Job ID = 10609026 sra ファイルのダウンロード中... Completed: 1711209K bytes transferred in 115 seconds (121705K 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 28934248 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3862162/SRR6914377.sra Written 28934248 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: 00:31:08 28934248 reads; of these: 28934248 (100.00%) were paired; of these: 2567544 (8.87%) aligned concordantly 0 times 17758901 (61.38%) aligned concordantly exactly 1 time 8607803 (29.75%) aligned concordantly >1 times ---- 2567544 pairs aligned concordantly 0 times; of these: 628997 (24.50%) aligned discordantly 1 time ---- 1938547 pairs aligned 0 times concordantly or discordantly; of these: 3877094 mates make up the pairs; of these: 2513783 (64.84%) aligned 0 times 418422 (10.79%) aligned exactly 1 time 944889 (24.37%) aligned >1 times 95.66% overall alignment rate Time searching: 00:31:08 Overall time: 00:31:08 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] 7386277 / 26949682 = 0.2741 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, 03 May 2018 23:59:21: # Command line: callpeak -t SRX3862162.bam -f BAM -g 12100000 -n SRX3862162.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3862162.20 # format = BAM # ChIP-seq file = ['SRX3862162.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, 03 May 2018 23:59:21: # Command line: callpeak -t SRX3862162.bam -f BAM -g 12100000 -n SRX3862162.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3862162.05 # format = BAM # ChIP-seq file = ['SRX3862162.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, 03 May 2018 23:59:21: # Command line: callpeak -t SRX3862162.bam -f BAM -g 12100000 -n SRX3862162.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3862162.10 # format = BAM # ChIP-seq file = ['SRX3862162.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, 03 May 2018 23:59:21: #1 read tag files... INFO @ Thu, 03 May 2018 23:59:21: #1 read tag files... INFO @ Thu, 03 May 2018 23:59:21: #1 read tag files... INFO @ Thu, 03 May 2018 23:59:21: #1 read treatment tags... INFO @ Thu, 03 May 2018 23:59:21: #1 read treatment tags... INFO @ Thu, 03 May 2018 23:59:21: #1 read treatment tags... INFO @ Thu, 03 May 2018 23:59:27: 1000000 INFO @ Thu, 03 May 2018 23:59:27: 1000000 INFO @ Thu, 03 May 2018 23:59:27: 1000000 INFO @ Thu, 03 May 2018 23:59:32: 2000000 INFO @ Thu, 03 May 2018 23:59:32: 2000000 INFO @ Thu, 03 May 2018 23:59:33: 2000000 INFO @ Thu, 03 May 2018 23:59:38: 3000000 INFO @ Thu, 03 May 2018 23:59:38: 3000000 INFO @ Thu, 03 May 2018 23:59:38: 3000000 INFO @ Thu, 03 May 2018 23:59:44: 4000000 INFO @ Thu, 03 May 2018 23:59:44: 4000000 INFO @ Thu, 03 May 2018 23:59:44: 4000000 INFO @ Thu, 03 May 2018 23:59:50: 5000000 INFO @ Thu, 03 May 2018 23:59:50: 5000000 INFO @ Thu, 03 May 2018 23:59:50: 5000000 INFO @ Thu, 03 May 2018 23:59:56: 6000000 INFO @ Thu, 03 May 2018 23:59:56: 6000000 INFO @ Thu, 03 May 2018 23:59:56: 6000000 INFO @ Fri, 04 May 2018 00:00:02: 7000000 INFO @ Fri, 04 May 2018 00:00:02: 7000000 INFO @ Fri, 04 May 2018 00:00:02: 7000000 INFO @ Fri, 04 May 2018 00:00:07: 8000000 INFO @ Fri, 04 May 2018 00:00:08: 8000000 INFO @ Fri, 04 May 2018 00:00:08: 8000000 INFO @ Fri, 04 May 2018 00:00:13: 9000000 INFO @ Fri, 04 May 2018 00:00:14: 9000000 INFO @ Fri, 04 May 2018 00:00:15: 9000000 INFO @ Fri, 04 May 2018 00:00:19: 10000000 INFO @ Fri, 04 May 2018 00:00:20: 10000000 INFO @ Fri, 04 May 2018 00:00:21: 10000000 INFO @ Fri, 04 May 2018 00:00:24: 11000000 INFO @ Fri, 04 May 2018 00:00:26: 11000000 INFO @ Fri, 04 May 2018 00:00:27: 11000000 INFO @ Fri, 04 May 2018 00:00:30: 12000000 INFO @ Fri, 04 May 2018 00:00:32: 12000000 INFO @ Fri, 04 May 2018 00:00:33: 12000000 INFO @ Fri, 04 May 2018 00:00:35: 13000000 INFO @ Fri, 04 May 2018 00:00:37: 13000000 INFO @ Fri, 04 May 2018 00:00:39: 13000000 INFO @ Fri, 04 May 2018 00:00:41: 14000000 INFO @ Fri, 04 May 2018 00:00:44: 14000000 INFO @ Fri, 04 May 2018 00:00:46: 14000000 INFO @ Fri, 04 May 2018 00:00:47: 15000000 INFO @ Fri, 04 May 2018 00:00:50: 15000000 INFO @ Fri, 04 May 2018 00:00:52: 15000000 INFO @ Fri, 04 May 2018 00:00:52: 16000000 INFO @ Fri, 04 May 2018 00:00:56: 16000000 INFO @ Fri, 04 May 2018 00:00:58: 17000000 INFO @ Fri, 04 May 2018 00:00:58: 16000000 INFO @ Fri, 04 May 2018 00:01:02: 17000000 INFO @ Fri, 04 May 2018 00:01:03: 18000000 INFO @ Fri, 04 May 2018 00:01:04: 17000000 INFO @ Fri, 04 May 2018 00:01:07: 18000000 INFO @ Fri, 04 May 2018 00:01:09: 19000000 INFO @ Fri, 04 May 2018 00:01:11: 18000000 INFO @ Fri, 04 May 2018 00:01:13: 19000000 INFO @ Fri, 04 May 2018 00:01:15: 20000000 INFO @ Fri, 04 May 2018 00:01:17: 19000000 INFO @ Fri, 04 May 2018 00:01:19: 20000000 INFO @ Fri, 04 May 2018 00:01:20: 21000000 INFO @ Fri, 04 May 2018 00:01:23: 20000000 INFO @ Fri, 04 May 2018 00:01:25: 21000000 INFO @ Fri, 04 May 2018 00:01:26: 22000000 INFO @ Fri, 04 May 2018 00:01:29: 21000000 INFO @ Fri, 04 May 2018 00:01:31: 22000000 INFO @ Fri, 04 May 2018 00:01:31: 23000000 INFO @ Fri, 04 May 2018 00:01:35: 22000000 INFO @ Fri, 04 May 2018 00:01:36: 23000000 INFO @ Fri, 04 May 2018 00:01:37: 24000000 INFO @ Fri, 04 May 2018 00:01:41: 23000000 INFO @ Fri, 04 May 2018 00:01:42: 25000000 INFO @ Fri, 04 May 2018 00:01:42: 24000000 INFO @ Fri, 04 May 2018 00:01:47: 24000000 INFO @ Fri, 04 May 2018 00:01:47: 26000000 INFO @ Fri, 04 May 2018 00:01:48: 25000000 INFO @ Fri, 04 May 2018 00:01:53: 27000000 INFO @ Fri, 04 May 2018 00:01:53: 25000000 INFO @ Fri, 04 May 2018 00:01:54: 26000000 INFO @ Fri, 04 May 2018 00:01:58: 28000000 INFO @ Fri, 04 May 2018 00:01:59: 26000000 INFO @ Fri, 04 May 2018 00:01:59: 27000000 INFO @ Fri, 04 May 2018 00:02:04: 29000000 INFO @ Fri, 04 May 2018 00:02:05: 27000000 INFO @ Fri, 04 May 2018 00:02:05: 28000000 INFO @ Fri, 04 May 2018 00:02:09: 30000000 INFO @ Fri, 04 May 2018 00:02:11: 28000000 INFO @ Fri, 04 May 2018 00:02:11: 29000000 INFO @ Fri, 04 May 2018 00:02:15: 31000000 INFO @ Fri, 04 May 2018 00:02:17: 30000000 INFO @ Fri, 04 May 2018 00:02:17: 29000000 INFO @ Fri, 04 May 2018 00:02:21: 32000000 INFO @ Fri, 04 May 2018 00:02:23: 31000000 INFO @ Fri, 04 May 2018 00:02:23: 30000000 INFO @ Fri, 04 May 2018 00:02:26: 33000000 INFO @ Fri, 04 May 2018 00:02:29: 32000000 INFO @ Fri, 04 May 2018 00:02:29: 31000000 INFO @ Fri, 04 May 2018 00:02:32: 34000000 INFO @ Fri, 04 May 2018 00:02:34: 33000000 INFO @ Fri, 04 May 2018 00:02:35: 32000000 INFO @ Fri, 04 May 2018 00:02:37: 35000000 INFO @ Fri, 04 May 2018 00:02:40: 34000000 INFO @ Fri, 04 May 2018 00:02:42: 33000000 INFO @ Fri, 04 May 2018 00:02:43: 36000000 INFO @ Fri, 04 May 2018 00:02:46: 35000000 INFO @ Fri, 04 May 2018 00:02:48: 34000000 INFO @ Fri, 04 May 2018 00:02:49: 37000000 INFO @ Fri, 04 May 2018 00:02:52: 36000000 INFO @ Fri, 04 May 2018 00:02:54: 35000000 INFO @ Fri, 04 May 2018 00:02:54: 38000000 INFO @ Fri, 04 May 2018 00:02:58: 37000000 INFO @ Fri, 04 May 2018 00:03:00: 39000000 INFO @ Fri, 04 May 2018 00:03:00: 36000000 INFO @ Fri, 04 May 2018 00:03:04: 38000000 INFO @ Fri, 04 May 2018 00:03:05: 40000000 INFO @ Fri, 04 May 2018 00:03:06: 37000000 INFO @ Fri, 04 May 2018 00:03:09: #1 tag size is determined as 75 bps INFO @ Fri, 04 May 2018 00:03:09: #1 tag size = 75 INFO @ Fri, 04 May 2018 00:03:09: #1 total tags in treatment: 19029117 INFO @ Fri, 04 May 2018 00:03:09: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 00:03:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 May 2018 00:03:09: #1 tags after filtering in treatment: 10472866 INFO @ Fri, 04 May 2018 00:03:09: #1 Redundant rate of treatment: 0.45 INFO @ Fri, 04 May 2018 00:03:09: #1 finished! INFO @ Fri, 04 May 2018 00:03:09: #2 Build Peak Model... INFO @ Fri, 04 May 2018 00:03:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 00:03:10: #2 number of paired peaks: 0 WARNING @ Fri, 04 May 2018 00:03:10: 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 @ Fri, 04 May 2018 00:03:10: Process for pairing-model is terminated! cat: SRX3862162.10_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 `SRX3862162.10_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 `SRX3862162.10_*.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 `SRX3862162.10_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 @ Fri, 04 May 2018 00:03:10: 39000000 INFO @ Fri, 04 May 2018 00:03:12: 38000000 INFO @ Fri, 04 May 2018 00:03:16: 40000000 INFO @ Fri, 04 May 2018 00:03:18: 39000000 INFO @ Fri, 04 May 2018 00:03:19: #1 tag size is determined as 75 bps INFO @ Fri, 04 May 2018 00:03:19: #1 tag size = 75 INFO @ Fri, 04 May 2018 00:03:19: #1 total tags in treatment: 19029117 INFO @ Fri, 04 May 2018 00:03:19: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 00:03:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 May 2018 00:03:20: #1 tags after filtering in treatment: 10472866 INFO @ Fri, 04 May 2018 00:03:20: #1 Redundant rate of treatment: 0.45 INFO @ Fri, 04 May 2018 00:03:20: #1 finished! INFO @ Fri, 04 May 2018 00:03:20: #2 Build Peak Model... INFO @ Fri, 04 May 2018 00:03:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 00:03:20: #2 number of paired peaks: 0 WARNING @ Fri, 04 May 2018 00:03:20: 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 @ Fri, 04 May 2018 00:03:20: Process for pairing-model is terminated! cat: SRX3862162.05_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 `SRX3862162.05_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 `SRX3862162.05_*.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 `SRX3862162.05_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 @ Fri, 04 May 2018 00:03:24: 40000000 INFO @ Fri, 04 May 2018 00:03:28: #1 tag size is determined as 75 bps INFO @ Fri, 04 May 2018 00:03:28: #1 tag size = 75 INFO @ Fri, 04 May 2018 00:03:28: #1 total tags in treatment: 19029117 INFO @ Fri, 04 May 2018 00:03:28: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 00:03:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 May 2018 00:03:28: #1 tags after filtering in treatment: 10472866 INFO @ Fri, 04 May 2018 00:03:28: #1 Redundant rate of treatment: 0.45 INFO @ Fri, 04 May 2018 00:03:28: #1 finished! INFO @ Fri, 04 May 2018 00:03:28: #2 Build Peak Model... INFO @ Fri, 04 May 2018 00:03:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 00:03:29: #2 number of paired peaks: 0 WARNING @ Fri, 04 May 2018 00:03:29: 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 @ Fri, 04 May 2018 00:03:29: Process for pairing-model is terminated! cat: SRX3862162.20_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 `SRX3862162.20_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 `SRX3862162.20_*.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 `SRX3862162.20_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。