Job ID = 9161959 sra ファイルのダウンロード中... Completed: 1826114K bytes transferred in 17 seconds (851433K 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 30295240 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1423693/SRR2930982.sra Written 30295240 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: 00:24:26 30295240 reads; of these: 30295240 (100.00%) were paired; of these: 1921224 (6.34%) aligned concordantly 0 times 25322864 (83.59%) aligned concordantly exactly 1 time 3051152 (10.07%) aligned concordantly >1 times ---- 1921224 pairs aligned concordantly 0 times; of these: 48908 (2.55%) aligned discordantly 1 time ---- 1872316 pairs aligned 0 times concordantly or discordantly; of these: 3744632 mates make up the pairs; of these: 3421812 (91.38%) aligned 0 times 263091 (7.03%) aligned exactly 1 time 59729 (1.60%) aligned >1 times 94.35% overall alignment rate Time searching: 00:24:26 Overall time: 00:24:26 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] 11772713 / 28387259 = 0.4147 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 @ Wed, 28 Jun 2017 05:46:23: # Command line: callpeak -t SRX1423693.bam -f BAM -g 12100000 -n SRX1423693.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1423693.05 # format = BAM # ChIP-seq file = ['SRX1423693.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 @ Wed, 28 Jun 2017 05:46:23: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:46:23: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:46:23: # Command line: callpeak -t SRX1423693.bam -f BAM -g 12100000 -n SRX1423693.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1423693.10 # format = BAM # ChIP-seq file = ['SRX1423693.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 @ Wed, 28 Jun 2017 05:46:23: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:46:23: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:46:23: # Command line: callpeak -t SRX1423693.bam -f BAM -g 12100000 -n SRX1423693.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1423693.20 # format = BAM # ChIP-seq file = ['SRX1423693.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 @ Wed, 28 Jun 2017 05:46:23: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:46:23: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:46:31: 1000000 INFO @ Wed, 28 Jun 2017 05:46:31: 1000000 INFO @ Wed, 28 Jun 2017 05:46:33: 1000000 INFO @ Wed, 28 Jun 2017 05:46:39: 2000000 INFO @ Wed, 28 Jun 2017 05:46:40: 2000000 INFO @ Wed, 28 Jun 2017 05:46:42: 2000000 INFO @ Wed, 28 Jun 2017 05:46:47: 3000000 INFO @ Wed, 28 Jun 2017 05:46:48: 3000000 INFO @ Wed, 28 Jun 2017 05:46:49: 3000000 INFO @ Wed, 28 Jun 2017 05:46:54: 4000000 INFO @ Wed, 28 Jun 2017 05:46:55: 4000000 INFO @ Wed, 28 Jun 2017 05:46:57: 4000000 INFO @ Wed, 28 Jun 2017 05:47:02: 5000000 INFO @ Wed, 28 Jun 2017 05:47:03: 5000000 INFO @ Wed, 28 Jun 2017 05:47:05: 5000000 INFO @ Wed, 28 Jun 2017 05:47:09: 6000000 INFO @ Wed, 28 Jun 2017 05:47:10: 6000000 INFO @ Wed, 28 Jun 2017 05:47:13: 6000000 INFO @ Wed, 28 Jun 2017 05:47:17: 7000000 INFO @ Wed, 28 Jun 2017 05:47:19: 7000000 INFO @ Wed, 28 Jun 2017 05:47:22: 7000000 INFO @ Wed, 28 Jun 2017 05:47:27: 8000000 INFO @ Wed, 28 Jun 2017 05:47:29: 8000000 INFO @ Wed, 28 Jun 2017 05:47:32: 8000000 INFO @ Wed, 28 Jun 2017 05:47:36: 9000000 INFO @ Wed, 28 Jun 2017 05:47:38: 9000000 INFO @ Wed, 28 Jun 2017 05:47:42: 9000000 INFO @ Wed, 28 Jun 2017 05:47:47: 10000000 INFO @ Wed, 28 Jun 2017 05:47:48: 10000000 INFO @ Wed, 28 Jun 2017 05:47:52: 10000000 INFO @ Wed, 28 Jun 2017 05:47:57: 11000000 INFO @ Wed, 28 Jun 2017 05:47:59: 11000000 INFO @ Wed, 28 Jun 2017 05:48:03: 11000000 INFO @ Wed, 28 Jun 2017 05:48:07: 12000000 INFO @ Wed, 28 Jun 2017 05:48:09: 12000000 INFO @ Wed, 28 Jun 2017 05:48:13: 12000000 INFO @ Wed, 28 Jun 2017 05:48:17: 13000000 INFO @ Wed, 28 Jun 2017 05:48:19: 13000000 INFO @ Wed, 28 Jun 2017 05:48:21: 13000000 INFO @ Wed, 28 Jun 2017 05:48:26: 14000000 INFO @ Wed, 28 Jun 2017 05:48:27: 14000000 INFO @ Wed, 28 Jun 2017 05:48:27: 14000000 INFO @ Wed, 28 Jun 2017 05:48:34: 15000000 INFO @ Wed, 28 Jun 2017 05:48:34: 15000000 INFO @ Wed, 28 Jun 2017 05:48:35: 15000000 INFO @ Wed, 28 Jun 2017 05:48:41: 16000000 INFO @ Wed, 28 Jun 2017 05:48:43: 16000000 INFO @ Wed, 28 Jun 2017 05:48:44: 16000000 INFO @ Wed, 28 Jun 2017 05:48:47: 17000000 INFO @ Wed, 28 Jun 2017 05:48:51: 17000000 INFO @ Wed, 28 Jun 2017 05:48:52: 17000000 INFO @ Wed, 28 Jun 2017 05:48:54: 18000000 INFO @ Wed, 28 Jun 2017 05:48:59: 18000000 INFO @ Wed, 28 Jun 2017 05:49:00: 18000000 INFO @ Wed, 28 Jun 2017 05:49:01: 19000000 INFO @ Wed, 28 Jun 2017 05:49:06: 19000000 INFO @ Wed, 28 Jun 2017 05:49:07: 20000000 INFO @ Wed, 28 Jun 2017 05:49:07: 19000000 INFO @ Wed, 28 Jun 2017 05:49:14: 21000000 INFO @ Wed, 28 Jun 2017 05:49:14: 20000000 INFO @ Wed, 28 Jun 2017 05:49:15: 20000000 INFO @ Wed, 28 Jun 2017 05:49:20: 22000000 INFO @ Wed, 28 Jun 2017 05:49:21: 21000000 INFO @ Wed, 28 Jun 2017 05:49:22: 21000000 INFO @ Wed, 28 Jun 2017 05:49:26: 23000000 INFO @ Wed, 28 Jun 2017 05:49:29: 22000000 INFO @ Wed, 28 Jun 2017 05:49:30: 22000000 INFO @ Wed, 28 Jun 2017 05:49:33: 24000000 INFO @ Wed, 28 Jun 2017 05:49:36: 23000000 INFO @ Wed, 28 Jun 2017 05:49:37: 23000000 INFO @ Wed, 28 Jun 2017 05:49:39: 25000000 INFO @ Wed, 28 Jun 2017 05:49:44: 24000000 INFO @ Wed, 28 Jun 2017 05:49:45: 24000000 INFO @ Wed, 28 Jun 2017 05:49:46: 26000000 INFO @ Wed, 28 Jun 2017 05:49:51: 25000000 INFO @ Wed, 28 Jun 2017 05:49:52: 27000000 INFO @ Wed, 28 Jun 2017 05:49:52: 25000000 INFO @ Wed, 28 Jun 2017 05:49:58: 28000000 INFO @ Wed, 28 Jun 2017 05:49:59: 26000000 INFO @ Wed, 28 Jun 2017 05:50:00: 26000000 INFO @ Wed, 28 Jun 2017 05:50:05: 29000000 INFO @ Wed, 28 Jun 2017 05:50:06: 27000000 INFO @ Wed, 28 Jun 2017 05:50:08: 27000000 INFO @ Wed, 28 Jun 2017 05:50:13: 30000000 INFO @ Wed, 28 Jun 2017 05:50:18: 28000000 INFO @ Wed, 28 Jun 2017 05:50:20: 28000000 INFO @ Wed, 28 Jun 2017 05:50:25: 31000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 28 Jun 2017 05:50:30: 29000000 INFO @ Wed, 28 Jun 2017 05:50:31: 29000000 INFO @ Wed, 28 Jun 2017 05:50:37: 32000000 INFO @ Wed, 28 Jun 2017 05:50:42: 30000000 INFO @ Wed, 28 Jun 2017 05:50:43: 30000000 INFO @ Wed, 28 Jun 2017 05:50:50: 33000000 BigWig に変換しました。 INFO @ Wed, 28 Jun 2017 05:50:53: 31000000 INFO @ Wed, 28 Jun 2017 05:50:55: 31000000 INFO @ Wed, 28 Jun 2017 05:50:57: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:50:57: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:50:57: #1 total tags in treatment: 16608309 INFO @ Wed, 28 Jun 2017 05:50:57: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:50:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 05:50:58: #1 tags after filtering in treatment: 11057118 INFO @ Wed, 28 Jun 2017 05:50:58: #1 Redundant rate of treatment: 0.33 INFO @ Wed, 28 Jun 2017 05:50:58: #1 finished! INFO @ Wed, 28 Jun 2017 05:50:58: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:50:58: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:50:58: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 05:50:58: 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 @ Wed, 28 Jun 2017 05:50:58: Process for pairing-model is terminated! cat: SRX1423693.20_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 `SRX1423693.20_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 `SRX1423693.20_*.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 `SRX1423693.20_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 @ Wed, 28 Jun 2017 05:51:02: 32000000 INFO @ Wed, 28 Jun 2017 05:51:06: 32000000 INFO @ Wed, 28 Jun 2017 05:51:11: 33000000 INFO @ Wed, 28 Jun 2017 05:51:17: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:51:17: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:51:17: #1 total tags in treatment: 16608309 INFO @ Wed, 28 Jun 2017 05:51:17: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:51:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 05:51:17: #1 tags after filtering in treatment: 11057118 INFO @ Wed, 28 Jun 2017 05:51:17: #1 Redundant rate of treatment: 0.33 INFO @ Wed, 28 Jun 2017 05:51:17: #1 finished! INFO @ Wed, 28 Jun 2017 05:51:17: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:51:17: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:51:17: 33000000 INFO @ Wed, 28 Jun 2017 05:51:18: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 05:51:18: 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 @ Wed, 28 Jun 2017 05:51:18: Process for pairing-model is terminated! cat: SRX1423693.10_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 `SRX1423693.10_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 `SRX1423693.10_*.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 `SRX1423693.10_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 @ Wed, 28 Jun 2017 05:51:23: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:51:23: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:51:23: #1 total tags in treatment: 16608309 INFO @ Wed, 28 Jun 2017 05:51:23: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:51:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 05:51:24: #1 tags after filtering in treatment: 11057118 INFO @ Wed, 28 Jun 2017 05:51:24: #1 Redundant rate of treatment: 0.33 INFO @ Wed, 28 Jun 2017 05:51:24: #1 finished! INFO @ Wed, 28 Jun 2017 05:51:24: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:51:24: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:51:25: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 05:51:25: 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 @ Wed, 28 Jun 2017 05:51:25: Process for pairing-model is terminated! cat: SRX1423693.05_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 `SRX1423693.05_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 `SRX1423693.05_*.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 `SRX1423693.05_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