Job ID = 11388935 sra ファイルのダウンロード中... Completed: 1474267K bytes transferred in 30 seconds (402348K 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... Read 26584369 spots for /home/okishinya/chipatlas/results/sacCer3/SRX5017454/SRR8198077.sra Written 26584369 spots for /home/okishinya/chipatlas/results/sacCer3/SRX5017454/SRR8198077.sra 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: 00:57:35 26584369 reads; of these: 26584369 (100.00%) were paired; of these: 1934948 (7.28%) aligned concordantly 0 times 22019261 (82.83%) aligned concordantly exactly 1 time 2630160 (9.89%) aligned concordantly >1 times ---- 1934948 pairs aligned concordantly 0 times; of these: 244381 (12.63%) aligned discordantly 1 time ---- 1690567 pairs aligned 0 times concordantly or discordantly; of these: 3381134 mates make up the pairs; of these: 3045444 (90.07%) aligned 0 times 219019 (6.48%) aligned exactly 1 time 116671 (3.45%) aligned >1 times 94.27% overall alignment rate Time searching: 00:57:35 Overall time: 00:57:35 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] 3035093 / 24769620 = 0.1225 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, 13 Dec 2018 01:38:44: # Command line: callpeak -t SRX5017454.bam -f BAM -g 12100000 -n SRX5017454.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX5017454.05 # format = BAM # ChIP-seq file = ['SRX5017454.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, 13 Dec 2018 01:38:44: #1 read tag files... INFO @ Thu, 13 Dec 2018 01:38:44: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 01:38:44: # Command line: callpeak -t SRX5017454.bam -f BAM -g 12100000 -n SRX5017454.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX5017454.20 # format = BAM # ChIP-seq file = ['SRX5017454.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, 13 Dec 2018 01:38:44: #1 read tag files... INFO @ Thu, 13 Dec 2018 01:38:44: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 01:38:44: # Command line: callpeak -t SRX5017454.bam -f BAM -g 12100000 -n SRX5017454.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX5017454.10 # format = BAM # ChIP-seq file = ['SRX5017454.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, 13 Dec 2018 01:38:44: #1 read tag files... INFO @ Thu, 13 Dec 2018 01:38:44: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 01:39:03: 1000000 INFO @ Thu, 13 Dec 2018 01:39:05: 1000000 INFO @ Thu, 13 Dec 2018 01:39:05: 1000000 INFO @ Thu, 13 Dec 2018 01:39:22: 2000000 INFO @ Thu, 13 Dec 2018 01:39:27: 2000000 INFO @ Thu, 13 Dec 2018 01:39:27: 2000000 INFO @ Thu, 13 Dec 2018 01:39:40: 3000000 INFO @ Thu, 13 Dec 2018 01:39:47: 3000000 INFO @ Thu, 13 Dec 2018 01:39:47: 3000000 INFO @ Thu, 13 Dec 2018 01:39:57: 4000000 INFO @ Thu, 13 Dec 2018 01:40:07: 4000000 INFO @ Thu, 13 Dec 2018 01:40:07: 4000000 INFO @ Thu, 13 Dec 2018 01:40:16: 5000000 INFO @ Thu, 13 Dec 2018 01:40:27: 5000000 INFO @ Thu, 13 Dec 2018 01:40:27: 5000000 INFO @ Thu, 13 Dec 2018 01:40:34: 6000000 INFO @ Thu, 13 Dec 2018 01:40:47: 6000000 INFO @ Thu, 13 Dec 2018 01:40:47: 6000000 INFO @ Thu, 13 Dec 2018 01:40:54: 7000000 INFO @ Thu, 13 Dec 2018 01:41:07: 7000000 INFO @ Thu, 13 Dec 2018 01:41:10: 7000000 INFO @ Thu, 13 Dec 2018 01:41:13: 8000000 INFO @ Thu, 13 Dec 2018 01:41:25: 8000000 INFO @ Thu, 13 Dec 2018 01:41:32: 9000000 INFO @ Thu, 13 Dec 2018 01:41:35: 8000000 INFO @ Thu, 13 Dec 2018 01:41:44: 9000000 INFO @ Thu, 13 Dec 2018 01:41:52: 10000000 INFO @ Thu, 13 Dec 2018 01:41:59: 9000000 INFO @ Thu, 13 Dec 2018 01:42:02: 10000000 INFO @ Thu, 13 Dec 2018 01:42:11: 11000000 INFO @ Thu, 13 Dec 2018 01:42:20: 11000000 INFO @ Thu, 13 Dec 2018 01:42:25: 10000000 INFO @ Thu, 13 Dec 2018 01:42:31: 12000000 INFO @ Thu, 13 Dec 2018 01:42:38: 12000000 INFO @ Thu, 13 Dec 2018 01:42:48: 11000000 INFO @ Thu, 13 Dec 2018 01:42:49: 13000000 INFO @ Thu, 13 Dec 2018 01:42:59: 13000000 INFO @ Thu, 13 Dec 2018 01:43:10: 14000000 INFO @ Thu, 13 Dec 2018 01:43:13: 12000000 INFO @ Thu, 13 Dec 2018 01:43:19: 14000000 INFO @ Thu, 13 Dec 2018 01:43:29: 15000000 INFO @ Thu, 13 Dec 2018 01:43:38: 15000000 INFO @ Thu, 13 Dec 2018 01:43:38: 13000000 INFO @ Thu, 13 Dec 2018 01:43:47: 16000000 INFO @ Thu, 13 Dec 2018 01:43:56: 16000000 INFO @ Thu, 13 Dec 2018 01:44:03: 14000000 INFO @ Thu, 13 Dec 2018 01:44:05: 17000000 INFO @ Thu, 13 Dec 2018 01:44:15: 17000000 INFO @ Thu, 13 Dec 2018 01:44:28: 18000000 INFO @ Thu, 13 Dec 2018 01:44:28: 15000000 INFO @ Thu, 13 Dec 2018 01:44:36: 18000000 INFO @ Thu, 13 Dec 2018 01:44:51: 19000000 INFO @ Thu, 13 Dec 2018 01:44:52: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 13 Dec 2018 01:45:01: 19000000 INFO @ Thu, 13 Dec 2018 01:45:14: 20000000 INFO @ Thu, 13 Dec 2018 01:45:17: 17000000 INFO @ Thu, 13 Dec 2018 01:45:25: 20000000 BigWig に変換しました。 INFO @ Thu, 13 Dec 2018 01:45:37: 21000000 INFO @ Thu, 13 Dec 2018 01:45:41: 18000000 INFO @ Thu, 13 Dec 2018 01:45:51: 21000000 INFO @ Thu, 13 Dec 2018 01:45:59: 22000000 INFO @ Thu, 13 Dec 2018 01:46:06: 19000000 INFO @ Thu, 13 Dec 2018 01:46:13: 22000000 INFO @ Thu, 13 Dec 2018 01:46:23: 23000000 INFO @ Thu, 13 Dec 2018 01:46:29: 20000000 INFO @ Thu, 13 Dec 2018 01:46:37: 23000000 INFO @ Thu, 13 Dec 2018 01:46:44: 24000000 INFO @ Thu, 13 Dec 2018 01:46:53: 21000000 INFO @ Thu, 13 Dec 2018 01:47:02: 25000000 INFO @ Thu, 13 Dec 2018 01:47:02: 24000000 INFO @ Thu, 13 Dec 2018 01:47:17: 22000000 INFO @ Thu, 13 Dec 2018 01:47:24: 26000000 INFO @ Thu, 13 Dec 2018 01:47:26: 25000000 INFO @ Thu, 13 Dec 2018 01:47:41: 23000000 INFO @ Thu, 13 Dec 2018 01:47:51: 27000000 INFO @ Thu, 13 Dec 2018 01:47:53: 26000000 INFO @ Thu, 13 Dec 2018 01:48:02: 24000000 INFO @ Thu, 13 Dec 2018 01:48:14: 28000000 INFO @ Thu, 13 Dec 2018 01:48:17: 27000000 INFO @ Thu, 13 Dec 2018 01:48:19: 25000000 INFO @ Thu, 13 Dec 2018 01:48:37: 29000000 INFO @ Thu, 13 Dec 2018 01:48:38: 26000000 INFO @ Thu, 13 Dec 2018 01:48:43: 28000000 INFO @ Thu, 13 Dec 2018 01:48:58: 27000000 INFO @ Thu, 13 Dec 2018 01:48:59: 30000000 INFO @ Thu, 13 Dec 2018 01:49:07: 29000000 INFO @ Thu, 13 Dec 2018 01:49:18: 28000000 INFO @ Thu, 13 Dec 2018 01:49:19: 31000000 INFO @ Thu, 13 Dec 2018 01:49:30: 30000000 INFO @ Thu, 13 Dec 2018 01:49:38: 29000000 INFO @ Thu, 13 Dec 2018 01:49:39: 32000000 INFO @ Thu, 13 Dec 2018 01:49:49: 31000000 INFO @ Thu, 13 Dec 2018 01:49:57: 30000000 INFO @ Thu, 13 Dec 2018 01:50:02: 33000000 INFO @ Thu, 13 Dec 2018 01:50:10: 32000000 INFO @ Thu, 13 Dec 2018 01:50:17: 31000000 INFO @ Thu, 13 Dec 2018 01:50:23: 34000000 INFO @ Thu, 13 Dec 2018 01:50:31: 33000000 INFO @ Thu, 13 Dec 2018 01:50:35: 32000000 INFO @ Thu, 13 Dec 2018 01:50:44: 35000000 INFO @ Thu, 13 Dec 2018 01:50:51: 34000000 INFO @ Thu, 13 Dec 2018 01:50:54: 33000000 INFO @ Thu, 13 Dec 2018 01:51:06: 36000000 INFO @ Thu, 13 Dec 2018 01:51:11: 35000000 INFO @ Thu, 13 Dec 2018 01:51:13: 34000000 INFO @ Thu, 13 Dec 2018 01:51:27: 37000000 INFO @ Thu, 13 Dec 2018 01:51:32: 35000000 INFO @ Thu, 13 Dec 2018 01:51:33: 36000000 INFO @ Thu, 13 Dec 2018 01:51:50: 38000000 INFO @ Thu, 13 Dec 2018 01:51:51: 36000000 INFO @ Thu, 13 Dec 2018 01:51:56: 37000000 INFO @ Thu, 13 Dec 2018 01:52:10: 37000000 INFO @ Thu, 13 Dec 2018 01:52:12: 39000000 INFO @ Thu, 13 Dec 2018 01:52:18: 38000000 INFO @ Thu, 13 Dec 2018 01:52:30: 38000000 INFO @ Thu, 13 Dec 2018 01:52:35: 40000000 INFO @ Thu, 13 Dec 2018 01:52:42: 39000000 INFO @ Thu, 13 Dec 2018 01:52:49: 39000000 INFO @ Thu, 13 Dec 2018 01:53:00: 41000000 INFO @ Thu, 13 Dec 2018 01:53:08: 40000000 INFO @ Thu, 13 Dec 2018 01:53:08: 40000000 INFO @ Thu, 13 Dec 2018 01:53:25: 42000000 INFO @ Thu, 13 Dec 2018 01:53:28: 41000000 INFO @ Thu, 13 Dec 2018 01:53:34: 41000000 INFO @ Thu, 13 Dec 2018 01:53:47: 42000000 INFO @ Thu, 13 Dec 2018 01:53:51: 43000000 INFO @ Thu, 13 Dec 2018 01:53:59: 42000000 INFO @ Thu, 13 Dec 2018 01:54:07: 43000000 INFO @ Thu, 13 Dec 2018 01:54:16: 44000000 INFO @ Thu, 13 Dec 2018 01:54:17: #1 tag size is determined as 75 bps INFO @ Thu, 13 Dec 2018 01:54:17: #1 tag size = 75 INFO @ Thu, 13 Dec 2018 01:54:17: #1 total tags in treatment: 21623501 INFO @ Thu, 13 Dec 2018 01:54:17: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 01:54:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 13 Dec 2018 01:54:18: #1 tags after filtering in treatment: 12332934 INFO @ Thu, 13 Dec 2018 01:54:18: #1 Redundant rate of treatment: 0.43 INFO @ Thu, 13 Dec 2018 01:54:18: #1 finished! INFO @ Thu, 13 Dec 2018 01:54:18: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 01:54:18: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 01:54:19: #2 number of paired peaks: 0 WARNING @ Thu, 13 Dec 2018 01:54:19: 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, 13 Dec 2018 01:54:19: Process for pairing-model is terminated! cat: SRX5017454.20_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): 6 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX5017454.20_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 `SRX5017454.20_*.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 `SRX5017454.20_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, 13 Dec 2018 01:54:23: 43000000 INFO @ Thu, 13 Dec 2018 01:54:26: 44000000 INFO @ Thu, 13 Dec 2018 01:54:27: #1 tag size is determined as 75 bps INFO @ Thu, 13 Dec 2018 01:54:27: #1 tag size = 75 INFO @ Thu, 13 Dec 2018 01:54:27: #1 total tags in treatment: 21623501 INFO @ Thu, 13 Dec 2018 01:54:27: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 01:54:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 13 Dec 2018 01:54:28: #1 tags after filtering in treatment: 12332934 INFO @ Thu, 13 Dec 2018 01:54:28: #1 Redundant rate of treatment: 0.43 INFO @ Thu, 13 Dec 2018 01:54:28: #1 finished! INFO @ Thu, 13 Dec 2018 01:54:28: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 01:54:28: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 01:54:29: #2 number of paired peaks: 0 WARNING @ Thu, 13 Dec 2018 01:54:29: 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 @ Thu, 13 Dec 2018 01:54:29: Process for pairing-model is terminated! cat: SRX5017454.10_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): 8 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX5017454.10_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 `SRX5017454.10_*.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 `SRX5017454.10_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, 13 Dec 2018 01:54:44: 44000000 INFO @ Thu, 13 Dec 2018 01:54:45: #1 tag size is determined as 75 bps INFO @ Thu, 13 Dec 2018 01:54:45: #1 tag size = 75 INFO @ Thu, 13 Dec 2018 01:54:45: #1 total tags in treatment: 21623501 INFO @ Thu, 13 Dec 2018 01:54:45: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 01:54:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 13 Dec 2018 01:54:46: #1 tags after filtering in treatment: 12332934 INFO @ Thu, 13 Dec 2018 01:54:46: #1 Redundant rate of treatment: 0.43 INFO @ Thu, 13 Dec 2018 01:54:46: #1 finished! INFO @ Thu, 13 Dec 2018 01:54:46: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 01:54:46: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 01:54:47: #2 number of paired peaks: 0 WARNING @ Thu, 13 Dec 2018 01:54:47: 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, 13 Dec 2018 01:54:47: Process for pairing-model is terminated! cat: SRX5017454.05_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): 6 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX5017454.05_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 `SRX5017454.05_*.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 `SRX5017454.05_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