Job ID = 9160018 sra ファイルのダウンロード中... Completed: 1230324K bytes transferred in 14 seconds (709763K 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 11837767 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2402743/SRR5085188.sra Written 11837767 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: 00:10:42 11837767 reads; of these: 11837767 (100.00%) were paired; of these: 325489 (2.75%) aligned concordantly 0 times 10932119 (92.35%) aligned concordantly exactly 1 time 580159 (4.90%) aligned concordantly >1 times ---- 325489 pairs aligned concordantly 0 times; of these: 47080 (14.46%) aligned discordantly 1 time ---- 278409 pairs aligned 0 times concordantly or discordantly; of these: 556818 mates make up the pairs; of these: 504891 (90.67%) aligned 0 times 44313 (7.96%) aligned exactly 1 time 7614 (1.37%) aligned >1 times 97.87% overall alignment rate Time searching: 00:10:42 Overall time: 00:10:42 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] 315446 / 11552650 = 0.0273 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 01:59:52: # Command line: callpeak -t SRX2402743.bam -f BAM -g 12100000 -n SRX2402743.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2402743.20 # format = BAM # ChIP-seq file = ['SRX2402743.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 01:59:52: #1 read tag files... INFO @ Wed, 28 Jun 2017 01:59:52: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 01:59:52: # Command line: callpeak -t SRX2402743.bam -f BAM -g 12100000 -n SRX2402743.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2402743.05 # format = BAM # ChIP-seq file = ['SRX2402743.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 01:59:52: #1 read tag files... INFO @ Wed, 28 Jun 2017 01:59:52: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 01:59:52: # Command line: callpeak -t SRX2402743.bam -f BAM -g 12100000 -n SRX2402743.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2402743.10 # format = BAM # ChIP-seq file = ['SRX2402743.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 01:59:52: #1 read tag files... INFO @ Wed, 28 Jun 2017 01:59:52: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 02:00:00: 1000000 INFO @ Wed, 28 Jun 2017 02:00:00: 1000000 INFO @ Wed, 28 Jun 2017 02:00:01: 1000000 INFO @ Wed, 28 Jun 2017 02:00:08: 2000000 INFO @ Wed, 28 Jun 2017 02:00:08: 2000000 INFO @ Wed, 28 Jun 2017 02:00:10: 2000000 INFO @ Wed, 28 Jun 2017 02:00:15: 3000000 INFO @ Wed, 28 Jun 2017 02:00:15: 3000000 INFO @ Wed, 28 Jun 2017 02:00:18: 3000000 INFO @ Wed, 28 Jun 2017 02:00:22: 4000000 INFO @ Wed, 28 Jun 2017 02:00:22: 4000000 INFO @ Wed, 28 Jun 2017 02:00:26: 4000000 INFO @ Wed, 28 Jun 2017 02:00:28: 5000000 INFO @ Wed, 28 Jun 2017 02:00:28: 5000000 INFO @ Wed, 28 Jun 2017 02:00:33: 5000000 INFO @ Wed, 28 Jun 2017 02:00:35: 6000000 INFO @ Wed, 28 Jun 2017 02:00:35: 6000000 INFO @ Wed, 28 Jun 2017 02:00:40: 6000000 INFO @ Wed, 28 Jun 2017 02:00:42: 7000000 INFO @ Wed, 28 Jun 2017 02:00:42: 7000000 INFO @ Wed, 28 Jun 2017 02:00:47: 7000000 INFO @ Wed, 28 Jun 2017 02:00:49: 8000000 INFO @ Wed, 28 Jun 2017 02:00:49: 8000000 INFO @ Wed, 28 Jun 2017 02:00:53: 8000000 INFO @ Wed, 28 Jun 2017 02:00:55: 9000000 INFO @ Wed, 28 Jun 2017 02:00:56: 9000000 INFO @ Wed, 28 Jun 2017 02:01:00: 9000000 INFO @ Wed, 28 Jun 2017 02:01:02: 10000000 INFO @ Wed, 28 Jun 2017 02:01:03: 10000000 INFO @ Wed, 28 Jun 2017 02:01:07: 10000000 INFO @ Wed, 28 Jun 2017 02:01:09: 11000000 INFO @ Wed, 28 Jun 2017 02:01:10: 11000000 INFO @ Wed, 28 Jun 2017 02:01:14: 11000000 INFO @ Wed, 28 Jun 2017 02:01:16: 12000000 INFO @ Wed, 28 Jun 2017 02:01:17: 12000000 INFO @ Wed, 28 Jun 2017 02:01:22: 12000000 INFO @ Wed, 28 Jun 2017 02:01:23: 13000000 INFO @ Wed, 28 Jun 2017 02:01:24: 13000000 INFO @ Wed, 28 Jun 2017 02:01:29: 13000000 INFO @ Wed, 28 Jun 2017 02:01:30: 14000000 INFO @ Wed, 28 Jun 2017 02:01:31: 14000000 INFO @ Wed, 28 Jun 2017 02:01:36: 14000000 INFO @ Wed, 28 Jun 2017 02:01:38: 15000000 INFO @ Wed, 28 Jun 2017 02:01:39: 15000000 INFO @ Wed, 28 Jun 2017 02:01:43: 15000000 INFO @ Wed, 28 Jun 2017 02:01:45: 16000000 INFO @ Wed, 28 Jun 2017 02:01:46: 16000000 INFO @ Wed, 28 Jun 2017 02:01:49: 16000000 INFO @ Wed, 28 Jun 2017 02:01:51: 17000000 INFO @ Wed, 28 Jun 2017 02:01:53: 17000000 INFO @ Wed, 28 Jun 2017 02:01:56: 17000000 INFO @ Wed, 28 Jun 2017 02:01:59: 18000000 INFO @ Wed, 28 Jun 2017 02:02:01: 18000000 INFO @ Wed, 28 Jun 2017 02:02:03: 18000000 INFO @ Wed, 28 Jun 2017 02:02:06: 19000000 INFO @ Wed, 28 Jun 2017 02:02:08: 19000000 INFO @ Wed, 28 Jun 2017 02:02:10: 19000000 INFO @ Wed, 28 Jun 2017 02:02:12: 20000000 INFO @ Wed, 28 Jun 2017 02:02:15: 20000000 INFO @ Wed, 28 Jun 2017 02:02:17: 20000000 INFO @ Wed, 28 Jun 2017 02:02:19: 21000000 INFO @ Wed, 28 Jun 2017 02:02:22: 21000000 INFO @ Wed, 28 Jun 2017 02:02:24: 21000000 INFO @ Wed, 28 Jun 2017 02:02:26: 22000000 INFO @ Wed, 28 Jun 2017 02:02:30: 22000000 INFO @ Wed, 28 Jun 2017 02:02:30: #1 tag size is determined as 75 bps INFO @ Wed, 28 Jun 2017 02:02:30: #1 tag size = 75 INFO @ Wed, 28 Jun 2017 02:02:30: #1 total tags in treatment: 11197153 INFO @ Wed, 28 Jun 2017 02:02:30: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 02:02:30: #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 02:02:30: #1 tags after filtering in treatment: 5975777 INFO @ Wed, 28 Jun 2017 02:02:30: #1 Redundant rate of treatment: 0.47 INFO @ Wed, 28 Jun 2017 02:02:30: #1 finished! INFO @ Wed, 28 Jun 2017 02:02:30: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 02:02:30: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 02:02:31: 22000000 INFO @ Wed, 28 Jun 2017 02:02:31: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 02:02:31: 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 @ Wed, 28 Jun 2017 02:02:31: Process for pairing-model is terminated! cat: SRX2402743.05_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 `SRX2402743.05_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 `SRX2402743.05_*.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 `SRX2402743.05_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 02:02:34: #1 tag size is determined as 75 bps INFO @ Wed, 28 Jun 2017 02:02:34: #1 tag size = 75 INFO @ Wed, 28 Jun 2017 02:02:34: #1 total tags in treatment: 11197153 INFO @ Wed, 28 Jun 2017 02:02:34: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 02:02:34: #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 02:02:34: #1 tags after filtering in treatment: 5975777 INFO @ Wed, 28 Jun 2017 02:02:34: #1 Redundant rate of treatment: 0.47 INFO @ Wed, 28 Jun 2017 02:02:34: #1 finished! INFO @ Wed, 28 Jun 2017 02:02:34: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 02:02:34: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 02:02:34: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 02:02:34: 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 02:02:34: Process for pairing-model is terminated! cat: SRX2402743.20_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 `SRX2402743.20_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 `SRX2402743.20_*.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 `SRX2402743.20_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 02:02:34: #1 tag size is determined as 75 bps INFO @ Wed, 28 Jun 2017 02:02:34: #1 tag size = 75 INFO @ Wed, 28 Jun 2017 02:02:34: #1 total tags in treatment: 11197153 INFO @ Wed, 28 Jun 2017 02:02:34: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 02:02:34: #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 02:02:35: #1 tags after filtering in treatment: 5975777 INFO @ Wed, 28 Jun 2017 02:02:35: #1 Redundant rate of treatment: 0.47 INFO @ Wed, 28 Jun 2017 02:02:35: #1 finished! INFO @ Wed, 28 Jun 2017 02:02:35: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 02:02:35: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 02:02:35: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 02:02:35: 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 02:02:35: Process for pairing-model is terminated! cat: SRX2402743.10_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 `SRX2402743.10_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 `SRX2402743.10_*.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 `SRX2402743.10_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。