Job ID = 9163664 sra ファイルのダウンロード中... Completed: 1578606K bytes transferred in 15 seconds (814975K 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 24620406 spots for /home/okishinya/chipatlas/results/sacCer3/SRX997487/SRR1976519.sra Written 24620406 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: 00:16:29 24620406 reads; of these: 24620406 (100.00%) were paired; of these: 3383208 (13.74%) aligned concordantly 0 times 19316718 (78.46%) aligned concordantly exactly 1 time 1920480 (7.80%) aligned concordantly >1 times ---- 3383208 pairs aligned concordantly 0 times; of these: 140313 (4.15%) aligned discordantly 1 time ---- 3242895 pairs aligned 0 times concordantly or discordantly; of these: 6485790 mates make up the pairs; of these: 5847808 (90.16%) aligned 0 times 417655 (6.44%) aligned exactly 1 time 220327 (3.40%) aligned >1 times 88.12% overall alignment rate Time searching: 00:16:29 Overall time: 00:16:29 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] 320315 / 21364289 = 0.0150 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 11:44:38: # Command line: callpeak -t SRX997487.bam -f BAM -g 12100000 -n SRX997487.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX997487.10 # format = BAM # ChIP-seq file = ['SRX997487.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 11:44:38: #1 read tag files... INFO @ Wed, 28 Jun 2017 11:44:38: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 11:44:38: # Command line: callpeak -t SRX997487.bam -f BAM -g 12100000 -n SRX997487.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX997487.20 # format = BAM # ChIP-seq file = ['SRX997487.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 11:44:38: #1 read tag files... INFO @ Wed, 28 Jun 2017 11:44:38: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 11:44:38: # Command line: callpeak -t SRX997487.bam -f BAM -g 12100000 -n SRX997487.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX997487.05 # format = BAM # ChIP-seq file = ['SRX997487.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 11:44:38: #1 read tag files... INFO @ Wed, 28 Jun 2017 11:44:38: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 11:44:44: 1000000 INFO @ Wed, 28 Jun 2017 11:44:44: 1000000 INFO @ Wed, 28 Jun 2017 11:44:44: 1000000 INFO @ Wed, 28 Jun 2017 11:44:51: 2000000 INFO @ Wed, 28 Jun 2017 11:44:51: 2000000 INFO @ Wed, 28 Jun 2017 11:44:51: 2000000 INFO @ Wed, 28 Jun 2017 11:44:57: 3000000 INFO @ Wed, 28 Jun 2017 11:44:57: 3000000 INFO @ Wed, 28 Jun 2017 11:44:57: 3000000 INFO @ Wed, 28 Jun 2017 11:45:03: 4000000 INFO @ Wed, 28 Jun 2017 11:45:03: 4000000 INFO @ Wed, 28 Jun 2017 11:45:03: 4000000 INFO @ Wed, 28 Jun 2017 11:45:09: 5000000 INFO @ Wed, 28 Jun 2017 11:45:09: 5000000 INFO @ Wed, 28 Jun 2017 11:45:09: 5000000 INFO @ Wed, 28 Jun 2017 11:45:15: 6000000 INFO @ Wed, 28 Jun 2017 11:45:15: 6000000 INFO @ Wed, 28 Jun 2017 11:45:16: 6000000 INFO @ Wed, 28 Jun 2017 11:45:22: 7000000 INFO @ Wed, 28 Jun 2017 11:45:22: 7000000 INFO @ Wed, 28 Jun 2017 11:45:22: 7000000 INFO @ Wed, 28 Jun 2017 11:45:28: 8000000 INFO @ Wed, 28 Jun 2017 11:45:28: 8000000 INFO @ Wed, 28 Jun 2017 11:45:29: 8000000 INFO @ Wed, 28 Jun 2017 11:45:34: 9000000 INFO @ Wed, 28 Jun 2017 11:45:34: 9000000 INFO @ Wed, 28 Jun 2017 11:45:35: 9000000 INFO @ Wed, 28 Jun 2017 11:45:40: 10000000 INFO @ Wed, 28 Jun 2017 11:45:41: 10000000 INFO @ Wed, 28 Jun 2017 11:45:42: 10000000 INFO @ Wed, 28 Jun 2017 11:45:46: 11000000 INFO @ Wed, 28 Jun 2017 11:45:47: 11000000 INFO @ Wed, 28 Jun 2017 11:45:48: 11000000 INFO @ Wed, 28 Jun 2017 11:45:52: 12000000 INFO @ Wed, 28 Jun 2017 11:45:53: 12000000 INFO @ Wed, 28 Jun 2017 11:45:54: 12000000 INFO @ Wed, 28 Jun 2017 11:45:58: 13000000 INFO @ Wed, 28 Jun 2017 11:45:59: 13000000 INFO @ Wed, 28 Jun 2017 11:46:01: 13000000 INFO @ Wed, 28 Jun 2017 11:46:04: 14000000 INFO @ Wed, 28 Jun 2017 11:46:05: 14000000 INFO @ Wed, 28 Jun 2017 11:46:07: 14000000 INFO @ Wed, 28 Jun 2017 11:46:10: 15000000 INFO @ Wed, 28 Jun 2017 11:46:11: 15000000 INFO @ Wed, 28 Jun 2017 11:46:14: 15000000 INFO @ Wed, 28 Jun 2017 11:46:16: 16000000 INFO @ Wed, 28 Jun 2017 11:46:18: 16000000 INFO @ Wed, 28 Jun 2017 11:46:20: 16000000 INFO @ Wed, 28 Jun 2017 11:46:23: 17000000 INFO @ Wed, 28 Jun 2017 11:46:24: 17000000 INFO @ Wed, 28 Jun 2017 11:46:26: 17000000 INFO @ Wed, 28 Jun 2017 11:46:29: 18000000 INFO @ Wed, 28 Jun 2017 11:46:30: 18000000 INFO @ Wed, 28 Jun 2017 11:46:32: 18000000 INFO @ Wed, 28 Jun 2017 11:46:35: 19000000 INFO @ Wed, 28 Jun 2017 11:46:36: 19000000 INFO @ Wed, 28 Jun 2017 11:46:39: 19000000 INFO @ Wed, 28 Jun 2017 11:46:42: 20000000 INFO @ Wed, 28 Jun 2017 11:46:42: 20000000 INFO @ Wed, 28 Jun 2017 11:46:45: 20000000 INFO @ Wed, 28 Jun 2017 11:46:48: 21000000 INFO @ Wed, 28 Jun 2017 11:46:48: 21000000 INFO @ Wed, 28 Jun 2017 11:46:51: 21000000 INFO @ Wed, 28 Jun 2017 11:46:53: 22000000 INFO @ Wed, 28 Jun 2017 11:46:54: 22000000 INFO @ Wed, 28 Jun 2017 11:46:58: 22000000 INFO @ Wed, 28 Jun 2017 11:46:59: 23000000 INFO @ Wed, 28 Jun 2017 11:47:01: 23000000 INFO @ Wed, 28 Jun 2017 11:47:04: 23000000 INFO @ Wed, 28 Jun 2017 11:47:05: 24000000 INFO @ Wed, 28 Jun 2017 11:47:07: 24000000 INFO @ Wed, 28 Jun 2017 11:47:10: 24000000 INFO @ Wed, 28 Jun 2017 11:47:11: 25000000 INFO @ Wed, 28 Jun 2017 11:47:13: 25000000 INFO @ Wed, 28 Jun 2017 11:47:16: 25000000 INFO @ Wed, 28 Jun 2017 11:47:17: 26000000 INFO @ Wed, 28 Jun 2017 11:47:19: 26000000 INFO @ Wed, 28 Jun 2017 11:47:23: 26000000 INFO @ Wed, 28 Jun 2017 11:47:23: 27000000 INFO @ Wed, 28 Jun 2017 11:47:26: 27000000 INFO @ Wed, 28 Jun 2017 11:47:29: 28000000 INFO @ Wed, 28 Jun 2017 11:47:29: 27000000 INFO @ Wed, 28 Jun 2017 11:47:32: 28000000 INFO @ Wed, 28 Jun 2017 11:47:35: 29000000 INFO @ Wed, 28 Jun 2017 11:47:35: 28000000 INFO @ Wed, 28 Jun 2017 11:47:38: 29000000 INFO @ Wed, 28 Jun 2017 11:47:41: 30000000 INFO @ Wed, 28 Jun 2017 11:47:41: 29000000 INFO @ Wed, 28 Jun 2017 11:47:44: 30000000 INFO @ Wed, 28 Jun 2017 11:47:46: 31000000 INFO @ Wed, 28 Jun 2017 11:47:47: 30000000 INFO @ Wed, 28 Jun 2017 11:47:50: 31000000 INFO @ Wed, 28 Jun 2017 11:47:52: 32000000 INFO @ Wed, 28 Jun 2017 11:47:54: 31000000 INFO @ Wed, 28 Jun 2017 11:47:57: 32000000 INFO @ Wed, 28 Jun 2017 11:47:58: 33000000 INFO @ Wed, 28 Jun 2017 11:48:00: 32000000 INFO @ Wed, 28 Jun 2017 11:48:03: 33000000 INFO @ Wed, 28 Jun 2017 11:48:04: 34000000 INFO @ Wed, 28 Jun 2017 11:48:06: 33000000 INFO @ Wed, 28 Jun 2017 11:48:09: 34000000 INFO @ Wed, 28 Jun 2017 11:48:10: 35000000 INFO @ Wed, 28 Jun 2017 11:48:13: 34000000 INFO @ Wed, 28 Jun 2017 11:48:16: 35000000 INFO @ Wed, 28 Jun 2017 11:48:16: 36000000 INFO @ Wed, 28 Jun 2017 11:48:19: 35000000 INFO @ Wed, 28 Jun 2017 11:48:22: 37000000 INFO @ Wed, 28 Jun 2017 11:48:22: 36000000 INFO @ Wed, 28 Jun 2017 11:48:26: 36000000 INFO @ Wed, 28 Jun 2017 11:48:28: 38000000 INFO @ Wed, 28 Jun 2017 11:48:29: 37000000 INFO @ Wed, 28 Jun 2017 11:48:32: 37000000 INFO @ Wed, 28 Jun 2017 11:48:34: 39000000 INFO @ Wed, 28 Jun 2017 11:48:35: 38000000 INFO @ Wed, 28 Jun 2017 11:48:38: 38000000 INFO @ Wed, 28 Jun 2017 11:48:40: 40000000 INFO @ Wed, 28 Jun 2017 11:48:42: 39000000 INFO @ Wed, 28 Jun 2017 11:48:45: 39000000 INFO @ Wed, 28 Jun 2017 11:48:46: 41000000 INFO @ Wed, 28 Jun 2017 11:48:48: 40000000 INFO @ Wed, 28 Jun 2017 11:48:51: 40000000 INFO @ Wed, 28 Jun 2017 11:48:52: 42000000 INFO @ Wed, 28 Jun 2017 11:48:55: 41000000 INFO @ Wed, 28 Jun 2017 11:48:56: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 11:48:56: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 11:48:56: #1 total tags in treatment: 20917921 INFO @ Wed, 28 Jun 2017 11:48:56: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 11:48:56: #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 11:48:57: #1 tags after filtering in treatment: 12995032 INFO @ Wed, 28 Jun 2017 11:48:57: #1 Redundant rate of treatment: 0.38 INFO @ Wed, 28 Jun 2017 11:48:57: #1 finished! INFO @ Wed, 28 Jun 2017 11:48:57: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 11:48:57: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 11:48:58: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 11:48:58: 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 @ Wed, 28 Jun 2017 11:48:58: Process for pairing-model is terminated! cat: SRX997487.20_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 `SRX997487.20_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 `SRX997487.20_*.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 `SRX997487.20_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 @ Wed, 28 Jun 2017 11:48:58: 41000000 INFO @ Wed, 28 Jun 2017 11:49:01: 42000000 INFO @ Wed, 28 Jun 2017 11:49:04: 42000000 INFO @ Wed, 28 Jun 2017 11:49:06: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 11:49:06: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 11:49:06: #1 total tags in treatment: 20917921 INFO @ Wed, 28 Jun 2017 11:49:06: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 11:49:06: #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 11:49:06: #1 tags after filtering in treatment: 12995032 INFO @ Wed, 28 Jun 2017 11:49:06: #1 Redundant rate of treatment: 0.38 INFO @ Wed, 28 Jun 2017 11:49:06: #1 finished! INFO @ Wed, 28 Jun 2017 11:49:06: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 11:49:06: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 28 Jun 2017 11:49:07: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 11:49:07: 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 @ Wed, 28 Jun 2017 11:49:07: Process for pairing-model is terminated! cat: SRX997487.05_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 `SRX997487.05_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 `SRX997487.05_*.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 `SRX997487.05_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 @ Wed, 28 Jun 2017 11:49:09: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 11:49:09: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 11:49:09: #1 total tags in treatment: 20917921 INFO @ Wed, 28 Jun 2017 11:49:09: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 11:49:09: #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 11:49:09: #1 tags after filtering in treatment: 12995032 INFO @ Wed, 28 Jun 2017 11:49:09: #1 Redundant rate of treatment: 0.38 INFO @ Wed, 28 Jun 2017 11:49:09: #1 finished! INFO @ Wed, 28 Jun 2017 11:49:09: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 11:49:09: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 11:49:10: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 11:49:10: 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 11:49:10: Process for pairing-model is terminated! cat: SRX997487.10_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 `SRX997487.10_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 `SRX997487.10_*.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 `SRX997487.10_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 BigWig に変換しました。