Job ID = 10536521 sra ファイルのダウンロード中... Completed: 1174484K bytes transferred in 30 seconds (314535K 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 32797960 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3671214/SRR6696966.sra Written 32797960 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: 00:23:29 32797960 reads; of these: 32797960 (100.00%) were paired; of these: 3947943 (12.04%) aligned concordantly 0 times 24912877 (75.96%) aligned concordantly exactly 1 time 3937140 (12.00%) aligned concordantly >1 times ---- 3947943 pairs aligned concordantly 0 times; of these: 169430 (4.29%) aligned discordantly 1 time ---- 3778513 pairs aligned 0 times concordantly or discordantly; of these: 7557026 mates make up the pairs; of these: 7332163 (97.02%) aligned 0 times 125081 (1.66%) aligned exactly 1 time 99782 (1.32%) aligned >1 times 88.82% overall alignment rate Time searching: 00:23:29 Overall time: 00:23:29 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 24 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] 9910995 / 28963251 = 0.3422 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 10:40:23: # Command line: callpeak -t SRX3671214.bam -f BAM -g 12100000 -n SRX3671214.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3671214.05 # format = BAM # ChIP-seq file = ['SRX3671214.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 10:40:23: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:40:23: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:40:23: # Command line: callpeak -t SRX3671214.bam -f BAM -g 12100000 -n SRX3671214.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3671214.20 # format = BAM # ChIP-seq file = ['SRX3671214.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 10:40:23: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:40:23: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:40:23: # Command line: callpeak -t SRX3671214.bam -f BAM -g 12100000 -n SRX3671214.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3671214.10 # format = BAM # ChIP-seq file = ['SRX3671214.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 10:40:23: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:40:23: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:40:28: 1000000 INFO @ Thu, 05 Apr 2018 10:40:28: 1000000 INFO @ Thu, 05 Apr 2018 10:40:28: 1000000 INFO @ Thu, 05 Apr 2018 10:40:33: 2000000 INFO @ Thu, 05 Apr 2018 10:40:33: 2000000 INFO @ Thu, 05 Apr 2018 10:40:33: 2000000 INFO @ Thu, 05 Apr 2018 10:40:37: 3000000 INFO @ Thu, 05 Apr 2018 10:40:38: 3000000 INFO @ Thu, 05 Apr 2018 10:40:38: 3000000 INFO @ Thu, 05 Apr 2018 10:40:42: 4000000 INFO @ Thu, 05 Apr 2018 10:40:43: 4000000 INFO @ Thu, 05 Apr 2018 10:40:43: 4000000 INFO @ Thu, 05 Apr 2018 10:40:47: 5000000 INFO @ Thu, 05 Apr 2018 10:40:48: 5000000 INFO @ Thu, 05 Apr 2018 10:40:48: 5000000 INFO @ Thu, 05 Apr 2018 10:40:52: 6000000 INFO @ Thu, 05 Apr 2018 10:40:53: 6000000 INFO @ Thu, 05 Apr 2018 10:40:53: 6000000 INFO @ Thu, 05 Apr 2018 10:40:57: 7000000 INFO @ Thu, 05 Apr 2018 10:40:58: 7000000 INFO @ Thu, 05 Apr 2018 10:40:58: 7000000 INFO @ Thu, 05 Apr 2018 10:41:02: 8000000 INFO @ Thu, 05 Apr 2018 10:41:03: 8000000 INFO @ Thu, 05 Apr 2018 10:41:03: 8000000 INFO @ Thu, 05 Apr 2018 10:41:08: 9000000 INFO @ Thu, 05 Apr 2018 10:41:08: 9000000 INFO @ Thu, 05 Apr 2018 10:41:08: 9000000 INFO @ Thu, 05 Apr 2018 10:41:13: 10000000 INFO @ Thu, 05 Apr 2018 10:41:13: 10000000 INFO @ Thu, 05 Apr 2018 10:41:13: 10000000 INFO @ Thu, 05 Apr 2018 10:41:18: 11000000 INFO @ Thu, 05 Apr 2018 10:41:18: 11000000 INFO @ Thu, 05 Apr 2018 10:41:18: 11000000 INFO @ Thu, 05 Apr 2018 10:41:23: 12000000 INFO @ Thu, 05 Apr 2018 10:41:23: 12000000 INFO @ Thu, 05 Apr 2018 10:41:23: 12000000 INFO @ Thu, 05 Apr 2018 10:41:28: 13000000 INFO @ Thu, 05 Apr 2018 10:41:28: 13000000 INFO @ Thu, 05 Apr 2018 10:41:28: 13000000 INFO @ Thu, 05 Apr 2018 10:41:33: 14000000 INFO @ Thu, 05 Apr 2018 10:41:33: 14000000 INFO @ Thu, 05 Apr 2018 10:41:33: 14000000 INFO @ Thu, 05 Apr 2018 10:41:38: 15000000 INFO @ Thu, 05 Apr 2018 10:41:38: 15000000 INFO @ Thu, 05 Apr 2018 10:41:38: 15000000 INFO @ Thu, 05 Apr 2018 10:41:43: 16000000 INFO @ Thu, 05 Apr 2018 10:41:43: 16000000 INFO @ Thu, 05 Apr 2018 10:41:43: 16000000 INFO @ Thu, 05 Apr 2018 10:41:48: 17000000 INFO @ Thu, 05 Apr 2018 10:41:48: 17000000 INFO @ Thu, 05 Apr 2018 10:41:49: 17000000 INFO @ Thu, 05 Apr 2018 10:41:53: 18000000 INFO @ Thu, 05 Apr 2018 10:41:53: 18000000 INFO @ Thu, 05 Apr 2018 10:41:54: 18000000 INFO @ Thu, 05 Apr 2018 10:41:58: 19000000 INFO @ Thu, 05 Apr 2018 10:41:58: 19000000 INFO @ Thu, 05 Apr 2018 10:41:59: 19000000 INFO @ Thu, 05 Apr 2018 10:42:03: 20000000 INFO @ Thu, 05 Apr 2018 10:42:03: 20000000 INFO @ Thu, 05 Apr 2018 10:42:04: 20000000 INFO @ Thu, 05 Apr 2018 10:42:08: 21000000 INFO @ Thu, 05 Apr 2018 10:42:08: 21000000 INFO @ Thu, 05 Apr 2018 10:42:09: 21000000 INFO @ Thu, 05 Apr 2018 10:42:13: 22000000 INFO @ Thu, 05 Apr 2018 10:42:13: 22000000 INFO @ Thu, 05 Apr 2018 10:42:14: 22000000 INFO @ Thu, 05 Apr 2018 10:42:18: 23000000 INFO @ Thu, 05 Apr 2018 10:42:19: 23000000 INFO @ Thu, 05 Apr 2018 10:42:20: 23000000 INFO @ Thu, 05 Apr 2018 10:42:23: 24000000 INFO @ Thu, 05 Apr 2018 10:42:24: 24000000 INFO @ Thu, 05 Apr 2018 10:42:24: 24000000 INFO @ Thu, 05 Apr 2018 10:42:28: 25000000 INFO @ Thu, 05 Apr 2018 10:42:28: 25000000 INFO @ Thu, 05 Apr 2018 10:42:29: 25000000 INFO @ Thu, 05 Apr 2018 10:42:33: 26000000 INFO @ Thu, 05 Apr 2018 10:42:33: 26000000 INFO @ Thu, 05 Apr 2018 10:42:35: 26000000 INFO @ Thu, 05 Apr 2018 10:42:38: 27000000 INFO @ Thu, 05 Apr 2018 10:42:38: 27000000 INFO @ Thu, 05 Apr 2018 10:42:40: 27000000 INFO @ Thu, 05 Apr 2018 10:42:43: 28000000 INFO @ Thu, 05 Apr 2018 10:42:44: 28000000 INFO @ Thu, 05 Apr 2018 10:42:45: 28000000 INFO @ Thu, 05 Apr 2018 10:42:48: 29000000 INFO @ Thu, 05 Apr 2018 10:42:49: 29000000 INFO @ Thu, 05 Apr 2018 10:42:51: 29000000 INFO @ Thu, 05 Apr 2018 10:42:54: 30000000 INFO @ Thu, 05 Apr 2018 10:42:55: 30000000 INFO @ Thu, 05 Apr 2018 10:42:56: 30000000 INFO @ Thu, 05 Apr 2018 10:43:00: 31000000 INFO @ Thu, 05 Apr 2018 10:43:01: 31000000 INFO @ Thu, 05 Apr 2018 10:43:02: 31000000 INFO @ Thu, 05 Apr 2018 10:43:06: 32000000 INFO @ Thu, 05 Apr 2018 10:43:07: 32000000 INFO @ Thu, 05 Apr 2018 10:43:08: 32000000 INFO @ Thu, 05 Apr 2018 10:43:12: 33000000 INFO @ Thu, 05 Apr 2018 10:43:12: 33000000 INFO @ Thu, 05 Apr 2018 10:43:13: 33000000 INFO @ Thu, 05 Apr 2018 10:43:18: 34000000 INFO @ Thu, 05 Apr 2018 10:43:18: 34000000 INFO @ Thu, 05 Apr 2018 10:43:19: 34000000 INFO @ Thu, 05 Apr 2018 10:43:23: 35000000 INFO @ Thu, 05 Apr 2018 10:43:24: 35000000 INFO @ Thu, 05 Apr 2018 10:43:24: 35000000 INFO @ Thu, 05 Apr 2018 10:43:29: 36000000 INFO @ Thu, 05 Apr 2018 10:43:29: 36000000 INFO @ Thu, 05 Apr 2018 10:43:29: 36000000 INFO @ Thu, 05 Apr 2018 10:43:34: 37000000 INFO @ Thu, 05 Apr 2018 10:43:34: 37000000 INFO @ Thu, 05 Apr 2018 10:43:34: 37000000 INFO @ Thu, 05 Apr 2018 10:43:39: 38000000 INFO @ Thu, 05 Apr 2018 10:43:39: 38000000 INFO @ Thu, 05 Apr 2018 10:43:40: 38000000 INFO @ Thu, 05 Apr 2018 10:43:42: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:43:42: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:43:42: #1 total tags in treatment: 18987638 INFO @ Thu, 05 Apr 2018 10:43:42: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:43:42: #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 10:43:42: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:43:42: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:43:42: #1 total tags in treatment: 18987638 INFO @ Thu, 05 Apr 2018 10:43:42: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:43:42: #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 10:43:42: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:43:42: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:43:42: #1 total tags in treatment: 18987638 INFO @ Thu, 05 Apr 2018 10:43:42: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:43:42: #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 10:43:42: #1 tags after filtering in treatment: 6972780 INFO @ Thu, 05 Apr 2018 10:43:42: #1 Redundant rate of treatment: 0.63 INFO @ Thu, 05 Apr 2018 10:43:42: #1 finished! INFO @ Thu, 05 Apr 2018 10:43:42: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:43:42: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:43:42: #1 tags after filtering in treatment: 6972780 INFO @ Thu, 05 Apr 2018 10:43:42: #1 Redundant rate of treatment: 0.63 INFO @ Thu, 05 Apr 2018 10:43:42: #1 finished! INFO @ Thu, 05 Apr 2018 10:43:42: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:43:42: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:43:43: #1 tags after filtering in treatment: 6972780 INFO @ Thu, 05 Apr 2018 10:43:43: #1 Redundant rate of treatment: 0.63 INFO @ Thu, 05 Apr 2018 10:43:43: #1 finished! INFO @ Thu, 05 Apr 2018 10:43:43: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:43:43: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:43:43: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:43:43: 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 10:43:43: Process for pairing-model is terminated! cat: SRX3671214.10_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 `SRX3671214.10_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 `SRX3671214.10_*.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 `SRX3671214.10_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 10:43:43: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:43:43: 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 10:43:43: Process for pairing-model is terminated! cat: SRX3671214.20_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 `SRX3671214.20_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 `SRX3671214.20_*.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 `SRX3671214.20_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 @ Thu, 05 Apr 2018 10:43:43: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:43:43: 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 10:43:43: Process for pairing-model is terminated! cat: SRX3671214.05_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 `SRX3671214.05_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 `SRX3671214.05_*.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 `SRX3671214.05_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 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。