Job ID = 10536527 sra ファイルのダウンロード中... Completed: 1673219K bytes transferred in 48 seconds (281721K bits/sec), in 1 file. 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 46142873 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3671219/SRR6696971.sra Written 46142873 spots total rm: cannot remove `[DSE]RX*': 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 `[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: 00:28:53 46142873 reads; of these: 46142873 (100.00%) were paired; of these: 13990182 (30.32%) aligned concordantly 0 times 27980333 (60.64%) aligned concordantly exactly 1 time 4172358 (9.04%) aligned concordantly >1 times ---- 13990182 pairs aligned concordantly 0 times; of these: 274590 (1.96%) aligned discordantly 1 time ---- 13715592 pairs aligned 0 times concordantly or discordantly; of these: 27431184 mates make up the pairs; of these: 27114285 (98.84%) aligned 0 times 162181 (0.59%) aligned exactly 1 time 154718 (0.56%) aligned >1 times 70.62% overall alignment rate Time searching: 00:28:53 Overall time: 00:28:53 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 28 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] 12182946 / 32339017 = 0.3767 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 @ Thu, 05 Apr 2018 10:58:34: # Command line: callpeak -t SRX3671219.bam -f BAM -g 12100000 -n SRX3671219.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3671219.10 # format = BAM # ChIP-seq file = ['SRX3671219.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 @ Thu, 05 Apr 2018 10:58:34: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:58:34: # Command line: callpeak -t SRX3671219.bam -f BAM -g 12100000 -n SRX3671219.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3671219.05 # format = BAM # ChIP-seq file = ['SRX3671219.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 @ Thu, 05 Apr 2018 10:58:34: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:58:34: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:58:34: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:58:34: # Command line: callpeak -t SRX3671219.bam -f BAM -g 12100000 -n SRX3671219.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3671219.20 # format = BAM # ChIP-seq file = ['SRX3671219.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 @ Thu, 05 Apr 2018 10:58:34: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:58:34: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:58:40: 1000000 INFO @ Thu, 05 Apr 2018 10:58:40: 1000000 INFO @ Thu, 05 Apr 2018 10:58:40: 1000000 INFO @ Thu, 05 Apr 2018 10:58:45: 2000000 INFO @ Thu, 05 Apr 2018 10:58:45: 2000000 INFO @ Thu, 05 Apr 2018 10:58:46: 2000000 INFO @ Thu, 05 Apr 2018 10:58:51: 3000000 INFO @ Thu, 05 Apr 2018 10:58:51: 3000000 INFO @ Thu, 05 Apr 2018 10:58:52: 3000000 INFO @ Thu, 05 Apr 2018 10:58:56: 4000000 INFO @ Thu, 05 Apr 2018 10:58:56: 4000000 INFO @ Thu, 05 Apr 2018 10:58:58: 4000000 INFO @ Thu, 05 Apr 2018 10:59:01: 5000000 INFO @ Thu, 05 Apr 2018 10:59:02: 5000000 INFO @ Thu, 05 Apr 2018 10:59:04: 5000000 INFO @ Thu, 05 Apr 2018 10:59:07: 6000000 INFO @ Thu, 05 Apr 2018 10:59:07: 6000000 INFO @ Thu, 05 Apr 2018 10:59:09: 6000000 INFO @ Thu, 05 Apr 2018 10:59:13: 7000000 INFO @ Thu, 05 Apr 2018 10:59:13: 7000000 INFO @ Thu, 05 Apr 2018 10:59:15: 7000000 INFO @ Thu, 05 Apr 2018 10:59:18: 8000000 INFO @ Thu, 05 Apr 2018 10:59:19: 8000000 INFO @ Thu, 05 Apr 2018 10:59:21: 8000000 INFO @ Thu, 05 Apr 2018 10:59:24: 9000000 INFO @ Thu, 05 Apr 2018 10:59:25: 9000000 INFO @ Thu, 05 Apr 2018 10:59:27: 9000000 INFO @ Thu, 05 Apr 2018 10:59:30: 10000000 INFO @ Thu, 05 Apr 2018 10:59:30: 10000000 INFO @ Thu, 05 Apr 2018 10:59:33: 10000000 INFO @ Thu, 05 Apr 2018 10:59:35: 11000000 INFO @ Thu, 05 Apr 2018 10:59:36: 11000000 INFO @ Thu, 05 Apr 2018 10:59:39: 11000000 INFO @ Thu, 05 Apr 2018 10:59:41: 12000000 INFO @ Thu, 05 Apr 2018 10:59:42: 12000000 INFO @ Thu, 05 Apr 2018 10:59:45: 12000000 INFO @ Thu, 05 Apr 2018 10:59:47: 13000000 INFO @ Thu, 05 Apr 2018 10:59:48: 13000000 INFO @ Thu, 05 Apr 2018 10:59:51: 13000000 INFO @ Thu, 05 Apr 2018 10:59:53: 14000000 INFO @ Thu, 05 Apr 2018 10:59:53: 14000000 INFO @ Thu, 05 Apr 2018 10:59:57: 14000000 INFO @ Thu, 05 Apr 2018 10:59:59: 15000000 INFO @ Thu, 05 Apr 2018 11:00:00: 15000000 INFO @ Thu, 05 Apr 2018 11:00:02: 15000000 INFO @ Thu, 05 Apr 2018 11:00:05: 16000000 INFO @ Thu, 05 Apr 2018 11:00:06: 16000000 INFO @ Thu, 05 Apr 2018 11:00:08: 16000000 INFO @ Thu, 05 Apr 2018 11:00:11: 17000000 INFO @ Thu, 05 Apr 2018 11:00:12: 17000000 INFO @ Thu, 05 Apr 2018 11:00:14: 17000000 INFO @ Thu, 05 Apr 2018 11:00:17: 18000000 INFO @ Thu, 05 Apr 2018 11:00:18: 18000000 INFO @ Thu, 05 Apr 2018 11:00:20: 18000000 INFO @ Thu, 05 Apr 2018 11:00:23: 19000000 INFO @ Thu, 05 Apr 2018 11:00:24: 19000000 INFO @ Thu, 05 Apr 2018 11:00:25: 19000000 INFO @ Thu, 05 Apr 2018 11:00:29: 20000000 INFO @ Thu, 05 Apr 2018 11:00:30: 20000000 INFO @ Thu, 05 Apr 2018 11:00:31: 20000000 INFO @ Thu, 05 Apr 2018 11:00:35: 21000000 INFO @ Thu, 05 Apr 2018 11:00:36: 21000000 INFO @ Thu, 05 Apr 2018 11:00:37: 21000000 INFO @ Thu, 05 Apr 2018 11:00:41: 22000000 INFO @ Thu, 05 Apr 2018 11:00:42: 22000000 INFO @ Thu, 05 Apr 2018 11:00:43: 22000000 INFO @ Thu, 05 Apr 2018 11:00:47: 23000000 INFO @ Thu, 05 Apr 2018 11:00:48: 23000000 INFO @ Thu, 05 Apr 2018 11:00:48: 23000000 INFO @ Thu, 05 Apr 2018 11:00:53: 24000000 INFO @ Thu, 05 Apr 2018 11:00:54: 24000000 INFO @ Thu, 05 Apr 2018 11:00:54: 24000000 INFO @ Thu, 05 Apr 2018 11:00:59: 25000000 INFO @ Thu, 05 Apr 2018 11:01:00: 25000000 INFO @ Thu, 05 Apr 2018 11:01:00: 25000000 INFO @ Thu, 05 Apr 2018 11:01:05: 26000000 INFO @ Thu, 05 Apr 2018 11:01:06: 26000000 INFO @ Thu, 05 Apr 2018 11:01:06: 26000000 INFO @ Thu, 05 Apr 2018 11:01:11: 27000000 INFO @ Thu, 05 Apr 2018 11:01:12: 27000000 INFO @ Thu, 05 Apr 2018 11:01:12: 27000000 INFO @ Thu, 05 Apr 2018 11:01:17: 28000000 INFO @ Thu, 05 Apr 2018 11:01:17: 28000000 INFO @ Thu, 05 Apr 2018 11:01:19: 28000000 INFO @ Thu, 05 Apr 2018 11:01:23: 29000000 INFO @ Thu, 05 Apr 2018 11:01:23: 29000000 INFO @ Thu, 05 Apr 2018 11:01:25: 29000000 INFO @ Thu, 05 Apr 2018 11:01:28: 30000000 INFO @ Thu, 05 Apr 2018 11:01:29: 30000000 INFO @ Thu, 05 Apr 2018 11:01:31: 30000000 INFO @ Thu, 05 Apr 2018 11:01:34: 31000000 INFO @ Thu, 05 Apr 2018 11:01:35: 31000000 INFO @ Thu, 05 Apr 2018 11:01:37: 31000000 INFO @ Thu, 05 Apr 2018 11:01:40: 32000000 INFO @ Thu, 05 Apr 2018 11:01:41: 32000000 INFO @ Thu, 05 Apr 2018 11:01:43: 32000000 INFO @ Thu, 05 Apr 2018 11:01:46: 33000000 INFO @ Thu, 05 Apr 2018 11:01:46: 33000000 INFO @ Thu, 05 Apr 2018 11:01:49: 33000000 INFO @ Thu, 05 Apr 2018 11:01:52: 34000000 INFO @ Thu, 05 Apr 2018 11:01:52: 34000000 INFO @ Thu, 05 Apr 2018 11:01:55: 34000000 INFO @ Thu, 05 Apr 2018 11:01:58: 35000000 INFO @ Thu, 05 Apr 2018 11:01:58: 35000000 INFO @ Thu, 05 Apr 2018 11:02:01: 35000000 INFO @ Thu, 05 Apr 2018 11:02:03: 36000000 INFO @ Thu, 05 Apr 2018 11:02:04: 36000000 INFO @ Thu, 05 Apr 2018 11:02:07: 36000000 INFO @ Thu, 05 Apr 2018 11:02:09: 37000000 INFO @ Thu, 05 Apr 2018 11:02:09: 37000000 INFO @ Thu, 05 Apr 2018 11:02:13: 37000000 INFO @ Thu, 05 Apr 2018 11:02:15: 38000000 INFO @ Thu, 05 Apr 2018 11:02:15: 38000000 INFO @ Thu, 05 Apr 2018 11:02:19: 38000000 INFO @ Thu, 05 Apr 2018 11:02:21: 39000000 INFO @ Thu, 05 Apr 2018 11:02:21: 39000000 INFO @ Thu, 05 Apr 2018 11:02:25: 39000000 INFO @ Thu, 05 Apr 2018 11:02:26: 40000000 INFO @ Thu, 05 Apr 2018 11:02:27: 40000000 INFO @ Thu, 05 Apr 2018 11:02:31: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 11:02:31: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 11:02:31: #1 total tags in treatment: 20064465 INFO @ Thu, 05 Apr 2018 11:02:31: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 11:02:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 05 Apr 2018 11:02:31: 40000000 INFO @ Thu, 05 Apr 2018 11:02:32: #1 tags after filtering in treatment: 7189221 INFO @ Thu, 05 Apr 2018 11:02:32: #1 Redundant rate of treatment: 0.64 INFO @ Thu, 05 Apr 2018 11:02:32: #1 finished! INFO @ Thu, 05 Apr 2018 11:02:32: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 11:02:32: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 11:02:32: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 11:02:32: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 11:02:32: #1 total tags in treatment: 20064465 INFO @ Thu, 05 Apr 2018 11:02:32: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 11:02:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Apr 2018 11:02:32: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 11:02:32: 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 @ Thu, 05 Apr 2018 11:02:32: Process for pairing-model is terminated! cat: SRX3671219.05_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 `SRX3671219.05_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 `SRX3671219.05_*.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 `SRX3671219.05_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 @ Thu, 05 Apr 2018 11:02:32: #1 tags after filtering in treatment: 7189221 INFO @ Thu, 05 Apr 2018 11:02:32: #1 Redundant rate of treatment: 0.64 INFO @ Thu, 05 Apr 2018 11:02:32: #1 finished! INFO @ Thu, 05 Apr 2018 11:02:32: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 11:02:32: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 11:02:33: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 11:02:33: 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 @ Thu, 05 Apr 2018 11:02:33: Process for pairing-model is terminated! cat: SRX3671219.20_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 `SRX3671219.20_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 `SRX3671219.20_*.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 `SRX3671219.20_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 @ Thu, 05 Apr 2018 11:02:36: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 11:02:36: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 11:02:36: #1 total tags in treatment: 20064465 INFO @ Thu, 05 Apr 2018 11:02:36: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 11:02:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Apr 2018 11:02:36: #1 tags after filtering in treatment: 7189221 INFO @ Thu, 05 Apr 2018 11:02:36: #1 Redundant rate of treatment: 0.64 INFO @ Thu, 05 Apr 2018 11:02:36: #1 finished! INFO @ Thu, 05 Apr 2018 11:02:36: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 11:02:36: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 11:02:37: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 11:02:37: 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 @ Thu, 05 Apr 2018 11:02:37: Process for pairing-model is terminated! cat: SRX3671219.10_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): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3671219.10_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 `SRX3671219.10_*.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 `SRX3671219.10_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 BigWig に変換しました。