Job ID = 9732102 sra ファイルのダウンロード中... Completed: 277854K bytes transferred in 6 seconds (338281K bits/sec), in 1 file, 2 directories. 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 12013385 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2675892/SRR5380668.sra Written 12013385 spots total 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: 00:05:19 12013385 reads; of these: 12013385 (100.00%) were paired; of these: 2783074 (23.17%) aligned concordantly 0 times 8289602 (69.00%) aligned concordantly exactly 1 time 940709 (7.83%) aligned concordantly >1 times ---- 2783074 pairs aligned concordantly 0 times; of these: 600167 (21.56%) aligned discordantly 1 time ---- 2182907 pairs aligned 0 times concordantly or discordantly; of these: 4365814 mates make up the pairs; of these: 3753519 (85.98%) aligned 0 times 421527 (9.66%) aligned exactly 1 time 190768 (4.37%) aligned >1 times 84.38% overall alignment rate Time searching: 00:05:19 Overall time: 00:05:19 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 8 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] 1138811 / 9587796 = 0.1188 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 @ Sun, 03 Sep 2017 19:43:45: # Command line: callpeak -t SRX2675892.bam -f BAM -g 12100000 -n SRX2675892.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2675892.20 # format = BAM # ChIP-seq file = ['SRX2675892.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 @ Sun, 03 Sep 2017 19:43:45: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:43:45: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:43:45: # Command line: callpeak -t SRX2675892.bam -f BAM -g 12100000 -n SRX2675892.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2675892.10 # format = BAM # ChIP-seq file = ['SRX2675892.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 @ Sun, 03 Sep 2017 19:43:45: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:43:45: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:43:45: # Command line: callpeak -t SRX2675892.bam -f BAM -g 12100000 -n SRX2675892.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2675892.05 # format = BAM # ChIP-seq file = ['SRX2675892.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 @ Sun, 03 Sep 2017 19:43:45: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:43:45: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:43:51: 1000000 INFO @ Sun, 03 Sep 2017 19:43:51: 1000000 INFO @ Sun, 03 Sep 2017 19:43:51: 1000000 INFO @ Sun, 03 Sep 2017 19:43:56: 2000000 INFO @ Sun, 03 Sep 2017 19:43:57: 2000000 INFO @ Sun, 03 Sep 2017 19:43:57: 2000000 INFO @ Sun, 03 Sep 2017 19:44:01: 3000000 INFO @ Sun, 03 Sep 2017 19:44:02: 3000000 INFO @ Sun, 03 Sep 2017 19:44:02: 3000000 INFO @ Sun, 03 Sep 2017 19:44:07: 4000000 INFO @ Sun, 03 Sep 2017 19:44:08: 4000000 INFO @ Sun, 03 Sep 2017 19:44:08: 4000000 INFO @ Sun, 03 Sep 2017 19:44:12: 5000000 INFO @ Sun, 03 Sep 2017 19:44:13: 5000000 INFO @ Sun, 03 Sep 2017 19:44:13: 5000000 INFO @ Sun, 03 Sep 2017 19:44:17: 6000000 INFO @ Sun, 03 Sep 2017 19:44:19: 6000000 INFO @ Sun, 03 Sep 2017 19:44:19: 6000000 INFO @ Sun, 03 Sep 2017 19:44:22: 7000000 INFO @ Sun, 03 Sep 2017 19:44:24: 7000000 INFO @ Sun, 03 Sep 2017 19:44:24: 7000000 INFO @ Sun, 03 Sep 2017 19:44:28: 8000000 INFO @ Sun, 03 Sep 2017 19:44:30: 8000000 INFO @ Sun, 03 Sep 2017 19:44:30: 8000000 INFO @ Sun, 03 Sep 2017 19:44:33: 9000000 INFO @ Sun, 03 Sep 2017 19:44:35: 9000000 INFO @ Sun, 03 Sep 2017 19:44:35: 9000000 INFO @ Sun, 03 Sep 2017 19:44:38: 10000000 INFO @ Sun, 03 Sep 2017 19:44:40: 10000000 INFO @ Sun, 03 Sep 2017 19:44:41: 10000000 INFO @ Sun, 03 Sep 2017 19:44:43: 11000000 INFO @ Sun, 03 Sep 2017 19:44:46: 11000000 INFO @ Sun, 03 Sep 2017 19:44:46: 11000000 INFO @ Sun, 03 Sep 2017 19:44:49: 12000000 INFO @ Sun, 03 Sep 2017 19:44:51: 12000000 INFO @ Sun, 03 Sep 2017 19:44:51: 12000000 INFO @ Sun, 03 Sep 2017 19:44:54: 13000000 INFO @ Sun, 03 Sep 2017 19:44:57: 13000000 INFO @ Sun, 03 Sep 2017 19:44:57: 13000000 INFO @ Sun, 03 Sep 2017 19:44:59: 14000000 INFO @ Sun, 03 Sep 2017 19:45:02: 14000000 INFO @ Sun, 03 Sep 2017 19:45:02: 14000000 INFO @ Sun, 03 Sep 2017 19:45:04: 15000000 INFO @ Sun, 03 Sep 2017 19:45:08: 15000000 INFO @ Sun, 03 Sep 2017 19:45:08: 15000000 INFO @ Sun, 03 Sep 2017 19:45:09: 16000000 INFO @ Sun, 03 Sep 2017 19:45:13: 16000000 INFO @ Sun, 03 Sep 2017 19:45:13: 16000000 INFO @ Sun, 03 Sep 2017 19:45:15: 17000000 INFO @ Sun, 03 Sep 2017 19:45:18: 17000000 INFO @ Sun, 03 Sep 2017 19:45:18: 17000000 INFO @ Sun, 03 Sep 2017 19:45:20: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:45:20: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:45:20: #1 total tags in treatment: 8096870 INFO @ Sun, 03 Sep 2017 19:45:20: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:45:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 19:45:20: #1 tags after filtering in treatment: 4102749 INFO @ Sun, 03 Sep 2017 19:45:20: #1 Redundant rate of treatment: 0.49 INFO @ Sun, 03 Sep 2017 19:45:20: #1 finished! INFO @ Sun, 03 Sep 2017 19:45:20: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:45:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:45:20: #2 number of paired peaks: 1 WARNING @ Sun, 03 Sep 2017 19:45:20: Too few paired peaks (1) 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 @ Sun, 03 Sep 2017 19:45:20: Process for pairing-model is terminated! cat: SRX2675892.05_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): 6 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2675892.05_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 `SRX2675892.05_*.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 `SRX2675892.05_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 @ Sun, 03 Sep 2017 19:45:24: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:45:24: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:45:24: #1 total tags in treatment: 8096870 INFO @ Sun, 03 Sep 2017 19:45:24: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:45:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 19:45:24: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:45:24: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:45:24: #1 total tags in treatment: 8096870 INFO @ Sun, 03 Sep 2017 19:45:24: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:45:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 19:45:24: #1 tags after filtering in treatment: 4102749 INFO @ Sun, 03 Sep 2017 19:45:24: #1 Redundant rate of treatment: 0.49 INFO @ Sun, 03 Sep 2017 19:45:24: #1 finished! INFO @ Sun, 03 Sep 2017 19:45:24: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:45:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:45:24: #1 tags after filtering in treatment: 4102749 INFO @ Sun, 03 Sep 2017 19:45:24: #1 Redundant rate of treatment: 0.49 INFO @ Sun, 03 Sep 2017 19:45:24: #1 finished! INFO @ Sun, 03 Sep 2017 19:45:24: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:45:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:45:24: #2 number of paired peaks: 1 WARNING @ Sun, 03 Sep 2017 19:45:24: Too few paired peaks (1) 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 @ Sun, 03 Sep 2017 19:45:24: Process for pairing-model is terminated! INFO @ Sun, 03 Sep 2017 19:45:24: #2 number of paired peaks: 1 WARNING @ Sun, 03 Sep 2017 19:45:24: Too few paired peaks (1) 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 @ Sun, 03 Sep 2017 19:45:24: Process for pairing-model is terminated! cat: SRX2675892.20_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): 5 millis cat: SRX2675892.10_peaks.narrowPeak: そのようなファイルやディレクトリはありません needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2675892.20_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 `SRX2675892.20_*.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 `SRX2675892.20_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 pass1 - making usageList (0 chroms): 6 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2675892.10_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 `SRX2675892.10_*.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 `SRX2675892.10_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 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。