Job ID = 9732082 sra ファイルのダウンロード中... Completed: 334286K bytes transferred in 17 seconds (153695K 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 14420903 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2675872/SRR5380648.sra Written 14420903 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: 00:06:17 14420903 reads; of these: 14420903 (100.00%) were paired; of these: 3782070 (26.23%) aligned concordantly 0 times 9664726 (67.02%) aligned concordantly exactly 1 time 974107 (6.75%) aligned concordantly >1 times ---- 3782070 pairs aligned concordantly 0 times; of these: 741061 (19.59%) aligned discordantly 1 time ---- 3041009 pairs aligned 0 times concordantly or discordantly; of these: 6082018 mates make up the pairs; of these: 5227414 (85.95%) aligned 0 times 613748 (10.09%) aligned exactly 1 time 240856 (3.96%) aligned >1 times 81.88% overall alignment rate Time searching: 00:06:17 Overall time: 00:06:17 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 8 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] 1730122 / 10990172 = 0.1574 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 @ Sun, 03 Sep 2017 19:36:17: # Command line: callpeak -t SRX2675872.bam -f BAM -g 12100000 -n SRX2675872.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2675872.05 # format = BAM # ChIP-seq file = ['SRX2675872.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 @ Sun, 03 Sep 2017 19:36:17: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:36:17: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:36:17: # Command line: callpeak -t SRX2675872.bam -f BAM -g 12100000 -n SRX2675872.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2675872.10 # format = BAM # ChIP-seq file = ['SRX2675872.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 @ Sun, 03 Sep 2017 19:36:17: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:36:17: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:36:17: # Command line: callpeak -t SRX2675872.bam -f BAM -g 12100000 -n SRX2675872.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2675872.20 # format = BAM # ChIP-seq file = ['SRX2675872.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 @ Sun, 03 Sep 2017 19:36:17: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:36:17: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:36:22: 1000000 INFO @ Sun, 03 Sep 2017 19:36:22: 1000000 INFO @ Sun, 03 Sep 2017 19:36:22: 1000000 INFO @ Sun, 03 Sep 2017 19:36:27: 2000000 INFO @ Sun, 03 Sep 2017 19:36:27: 2000000 INFO @ Sun, 03 Sep 2017 19:36:27: 2000000 INFO @ Sun, 03 Sep 2017 19:36:32: 3000000 INFO @ Sun, 03 Sep 2017 19:36:32: 3000000 INFO @ Sun, 03 Sep 2017 19:36:33: 3000000 INFO @ Sun, 03 Sep 2017 19:36:37: 4000000 INFO @ Sun, 03 Sep 2017 19:36:37: 4000000 INFO @ Sun, 03 Sep 2017 19:36:38: 4000000 INFO @ Sun, 03 Sep 2017 19:36:42: 5000000 INFO @ Sun, 03 Sep 2017 19:36:42: 5000000 INFO @ Sun, 03 Sep 2017 19:36:43: 5000000 INFO @ Sun, 03 Sep 2017 19:36:48: 6000000 INFO @ Sun, 03 Sep 2017 19:36:48: 6000000 INFO @ Sun, 03 Sep 2017 19:36:48: 6000000 INFO @ Sun, 03 Sep 2017 19:36:53: 7000000 INFO @ Sun, 03 Sep 2017 19:36:53: 7000000 INFO @ Sun, 03 Sep 2017 19:36:54: 7000000 INFO @ Sun, 03 Sep 2017 19:36:58: 8000000 INFO @ Sun, 03 Sep 2017 19:36:58: 8000000 INFO @ Sun, 03 Sep 2017 19:36:59: 8000000 INFO @ Sun, 03 Sep 2017 19:37:03: 9000000 INFO @ Sun, 03 Sep 2017 19:37:03: 9000000 INFO @ Sun, 03 Sep 2017 19:37:04: 9000000 INFO @ Sun, 03 Sep 2017 19:37:08: 10000000 INFO @ Sun, 03 Sep 2017 19:37:08: 10000000 INFO @ Sun, 03 Sep 2017 19:37:09: 10000000 INFO @ Sun, 03 Sep 2017 19:37:13: 11000000 INFO @ Sun, 03 Sep 2017 19:37:13: 11000000 INFO @ Sun, 03 Sep 2017 19:37:15: 11000000 INFO @ Sun, 03 Sep 2017 19:37:18: 12000000 INFO @ Sun, 03 Sep 2017 19:37:18: 12000000 INFO @ Sun, 03 Sep 2017 19:37:20: 12000000 INFO @ Sun, 03 Sep 2017 19:37:23: 13000000 INFO @ Sun, 03 Sep 2017 19:37:23: 13000000 INFO @ Sun, 03 Sep 2017 19:37:25: 13000000 INFO @ Sun, 03 Sep 2017 19:37:28: 14000000 INFO @ Sun, 03 Sep 2017 19:37:28: 14000000 INFO @ Sun, 03 Sep 2017 19:37:30: 14000000 INFO @ Sun, 03 Sep 2017 19:37:33: 15000000 INFO @ Sun, 03 Sep 2017 19:37:33: 15000000 INFO @ Sun, 03 Sep 2017 19:37:35: 15000000 INFO @ Sun, 03 Sep 2017 19:37:38: 16000000 INFO @ Sun, 03 Sep 2017 19:37:38: 16000000 INFO @ Sun, 03 Sep 2017 19:37:41: 16000000 INFO @ Sun, 03 Sep 2017 19:37:43: 17000000 INFO @ Sun, 03 Sep 2017 19:37:43: 17000000 INFO @ Sun, 03 Sep 2017 19:37:46: 17000000 INFO @ Sun, 03 Sep 2017 19:37:48: 18000000 INFO @ Sun, 03 Sep 2017 19:37:48: 18000000 INFO @ Sun, 03 Sep 2017 19:37:51: 18000000 INFO @ Sun, 03 Sep 2017 19:37:53: 19000000 INFO @ Sun, 03 Sep 2017 19:37:53: 19000000 INFO @ Sun, 03 Sep 2017 19:37:56: 19000000 INFO @ Sun, 03 Sep 2017 19:37:58: 20000000 INFO @ Sun, 03 Sep 2017 19:37:58: 20000000 INFO @ Sun, 03 Sep 2017 19:37:59: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:37:59: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:37:59: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:37:59: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:37:59: #1 total tags in treatment: 8914594 INFO @ Sun, 03 Sep 2017 19:37:59: #1 total tags in treatment: 8914594 INFO @ Sun, 03 Sep 2017 19:37:59: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:37:59: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:37:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 19:37:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 19:37:59: #1 tags after filtering in treatment: 4235054 INFO @ Sun, 03 Sep 2017 19:37:59: #1 Redundant rate of treatment: 0.52 INFO @ Sun, 03 Sep 2017 19:37:59: #1 finished! INFO @ Sun, 03 Sep 2017 19:37:59: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:37:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:37:59: #1 tags after filtering in treatment: 4235054 INFO @ Sun, 03 Sep 2017 19:37:59: #1 Redundant rate of treatment: 0.52 INFO @ Sun, 03 Sep 2017 19:37:59: #1 finished! INFO @ Sun, 03 Sep 2017 19:37:59: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:37:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:38:00: #2 number of paired peaks: 0 WARNING @ Sun, 03 Sep 2017 19:38:00: 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 @ Sun, 03 Sep 2017 19:38:00: Process for pairing-model is terminated! INFO @ Sun, 03 Sep 2017 19:38:00: #2 number of paired peaks: 0 WARNING @ Sun, 03 Sep 2017 19:38:00: 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 @ Sun, 03 Sep 2017 19:38:00: Process for pairing-model is terminated! cat: SRX2675872.10_peaks.narrowPeak: そのようなファイルやディレクトリはありません cat: SRX2675872.20_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): 31 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) pass1 - making usageList (0 chroms): 20 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2675872.10_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 `SRX2675872.10_*.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 `SRX2675872.10_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 rm: cannot remove `SRX2675872.20_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 `SRX2675872.20_*.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 `SRX2675872.20_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 @ Sun, 03 Sep 2017 19:38:01: 20000000 INFO @ Sun, 03 Sep 2017 19:38:02: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:38:02: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:38:02: #1 total tags in treatment: 8914594 INFO @ Sun, 03 Sep 2017 19:38:02: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:38:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 19:38:03: #1 tags after filtering in treatment: 4235054 INFO @ Sun, 03 Sep 2017 19:38:03: #1 Redundant rate of treatment: 0.52 INFO @ Sun, 03 Sep 2017 19:38:03: #1 finished! INFO @ Sun, 03 Sep 2017 19:38:03: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:38:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:38:03: #2 number of paired peaks: 0 WARNING @ Sun, 03 Sep 2017 19:38:03: 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 @ Sun, 03 Sep 2017 19:38:03: Process for pairing-model is terminated! cat: SRX2675872.05_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): 10 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2675872.05_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 `SRX2675872.05_*.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 `SRX2675872.05_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 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。