Job ID = 10488211 sra ファイルのダウンロード中... Completed: 942862K bytes transferred in 22 seconds (343914K 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 19426712 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3188112/SRR6039984.sra Written 19426712 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: 00:12:54 19426712 reads; of these: 19426712 (100.00%) were paired; of these: 3092177 (15.92%) aligned concordantly 0 times 14816859 (76.27%) aligned concordantly exactly 1 time 1517676 (7.81%) aligned concordantly >1 times ---- 3092177 pairs aligned concordantly 0 times; of these: 641810 (20.76%) aligned discordantly 1 time ---- 2450367 pairs aligned 0 times concordantly or discordantly; of these: 4900734 mates make up the pairs; of these: 4042943 (82.50%) aligned 0 times 540480 (11.03%) aligned exactly 1 time 317311 (6.47%) aligned >1 times 89.59% overall alignment rate Time searching: 00:12:54 Overall time: 00:12:54 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 16 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] 665915 / 16968375 = 0.0392 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, 18 Mar 2018 12:41:48: # Command line: callpeak -t SRX3188112.bam -f BAM -g 12100000 -n SRX3188112.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3188112.20 # format = BAM # ChIP-seq file = ['SRX3188112.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, 18 Mar 2018 12:41:48: #1 read tag files... INFO @ Sun, 18 Mar 2018 12:41:48: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 12:41:48: # Command line: callpeak -t SRX3188112.bam -f BAM -g 12100000 -n SRX3188112.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3188112.05 # format = BAM # ChIP-seq file = ['SRX3188112.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, 18 Mar 2018 12:41:48: #1 read tag files... INFO @ Sun, 18 Mar 2018 12:41:48: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 12:41:48: # Command line: callpeak -t SRX3188112.bam -f BAM -g 12100000 -n SRX3188112.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3188112.10 # format = BAM # ChIP-seq file = ['SRX3188112.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, 18 Mar 2018 12:41:48: #1 read tag files... INFO @ Sun, 18 Mar 2018 12:41:48: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 12:41:54: 1000000 INFO @ Sun, 18 Mar 2018 12:41:54: 1000000 INFO @ Sun, 18 Mar 2018 12:41:54: 1000000 INFO @ Sun, 18 Mar 2018 12:42:00: 2000000 INFO @ Sun, 18 Mar 2018 12:42:00: 2000000 INFO @ Sun, 18 Mar 2018 12:42:00: 2000000 INFO @ Sun, 18 Mar 2018 12:42:05: 3000000 INFO @ Sun, 18 Mar 2018 12:42:06: 3000000 INFO @ Sun, 18 Mar 2018 12:42:06: 3000000 INFO @ Sun, 18 Mar 2018 12:42:11: 4000000 INFO @ Sun, 18 Mar 2018 12:42:11: 4000000 INFO @ Sun, 18 Mar 2018 12:42:11: 4000000 INFO @ Sun, 18 Mar 2018 12:42:17: 5000000 INFO @ Sun, 18 Mar 2018 12:42:17: 5000000 INFO @ Sun, 18 Mar 2018 12:42:17: 5000000 INFO @ Sun, 18 Mar 2018 12:42:22: 6000000 INFO @ Sun, 18 Mar 2018 12:42:22: 6000000 INFO @ Sun, 18 Mar 2018 12:42:23: 6000000 INFO @ Sun, 18 Mar 2018 12:42:28: 7000000 INFO @ Sun, 18 Mar 2018 12:42:28: 7000000 INFO @ Sun, 18 Mar 2018 12:42:28: 7000000 INFO @ Sun, 18 Mar 2018 12:42:34: 8000000 INFO @ Sun, 18 Mar 2018 12:42:34: 8000000 INFO @ Sun, 18 Mar 2018 12:42:34: 8000000 INFO @ Sun, 18 Mar 2018 12:42:39: 9000000 INFO @ Sun, 18 Mar 2018 12:42:39: 9000000 INFO @ Sun, 18 Mar 2018 12:42:39: 9000000 INFO @ Sun, 18 Mar 2018 12:42:45: 10000000 INFO @ Sun, 18 Mar 2018 12:42:45: 10000000 INFO @ Sun, 18 Mar 2018 12:42:45: 10000000 INFO @ Sun, 18 Mar 2018 12:42:50: 11000000 INFO @ Sun, 18 Mar 2018 12:42:50: 11000000 INFO @ Sun, 18 Mar 2018 12:42:51: 11000000 INFO @ Sun, 18 Mar 2018 12:42:56: 12000000 INFO @ Sun, 18 Mar 2018 12:42:56: 12000000 INFO @ Sun, 18 Mar 2018 12:42:56: 12000000 INFO @ Sun, 18 Mar 2018 12:43:01: 13000000 INFO @ Sun, 18 Mar 2018 12:43:02: 13000000 INFO @ Sun, 18 Mar 2018 12:43:02: 13000000 INFO @ Sun, 18 Mar 2018 12:43:07: 14000000 INFO @ Sun, 18 Mar 2018 12:43:07: 14000000 INFO @ Sun, 18 Mar 2018 12:43:08: 14000000 INFO @ Sun, 18 Mar 2018 12:43:13: 15000000 INFO @ Sun, 18 Mar 2018 12:43:13: 15000000 INFO @ Sun, 18 Mar 2018 12:43:13: 15000000 INFO @ Sun, 18 Mar 2018 12:43:18: 16000000 INFO @ Sun, 18 Mar 2018 12:43:19: 16000000 INFO @ Sun, 18 Mar 2018 12:43:19: 16000000 INFO @ Sun, 18 Mar 2018 12:43:24: 17000000 INFO @ Sun, 18 Mar 2018 12:43:24: 17000000 INFO @ Sun, 18 Mar 2018 12:43:24: 17000000 INFO @ Sun, 18 Mar 2018 12:43:29: 18000000 INFO @ Sun, 18 Mar 2018 12:43:30: 18000000 INFO @ Sun, 18 Mar 2018 12:43:30: 18000000 INFO @ Sun, 18 Mar 2018 12:43:35: 19000000 INFO @ Sun, 18 Mar 2018 12:43:35: 19000000 INFO @ Sun, 18 Mar 2018 12:43:36: 19000000 INFO @ Sun, 18 Mar 2018 12:43:40: 20000000 INFO @ Sun, 18 Mar 2018 12:43:41: 20000000 INFO @ Sun, 18 Mar 2018 12:43:41: 20000000 INFO @ Sun, 18 Mar 2018 12:43:46: 21000000 INFO @ Sun, 18 Mar 2018 12:43:46: 21000000 INFO @ Sun, 18 Mar 2018 12:43:47: 21000000 INFO @ Sun, 18 Mar 2018 12:43:51: 22000000 INFO @ Sun, 18 Mar 2018 12:43:52: 22000000 INFO @ Sun, 18 Mar 2018 12:43:52: 22000000 INFO @ Sun, 18 Mar 2018 12:43:56: 23000000 INFO @ Sun, 18 Mar 2018 12:43:57: 23000000 INFO @ Sun, 18 Mar 2018 12:43:58: 23000000 INFO @ Sun, 18 Mar 2018 12:44:02: 24000000 INFO @ Sun, 18 Mar 2018 12:44:03: 24000000 INFO @ Sun, 18 Mar 2018 12:44:04: 24000000 INFO @ Sun, 18 Mar 2018 12:44:08: 25000000 INFO @ Sun, 18 Mar 2018 12:44:09: 25000000 INFO @ Sun, 18 Mar 2018 12:44:09: 25000000 INFO @ Sun, 18 Mar 2018 12:44:13: 26000000 INFO @ Sun, 18 Mar 2018 12:44:14: 26000000 INFO @ Sun, 18 Mar 2018 12:44:15: 26000000 INFO @ Sun, 18 Mar 2018 12:44:19: 27000000 INFO @ Sun, 18 Mar 2018 12:44:20: 27000000 INFO @ Sun, 18 Mar 2018 12:44:21: 27000000 INFO @ Sun, 18 Mar 2018 12:44:24: 28000000 INFO @ Sun, 18 Mar 2018 12:44:26: 28000000 INFO @ Sun, 18 Mar 2018 12:44:27: 28000000 INFO @ Sun, 18 Mar 2018 12:44:30: 29000000 INFO @ Sun, 18 Mar 2018 12:44:31: 29000000 INFO @ Sun, 18 Mar 2018 12:44:32: 29000000 INFO @ Sun, 18 Mar 2018 12:44:35: 30000000 INFO @ Sun, 18 Mar 2018 12:44:37: 30000000 INFO @ Sun, 18 Mar 2018 12:44:38: 30000000 INFO @ Sun, 18 Mar 2018 12:44:41: 31000000 INFO @ Sun, 18 Mar 2018 12:44:43: 31000000 INFO @ Sun, 18 Mar 2018 12:44:44: 31000000 INFO @ Sun, 18 Mar 2018 12:44:46: 32000000 INFO @ Sun, 18 Mar 2018 12:44:48: 32000000 INFO @ Sun, 18 Mar 2018 12:44:49: 32000000 INFO @ Sun, 18 Mar 2018 12:44:52: 33000000 INFO @ Sun, 18 Mar 2018 12:44:54: 33000000 INFO @ Sun, 18 Mar 2018 12:44:54: #1 tag size is determined as 51 bps INFO @ Sun, 18 Mar 2018 12:44:54: #1 tag size = 51 INFO @ Sun, 18 Mar 2018 12:44:54: #1 total tags in treatment: 15675988 INFO @ Sun, 18 Mar 2018 12:44:54: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 12:44:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 18 Mar 2018 12:44:55: #1 tags after filtering in treatment: 10280176 INFO @ Sun, 18 Mar 2018 12:44:55: #1 Redundant rate of treatment: 0.34 INFO @ Sun, 18 Mar 2018 12:44:55: #1 finished! INFO @ Sun, 18 Mar 2018 12:44:55: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 12:44:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 12:44:55: 33000000 INFO @ Sun, 18 Mar 2018 12:44:55: #2 number of paired peaks: 0 WARNING @ Sun, 18 Mar 2018 12:44:55: 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, 18 Mar 2018 12:44:55: Process for pairing-model is terminated! cat: SRX3188112.10_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 `SRX3188112.10_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 `SRX3188112.10_*.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 `SRX3188112.10_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 @ Sun, 18 Mar 2018 12:44:57: #1 tag size is determined as 51 bps INFO @ Sun, 18 Mar 2018 12:44:57: #1 tag size = 51 INFO @ Sun, 18 Mar 2018 12:44:57: #1 total tags in treatment: 15675988 INFO @ Sun, 18 Mar 2018 12:44:57: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 12:44:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 18 Mar 2018 12:44:57: #1 tags after filtering in treatment: 10280176 INFO @ Sun, 18 Mar 2018 12:44:57: #1 Redundant rate of treatment: 0.34 INFO @ Sun, 18 Mar 2018 12:44:57: #1 finished! INFO @ Sun, 18 Mar 2018 12:44:57: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 12:44:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 12:44:58: #2 number of paired peaks: 0 WARNING @ Sun, 18 Mar 2018 12:44:58: 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 @ Sun, 18 Mar 2018 12:44:58: Process for pairing-model is terminated! cat: SRX3188112.20_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 `SRX3188112.20_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 `SRX3188112.20_*.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 `SRX3188112.20_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, 18 Mar 2018 12:44:58: #1 tag size is determined as 51 bps INFO @ Sun, 18 Mar 2018 12:44:58: #1 tag size = 51 INFO @ Sun, 18 Mar 2018 12:44:58: #1 total tags in treatment: 15675988 INFO @ Sun, 18 Mar 2018 12:44:58: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 12:44:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 18 Mar 2018 12:44:58: #1 tags after filtering in treatment: 10280176 INFO @ Sun, 18 Mar 2018 12:44:58: #1 Redundant rate of treatment: 0.34 INFO @ Sun, 18 Mar 2018 12:44:58: #1 finished! INFO @ Sun, 18 Mar 2018 12:44:58: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 12:44:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 12:44:59: #2 number of paired peaks: 0 WARNING @ Sun, 18 Mar 2018 12:44:59: 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, 18 Mar 2018 12:44:59: Process for pairing-model is terminated! cat: SRX3188112.05_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 `SRX3188112.05_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 `SRX3188112.05_*.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 `SRX3188112.05_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。