Job ID = 10536536 sra ファイルのダウンロード中... Completed: 1250185K bytes transferred in 41 seconds (248595K 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 34056603 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3671227/SRR6696979.sra Written 34056603 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: 00:21:46 34056603 reads; of these: 34056603 (100.00%) were paired; of these: 7262576 (21.33%) aligned concordantly 0 times 23305020 (68.43%) aligned concordantly exactly 1 time 3489007 (10.24%) aligned concordantly >1 times ---- 7262576 pairs aligned concordantly 0 times; of these: 133358 (1.84%) aligned discordantly 1 time ---- 7129218 pairs aligned 0 times concordantly or discordantly; of these: 14258436 mates make up the pairs; of these: 14034206 (98.43%) aligned 0 times 130423 (0.91%) aligned exactly 1 time 93807 (0.66%) aligned >1 times 79.40% overall alignment rate Time searching: 00:21:46 Overall time: 00:21:46 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 24 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] 9812714 / 26884682 = 0.3650 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 10:52:18: # Command line: callpeak -t SRX3671227.bam -f BAM -g 12100000 -n SRX3671227.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3671227.20 # format = BAM # ChIP-seq file = ['SRX3671227.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 10:52:18: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:52:18: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:52:18: # Command line: callpeak -t SRX3671227.bam -f BAM -g 12100000 -n SRX3671227.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3671227.05 # format = BAM # ChIP-seq file = ['SRX3671227.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 10:52:18: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:52:18: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:52:18: # Command line: callpeak -t SRX3671227.bam -f BAM -g 12100000 -n SRX3671227.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3671227.10 # format = BAM # ChIP-seq file = ['SRX3671227.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 10:52:18: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:52:18: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:52:23: 1000000 INFO @ Thu, 05 Apr 2018 10:52:23: 1000000 INFO @ Thu, 05 Apr 2018 10:52:24: 1000000 INFO @ Thu, 05 Apr 2018 10:52:29: 2000000 INFO @ Thu, 05 Apr 2018 10:52:29: 2000000 INFO @ Thu, 05 Apr 2018 10:52:29: 2000000 INFO @ Thu, 05 Apr 2018 10:52:34: 3000000 INFO @ Thu, 05 Apr 2018 10:52:35: 3000000 INFO @ Thu, 05 Apr 2018 10:52:35: 3000000 INFO @ Thu, 05 Apr 2018 10:52:40: 4000000 INFO @ Thu, 05 Apr 2018 10:52:40: 4000000 INFO @ Thu, 05 Apr 2018 10:52:41: 4000000 INFO @ Thu, 05 Apr 2018 10:52:46: 5000000 INFO @ Thu, 05 Apr 2018 10:52:46: 5000000 INFO @ Thu, 05 Apr 2018 10:52:47: 5000000 INFO @ Thu, 05 Apr 2018 10:52:51: 6000000 INFO @ Thu, 05 Apr 2018 10:52:51: 6000000 INFO @ Thu, 05 Apr 2018 10:52:53: 6000000 INFO @ Thu, 05 Apr 2018 10:52:57: 7000000 INFO @ Thu, 05 Apr 2018 10:52:57: 7000000 INFO @ Thu, 05 Apr 2018 10:52:58: 7000000 INFO @ Thu, 05 Apr 2018 10:53:02: 8000000 INFO @ Thu, 05 Apr 2018 10:53:02: 8000000 INFO @ Thu, 05 Apr 2018 10:53:04: 8000000 INFO @ Thu, 05 Apr 2018 10:53:08: 9000000 INFO @ Thu, 05 Apr 2018 10:53:08: 9000000 INFO @ Thu, 05 Apr 2018 10:53:10: 9000000 INFO @ Thu, 05 Apr 2018 10:53:13: 10000000 INFO @ Thu, 05 Apr 2018 10:53:14: 10000000 INFO @ Thu, 05 Apr 2018 10:53:16: 10000000 INFO @ Thu, 05 Apr 2018 10:53:19: 11000000 INFO @ Thu, 05 Apr 2018 10:53:20: 11000000 INFO @ Thu, 05 Apr 2018 10:53:22: 11000000 INFO @ Thu, 05 Apr 2018 10:53:24: 12000000 INFO @ Thu, 05 Apr 2018 10:53:26: 12000000 INFO @ Thu, 05 Apr 2018 10:53:28: 12000000 INFO @ Thu, 05 Apr 2018 10:53:30: 13000000 INFO @ Thu, 05 Apr 2018 10:53:32: 13000000 INFO @ Thu, 05 Apr 2018 10:53:35: 13000000 INFO @ Thu, 05 Apr 2018 10:53:35: 14000000 INFO @ Thu, 05 Apr 2018 10:53:38: 14000000 INFO @ Thu, 05 Apr 2018 10:53:40: 14000000 INFO @ Thu, 05 Apr 2018 10:53:41: 15000000 INFO @ Thu, 05 Apr 2018 10:53:43: 15000000 INFO @ Thu, 05 Apr 2018 10:53:46: 15000000 INFO @ Thu, 05 Apr 2018 10:53:47: 16000000 INFO @ Thu, 05 Apr 2018 10:53:49: 16000000 INFO @ Thu, 05 Apr 2018 10:53:52: 16000000 INFO @ Thu, 05 Apr 2018 10:53:53: 17000000 INFO @ Thu, 05 Apr 2018 10:53:54: 17000000 INFO @ Thu, 05 Apr 2018 10:53:58: 18000000 INFO @ Thu, 05 Apr 2018 10:53:58: 17000000 INFO @ Thu, 05 Apr 2018 10:54:00: 18000000 INFO @ Thu, 05 Apr 2018 10:54:04: 19000000 INFO @ Thu, 05 Apr 2018 10:54:04: 18000000 INFO @ Thu, 05 Apr 2018 10:54:06: 19000000 INFO @ Thu, 05 Apr 2018 10:54:09: 20000000 INFO @ Thu, 05 Apr 2018 10:54:11: 19000000 INFO @ Thu, 05 Apr 2018 10:54:12: 20000000 INFO @ Thu, 05 Apr 2018 10:54:15: 21000000 INFO @ Thu, 05 Apr 2018 10:54:17: 20000000 INFO @ Thu, 05 Apr 2018 10:54:18: 21000000 INFO @ Thu, 05 Apr 2018 10:54:20: 22000000 INFO @ Thu, 05 Apr 2018 10:54:23: 21000000 INFO @ Thu, 05 Apr 2018 10:54:23: 22000000 INFO @ Thu, 05 Apr 2018 10:54:26: 23000000 INFO @ Thu, 05 Apr 2018 10:54:29: 23000000 INFO @ Thu, 05 Apr 2018 10:54:29: 22000000 INFO @ Thu, 05 Apr 2018 10:54:32: 24000000 INFO @ Thu, 05 Apr 2018 10:54:34: 24000000 INFO @ Thu, 05 Apr 2018 10:54:35: 23000000 INFO @ Thu, 05 Apr 2018 10:54:37: 25000000 INFO @ Thu, 05 Apr 2018 10:54:40: 25000000 INFO @ Thu, 05 Apr 2018 10:54:41: 24000000 INFO @ Thu, 05 Apr 2018 10:54:43: 26000000 INFO @ Thu, 05 Apr 2018 10:54:46: 26000000 INFO @ Thu, 05 Apr 2018 10:54:47: 25000000 INFO @ Thu, 05 Apr 2018 10:54:48: 27000000 INFO @ Thu, 05 Apr 2018 10:54:51: 27000000 INFO @ Thu, 05 Apr 2018 10:54:53: 26000000 INFO @ Thu, 05 Apr 2018 10:54:54: 28000000 INFO @ Thu, 05 Apr 2018 10:54:56: 28000000 INFO @ Thu, 05 Apr 2018 10:54:59: 27000000 INFO @ Thu, 05 Apr 2018 10:55:00: 29000000 INFO @ Thu, 05 Apr 2018 10:55:02: 29000000 INFO @ Thu, 05 Apr 2018 10:55:05: 28000000 INFO @ Thu, 05 Apr 2018 10:55:05: 30000000 INFO @ Thu, 05 Apr 2018 10:55:07: 30000000 INFO @ Thu, 05 Apr 2018 10:55:11: 31000000 INFO @ Thu, 05 Apr 2018 10:55:11: 29000000 INFO @ Thu, 05 Apr 2018 10:55:13: 31000000 INFO @ Thu, 05 Apr 2018 10:55:17: 32000000 INFO @ Thu, 05 Apr 2018 10:55:17: 30000000 INFO @ Thu, 05 Apr 2018 10:55:18: 32000000 INFO @ Thu, 05 Apr 2018 10:55:22: 33000000 INFO @ Thu, 05 Apr 2018 10:55:23: 31000000 INFO @ Thu, 05 Apr 2018 10:55:24: 33000000 INFO @ Thu, 05 Apr 2018 10:55:28: 34000000 INFO @ Thu, 05 Apr 2018 10:55:29: 32000000 INFO @ Thu, 05 Apr 2018 10:55:30: 34000000 INFO @ Thu, 05 Apr 2018 10:55:30: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:55:30: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:55:30: #1 total tags in treatment: 17017731 INFO @ Thu, 05 Apr 2018 10:55:30: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:55:30: #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 10:55:31: #1 tags after filtering in treatment: 6793466 INFO @ Thu, 05 Apr 2018 10:55:31: #1 Redundant rate of treatment: 0.60 INFO @ Thu, 05 Apr 2018 10:55:31: #1 finished! INFO @ Thu, 05 Apr 2018 10:55:31: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:55:31: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:55:31: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:55:31: 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 @ Thu, 05 Apr 2018 10:55:31: Process for pairing-model is terminated! cat: SRX3671227.05_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 `SRX3671227.05_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 `SRX3671227.05_*.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 `SRX3671227.05_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 10:55:33: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:55:33: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:55:33: #1 total tags in treatment: 17017731 INFO @ Thu, 05 Apr 2018 10:55:33: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:55:33: #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 10:55:33: #1 tags after filtering in treatment: 6793466 INFO @ Thu, 05 Apr 2018 10:55:33: #1 Redundant rate of treatment: 0.60 INFO @ Thu, 05 Apr 2018 10:55:33: #1 finished! INFO @ Thu, 05 Apr 2018 10:55:33: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:55:33: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:55:34: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:55:34: 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 @ Thu, 05 Apr 2018 10:55:34: Process for pairing-model is terminated! cat: SRX3671227.20_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 `SRX3671227.20_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 `SRX3671227.20_*.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 `SRX3671227.20_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 10:55:35: 33000000 INFO @ Thu, 05 Apr 2018 10:55:41: 34000000 INFO @ Thu, 05 Apr 2018 10:55:43: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:55:43: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:55:43: #1 total tags in treatment: 17017731 INFO @ Thu, 05 Apr 2018 10:55:43: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:55:43: #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 10:55:44: #1 tags after filtering in treatment: 6793466 INFO @ Thu, 05 Apr 2018 10:55:44: #1 Redundant rate of treatment: 0.60 INFO @ Thu, 05 Apr 2018 10:55:44: #1 finished! INFO @ Thu, 05 Apr 2018 10:55:44: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:55:44: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:55:44: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:55:44: 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 10:55:44: Process for pairing-model is terminated! cat: SRX3671227.10_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 `SRX3671227.10_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 `SRX3671227.10_*.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 `SRX3671227.10_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。