Job ID = 10536529 sra ファイルのダウンロード中... Completed: 1452885K bytes transferred in 44 seconds (264533K 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 39531974 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3671221/SRR6696973.sra Written 39531974 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:25:48 39531974 reads; of these: 39531974 (100.00%) were paired; of these: 9695406 (24.53%) aligned concordantly 0 times 24880874 (62.94%) aligned concordantly exactly 1 time 4955694 (12.54%) aligned concordantly >1 times ---- 9695406 pairs aligned concordantly 0 times; of these: 49380 (0.51%) aligned discordantly 1 time ---- 9646026 pairs aligned 0 times concordantly or discordantly; of these: 19292052 mates make up the pairs; of these: 19073585 (98.87%) aligned 0 times 155537 (0.81%) aligned exactly 1 time 62930 (0.33%) aligned >1 times 75.88% overall alignment rate Time searching: 00:25:49 Overall time: 00:25:49 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] 13851108 / 29851330 = 0.4640 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 10:56:25: # Command line: callpeak -t SRX3671221.bam -f BAM -g 12100000 -n SRX3671221.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3671221.20 # format = BAM # ChIP-seq file = ['SRX3671221.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 10:56:25: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:56:25: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:56:25: # Command line: callpeak -t SRX3671221.bam -f BAM -g 12100000 -n SRX3671221.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3671221.10 # format = BAM # ChIP-seq file = ['SRX3671221.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 10:56:25: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:56:25: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:56:25: # Command line: callpeak -t SRX3671221.bam -f BAM -g 12100000 -n SRX3671221.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3671221.05 # format = BAM # ChIP-seq file = ['SRX3671221.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 10:56:25: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:56:25: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:56:34: 1000000 INFO @ Thu, 05 Apr 2018 10:56:34: 1000000 INFO @ Thu, 05 Apr 2018 10:56:35: 1000000 INFO @ Thu, 05 Apr 2018 10:56:41: 2000000 INFO @ Thu, 05 Apr 2018 10:56:41: 2000000 INFO @ Thu, 05 Apr 2018 10:56:42: 2000000 INFO @ Thu, 05 Apr 2018 10:56:49: 3000000 INFO @ Thu, 05 Apr 2018 10:56:52: 3000000 INFO @ Thu, 05 Apr 2018 10:56:52: 3000000 INFO @ Thu, 05 Apr 2018 10:56:59: 4000000 INFO @ Thu, 05 Apr 2018 10:57:00: 4000000 INFO @ Thu, 05 Apr 2018 10:57:00: 4000000 INFO @ Thu, 05 Apr 2018 10:57:05: 5000000 INFO @ Thu, 05 Apr 2018 10:57:06: 5000000 INFO @ Thu, 05 Apr 2018 10:57:06: 5000000 INFO @ Thu, 05 Apr 2018 10:57:11: 6000000 INFO @ Thu, 05 Apr 2018 10:57:12: 6000000 INFO @ Thu, 05 Apr 2018 10:57:12: 6000000 INFO @ Thu, 05 Apr 2018 10:57:17: 7000000 INFO @ Thu, 05 Apr 2018 10:57:18: 7000000 INFO @ Thu, 05 Apr 2018 10:57:18: 7000000 INFO @ Thu, 05 Apr 2018 10:57:23: 8000000 INFO @ Thu, 05 Apr 2018 10:57:24: 8000000 INFO @ Thu, 05 Apr 2018 10:57:25: 8000000 INFO @ Thu, 05 Apr 2018 10:57:29: 9000000 INFO @ Thu, 05 Apr 2018 10:57:30: 9000000 INFO @ Thu, 05 Apr 2018 10:57:31: 9000000 INFO @ Thu, 05 Apr 2018 10:57:35: 10000000 INFO @ Thu, 05 Apr 2018 10:57:36: 10000000 INFO @ Thu, 05 Apr 2018 10:57:37: 10000000 INFO @ Thu, 05 Apr 2018 10:57:42: 11000000 INFO @ Thu, 05 Apr 2018 10:57:44: 11000000 INFO @ Thu, 05 Apr 2018 10:57:46: 11000000 INFO @ Thu, 05 Apr 2018 10:57:53: 12000000 INFO @ Thu, 05 Apr 2018 10:57:56: 12000000 INFO @ Thu, 05 Apr 2018 10:57:56: 12000000 INFO @ Thu, 05 Apr 2018 10:58:02: 13000000 INFO @ Thu, 05 Apr 2018 10:58:05: 13000000 INFO @ Thu, 05 Apr 2018 10:58:07: 13000000 INFO @ Thu, 05 Apr 2018 10:58:11: 14000000 INFO @ Thu, 05 Apr 2018 10:58:13: 14000000 INFO @ Thu, 05 Apr 2018 10:58:13: 14000000 INFO @ Thu, 05 Apr 2018 10:58:18: 15000000 INFO @ Thu, 05 Apr 2018 10:58:18: 15000000 INFO @ Thu, 05 Apr 2018 10:58:19: 15000000 INFO @ Thu, 05 Apr 2018 10:58:24: 16000000 INFO @ Thu, 05 Apr 2018 10:58:24: 16000000 INFO @ Thu, 05 Apr 2018 10:58:26: 16000000 INFO @ Thu, 05 Apr 2018 10:58:31: 17000000 INFO @ Thu, 05 Apr 2018 10:58:31: 17000000 INFO @ Thu, 05 Apr 2018 10:58:32: 17000000 INFO @ Thu, 05 Apr 2018 10:58:37: 18000000 INFO @ Thu, 05 Apr 2018 10:58:37: 18000000 INFO @ Thu, 05 Apr 2018 10:58:39: 18000000 INFO @ Thu, 05 Apr 2018 10:58:46: 19000000 INFO @ Thu, 05 Apr 2018 10:58:46: 19000000 INFO @ Thu, 05 Apr 2018 10:58:50: 19000000 INFO @ Thu, 05 Apr 2018 10:58:54: 20000000 INFO @ Thu, 05 Apr 2018 10:58:56: 20000000 INFO @ Thu, 05 Apr 2018 10:59:00: 20000000 INFO @ Thu, 05 Apr 2018 10:59:02: 21000000 INFO @ Thu, 05 Apr 2018 10:59:04: 21000000 INFO @ Thu, 05 Apr 2018 10:59:08: 22000000 INFO @ Thu, 05 Apr 2018 10:59:11: 21000000 INFO @ Thu, 05 Apr 2018 10:59:11: 22000000 INFO @ Thu, 05 Apr 2018 10:59:14: 23000000 INFO @ Thu, 05 Apr 2018 10:59:17: 23000000 INFO @ Thu, 05 Apr 2018 10:59:17: 22000000 INFO @ Thu, 05 Apr 2018 10:59:21: 24000000 INFO @ Thu, 05 Apr 2018 10:59:23: 24000000 INFO @ Thu, 05 Apr 2018 10:59:23: 23000000 INFO @ Thu, 05 Apr 2018 10:59:27: 25000000 INFO @ Thu, 05 Apr 2018 10:59:29: 25000000 INFO @ Thu, 05 Apr 2018 10:59:34: 26000000 INFO @ Thu, 05 Apr 2018 10:59:35: 24000000 INFO @ Thu, 05 Apr 2018 10:59:37: 26000000 INFO @ Thu, 05 Apr 2018 10:59:42: 27000000 INFO @ Thu, 05 Apr 2018 10:59:43: 25000000 INFO @ Thu, 05 Apr 2018 10:59:45: 27000000 INFO @ Thu, 05 Apr 2018 10:59:48: 28000000 INFO @ Thu, 05 Apr 2018 10:59:49: 26000000 INFO @ Thu, 05 Apr 2018 10:59:51: 28000000 INFO @ Thu, 05 Apr 2018 10:59:54: 29000000 INFO @ Thu, 05 Apr 2018 10:59:55: 27000000 INFO @ Thu, 05 Apr 2018 10:59:57: 29000000 INFO @ Thu, 05 Apr 2018 11:00:00: 30000000 INFO @ Thu, 05 Apr 2018 11:00:01: 28000000 INFO @ Thu, 05 Apr 2018 11:00:02: 30000000 INFO @ Thu, 05 Apr 2018 11:00:07: 31000000 INFO @ Thu, 05 Apr 2018 11:00:07: 29000000 INFO @ Thu, 05 Apr 2018 11:00:08: 31000000 INFO @ Thu, 05 Apr 2018 11:00:14: 32000000 INFO @ Thu, 05 Apr 2018 11:00:14: 32000000 INFO @ Thu, 05 Apr 2018 11:00:14: 30000000 INFO @ Thu, 05 Apr 2018 11:00:15: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 11:00:15: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 11:00:15: #1 total tags in treatment: 15995300 INFO @ Thu, 05 Apr 2018 11:00:15: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 11:00:15: #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 11:00:16: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 11:00:16: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 11:00:16: #1 total tags in treatment: 15995300 INFO @ Thu, 05 Apr 2018 11:00:16: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 11:00:16: #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 11:00:16: #1 tags after filtering in treatment: 6677820 INFO @ Thu, 05 Apr 2018 11:00:16: #1 Redundant rate of treatment: 0.58 INFO @ Thu, 05 Apr 2018 11:00:16: #1 finished! INFO @ Thu, 05 Apr 2018 11:00:16: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 11:00:16: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 11:00:16: #1 tags after filtering in treatment: 6677820 INFO @ Thu, 05 Apr 2018 11:00:16: #1 Redundant rate of treatment: 0.58 INFO @ Thu, 05 Apr 2018 11:00:16: #1 finished! INFO @ Thu, 05 Apr 2018 11:00:16: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 11:00:16: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 11:00:16: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 11:00:16: 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 11:00:16: Process for pairing-model is terminated! cat: SRX3671221.10_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 `SRX3671221.10_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 `SRX3671221.10_*.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 `SRX3671221.10_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 11:00:16: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 11:00:16: 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 11:00:16: Process for pairing-model is terminated! cat: SRX3671221.05_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 `SRX3671221.05_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 `SRX3671221.05_*.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 `SRX3671221.05_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, 05 Apr 2018 11:00:20: 31000000 INFO @ Thu, 05 Apr 2018 11:00:25: 32000000 INFO @ Thu, 05 Apr 2018 11:00:27: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 11:00:27: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 11:00:27: #1 total tags in treatment: 15995300 INFO @ Thu, 05 Apr 2018 11:00:27: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 11:00:27: #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 11:00:27: #1 tags after filtering in treatment: 6677820 INFO @ Thu, 05 Apr 2018 11:00:27: #1 Redundant rate of treatment: 0.58 INFO @ Thu, 05 Apr 2018 11:00:27: #1 finished! INFO @ Thu, 05 Apr 2018 11:00:27: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 11:00:27: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 11:00:28: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 11:00:28: 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 11:00:28: Process for pairing-model is terminated! cat: SRX3671221.20_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 `SRX3671221.20_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 `SRX3671221.20_*.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 `SRX3671221.20_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 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。