Job ID = 10608973 sra ファイルのダウンロード中... Completed: 2299300K bytes transferred in 284 seconds (66158K 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 18271331 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2741972/SRR5453806.sra Written 18271331 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: 00:22:23 18271331 reads; of these: 18271331 (100.00%) were paired; of these: 2004935 (10.97%) aligned concordantly 0 times 14351629 (78.55%) aligned concordantly exactly 1 time 1914767 (10.48%) aligned concordantly >1 times ---- 2004935 pairs aligned concordantly 0 times; of these: 302191 (15.07%) aligned discordantly 1 time ---- 1702744 pairs aligned 0 times concordantly or discordantly; of these: 3405488 mates make up the pairs; of these: 2668732 (78.37%) aligned 0 times 549393 (16.13%) aligned exactly 1 time 187363 (5.50%) aligned >1 times 92.70% overall alignment rate Time searching: 00:22:23 Overall time: 00:22:23 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 16 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] 9515799 / 16530055 = 0.5757 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 23:31:39: # Command line: callpeak -t SRX2741972.bam -f BAM -g 12100000 -n SRX2741972.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2741972.10 # format = BAM # ChIP-seq file = ['SRX2741972.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 23:31:39: #1 read tag files... INFO @ Thu, 03 May 2018 23:31:39: #1 read treatment tags... INFO @ Thu, 03 May 2018 23:31:39: # Command line: callpeak -t SRX2741972.bam -f BAM -g 12100000 -n SRX2741972.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2741972.20 # format = BAM # ChIP-seq file = ['SRX2741972.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 23:31:39: #1 read tag files... INFO @ Thu, 03 May 2018 23:31:39: #1 read treatment tags... INFO @ Thu, 03 May 2018 23:31:39: # Command line: callpeak -t SRX2741972.bam -f BAM -g 12100000 -n SRX2741972.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2741972.05 # format = BAM # ChIP-seq file = ['SRX2741972.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 23:31:39: #1 read tag files... INFO @ Thu, 03 May 2018 23:31:39: #1 read treatment tags... INFO @ Thu, 03 May 2018 23:31:47: 1000000 INFO @ Thu, 03 May 2018 23:31:47: 1000000 INFO @ Thu, 03 May 2018 23:31:47: 1000000 INFO @ Thu, 03 May 2018 23:31:54: 2000000 INFO @ Thu, 03 May 2018 23:31:55: 2000000 INFO @ Thu, 03 May 2018 23:31:57: 2000000 INFO @ Thu, 03 May 2018 23:32:02: 3000000 INFO @ Thu, 03 May 2018 23:32:04: 3000000 INFO @ Thu, 03 May 2018 23:32:06: 3000000 INFO @ Thu, 03 May 2018 23:32:09: 4000000 INFO @ Thu, 03 May 2018 23:32:12: 4000000 INFO @ Thu, 03 May 2018 23:32:15: 4000000 INFO @ Thu, 03 May 2018 23:32:17: 5000000 INFO @ Thu, 03 May 2018 23:32:20: 5000000 INFO @ Thu, 03 May 2018 23:32:24: 5000000 INFO @ Thu, 03 May 2018 23:32:24: 6000000 INFO @ Thu, 03 May 2018 23:32:29: 6000000 INFO @ Thu, 03 May 2018 23:32:32: 7000000 INFO @ Thu, 03 May 2018 23:32:33: 6000000 INFO @ Thu, 03 May 2018 23:32:37: 7000000 INFO @ Thu, 03 May 2018 23:32:39: 8000000 INFO @ Thu, 03 May 2018 23:32:42: 7000000 INFO @ Thu, 03 May 2018 23:32:46: 8000000 INFO @ Thu, 03 May 2018 23:32:46: 9000000 INFO @ Thu, 03 May 2018 23:32:52: 8000000 INFO @ Thu, 03 May 2018 23:32:54: 10000000 INFO @ Thu, 03 May 2018 23:32:54: 9000000 INFO @ Thu, 03 May 2018 23:33:01: 9000000 INFO @ Thu, 03 May 2018 23:33:01: 11000000 INFO @ Thu, 03 May 2018 23:33:02: 10000000 INFO @ Thu, 03 May 2018 23:33:09: 12000000 INFO @ Thu, 03 May 2018 23:33:10: 10000000 INFO @ Thu, 03 May 2018 23:33:10: 11000000 INFO @ Thu, 03 May 2018 23:33:16: 13000000 INFO @ Thu, 03 May 2018 23:33:19: 12000000 INFO @ Thu, 03 May 2018 23:33:19: 11000000 INFO @ Thu, 03 May 2018 23:33:24: 14000000 INFO @ Thu, 03 May 2018 23:33:27: 13000000 INFO @ Thu, 03 May 2018 23:33:28: 12000000 INFO @ Thu, 03 May 2018 23:33:30: #1 tag size is determined as 100 bps INFO @ Thu, 03 May 2018 23:33:30: #1 tag size = 100 INFO @ Thu, 03 May 2018 23:33:30: #1 total tags in treatment: 6792718 INFO @ Thu, 03 May 2018 23:33:30: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 23:33:30: #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 23:33:30: #1 tags after filtering in treatment: 5204208 INFO @ Thu, 03 May 2018 23:33:30: #1 Redundant rate of treatment: 0.23 INFO @ Thu, 03 May 2018 23:33:30: #1 finished! INFO @ Thu, 03 May 2018 23:33:30: #2 Build Peak Model... INFO @ Thu, 03 May 2018 23:33:30: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 23:33:31: #2 number of paired peaks: 0 WARNING @ Thu, 03 May 2018 23:33:31: 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 23:33:31: Process for pairing-model is terminated! cat: SRX2741972.10_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 `SRX2741972.10_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 `SRX2741972.10_*.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 `SRX2741972.10_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 23:33:36: 14000000 INFO @ Thu, 03 May 2018 23:33:37: 13000000 INFO @ Thu, 03 May 2018 23:33:42: #1 tag size is determined as 100 bps INFO @ Thu, 03 May 2018 23:33:42: #1 tag size = 100 INFO @ Thu, 03 May 2018 23:33:42: #1 total tags in treatment: 6792718 INFO @ Thu, 03 May 2018 23:33:42: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 23:33:42: #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 23:33:43: #1 tags after filtering in treatment: 5204208 INFO @ Thu, 03 May 2018 23:33:43: #1 Redundant rate of treatment: 0.23 INFO @ Thu, 03 May 2018 23:33:43: #1 finished! INFO @ Thu, 03 May 2018 23:33:43: #2 Build Peak Model... INFO @ Thu, 03 May 2018 23:33:43: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 23:33:43: #2 number of paired peaks: 0 WARNING @ Thu, 03 May 2018 23:33:43: 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, 03 May 2018 23:33:43: Process for pairing-model is terminated! cat: SRX2741972.20_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 `SRX2741972.20_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 `SRX2741972.20_*.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 `SRX2741972.20_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, 03 May 2018 23:33:46: 14000000 INFO @ Thu, 03 May 2018 23:33:53: #1 tag size is determined as 100 bps INFO @ Thu, 03 May 2018 23:33:53: #1 tag size = 100 INFO @ Thu, 03 May 2018 23:33:53: #1 total tags in treatment: 6792718 INFO @ Thu, 03 May 2018 23:33:53: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 23:33:53: #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 23:33:53: #1 tags after filtering in treatment: 5204208 INFO @ Thu, 03 May 2018 23:33:53: #1 Redundant rate of treatment: 0.23 INFO @ Thu, 03 May 2018 23:33:53: #1 finished! INFO @ Thu, 03 May 2018 23:33:53: #2 Build Peak Model... INFO @ Thu, 03 May 2018 23:33:53: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 23:33:54: #2 number of paired peaks: 0 WARNING @ Thu, 03 May 2018 23:33:54: 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 23:33:54: Process for pairing-model is terminated! cat: SRX2741972.05_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 `SRX2741972.05_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 `SRX2741972.05_*.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 `SRX2741972.05_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。