Job ID = 10536513 sra ファイルのダウンロード中... Completed: 1344277K bytes transferred in 31 seconds (351028K 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 37439905 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3671207/SRR6696959.sra Written 37439905 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:26:25 37439905 reads; of these: 37439905 (100.00%) were paired; of these: 3956931 (10.57%) aligned concordantly 0 times 27323767 (72.98%) aligned concordantly exactly 1 time 6159207 (16.45%) aligned concordantly >1 times ---- 3956931 pairs aligned concordantly 0 times; of these: 135965 (3.44%) aligned discordantly 1 time ---- 3820966 pairs aligned 0 times concordantly or discordantly; of these: 7641932 mates make up the pairs; of these: 7400079 (96.84%) aligned 0 times 119198 (1.56%) aligned exactly 1 time 122655 (1.61%) aligned >1 times 90.12% overall alignment rate Time searching: 00:26:25 Overall time: 00:26:25 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] 13103747 / 33569214 = 0.3904 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 10:40:17: # Command line: callpeak -t SRX3671207.bam -f BAM -g 12100000 -n SRX3671207.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3671207.05 # format = BAM # ChIP-seq file = ['SRX3671207.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 10:40:17: # Command line: callpeak -t SRX3671207.bam -f BAM -g 12100000 -n SRX3671207.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3671207.10 # format = BAM # ChIP-seq file = ['SRX3671207.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 10:40:17: # Command line: callpeak -t SRX3671207.bam -f BAM -g 12100000 -n SRX3671207.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3671207.20 # format = BAM # ChIP-seq file = ['SRX3671207.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 10:40:17: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:40:17: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:40:17: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:40:17: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:40:17: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:40:17: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:40:23: 1000000 INFO @ Thu, 05 Apr 2018 10:40:23: 1000000 INFO @ Thu, 05 Apr 2018 10:40:23: 1000000 INFO @ Thu, 05 Apr 2018 10:40:28: 2000000 INFO @ Thu, 05 Apr 2018 10:40:29: 2000000 INFO @ Thu, 05 Apr 2018 10:40:29: 2000000 INFO @ Thu, 05 Apr 2018 10:40:34: 3000000 INFO @ Thu, 05 Apr 2018 10:40:34: 3000000 INFO @ Thu, 05 Apr 2018 10:40:35: 3000000 INFO @ Thu, 05 Apr 2018 10:40:40: 4000000 INFO @ Thu, 05 Apr 2018 10:40:40: 4000000 INFO @ Thu, 05 Apr 2018 10:40:41: 4000000 INFO @ Thu, 05 Apr 2018 10:40:46: 5000000 INFO @ Thu, 05 Apr 2018 10:40:46: 5000000 INFO @ Thu, 05 Apr 2018 10:40:47: 5000000 INFO @ Thu, 05 Apr 2018 10:40:51: 6000000 INFO @ Thu, 05 Apr 2018 10:40:52: 6000000 INFO @ Thu, 05 Apr 2018 10:40:54: 6000000 INFO @ Thu, 05 Apr 2018 10:40:57: 7000000 INFO @ Thu, 05 Apr 2018 10:40:58: 7000000 INFO @ Thu, 05 Apr 2018 10:41:00: 7000000 INFO @ Thu, 05 Apr 2018 10:41:03: 8000000 INFO @ Thu, 05 Apr 2018 10:41:04: 8000000 INFO @ Thu, 05 Apr 2018 10:41:06: 8000000 INFO @ Thu, 05 Apr 2018 10:41:08: 9000000 INFO @ Thu, 05 Apr 2018 10:41:10: 9000000 INFO @ Thu, 05 Apr 2018 10:41:12: 9000000 INFO @ Thu, 05 Apr 2018 10:41:14: 10000000 INFO @ Thu, 05 Apr 2018 10:41:16: 10000000 INFO @ Thu, 05 Apr 2018 10:41:19: 10000000 INFO @ Thu, 05 Apr 2018 10:41:19: 11000000 INFO @ Thu, 05 Apr 2018 10:41:22: 11000000 INFO @ Thu, 05 Apr 2018 10:41:25: 11000000 INFO @ Thu, 05 Apr 2018 10:41:25: 12000000 INFO @ Thu, 05 Apr 2018 10:41:28: 12000000 INFO @ Thu, 05 Apr 2018 10:41:31: 13000000 INFO @ Thu, 05 Apr 2018 10:41:31: 12000000 INFO @ Thu, 05 Apr 2018 10:41:33: 13000000 INFO @ Thu, 05 Apr 2018 10:41:36: 14000000 INFO @ Thu, 05 Apr 2018 10:41:37: 13000000 INFO @ Thu, 05 Apr 2018 10:41:39: 14000000 INFO @ Thu, 05 Apr 2018 10:41:42: 15000000 INFO @ Thu, 05 Apr 2018 10:41:44: 14000000 INFO @ Thu, 05 Apr 2018 10:41:45: 15000000 INFO @ Thu, 05 Apr 2018 10:41:47: 16000000 INFO @ Thu, 05 Apr 2018 10:41:50: 15000000 INFO @ Thu, 05 Apr 2018 10:41:51: 16000000 INFO @ Thu, 05 Apr 2018 10:41:53: 17000000 INFO @ Thu, 05 Apr 2018 10:41:56: 16000000 INFO @ Thu, 05 Apr 2018 10:41:57: 17000000 INFO @ Thu, 05 Apr 2018 10:41:59: 18000000 INFO @ Thu, 05 Apr 2018 10:42:02: 17000000 INFO @ Thu, 05 Apr 2018 10:42:03: 18000000 INFO @ Thu, 05 Apr 2018 10:42:04: 19000000 INFO @ Thu, 05 Apr 2018 10:42:09: 18000000 INFO @ Thu, 05 Apr 2018 10:42:09: 19000000 INFO @ Thu, 05 Apr 2018 10:42:10: 20000000 INFO @ Thu, 05 Apr 2018 10:42:15: 19000000 INFO @ Thu, 05 Apr 2018 10:42:15: 20000000 INFO @ Thu, 05 Apr 2018 10:42:16: 21000000 INFO @ Thu, 05 Apr 2018 10:42:21: 21000000 INFO @ Thu, 05 Apr 2018 10:42:21: 20000000 INFO @ Thu, 05 Apr 2018 10:42:21: 22000000 INFO @ Thu, 05 Apr 2018 10:42:27: 22000000 INFO @ Thu, 05 Apr 2018 10:42:27: 23000000 INFO @ Thu, 05 Apr 2018 10:42:27: 21000000 INFO @ Thu, 05 Apr 2018 10:42:32: 24000000 INFO @ Thu, 05 Apr 2018 10:42:33: 23000000 INFO @ Thu, 05 Apr 2018 10:42:34: 22000000 INFO @ Thu, 05 Apr 2018 10:42:38: 25000000 INFO @ Thu, 05 Apr 2018 10:42:38: 24000000 INFO @ Thu, 05 Apr 2018 10:42:40: 23000000 INFO @ Thu, 05 Apr 2018 10:42:43: 26000000 INFO @ Thu, 05 Apr 2018 10:42:44: 25000000 INFO @ Thu, 05 Apr 2018 10:42:46: 24000000 INFO @ Thu, 05 Apr 2018 10:42:49: 27000000 INFO @ Thu, 05 Apr 2018 10:42:50: 26000000 INFO @ Thu, 05 Apr 2018 10:42:52: 25000000 INFO @ Thu, 05 Apr 2018 10:42:54: 28000000 INFO @ Thu, 05 Apr 2018 10:42:56: 27000000 INFO @ Thu, 05 Apr 2018 10:42:58: 26000000 INFO @ Thu, 05 Apr 2018 10:43:00: 29000000 INFO @ Thu, 05 Apr 2018 10:43:02: 28000000 INFO @ Thu, 05 Apr 2018 10:43:04: 27000000 INFO @ Thu, 05 Apr 2018 10:43:06: 30000000 INFO @ Thu, 05 Apr 2018 10:43:08: 29000000 INFO @ Thu, 05 Apr 2018 10:43:11: 28000000 INFO @ Thu, 05 Apr 2018 10:43:11: 31000000 INFO @ Thu, 05 Apr 2018 10:43:13: 30000000 INFO @ Thu, 05 Apr 2018 10:43:17: 32000000 INFO @ Thu, 05 Apr 2018 10:43:17: 29000000 INFO @ Thu, 05 Apr 2018 10:43:19: 31000000 INFO @ Thu, 05 Apr 2018 10:43:22: 33000000 INFO @ Thu, 05 Apr 2018 10:43:23: 30000000 INFO @ Thu, 05 Apr 2018 10:43:25: 32000000 INFO @ Thu, 05 Apr 2018 10:43:28: 34000000 INFO @ Thu, 05 Apr 2018 10:43:29: 31000000 INFO @ Thu, 05 Apr 2018 10:43:31: 33000000 INFO @ Thu, 05 Apr 2018 10:43:34: 35000000 INFO @ Thu, 05 Apr 2018 10:43:35: 32000000 INFO @ Thu, 05 Apr 2018 10:43:37: 34000000 INFO @ Thu, 05 Apr 2018 10:43:39: 36000000 INFO @ Thu, 05 Apr 2018 10:43:42: 33000000 INFO @ Thu, 05 Apr 2018 10:43:43: 35000000 INFO @ Thu, 05 Apr 2018 10:43:45: 37000000 INFO @ Thu, 05 Apr 2018 10:43:48: 34000000 INFO @ Thu, 05 Apr 2018 10:43:49: 36000000 INFO @ Thu, 05 Apr 2018 10:43:50: 38000000 INFO @ Thu, 05 Apr 2018 10:43:54: 35000000 INFO @ Thu, 05 Apr 2018 10:43:54: 37000000 INFO @ Thu, 05 Apr 2018 10:43:56: 39000000 INFO @ Thu, 05 Apr 2018 10:44:00: 36000000 INFO @ Thu, 05 Apr 2018 10:44:00: 38000000 INFO @ Thu, 05 Apr 2018 10:44:01: 40000000 INFO @ Thu, 05 Apr 2018 10:44:06: 39000000 INFO @ Thu, 05 Apr 2018 10:44:06: 37000000 INFO @ Thu, 05 Apr 2018 10:44:07: 41000000 INFO @ Thu, 05 Apr 2018 10:44:09: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:44:09: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:44:09: #1 total tags in treatment: 20416108 INFO @ Thu, 05 Apr 2018 10:44:09: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:44:09: #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 10:44:09: #1 tags after filtering in treatment: 7274489 INFO @ Thu, 05 Apr 2018 10:44:09: #1 Redundant rate of treatment: 0.64 INFO @ Thu, 05 Apr 2018 10:44:09: #1 finished! INFO @ Thu, 05 Apr 2018 10:44:09: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:44:09: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:44:10: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:44:10: 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 @ Thu, 05 Apr 2018 10:44:10: Process for pairing-model is terminated! cat: SRX3671207.05_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 `SRX3671207.05_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 `SRX3671207.05_*.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 `SRX3671207.05_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 10:44:12: 40000000 INFO @ Thu, 05 Apr 2018 10:44:12: 38000000 INFO @ Thu, 05 Apr 2018 10:44:18: 41000000 INFO @ Thu, 05 Apr 2018 10:44:18: 39000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 05 Apr 2018 10:44:19: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:44:19: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:44:19: #1 total tags in treatment: 20416108 INFO @ Thu, 05 Apr 2018 10:44:19: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:44:19: #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 10:44:20: #1 tags after filtering in treatment: 7274489 INFO @ Thu, 05 Apr 2018 10:44:20: #1 Redundant rate of treatment: 0.64 INFO @ Thu, 05 Apr 2018 10:44:20: #1 finished! INFO @ Thu, 05 Apr 2018 10:44:20: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:44:20: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:44:20: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:44:20: 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, 05 Apr 2018 10:44:20: Process for pairing-model is terminated! cat: SRX3671207.10_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 `SRX3671207.10_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 `SRX3671207.10_*.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 `SRX3671207.10_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 10:44:24: 40000000 INFO @ Thu, 05 Apr 2018 10:44:30: 41000000 INFO @ Thu, 05 Apr 2018 10:44:32: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:44:32: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:44:32: #1 total tags in treatment: 20416108 INFO @ Thu, 05 Apr 2018 10:44:32: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:44:32: #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 10:44:32: #1 tags after filtering in treatment: 7274489 INFO @ Thu, 05 Apr 2018 10:44:32: #1 Redundant rate of treatment: 0.64 INFO @ Thu, 05 Apr 2018 10:44:32: #1 finished! INFO @ Thu, 05 Apr 2018 10:44:32: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:44:32: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:44:33: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:44:33: 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 10:44:33: Process for pairing-model is terminated! cat: SRX3671207.20_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): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3671207.20_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 `SRX3671207.20_*.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 `SRX3671207.20_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 BigWig に変換しました。