `SRX1423721.20_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 05:31:39: 17000000 INFO @ Wed, 28 Jun 2017 05:31:46: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:31:46: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:31:46: #1 total tags in treatment: 8874128 INFO @ Wed, 28 Jun 2017 05:31:46: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:31:46: #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 05:31:46: #1 tags after filtering in treatment: 6071965 INFO @ Wed, 28 Jun 2017 05:31:46: #1 Redundant rate of treatment: 0.32 INFO @ Wed, 28 Jun 2017 05:31:46: #1 finished! INFO @ Wed, 28 Jun 2017 05:31:46: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:31:46: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:31:46: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 05:31:46: 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 05:31:46: Process for pairing-model is terminated! cat: SRX1423721.10_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 `SRX1423721.10_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 `SRX1423721.10_*.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 `SRX1423721.10_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。