Job ID = 9162104 sra ファイルのダウンロード中... Completed: 973732K bytes transferred in 10 seconds (734542K 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 22547840 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1631840/SRR3225773.sra Written 22547840 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: 00:18:58 22547840 reads; of these: 22547840 (100.00%) were paired; of these: 1072912 (4.76%) aligned concordantly 0 times 19014160 (84.33%) aligned concordantly exactly 1 time 2460768 (10.91%) aligned concordantly >1 times ---- 1072912 pairs aligned concordantly 0 times; of these: 448185 (41.77%) aligned discordantly 1 time ---- 624727 pairs aligned 0 times concordantly or discordantly; of these: 1249454 mates make up the pairs; of these: 940005 (75.23%) aligned 0 times 141690 (11.34%) aligned exactly 1 time 167759 (13.43%) aligned >1 times 97.92% overall alignment rate Time searching: 00:18:58 Overall time: 00:18:58 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 20 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] 750036 / 21814448 = 0.0344 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 06:24:30: # Command line: callpeak -t SRX1631840.bam -f BAM -g 12100000 -n SRX1631840.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1631840.10 # format = BAM # ChIP-seq file = ['SRX1631840.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 06:24:30: #1 read tag files... INFO @ Wed, 28 Jun 2017 06:24:30: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 06:24:30: # Command line: callpeak -t SRX1631840.bam -f BAM -g 12100000 -n SRX1631840.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1631840.05 # format = BAM # ChIP-seq file = ['SRX1631840.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 06:24:30: #1 read tag files... INFO @ Wed, 28 Jun 2017 06:24:30: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 06:24:30: # Command line: callpeak -t SRX1631840.bam -f BAM -g 12100000 -n SRX1631840.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1631840.20 # format = BAM # ChIP-seq file = ['SRX1631840.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 06:24:30: #1 read tag files... INFO @ Wed, 28 Jun 2017 06:24:30: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 06:24:37: 1000000 INFO @ Wed, 28 Jun 2017 06:24:37: 1000000 INFO @ Wed, 28 Jun 2017 06:24:37: 1000000 INFO @ Wed, 28 Jun 2017 06:24:43: 2000000 INFO @ Wed, 28 Jun 2017 06:24:43: 2000000 INFO @ Wed, 28 Jun 2017 06:24:43: 2000000 INFO @ Wed, 28 Jun 2017 06:24:50: 3000000 INFO @ Wed, 28 Jun 2017 06:24:50: 3000000 INFO @ Wed, 28 Jun 2017 06:24:50: 3000000 INFO @ Wed, 28 Jun 2017 06:24:57: 4000000 INFO @ Wed, 28 Jun 2017 06:24:57: 4000000 INFO @ Wed, 28 Jun 2017 06:24:57: 4000000 INFO @ Wed, 28 Jun 2017 06:25:04: 5000000 INFO @ Wed, 28 Jun 2017 06:25:04: 5000000 INFO @ Wed, 28 Jun 2017 06:25:04: 5000000 INFO @ Wed, 28 Jun 2017 06:25:10: 6000000 INFO @ Wed, 28 Jun 2017 06:25:10: 6000000 INFO @ Wed, 28 Jun 2017 06:25:10: 6000000 INFO @ Wed, 28 Jun 2017 06:25:17: 7000000 INFO @ Wed, 28 Jun 2017 06:25:17: 7000000 INFO @ Wed, 28 Jun 2017 06:25:17: 7000000 INFO @ Wed, 28 Jun 2017 06:25:24: 8000000 INFO @ Wed, 28 Jun 2017 06:25:24: 8000000 INFO @ Wed, 28 Jun 2017 06:25:24: 8000000 INFO @ Wed, 28 Jun 2017 06:25:30: 9000000 INFO @ Wed, 28 Jun 2017 06:25:30: 9000000 INFO @ Wed, 28 Jun 2017 06:25:30: 9000000 INFO @ Wed, 28 Jun 2017 06:25:37: 10000000 INFO @ Wed, 28 Jun 2017 06:25:37: 10000000 INFO @ Wed, 28 Jun 2017 06:25:37: 10000000 INFO @ Wed, 28 Jun 2017 06:25:44: 11000000 INFO @ Wed, 28 Jun 2017 06:25:44: 11000000 INFO @ Wed, 28 Jun 2017 06:25:44: 11000000 INFO @ Wed, 28 Jun 2017 06:25:50: 12000000 INFO @ Wed, 28 Jun 2017 06:25:50: 12000000 INFO @ Wed, 28 Jun 2017 06:25:50: 12000000 INFO @ Wed, 28 Jun 2017 06:25:57: 13000000 INFO @ Wed, 28 Jun 2017 06:25:57: 13000000 INFO @ Wed, 28 Jun 2017 06:25:57: 13000000 INFO @ Wed, 28 Jun 2017 06:26:04: 14000000 INFO @ Wed, 28 Jun 2017 06:26:04: 14000000 INFO @ Wed, 28 Jun 2017 06:26:04: 14000000 INFO @ Wed, 28 Jun 2017 06:26:11: 15000000 INFO @ Wed, 28 Jun 2017 06:26:11: 15000000 INFO @ Wed, 28 Jun 2017 06:26:11: 15000000 INFO @ Wed, 28 Jun 2017 06:26:18: 16000000 INFO @ Wed, 28 Jun 2017 06:26:18: 16000000 INFO @ Wed, 28 Jun 2017 06:26:18: 16000000 INFO @ Wed, 28 Jun 2017 06:26:25: 17000000 INFO @ Wed, 28 Jun 2017 06:26:25: 17000000 INFO @ Wed, 28 Jun 2017 06:26:25: 17000000 INFO @ Wed, 28 Jun 2017 06:26:31: 18000000 INFO @ Wed, 28 Jun 2017 06:26:31: 18000000 INFO @ Wed, 28 Jun 2017 06:26:32: 18000000 INFO @ Wed, 28 Jun 2017 06:26:39: 19000000 INFO @ Wed, 28 Jun 2017 06:26:39: 19000000 INFO @ Wed, 28 Jun 2017 06:26:39: 19000000 INFO @ Wed, 28 Jun 2017 06:26:45: 20000000 INFO @ Wed, 28 Jun 2017 06:26:45: 20000000 INFO @ Wed, 28 Jun 2017 06:26:46: 20000000 INFO @ Wed, 28 Jun 2017 06:26:53: 21000000 INFO @ Wed, 28 Jun 2017 06:26:53: 21000000 INFO @ Wed, 28 Jun 2017 06:26:54: 21000000 INFO @ Wed, 28 Jun 2017 06:27:00: 22000000 INFO @ Wed, 28 Jun 2017 06:27:00: 22000000 INFO @ Wed, 28 Jun 2017 06:27:02: 22000000 INFO @ Wed, 28 Jun 2017 06:27:07: 23000000 INFO @ Wed, 28 Jun 2017 06:27:07: 23000000 INFO @ Wed, 28 Jun 2017 06:27:09: 23000000 INFO @ Wed, 28 Jun 2017 06:27:14: 24000000 INFO @ Wed, 28 Jun 2017 06:27:14: 24000000 INFO @ Wed, 28 Jun 2017 06:27:16: 24000000 INFO @ Wed, 28 Jun 2017 06:27:21: 25000000 INFO @ Wed, 28 Jun 2017 06:27:21: 25000000 INFO @ Wed, 28 Jun 2017 06:27:24: 25000000 INFO @ Wed, 28 Jun 2017 06:27:29: 26000000 INFO @ Wed, 28 Jun 2017 06:27:29: 26000000 INFO @ Wed, 28 Jun 2017 06:27:33: 26000000 INFO @ Wed, 28 Jun 2017 06:27:37: 27000000 INFO @ Wed, 28 Jun 2017 06:27:37: 27000000 INFO @ Wed, 28 Jun 2017 06:27:41: 27000000 INFO @ Wed, 28 Jun 2017 06:27:45: 28000000 INFO @ Wed, 28 Jun 2017 06:27:46: 28000000 INFO @ Wed, 28 Jun 2017 06:27:49: 28000000 INFO @ Wed, 28 Jun 2017 06:27:53: 29000000 INFO @ Wed, 28 Jun 2017 06:27:54: 29000000 INFO @ Wed, 28 Jun 2017 06:27:57: 29000000 INFO @ Wed, 28 Jun 2017 06:28:01: 30000000 INFO @ Wed, 28 Jun 2017 06:28:02: 30000000 INFO @ Wed, 28 Jun 2017 06:28:05: 30000000 INFO @ Wed, 28 Jun 2017 06:28:09: 31000000 INFO @ Wed, 28 Jun 2017 06:28:09: 31000000 INFO @ Wed, 28 Jun 2017 06:28:14: 31000000 INFO @ Wed, 28 Jun 2017 06:28:18: 32000000 INFO @ Wed, 28 Jun 2017 06:28:18: 32000000 INFO @ Wed, 28 Jun 2017 06:28:22: 32000000 INFO @ Wed, 28 Jun 2017 06:28:26: 33000000 INFO @ Wed, 28 Jun 2017 06:28:26: 33000000 INFO @ Wed, 28 Jun 2017 06:28:30: 33000000 INFO @ Wed, 28 Jun 2017 06:28:33: 34000000 INFO @ Wed, 28 Jun 2017 06:28:34: 34000000 INFO @ Wed, 28 Jun 2017 06:28:38: 34000000 INFO @ Wed, 28 Jun 2017 06:28:41: 35000000 INFO @ Wed, 28 Jun 2017 06:28:42: 35000000 INFO @ Wed, 28 Jun 2017 06:28:46: 35000000 INFO @ Wed, 28 Jun 2017 06:28:50: 36000000 INFO @ Wed, 28 Jun 2017 06:28:50: 36000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 28 Jun 2017 06:28:54: 36000000 INFO @ Wed, 28 Jun 2017 06:28:58: 37000000 INFO @ Wed, 28 Jun 2017 06:28:58: 37000000 INFO @ Wed, 28 Jun 2017 06:29:03: 37000000 INFO @ Wed, 28 Jun 2017 06:29:06: 38000000 INFO @ Wed, 28 Jun 2017 06:29:06: 38000000 INFO @ Wed, 28 Jun 2017 06:29:11: 38000000 INFO @ Wed, 28 Jun 2017 06:29:14: 39000000 BigWig に変換しました。 INFO @ Wed, 28 Jun 2017 06:29:14: 39000000 INFO @ Wed, 28 Jun 2017 06:29:19: 39000000 INFO @ Wed, 28 Jun 2017 06:29:22: 40000000 INFO @ Wed, 28 Jun 2017 06:29:22: 40000000 INFO @ Wed, 28 Jun 2017 06:29:27: 40000000 INFO @ Wed, 28 Jun 2017 06:29:30: 41000000 INFO @ Wed, 28 Jun 2017 06:29:30: 41000000 INFO @ Wed, 28 Jun 2017 06:29:35: 41000000 INFO @ Wed, 28 Jun 2017 06:29:38: 42000000 INFO @ Wed, 28 Jun 2017 06:29:38: 42000000 INFO @ Wed, 28 Jun 2017 06:29:43: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 06:29:43: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 06:29:43: #1 total tags in treatment: 20729277 INFO @ Wed, 28 Jun 2017 06:29:43: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 06:29:43: #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 06:29:43: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 06:29:43: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 06:29:43: #1 total tags in treatment: 20729277 INFO @ Wed, 28 Jun 2017 06:29:43: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 06:29:43: #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 06:29:43: #1 tags after filtering in treatment: 12886469 INFO @ Wed, 28 Jun 2017 06:29:43: #1 Redundant rate of treatment: 0.38 INFO @ Wed, 28 Jun 2017 06:29:43: #1 finished! INFO @ Wed, 28 Jun 2017 06:29:43: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 06:29:43: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 06:29:43: #1 tags after filtering in treatment: 12886469 INFO @ Wed, 28 Jun 2017 06:29:43: #1 Redundant rate of treatment: 0.38 INFO @ Wed, 28 Jun 2017 06:29:43: #1 finished! INFO @ Wed, 28 Jun 2017 06:29:43: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 06:29:43: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 06:29:43: 42000000 INFO @ Wed, 28 Jun 2017 06:29:44: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 06:29:44: 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 06:29:44: Process for pairing-model is terminated! INFO @ Wed, 28 Jun 2017 06:29:44: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 06:29:44: 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 06:29:44: Process for pairing-model is terminated! cat: SRX1631840.05_peaks.narrowPeak: そのようなファイルやディレクトリはありません cat: SRX1631840.10_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 pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: rm: cannot remove `SRX1631840.10_model.r'cannot remove `SRX1631840.05_model.r': そのようなファイルやディレクトリはありません: そのようなファイルやディレクトリはありません rm: rm: cannot remove `SRX1631840.10_*.xls'cannot remove `SRX1631840.05_*.xls': そのようなファイルやディレクトリはありません: そのようなファイルやディレクトリはありません rm: rm: cannot remove `SRX1631840.10_peaks.narrowPeak'cannot remove `SRX1631840.05_peaks.narrowPeak': そのようなファイルやディレクトリはありません: そのようなファイルやディレクトリはありません CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 06:29:48: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 06:29:48: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 06:29:48: #1 total tags in treatment: 20729277 INFO @ Wed, 28 Jun 2017 06:29:48: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 06:29:48: #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 06:29:49: #1 tags after filtering in treatment: 12886469 INFO @ Wed, 28 Jun 2017 06:29:49: #1 Redundant rate of treatment: 0.38 INFO @ Wed, 28 Jun 2017 06:29:49: #1 finished! INFO @ Wed, 28 Jun 2017 06:29:49: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 06:29:49: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 06:29:50: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 06:29:50: 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 @ Wed, 28 Jun 2017 06:29:50: Process for pairing-model is terminated! cat: SRX1631840.20_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 `SRX1631840.20_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 `SRX1631840.20_*.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 `SRX1631840.20_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