Job ID = 9161692 sra ファイルのダウンロード中... Completed: 974071K bytes transferred in 11 seconds (719218K 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 25930354 spots for /home/okishinya/chipatlas/results/sacCer3/SRX079675/SRR292346.sra Written 25930354 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 25930354 reads; of these: 25930354 (100.00%) were paired; of these: 11771085 (45.40%) aligned concordantly 0 times 10892619 (42.01%) aligned concordantly exactly 1 time 3266650 (12.60%) aligned concordantly >1 times ---- 11771085 pairs aligned concordantly 0 times; of these: 1884677 (16.01%) aligned discordantly 1 time ---- 9886408 pairs aligned 0 times concordantly or discordantly; of these: 19772816 mates make up the pairs; of these: 15746802 (79.64%) aligned 0 times 1022850 (5.17%) aligned exactly 1 time 3003164 (15.19%) aligned >1 times 69.64% 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] 4866585 / 15602766 = 0.3119 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 04:44:31: # Command line: callpeak -t SRX079675.bam -f BAM -g 12100000 -n SRX079675.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX079675.10 # format = BAM # ChIP-seq file = ['SRX079675.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 04:44:31: #1 read tag files... INFO @ Wed, 28 Jun 2017 04:44:31: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 04:44:31: # Command line: callpeak -t SRX079675.bam -f BAM -g 12100000 -n SRX079675.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX079675.05 # format = BAM # ChIP-seq file = ['SRX079675.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 04:44:31: #1 read tag files... INFO @ Wed, 28 Jun 2017 04:44:31: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 04:44:31: # Command line: callpeak -t SRX079675.bam -f BAM -g 12100000 -n SRX079675.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX079675.20 # format = BAM # ChIP-seq file = ['SRX079675.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 04:44:31: #1 read tag files... INFO @ Wed, 28 Jun 2017 04:44:31: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 04:44:37: 1000000 INFO @ Wed, 28 Jun 2017 04:44:37: 1000000 INFO @ Wed, 28 Jun 2017 04:44:37: 1000000 INFO @ Wed, 28 Jun 2017 04:44:42: 2000000 INFO @ Wed, 28 Jun 2017 04:44:42: 2000000 INFO @ Wed, 28 Jun 2017 04:44:44: 2000000 INFO @ Wed, 28 Jun 2017 04:44:47: 3000000 INFO @ Wed, 28 Jun 2017 04:44:47: 3000000 INFO @ Wed, 28 Jun 2017 04:44:49: 3000000 INFO @ Wed, 28 Jun 2017 04:44:52: 4000000 INFO @ Wed, 28 Jun 2017 04:44:53: 4000000 INFO @ Wed, 28 Jun 2017 04:44:55: 4000000 INFO @ Wed, 28 Jun 2017 04:44:57: 5000000 INFO @ Wed, 28 Jun 2017 04:44:58: 5000000 INFO @ Wed, 28 Jun 2017 04:45:00: 5000000 INFO @ Wed, 28 Jun 2017 04:45:02: 6000000 INFO @ Wed, 28 Jun 2017 04:45:03: 6000000 INFO @ Wed, 28 Jun 2017 04:45:05: 6000000 INFO @ Wed, 28 Jun 2017 04:45:07: 7000000 INFO @ Wed, 28 Jun 2017 04:45:08: 7000000 INFO @ Wed, 28 Jun 2017 04:45:11: 7000000 INFO @ Wed, 28 Jun 2017 04:45:12: 8000000 INFO @ Wed, 28 Jun 2017 04:45:13: 8000000 INFO @ Wed, 28 Jun 2017 04:45:16: 8000000 INFO @ Wed, 28 Jun 2017 04:45:17: 9000000 INFO @ Wed, 28 Jun 2017 04:45:18: 9000000 INFO @ Wed, 28 Jun 2017 04:45:21: 9000000 INFO @ Wed, 28 Jun 2017 04:45:22: 10000000 INFO @ Wed, 28 Jun 2017 04:45:24: 10000000 INFO @ Wed, 28 Jun 2017 04:45:26: 10000000 INFO @ Wed, 28 Jun 2017 04:45:27: 11000000 INFO @ Wed, 28 Jun 2017 04:45:29: 11000000 INFO @ Wed, 28 Jun 2017 04:45:32: 11000000 INFO @ Wed, 28 Jun 2017 04:45:32: 12000000 INFO @ Wed, 28 Jun 2017 04:45:34: 12000000 INFO @ Wed, 28 Jun 2017 04:45:37: 12000000 INFO @ Wed, 28 Jun 2017 04:45:37: 13000000 INFO @ Wed, 28 Jun 2017 04:45:39: 13000000 INFO @ Wed, 28 Jun 2017 04:45:42: 13000000 INFO @ Wed, 28 Jun 2017 04:45:42: 14000000 INFO @ Wed, 28 Jun 2017 04:45:44: 14000000 INFO @ Wed, 28 Jun 2017 04:45:47: 15000000 INFO @ Wed, 28 Jun 2017 04:45:47: 14000000 INFO @ Wed, 28 Jun 2017 04:45:49: 15000000 INFO @ Wed, 28 Jun 2017 04:45:51: 16000000 INFO @ Wed, 28 Jun 2017 04:45:52: 15000000 INFO @ Wed, 28 Jun 2017 04:45:53: 16000000 INFO @ Wed, 28 Jun 2017 04:45:56: 17000000 INFO @ Wed, 28 Jun 2017 04:45:57: 16000000 INFO @ Wed, 28 Jun 2017 04:45:58: 17000000 INFO @ Wed, 28 Jun 2017 04:46:00: 18000000 INFO @ Wed, 28 Jun 2017 04:46:01: 17000000 INFO @ Wed, 28 Jun 2017 04:46:02: 18000000 INFO @ Wed, 28 Jun 2017 04:46:05: 19000000 INFO @ Wed, 28 Jun 2017 04:46:06: 18000000 INFO @ Wed, 28 Jun 2017 04:46:08: 19000000 INFO @ Wed, 28 Jun 2017 04:46:10: 20000000 INFO @ Wed, 28 Jun 2017 04:46:11: 19000000 INFO @ Wed, 28 Jun 2017 04:46:13: 20000000 INFO @ Wed, 28 Jun 2017 04:46:15: 21000000 INFO @ Wed, 28 Jun 2017 04:46:16: 20000000 INFO @ Wed, 28 Jun 2017 04:46:19: 21000000 INFO @ Wed, 28 Jun 2017 04:46:20: 22000000 INFO @ Wed, 28 Jun 2017 04:46:22: 21000000 INFO @ Wed, 28 Jun 2017 04:46:25: 23000000 INFO @ Wed, 28 Jun 2017 04:46:25: 22000000 INFO @ Wed, 28 Jun 2017 04:46:28: 22000000 INFO @ Wed, 28 Jun 2017 04:46:29: 24000000 INFO @ Wed, 28 Jun 2017 04:46:31: 23000000 INFO @ Wed, 28 Jun 2017 04:46:34: 23000000 INFO @ Wed, 28 Jun 2017 04:46:34: 25000000 INFO @ Wed, 28 Jun 2017 04:46:36: 24000000 INFO @ Wed, 28 Jun 2017 04:46:39: 26000000 INFO @ Wed, 28 Jun 2017 04:46:39: 24000000 INFO @ Wed, 28 Jun 2017 04:46:41: #1 tag size is determined as 36 bps INFO @ Wed, 28 Jun 2017 04:46:41: #1 tag size = 36 INFO @ Wed, 28 Jun 2017 04:46:41: #1 total tags in treatment: 10159781 INFO @ Wed, 28 Jun 2017 04:46:41: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 04:46:41: #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 04:46:41: #1 tags after filtering in treatment: 5145184 INFO @ Wed, 28 Jun 2017 04:46:41: #1 Redundant rate of treatment: 0.49 INFO @ Wed, 28 Jun 2017 04:46:41: #1 finished! INFO @ Wed, 28 Jun 2017 04:46:41: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 04:46:41: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 04:46:41: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 04:46:41: 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 04:46:41: Process for pairing-model is terminated! cat: SRX079675.05_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 `SRX079675.05_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 `SRX079675.05_*.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 `SRX079675.05_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 04:46:42: 25000000 INFO @ Wed, 28 Jun 2017 04:46:45: 25000000 INFO @ Wed, 28 Jun 2017 04:46:49: 26000000 INFO @ Wed, 28 Jun 2017 04:46:51: #1 tag size is determined as 36 bps INFO @ Wed, 28 Jun 2017 04:46:51: #1 tag size = 36 INFO @ Wed, 28 Jun 2017 04:46:51: #1 total tags in treatment: 10159781 INFO @ Wed, 28 Jun 2017 04:46:51: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 04:46:51: #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 04:46:51: 26000000 INFO @ Wed, 28 Jun 2017 04:46:51: #1 tags after filtering in treatment: 5145184 INFO @ Wed, 28 Jun 2017 04:46:51: #1 Redundant rate of treatment: 0.49 INFO @ Wed, 28 Jun 2017 04:46:51: #1 finished! INFO @ Wed, 28 Jun 2017 04:46:51: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 04:46:51: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 04:46:52: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 04:46:52: 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 04:46:52: Process for pairing-model is terminated! cat: SRX079675.10_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 `SRX079675.10_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 `SRX079675.10_*.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 `SRX079675.10_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 04:46:53: #1 tag size is determined as 36 bps INFO @ Wed, 28 Jun 2017 04:46:53: #1 tag size = 36 INFO @ Wed, 28 Jun 2017 04:46:53: #1 total tags in treatment: 10159781 INFO @ Wed, 28 Jun 2017 04:46:53: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 04:46:53: #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 04:46:53: #1 tags after filtering in treatment: 5145184 INFO @ Wed, 28 Jun 2017 04:46:53: #1 Redundant rate of treatment: 0.49 INFO @ Wed, 28 Jun 2017 04:46:53: #1 finished! INFO @ Wed, 28 Jun 2017 04:46:53: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 04:46:53: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 04:46:54: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 04:46:54: 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 04:46:54: Process for pairing-model is terminated! cat: SRX079675.20_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 `SRX079675.20_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 `SRX079675.20_*.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 `SRX079675.20_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。