Job ID = 11388934 sra ファイルのダウンロード中... Completed: 1725959K bytes transferred in 31 seconds (454093K 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 31543484 spots for /home/okishinya/chipatlas/results/sacCer3/SRX5017453/SRR8198076.sra Written 31543484 spots for /home/okishinya/chipatlas/results/sacCer3/SRX5017453/SRR8198076.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: 01:04:35 31543484 reads; of these: 31543484 (100.00%) were paired; of these: 2101702 (6.66%) aligned concordantly 0 times 26297008 (83.37%) aligned concordantly exactly 1 time 3144774 (9.97%) aligned concordantly >1 times ---- 2101702 pairs aligned concordantly 0 times; of these: 354619 (16.87%) aligned discordantly 1 time ---- 1747083 pairs aligned 0 times concordantly or discordantly; of these: 3494166 mates make up the pairs; of these: 3124336 (89.42%) aligned 0 times 223304 (6.39%) aligned exactly 1 time 146526 (4.19%) aligned >1 times 95.05% overall alignment rate Time searching: 01:04:35 Overall time: 01:04:35 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 28 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] 3889756 / 29692933 = 0.1310 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 01:50:20: # Command line: callpeak -t SRX5017453.bam -f BAM -g 12100000 -n SRX5017453.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX5017453.20 # format = BAM # ChIP-seq file = ['SRX5017453.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 01:50:20: #1 read tag files... INFO @ Thu, 13 Dec 2018 01:50:20: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 01:50:20: # Command line: callpeak -t SRX5017453.bam -f BAM -g 12100000 -n SRX5017453.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX5017453.10 # format = BAM # ChIP-seq file = ['SRX5017453.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 01:50:20: #1 read tag files... INFO @ Thu, 13 Dec 2018 01:50:20: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 01:50:20: # Command line: callpeak -t SRX5017453.bam -f BAM -g 12100000 -n SRX5017453.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX5017453.05 # format = BAM # ChIP-seq file = ['SRX5017453.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 01:50:20: #1 read tag files... INFO @ Thu, 13 Dec 2018 01:50:20: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 01:50:31: 1000000 INFO @ Thu, 13 Dec 2018 01:50:33: 1000000 INFO @ Thu, 13 Dec 2018 01:50:35: 1000000 INFO @ Thu, 13 Dec 2018 01:50:43: 2000000 INFO @ Thu, 13 Dec 2018 01:50:44: 2000000 INFO @ Thu, 13 Dec 2018 01:50:46: 2000000 INFO @ Thu, 13 Dec 2018 01:50:54: 3000000 INFO @ Thu, 13 Dec 2018 01:50:56: 3000000 INFO @ Thu, 13 Dec 2018 01:50:57: 3000000 INFO @ Thu, 13 Dec 2018 01:51:04: 4000000 INFO @ Thu, 13 Dec 2018 01:51:08: 4000000 INFO @ Thu, 13 Dec 2018 01:51:13: 4000000 INFO @ Thu, 13 Dec 2018 01:51:15: 5000000 INFO @ Thu, 13 Dec 2018 01:51:24: 5000000 INFO @ Thu, 13 Dec 2018 01:51:25: 6000000 INFO @ Thu, 13 Dec 2018 01:51:30: 5000000 INFO @ Thu, 13 Dec 2018 01:51:37: 7000000 INFO @ Thu, 13 Dec 2018 01:51:40: 6000000 INFO @ Thu, 13 Dec 2018 01:51:45: 6000000 INFO @ Thu, 13 Dec 2018 01:51:48: 8000000 INFO @ Thu, 13 Dec 2018 01:51:53: 7000000 INFO @ Thu, 13 Dec 2018 01:52:00: 9000000 INFO @ Thu, 13 Dec 2018 01:52:00: 7000000 INFO @ Thu, 13 Dec 2018 01:52:07: 8000000 INFO @ Thu, 13 Dec 2018 01:52:13: 8000000 INFO @ Thu, 13 Dec 2018 01:52:15: 10000000 INFO @ Thu, 13 Dec 2018 01:52:25: 9000000 INFO @ Thu, 13 Dec 2018 01:52:30: 9000000 INFO @ Thu, 13 Dec 2018 01:52:31: 11000000 INFO @ Thu, 13 Dec 2018 01:52:41: 10000000 INFO @ Thu, 13 Dec 2018 01:52:45: 10000000 INFO @ Thu, 13 Dec 2018 01:52:45: 12000000 INFO @ Thu, 13 Dec 2018 01:52:58: 11000000 INFO @ Thu, 13 Dec 2018 01:52:59: 13000000 INFO @ Thu, 13 Dec 2018 01:53:02: 11000000 INFO @ Thu, 13 Dec 2018 01:53:12: 14000000 INFO @ Thu, 13 Dec 2018 01:53:15: 12000000 INFO @ Thu, 13 Dec 2018 01:53:20: 12000000 INFO @ Thu, 13 Dec 2018 01:53:26: 15000000 INFO @ Thu, 13 Dec 2018 01:53:30: 13000000 INFO @ Thu, 13 Dec 2018 01:53:37: 13000000 INFO @ Thu, 13 Dec 2018 01:53:47: 14000000 INFO @ Thu, 13 Dec 2018 01:53:49: 16000000 INFO @ Thu, 13 Dec 2018 01:53:51: 14000000 INFO @ Thu, 13 Dec 2018 01:54:03: 15000000 INFO @ Thu, 13 Dec 2018 01:54:10: 17000000 INFO @ Thu, 13 Dec 2018 01:54:11: 15000000 INFO @ Thu, 13 Dec 2018 01:54:17: 16000000 INFO @ Thu, 13 Dec 2018 01:54:22: 16000000 INFO @ Thu, 13 Dec 2018 01:54:31: 17000000 INFO @ Thu, 13 Dec 2018 01:54:33: 18000000 INFO @ Thu, 13 Dec 2018 01:54:35: 17000000 INFO @ Thu, 13 Dec 2018 01:54:47: 18000000 INFO @ Thu, 13 Dec 2018 01:54:47: 18000000 INFO @ Thu, 13 Dec 2018 01:54:55: 19000000 INFO @ Thu, 13 Dec 2018 01:55:01: 19000000 INFO @ Thu, 13 Dec 2018 01:55:04: 19000000 INFO @ Thu, 13 Dec 2018 01:55:12: 20000000 INFO @ Thu, 13 Dec 2018 01:55:19: 20000000 INFO @ Thu, 13 Dec 2018 01:55:25: 20000000 INFO @ Thu, 13 Dec 2018 01:55:29: 21000000 INFO @ Thu, 13 Dec 2018 01:55:42: 21000000 INFO @ Thu, 13 Dec 2018 01:55:47: 21000000 INFO @ Thu, 13 Dec 2018 01:55:47: 22000000 INFO @ Thu, 13 Dec 2018 01:56:01: 23000000 INFO @ Thu, 13 Dec 2018 01:56:02: 22000000 INFO @ Thu, 13 Dec 2018 01:56:04: 22000000 INFO @ Thu, 13 Dec 2018 01:56:18: 24000000 INFO @ Thu, 13 Dec 2018 01:56:26: 23000000 INFO @ Thu, 13 Dec 2018 01:56:26: 23000000 INFO @ Thu, 13 Dec 2018 01:56:34: 25000000 INFO @ Thu, 13 Dec 2018 01:56:45: 24000000 INFO @ Thu, 13 Dec 2018 01:56:45: 24000000 INFO @ Thu, 13 Dec 2018 01:56:51: 26000000 INFO @ Thu, 13 Dec 2018 01:57:02: 25000000 INFO @ Thu, 13 Dec 2018 01:57:02: 25000000 INFO @ Thu, 13 Dec 2018 01:57:10: 27000000 INFO @ Thu, 13 Dec 2018 01:57:18: 26000000 INFO @ Thu, 13 Dec 2018 01:57:19: 26000000 INFO @ Thu, 13 Dec 2018 01:57:25: 28000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 13 Dec 2018 01:57:36: 27000000 INFO @ Thu, 13 Dec 2018 01:57:37: 27000000 INFO @ Thu, 13 Dec 2018 01:57:48: 29000000 INFO @ Thu, 13 Dec 2018 01:57:53: 28000000 INFO @ Thu, 13 Dec 2018 01:57:55: 28000000 BigWig に変換しました。 INFO @ Thu, 13 Dec 2018 01:58:06: 29000000 INFO @ Thu, 13 Dec 2018 01:58:09: 30000000 INFO @ Thu, 13 Dec 2018 01:58:12: 29000000 INFO @ Thu, 13 Dec 2018 01:58:25: 30000000 INFO @ Thu, 13 Dec 2018 01:58:31: 31000000 INFO @ Thu, 13 Dec 2018 01:58:34: 30000000 INFO @ Thu, 13 Dec 2018 01:58:48: 32000000 INFO @ Thu, 13 Dec 2018 01:58:53: 31000000 INFO @ Thu, 13 Dec 2018 01:58:58: 31000000 INFO @ Thu, 13 Dec 2018 01:59:04: 33000000 INFO @ Thu, 13 Dec 2018 01:59:14: 32000000 INFO @ Thu, 13 Dec 2018 01:59:16: 34000000 INFO @ Thu, 13 Dec 2018 01:59:17: 32000000 INFO @ Thu, 13 Dec 2018 01:59:24: 33000000 INFO @ Thu, 13 Dec 2018 01:59:39: 33000000 INFO @ Thu, 13 Dec 2018 01:59:39: 34000000 INFO @ Thu, 13 Dec 2018 01:59:39: 35000000 INFO @ Thu, 13 Dec 2018 01:59:53: 35000000 INFO @ Thu, 13 Dec 2018 01:59:54: 36000000 INFO @ Thu, 13 Dec 2018 01:59:58: 34000000 INFO @ Thu, 13 Dec 2018 02:00:09: 36000000 INFO @ Thu, 13 Dec 2018 02:00:09: 37000000 INFO @ Thu, 13 Dec 2018 02:00:16: 35000000 INFO @ Thu, 13 Dec 2018 02:00:24: 37000000 INFO @ Thu, 13 Dec 2018 02:00:30: 38000000 INFO @ Thu, 13 Dec 2018 02:00:36: 36000000 INFO @ Thu, 13 Dec 2018 02:00:39: 38000000 INFO @ Thu, 13 Dec 2018 02:00:43: 39000000 INFO @ Thu, 13 Dec 2018 02:00:53: 37000000 INFO @ Thu, 13 Dec 2018 02:00:54: 39000000 INFO @ Thu, 13 Dec 2018 02:00:58: 40000000 INFO @ Thu, 13 Dec 2018 02:01:09: 38000000 INFO @ Thu, 13 Dec 2018 02:01:13: 40000000 INFO @ Thu, 13 Dec 2018 02:01:14: 41000000 INFO @ Thu, 13 Dec 2018 02:01:24: 39000000 INFO @ Thu, 13 Dec 2018 02:01:29: 41000000 INFO @ Thu, 13 Dec 2018 02:01:33: 42000000 INFO @ Thu, 13 Dec 2018 02:01:39: 40000000 INFO @ Thu, 13 Dec 2018 02:01:47: 42000000 INFO @ Thu, 13 Dec 2018 02:01:48: 43000000 INFO @ Thu, 13 Dec 2018 02:02:01: 43000000 INFO @ Thu, 13 Dec 2018 02:02:02: 41000000 INFO @ Thu, 13 Dec 2018 02:02:05: 44000000 INFO @ Thu, 13 Dec 2018 02:02:17: 44000000 INFO @ Thu, 13 Dec 2018 02:02:21: 42000000 INFO @ Thu, 13 Dec 2018 02:02:21: 45000000 INFO @ Thu, 13 Dec 2018 02:02:29: 45000000 INFO @ Thu, 13 Dec 2018 02:02:37: 43000000 INFO @ Thu, 13 Dec 2018 02:02:37: 46000000 INFO @ Thu, 13 Dec 2018 02:02:41: 46000000 INFO @ Thu, 13 Dec 2018 02:02:53: 47000000 INFO @ Thu, 13 Dec 2018 02:02:54: 44000000 INFO @ Thu, 13 Dec 2018 02:02:58: 47000000 INFO @ Thu, 13 Dec 2018 02:03:06: 48000000 INFO @ Thu, 13 Dec 2018 02:03:16: 45000000 INFO @ Thu, 13 Dec 2018 02:03:17: 48000000 INFO @ Thu, 13 Dec 2018 02:03:22: 49000000 INFO @ Thu, 13 Dec 2018 02:03:34: 49000000 INFO @ Thu, 13 Dec 2018 02:03:34: 46000000 INFO @ Thu, 13 Dec 2018 02:03:35: 50000000 INFO @ Thu, 13 Dec 2018 02:03:51: 51000000 INFO @ Thu, 13 Dec 2018 02:03:56: 50000000 INFO @ Thu, 13 Dec 2018 02:03:59: 47000000 INFO @ Thu, 13 Dec 2018 02:04:14: 52000000 INFO @ Thu, 13 Dec 2018 02:04:17: #1 tag size is determined as 75 bps INFO @ Thu, 13 Dec 2018 02:04:17: #1 tag size = 75 INFO @ Thu, 13 Dec 2018 02:04:17: #1 total tags in treatment: 25573324 INFO @ Thu, 13 Dec 2018 02:04:17: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 02:04:17: #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 02:04:18: #1 tags after filtering in treatment: 13556166 INFO @ Thu, 13 Dec 2018 02:04:18: #1 Redundant rate of treatment: 0.47 INFO @ Thu, 13 Dec 2018 02:04:18: #1 finished! INFO @ Thu, 13 Dec 2018 02:04:18: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 02:04:18: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 02:04:20: #2 number of paired peaks: 0 WARNING @ Thu, 13 Dec 2018 02:04:20: 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 02:04:20: Process for pairing-model is terminated! cat: SRX5017453.10_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): 9 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX5017453.10_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 `SRX5017453.10_*.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 `SRX5017453.10_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 02:04:20: 51000000 INFO @ Thu, 13 Dec 2018 02:04:21: 48000000 INFO @ Thu, 13 Dec 2018 02:04:33: 49000000 INFO @ Thu, 13 Dec 2018 02:04:43: 52000000 INFO @ Thu, 13 Dec 2018 02:04:44: 50000000 INFO @ Thu, 13 Dec 2018 02:04:47: #1 tag size is determined as 75 bps INFO @ Thu, 13 Dec 2018 02:04:47: #1 tag size = 75 INFO @ Thu, 13 Dec 2018 02:04:47: #1 total tags in treatment: 25573324 INFO @ Thu, 13 Dec 2018 02:04:47: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 02:04:47: #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 02:04:48: #1 tags after filtering in treatment: 13556166 INFO @ Thu, 13 Dec 2018 02:04:48: #1 Redundant rate of treatment: 0.47 INFO @ Thu, 13 Dec 2018 02:04:48: #1 finished! INFO @ Thu, 13 Dec 2018 02:04:48: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 02:04:48: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 02:04:49: #2 number of paired peaks: 0 WARNING @ Thu, 13 Dec 2018 02:04:49: 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 02:04:49: Process for pairing-model is terminated! cat: SRX5017453.05_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): 9 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX5017453.05_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 `SRX5017453.05_*.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 `SRX5017453.05_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 INFO @ Thu, 13 Dec 2018 02:04:53: 51000000 INFO @ Thu, 13 Dec 2018 02:05:03: 52000000 INFO @ Thu, 13 Dec 2018 02:05:05: #1 tag size is determined as 75 bps INFO @ Thu, 13 Dec 2018 02:05:05: #1 tag size = 75 INFO @ Thu, 13 Dec 2018 02:05:05: #1 total tags in treatment: 25573324 INFO @ Thu, 13 Dec 2018 02:05:05: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 02:05:05: #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 02:05:06: #1 tags after filtering in treatment: 13556166 INFO @ Thu, 13 Dec 2018 02:05:06: #1 Redundant rate of treatment: 0.47 INFO @ Thu, 13 Dec 2018 02:05:06: #1 finished! INFO @ Thu, 13 Dec 2018 02:05:06: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 02:05:06: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 02:05:07: #2 number of paired peaks: 0 WARNING @ Thu, 13 Dec 2018 02:05:07: 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 02:05:07: Process for pairing-model is terminated! cat: SRX5017453.20_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): 10 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX5017453.20_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 `SRX5017453.20_*.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 `SRX5017453.20_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