Job ID = 10536417 sra ファイルのダウンロード中... Completed: 1211839K bytes transferred in 41 seconds (237050K 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 26774888 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3671157/SRR6696909.sra Written 26774888 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: 00:20:00 26774888 reads; of these: 26774888 (100.00%) were paired; of these: 2003254 (7.48%) aligned concordantly 0 times 22084351 (82.48%) aligned concordantly exactly 1 time 2687283 (10.04%) aligned concordantly >1 times ---- 2003254 pairs aligned concordantly 0 times; of these: 34806 (1.74%) aligned discordantly 1 time ---- 1968448 pairs aligned 0 times concordantly or discordantly; of these: 3936896 mates make up the pairs; of these: 3729236 (94.73%) aligned 0 times 167699 (4.26%) aligned exactly 1 time 39961 (1.02%) aligned >1 times 93.04% overall alignment rate Time searching: 00:20:00 Overall time: 00:20:00 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 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] 12158766 / 24779695 = 0.4907 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 09:52:02: # Command line: callpeak -t SRX3671157.bam -f BAM -g 12100000 -n SRX3671157.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3671157.10 # format = BAM # ChIP-seq file = ['SRX3671157.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 09:52:02: # Command line: callpeak -t SRX3671157.bam -f BAM -g 12100000 -n SRX3671157.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3671157.20 # format = BAM # ChIP-seq file = ['SRX3671157.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 09:52:02: # Command line: callpeak -t SRX3671157.bam -f BAM -g 12100000 -n SRX3671157.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3671157.05 # format = BAM # ChIP-seq file = ['SRX3671157.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 09:52:02: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:52:02: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:52:02: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:52:02: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:52:02: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:52:02: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:52:08: 1000000 INFO @ Thu, 05 Apr 2018 09:52:09: 1000000 INFO @ Thu, 05 Apr 2018 09:52:09: 1000000 INFO @ Thu, 05 Apr 2018 09:52:14: 2000000 INFO @ Thu, 05 Apr 2018 09:52:15: 2000000 INFO @ Thu, 05 Apr 2018 09:52:15: 2000000 INFO @ Thu, 05 Apr 2018 09:52:20: 3000000 INFO @ Thu, 05 Apr 2018 09:52:22: 3000000 INFO @ Thu, 05 Apr 2018 09:52:22: 3000000 INFO @ Thu, 05 Apr 2018 09:52:26: 4000000 INFO @ Thu, 05 Apr 2018 09:52:28: 4000000 INFO @ Thu, 05 Apr 2018 09:52:28: 4000000 INFO @ Thu, 05 Apr 2018 09:52:32: 5000000 INFO @ Thu, 05 Apr 2018 09:52:35: 5000000 INFO @ Thu, 05 Apr 2018 09:52:35: 5000000 INFO @ Thu, 05 Apr 2018 09:52:37: 6000000 INFO @ Thu, 05 Apr 2018 09:52:41: 6000000 INFO @ Thu, 05 Apr 2018 09:52:41: 6000000 INFO @ Thu, 05 Apr 2018 09:52:43: 7000000 INFO @ Thu, 05 Apr 2018 09:52:48: 7000000 INFO @ Thu, 05 Apr 2018 09:52:48: 7000000 INFO @ Thu, 05 Apr 2018 09:52:49: 8000000 INFO @ Thu, 05 Apr 2018 09:52:54: 8000000 INFO @ Thu, 05 Apr 2018 09:52:54: 8000000 INFO @ Thu, 05 Apr 2018 09:52:55: 9000000 INFO @ Thu, 05 Apr 2018 09:53:01: 9000000 INFO @ Thu, 05 Apr 2018 09:53:01: 9000000 INFO @ Thu, 05 Apr 2018 09:53:01: 10000000 INFO @ Thu, 05 Apr 2018 09:53:07: 11000000 INFO @ Thu, 05 Apr 2018 09:53:07: 10000000 INFO @ Thu, 05 Apr 2018 09:53:07: 10000000 INFO @ Thu, 05 Apr 2018 09:53:13: 12000000 INFO @ Thu, 05 Apr 2018 09:53:14: 11000000 INFO @ Thu, 05 Apr 2018 09:53:14: 11000000 INFO @ Thu, 05 Apr 2018 09:53:18: 13000000 INFO @ Thu, 05 Apr 2018 09:53:20: 12000000 INFO @ Thu, 05 Apr 2018 09:53:20: 12000000 INFO @ Thu, 05 Apr 2018 09:53:24: 14000000 INFO @ Thu, 05 Apr 2018 09:53:27: 13000000 INFO @ Thu, 05 Apr 2018 09:53:27: 13000000 INFO @ Thu, 05 Apr 2018 09:53:30: 15000000 INFO @ Thu, 05 Apr 2018 09:53:33: 14000000 INFO @ Thu, 05 Apr 2018 09:53:33: 14000000 INFO @ Thu, 05 Apr 2018 09:53:36: 16000000 INFO @ Thu, 05 Apr 2018 09:53:40: 15000000 INFO @ Thu, 05 Apr 2018 09:53:40: 15000000 INFO @ Thu, 05 Apr 2018 09:53:42: 17000000 INFO @ Thu, 05 Apr 2018 09:53:46: 16000000 INFO @ Thu, 05 Apr 2018 09:53:46: 16000000 INFO @ Thu, 05 Apr 2018 09:53:47: 18000000 INFO @ Thu, 05 Apr 2018 09:53:53: 17000000 INFO @ Thu, 05 Apr 2018 09:53:53: 17000000 INFO @ Thu, 05 Apr 2018 09:53:53: 19000000 INFO @ Thu, 05 Apr 2018 09:53:59: 18000000 INFO @ Thu, 05 Apr 2018 09:53:59: 18000000 INFO @ Thu, 05 Apr 2018 09:53:59: 20000000 INFO @ Thu, 05 Apr 2018 09:54:05: 21000000 INFO @ Thu, 05 Apr 2018 09:54:06: 19000000 INFO @ Thu, 05 Apr 2018 09:54:06: 19000000 INFO @ Thu, 05 Apr 2018 09:54:11: 22000000 INFO @ Thu, 05 Apr 2018 09:54:12: 20000000 INFO @ Thu, 05 Apr 2018 09:54:12: 20000000 INFO @ Thu, 05 Apr 2018 09:54:17: 23000000 INFO @ Thu, 05 Apr 2018 09:54:19: 21000000 INFO @ Thu, 05 Apr 2018 09:54:19: 21000000 INFO @ Thu, 05 Apr 2018 09:54:23: 24000000 INFO @ Thu, 05 Apr 2018 09:54:25: 22000000 INFO @ Thu, 05 Apr 2018 09:54:25: 22000000 INFO @ Thu, 05 Apr 2018 09:54:29: 25000000 INFO @ Thu, 05 Apr 2018 09:54:31: 23000000 INFO @ Thu, 05 Apr 2018 09:54:32: 23000000 INFO @ Thu, 05 Apr 2018 09:54:32: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:54:32: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:54:32: #1 total tags in treatment: 12615887 INFO @ Thu, 05 Apr 2018 09:54:32: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:54:32: #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 09:54:33: #1 tags after filtering in treatment: 9085947 INFO @ Thu, 05 Apr 2018 09:54:33: #1 Redundant rate of treatment: 0.28 INFO @ Thu, 05 Apr 2018 09:54:33: #1 finished! INFO @ Thu, 05 Apr 2018 09:54:33: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:54:33: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:54:33: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 09:54:33: 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 09:54:33: Process for pairing-model is terminated! cat: SRX3671157.05_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 `SRX3671157.05_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 `SRX3671157.05_*.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 `SRX3671157.05_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 09:54:37: 24000000 INFO @ Thu, 05 Apr 2018 09:54:37: 24000000 INFO @ Thu, 05 Apr 2018 09:54:43: 25000000 INFO @ Thu, 05 Apr 2018 09:54:43: 25000000 INFO @ Thu, 05 Apr 2018 09:54:46: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:54:46: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:54:46: #1 total tags in treatment: 12615887 INFO @ Thu, 05 Apr 2018 09:54:46: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:54:46: #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 09:54:46: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:54:46: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:54:46: #1 total tags in treatment: 12615887 INFO @ Thu, 05 Apr 2018 09:54:46: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:54:46: #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 09:54:46: #1 tags after filtering in treatment: 9085947 INFO @ Thu, 05 Apr 2018 09:54:46: #1 Redundant rate of treatment: 0.28 INFO @ Thu, 05 Apr 2018 09:54:46: #1 finished! INFO @ Thu, 05 Apr 2018 09:54:46: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:54:46: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:54:46: #1 tags after filtering in treatment: 9085947 INFO @ Thu, 05 Apr 2018 09:54:46: #1 Redundant rate of treatment: 0.28 INFO @ Thu, 05 Apr 2018 09:54:46: #1 finished! INFO @ Thu, 05 Apr 2018 09:54:46: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:54:46: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:54:47: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 09:54:47: 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 09:54:47: Process for pairing-model is terminated! cat: SRX3671157.20_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 `SRX3671157.20_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 `SRX3671157.20_*.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 `SRX3671157.20_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 09:54:47: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 09:54:47: 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 09:54:47: Process for pairing-model is terminated! cat: SRX3671157.10_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 `SRX3671157.10_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 `SRX3671157.10_*.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 `SRX3671157.10_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。