Job ID = 10608977 sra ファイルのダウンロード中... Completed: 2794834K bytes transferred in 175 seconds (130616K 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 22134484 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2741984/SRR5453818.sra Written 22134484 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: 00:38:57 22134484 reads; of these: 22134484 (100.00%) were paired; of these: 1558180 (7.04%) aligned concordantly 0 times 18645362 (84.24%) aligned concordantly exactly 1 time 1930942 (8.72%) aligned concordantly >1 times ---- 1558180 pairs aligned concordantly 0 times; of these: 287401 (18.44%) aligned discordantly 1 time ---- 1270779 pairs aligned 0 times concordantly or discordantly; of these: 2541558 mates make up the pairs; of these: 1497961 (58.94%) aligned 0 times 769811 (30.29%) aligned exactly 1 time 273786 (10.77%) aligned >1 times 96.62% overall alignment rate Time searching: 00:38:57 Overall time: 00:38:57 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] 10846761 / 20837550 = 0.5205 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, 03 May 2018 23:51:03: # Command line: callpeak -t SRX2741984.bam -f BAM -g 12100000 -n SRX2741984.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2741984.05 # format = BAM # ChIP-seq file = ['SRX2741984.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, 03 May 2018 23:51:03: #1 read tag files... INFO @ Thu, 03 May 2018 23:51:03: #1 read treatment tags... INFO @ Thu, 03 May 2018 23:51:03: # Command line: callpeak -t SRX2741984.bam -f BAM -g 12100000 -n SRX2741984.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2741984.10 # format = BAM # ChIP-seq file = ['SRX2741984.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, 03 May 2018 23:51:03: #1 read tag files... INFO @ Thu, 03 May 2018 23:51:03: # Command line: callpeak -t SRX2741984.bam -f BAM -g 12100000 -n SRX2741984.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2741984.20 # format = BAM # ChIP-seq file = ['SRX2741984.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, 03 May 2018 23:51:03: #1 read treatment tags... INFO @ Thu, 03 May 2018 23:51:03: #1 read tag files... INFO @ Thu, 03 May 2018 23:51:03: #1 read treatment tags... INFO @ Thu, 03 May 2018 23:51:10: 1000000 INFO @ Thu, 03 May 2018 23:51:10: 1000000 INFO @ Thu, 03 May 2018 23:51:10: 1000000 INFO @ Thu, 03 May 2018 23:51:17: 2000000 INFO @ Thu, 03 May 2018 23:51:17: 2000000 INFO @ Thu, 03 May 2018 23:51:17: 2000000 INFO @ Thu, 03 May 2018 23:51:24: 3000000 INFO @ Thu, 03 May 2018 23:51:24: 3000000 INFO @ Thu, 03 May 2018 23:51:25: 3000000 INFO @ Thu, 03 May 2018 23:51:31: 4000000 INFO @ Thu, 03 May 2018 23:51:32: 4000000 INFO @ Thu, 03 May 2018 23:51:32: 4000000 INFO @ Thu, 03 May 2018 23:51:39: 5000000 INFO @ Thu, 03 May 2018 23:51:39: 5000000 INFO @ Thu, 03 May 2018 23:51:40: 5000000 INFO @ Thu, 03 May 2018 23:51:46: 6000000 INFO @ Thu, 03 May 2018 23:51:47: 6000000 INFO @ Thu, 03 May 2018 23:51:47: 6000000 INFO @ Thu, 03 May 2018 23:51:53: 7000000 INFO @ Thu, 03 May 2018 23:51:54: 7000000 INFO @ Thu, 03 May 2018 23:51:55: 7000000 INFO @ Thu, 03 May 2018 23:52:00: 8000000 INFO @ Thu, 03 May 2018 23:52:02: 8000000 INFO @ Thu, 03 May 2018 23:52:03: 8000000 INFO @ Thu, 03 May 2018 23:52:07: 9000000 INFO @ Thu, 03 May 2018 23:52:09: 9000000 INFO @ Thu, 03 May 2018 23:52:11: 9000000 INFO @ Thu, 03 May 2018 23:52:14: 10000000 INFO @ Thu, 03 May 2018 23:52:17: 10000000 INFO @ Thu, 03 May 2018 23:52:18: 10000000 INFO @ Thu, 03 May 2018 23:52:21: 11000000 INFO @ Thu, 03 May 2018 23:52:24: 11000000 INFO @ Thu, 03 May 2018 23:52:26: 11000000 INFO @ Thu, 03 May 2018 23:52:28: 12000000 INFO @ Thu, 03 May 2018 23:52:32: 12000000 INFO @ Thu, 03 May 2018 23:52:34: 12000000 INFO @ Thu, 03 May 2018 23:52:34: 13000000 INFO @ Thu, 03 May 2018 23:52:39: 13000000 INFO @ Thu, 03 May 2018 23:52:42: 14000000 INFO @ Thu, 03 May 2018 23:52:42: 13000000 INFO @ Thu, 03 May 2018 23:52:47: 14000000 INFO @ Thu, 03 May 2018 23:52:49: 15000000 INFO @ Thu, 03 May 2018 23:52:49: 14000000 INFO @ Thu, 03 May 2018 23:52:55: 15000000 INFO @ Thu, 03 May 2018 23:52:56: 16000000 INFO @ Thu, 03 May 2018 23:52:57: 15000000 INFO @ Thu, 03 May 2018 23:53:02: 16000000 INFO @ Thu, 03 May 2018 23:53:03: 17000000 INFO @ Thu, 03 May 2018 23:53:05: 16000000 INFO @ Thu, 03 May 2018 23:53:10: 18000000 INFO @ Thu, 03 May 2018 23:53:10: 17000000 INFO @ Thu, 03 May 2018 23:53:13: 17000000 INFO @ Thu, 03 May 2018 23:53:17: 19000000 INFO @ Thu, 03 May 2018 23:53:17: 18000000 INFO @ Thu, 03 May 2018 23:53:20: 18000000 INFO @ Thu, 03 May 2018 23:53:24: 20000000 INFO @ Thu, 03 May 2018 23:53:25: 19000000 INFO @ Thu, 03 May 2018 23:53:28: 19000000 INFO @ Thu, 03 May 2018 23:53:30: 21000000 INFO @ Thu, 03 May 2018 23:53:31: #1 tag size is determined as 100 bps INFO @ Thu, 03 May 2018 23:53:31: #1 tag size = 100 INFO @ Thu, 03 May 2018 23:53:31: #1 total tags in treatment: 9759899 INFO @ Thu, 03 May 2018 23:53:31: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 23:53:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 03 May 2018 23:53:31: #1 tags after filtering in treatment: 5104957 INFO @ Thu, 03 May 2018 23:53:31: #1 Redundant rate of treatment: 0.48 INFO @ Thu, 03 May 2018 23:53:31: #1 finished! INFO @ Thu, 03 May 2018 23:53:31: #2 Build Peak Model... INFO @ Thu, 03 May 2018 23:53:31: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 23:53:32: #2 number of paired peaks: 0 WARNING @ Thu, 03 May 2018 23:53:32: 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, 03 May 2018 23:53:32: Process for pairing-model is terminated! cat: SRX2741984.10_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 `SRX2741984.10_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 `SRX2741984.10_*.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 `SRX2741984.10_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, 03 May 2018 23:53:32: 20000000 INFO @ Thu, 03 May 2018 23:53:36: 20000000 INFO @ Thu, 03 May 2018 23:53:39: 21000000 INFO @ Thu, 03 May 2018 23:53:40: #1 tag size is determined as 100 bps INFO @ Thu, 03 May 2018 23:53:40: #1 tag size = 100 INFO @ Thu, 03 May 2018 23:53:40: #1 total tags in treatment: 9759899 INFO @ Thu, 03 May 2018 23:53:40: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 23:53:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 03 May 2018 23:53:40: #1 tags after filtering in treatment: 5104957 INFO @ Thu, 03 May 2018 23:53:40: #1 Redundant rate of treatment: 0.48 INFO @ Thu, 03 May 2018 23:53:40: #1 finished! INFO @ Thu, 03 May 2018 23:53:40: #2 Build Peak Model... INFO @ Thu, 03 May 2018 23:53:40: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 23:53:41: #2 number of paired peaks: 0 WARNING @ Thu, 03 May 2018 23:53:41: 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, 03 May 2018 23:53:41: Process for pairing-model is terminated! cat: SRX2741984.05_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 `SRX2741984.05_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 `SRX2741984.05_*.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 `SRX2741984.05_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, 03 May 2018 23:53:43: 21000000 INFO @ Thu, 03 May 2018 23:53:43: #1 tag size is determined as 100 bps INFO @ Thu, 03 May 2018 23:53:43: #1 tag size = 100 INFO @ Thu, 03 May 2018 23:53:43: #1 total tags in treatment: 9759899 INFO @ Thu, 03 May 2018 23:53:43: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 23:53:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 03 May 2018 23:53:44: #1 tags after filtering in treatment: 5104957 INFO @ Thu, 03 May 2018 23:53:44: #1 Redundant rate of treatment: 0.48 INFO @ Thu, 03 May 2018 23:53:44: #1 finished! INFO @ Thu, 03 May 2018 23:53:44: #2 Build Peak Model... INFO @ Thu, 03 May 2018 23:53:44: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 23:53:44: #2 number of paired peaks: 0 WARNING @ Thu, 03 May 2018 23:53:44: 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 @ Thu, 03 May 2018 23:53:44: Process for pairing-model is terminated! cat: SRX2741984.20_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 `SRX2741984.20_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 `SRX2741984.20_*.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 `SRX2741984.20_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。