Job ID = 10536367 sra ファイルのダウンロード中... Completed: 1055028K bytes transferred in 27 seconds (314564K 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 29583083 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3433229/SRR6333870.sra Written 29583083 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: 00:22:26 29583083 reads; of these: 29583083 (100.00%) were paired; of these: 3957777 (13.38%) aligned concordantly 0 times 23570483 (79.68%) aligned concordantly exactly 1 time 2054823 (6.95%) aligned concordantly >1 times ---- 3957777 pairs aligned concordantly 0 times; of these: 1169958 (29.56%) aligned discordantly 1 time ---- 2787819 pairs aligned 0 times concordantly or discordantly; of these: 5575638 mates make up the pairs; of these: 3846469 (68.99%) aligned 0 times 1406483 (25.23%) aligned exactly 1 time 322686 (5.79%) aligned >1 times 93.50% overall alignment rate Time searching: 00:22:26 Overall time: 00:22:26 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] 5638011 / 25732597 = 0.2191 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 09:38:40: # Command line: callpeak -t SRX3433229.bam -f BAM -g 12100000 -n SRX3433229.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3433229.05 # format = BAM # ChIP-seq file = ['SRX3433229.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 09:38:40: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:38:40: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:38:40: # Command line: callpeak -t SRX3433229.bam -f BAM -g 12100000 -n SRX3433229.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3433229.20 # format = BAM # ChIP-seq file = ['SRX3433229.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 09:38:40: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:38:40: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:38:40: # Command line: callpeak -t SRX3433229.bam -f BAM -g 12100000 -n SRX3433229.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3433229.10 # format = BAM # ChIP-seq file = ['SRX3433229.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 09:38:40: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:38:40: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:38:46: 1000000 INFO @ Thu, 05 Apr 2018 09:38:47: 1000000 INFO @ Thu, 05 Apr 2018 09:38:47: 1000000 INFO @ Thu, 05 Apr 2018 09:38:52: 2000000 INFO @ Thu, 05 Apr 2018 09:38:54: 2000000 INFO @ Thu, 05 Apr 2018 09:38:54: 2000000 INFO @ Thu, 05 Apr 2018 09:38:58: 3000000 INFO @ Thu, 05 Apr 2018 09:39:01: 3000000 INFO @ Thu, 05 Apr 2018 09:39:01: 3000000 INFO @ Thu, 05 Apr 2018 09:39:05: 4000000 INFO @ Thu, 05 Apr 2018 09:39:07: 4000000 INFO @ Thu, 05 Apr 2018 09:39:07: 4000000 INFO @ Thu, 05 Apr 2018 09:39:10: 5000000 INFO @ Thu, 05 Apr 2018 09:39:13: 5000000 INFO @ Thu, 05 Apr 2018 09:39:13: 5000000 INFO @ Thu, 05 Apr 2018 09:39:15: 6000000 INFO @ Thu, 05 Apr 2018 09:39:19: 6000000 INFO @ Thu, 05 Apr 2018 09:39:19: 6000000 INFO @ Thu, 05 Apr 2018 09:39:21: 7000000 INFO @ Thu, 05 Apr 2018 09:39:24: 7000000 INFO @ Thu, 05 Apr 2018 09:39:24: 7000000 INFO @ Thu, 05 Apr 2018 09:39:26: 8000000 INFO @ Thu, 05 Apr 2018 09:39:30: 8000000 INFO @ Thu, 05 Apr 2018 09:39:30: 8000000 INFO @ Thu, 05 Apr 2018 09:39:32: 9000000 INFO @ Thu, 05 Apr 2018 09:39:35: 9000000 INFO @ Thu, 05 Apr 2018 09:39:36: 9000000 INFO @ Thu, 05 Apr 2018 09:39:38: 10000000 INFO @ Thu, 05 Apr 2018 09:39:41: 10000000 INFO @ Thu, 05 Apr 2018 09:39:42: 10000000 INFO @ Thu, 05 Apr 2018 09:39:43: 11000000 INFO @ Thu, 05 Apr 2018 09:39:47: 11000000 INFO @ Thu, 05 Apr 2018 09:39:48: 11000000 INFO @ Thu, 05 Apr 2018 09:39:49: 12000000 INFO @ Thu, 05 Apr 2018 09:39:52: 12000000 INFO @ Thu, 05 Apr 2018 09:39:54: 12000000 INFO @ Thu, 05 Apr 2018 09:39:55: 13000000 INFO @ Thu, 05 Apr 2018 09:39:58: 13000000 INFO @ Thu, 05 Apr 2018 09:40:00: 13000000 INFO @ Thu, 05 Apr 2018 09:40:01: 14000000 INFO @ Thu, 05 Apr 2018 09:40:03: 14000000 INFO @ Thu, 05 Apr 2018 09:40:06: 14000000 INFO @ Thu, 05 Apr 2018 09:40:06: 15000000 INFO @ Thu, 05 Apr 2018 09:40:09: 15000000 INFO @ Thu, 05 Apr 2018 09:40:11: 15000000 INFO @ Thu, 05 Apr 2018 09:40:12: 16000000 INFO @ Thu, 05 Apr 2018 09:40:15: 16000000 INFO @ Thu, 05 Apr 2018 09:40:17: 16000000 INFO @ Thu, 05 Apr 2018 09:40:17: 17000000 INFO @ Thu, 05 Apr 2018 09:40:20: 17000000 INFO @ Thu, 05 Apr 2018 09:40:23: 17000000 INFO @ Thu, 05 Apr 2018 09:40:23: 18000000 INFO @ Thu, 05 Apr 2018 09:40:26: 18000000 INFO @ Thu, 05 Apr 2018 09:40:29: 19000000 INFO @ Thu, 05 Apr 2018 09:40:29: 18000000 INFO @ Thu, 05 Apr 2018 09:40:31: 19000000 INFO @ Thu, 05 Apr 2018 09:40:34: 20000000 INFO @ Thu, 05 Apr 2018 09:40:35: 19000000 INFO @ Thu, 05 Apr 2018 09:40:37: 20000000 INFO @ Thu, 05 Apr 2018 09:40:40: 21000000 INFO @ Thu, 05 Apr 2018 09:40:40: 20000000 INFO @ Thu, 05 Apr 2018 09:40:43: 21000000 INFO @ Thu, 05 Apr 2018 09:40:46: 22000000 INFO @ Thu, 05 Apr 2018 09:40:46: 21000000 INFO @ Thu, 05 Apr 2018 09:40:48: 22000000 INFO @ Thu, 05 Apr 2018 09:40:51: 23000000 INFO @ Thu, 05 Apr 2018 09:40:52: 22000000 INFO @ Thu, 05 Apr 2018 09:40:54: 23000000 INFO @ Thu, 05 Apr 2018 09:40:57: 24000000 INFO @ Thu, 05 Apr 2018 09:40:58: 23000000 INFO @ Thu, 05 Apr 2018 09:40:59: 24000000 INFO @ Thu, 05 Apr 2018 09:41:03: 25000000 INFO @ Thu, 05 Apr 2018 09:41:04: 24000000 INFO @ Thu, 05 Apr 2018 09:41:05: 25000000 INFO @ Thu, 05 Apr 2018 09:41:08: 26000000 INFO @ Thu, 05 Apr 2018 09:41:10: 25000000 INFO @ Thu, 05 Apr 2018 09:41:11: 26000000 INFO @ Thu, 05 Apr 2018 09:41:14: 27000000 INFO @ Thu, 05 Apr 2018 09:41:15: 26000000 INFO @ Thu, 05 Apr 2018 09:41:16: 27000000 INFO @ Thu, 05 Apr 2018 09:41:19: 28000000 INFO @ Thu, 05 Apr 2018 09:41:21: 27000000 INFO @ Thu, 05 Apr 2018 09:41:22: 28000000 INFO @ Thu, 05 Apr 2018 09:41:25: 29000000 INFO @ Thu, 05 Apr 2018 09:41:27: 28000000 INFO @ Thu, 05 Apr 2018 09:41:27: 29000000 INFO @ Thu, 05 Apr 2018 09:41:31: 30000000 INFO @ Thu, 05 Apr 2018 09:41:33: 29000000 INFO @ Thu, 05 Apr 2018 09:41:33: 30000000 INFO @ Thu, 05 Apr 2018 09:41:36: 31000000 INFO @ Thu, 05 Apr 2018 09:41:39: 30000000 INFO @ Thu, 05 Apr 2018 09:41:39: 31000000 INFO @ Thu, 05 Apr 2018 09:41:42: 32000000 INFO @ Thu, 05 Apr 2018 09:41:44: 32000000 INFO @ Thu, 05 Apr 2018 09:41:44: 31000000 INFO @ Thu, 05 Apr 2018 09:41:47: 33000000 INFO @ Thu, 05 Apr 2018 09:41:50: 33000000 INFO @ Thu, 05 Apr 2018 09:41:50: 32000000 INFO @ Thu, 05 Apr 2018 09:41:53: 34000000 INFO @ Thu, 05 Apr 2018 09:41:55: 34000000 INFO @ Thu, 05 Apr 2018 09:41:56: 33000000 INFO @ Thu, 05 Apr 2018 09:41:59: 35000000 INFO @ Thu, 05 Apr 2018 09:42:01: 35000000 INFO @ Thu, 05 Apr 2018 09:42:01: 34000000 INFO @ Thu, 05 Apr 2018 09:42:04: 36000000 INFO @ Thu, 05 Apr 2018 09:42:06: 36000000 INFO @ Thu, 05 Apr 2018 09:42:07: 35000000 INFO @ Thu, 05 Apr 2018 09:42:10: 37000000 INFO @ Thu, 05 Apr 2018 09:42:12: 37000000 INFO @ Thu, 05 Apr 2018 09:42:13: 36000000 INFO @ Thu, 05 Apr 2018 09:42:15: 38000000 INFO @ Thu, 05 Apr 2018 09:42:17: 38000000 INFO @ Thu, 05 Apr 2018 09:42:19: 37000000 INFO @ Thu, 05 Apr 2018 09:42:21: 39000000 INFO @ Thu, 05 Apr 2018 09:42:23: 39000000 INFO @ Thu, 05 Apr 2018 09:42:24: 38000000 INFO @ Thu, 05 Apr 2018 09:42:26: 40000000 INFO @ Thu, 05 Apr 2018 09:42:28: 40000000 INFO @ Thu, 05 Apr 2018 09:42:30: 39000000 INFO @ Thu, 05 Apr 2018 09:42:32: 41000000 INFO @ Thu, 05 Apr 2018 09:42:34: 41000000 INFO @ Thu, 05 Apr 2018 09:42:36: 40000000 INFO @ Thu, 05 Apr 2018 09:42:37: 42000000 INFO @ Thu, 05 Apr 2018 09:42:40: 42000000 INFO @ Thu, 05 Apr 2018 09:42:41: 41000000 INFO @ Thu, 05 Apr 2018 09:42:43: 43000000 INFO @ Thu, 05 Apr 2018 09:42:45: 43000000 INFO @ Thu, 05 Apr 2018 09:42:47: 42000000 INFO @ Thu, 05 Apr 2018 09:42:48: 44000000 INFO @ Thu, 05 Apr 2018 09:42:49: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:42:49: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:42:49: #1 total tags in treatment: 20010455 INFO @ Thu, 05 Apr 2018 09:42:49: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:42:49: #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 09:42:49: #1 tags after filtering in treatment: 11093553 INFO @ Thu, 05 Apr 2018 09:42:49: #1 Redundant rate of treatment: 0.45 INFO @ Thu, 05 Apr 2018 09:42:49: #1 finished! INFO @ Thu, 05 Apr 2018 09:42:49: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:42:49: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:42:50: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 09:42:50: 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 09:42:50: Process for pairing-model is terminated! cat: SRX3433229.10_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 `SRX3433229.10_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 `SRX3433229.10_*.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 `SRX3433229.10_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 @ Thu, 05 Apr 2018 09:42:51: 44000000 INFO @ Thu, 05 Apr 2018 09:42:51: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:42:51: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:42:51: #1 total tags in treatment: 20010455 INFO @ Thu, 05 Apr 2018 09:42:51: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:42:51: #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 09:42:51: #1 tags after filtering in treatment: 11093553 INFO @ Thu, 05 Apr 2018 09:42:51: #1 Redundant rate of treatment: 0.45 INFO @ Thu, 05 Apr 2018 09:42:51: #1 finished! INFO @ Thu, 05 Apr 2018 09:42:51: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:42:51: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:42:52: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 09:42:52: 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 09:42:52: Process for pairing-model is terminated! cat: SRX3433229.20_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 `SRX3433229.20_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 `SRX3433229.20_*.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 `SRX3433229.20_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 09:42:52: 43000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 05 Apr 2018 09:42:58: 44000000 INFO @ Thu, 05 Apr 2018 09:42:58: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:42:58: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:42:58: #1 total tags in treatment: 20010455 INFO @ Thu, 05 Apr 2018 09:42:58: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:42:58: #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 09:42:59: #1 tags after filtering in treatment: 11093553 INFO @ Thu, 05 Apr 2018 09:42:59: #1 Redundant rate of treatment: 0.45 INFO @ Thu, 05 Apr 2018 09:42:59: #1 finished! INFO @ Thu, 05 Apr 2018 09:42:59: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:42:59: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:42:59: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 09:42:59: 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 @ Thu, 05 Apr 2018 09:42:59: Process for pairing-model is terminated! cat: SRX3433229.05_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 `SRX3433229.05_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 `SRX3433229.05_*.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 `SRX3433229.05_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 BigWig に変換しました。