Job ID = 9732098 sra ファイルのダウンロード中... Completed: 328860K bytes transferred in 8 seconds (328982K 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 14183723 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2675889/SRR5380665.sra Written 14183723 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: 00:05:55 14183723 reads; of these: 14183723 (100.00%) were paired; of these: 4692039 (33.08%) aligned concordantly 0 times 8358229 (58.93%) aligned concordantly exactly 1 time 1133455 (7.99%) aligned concordantly >1 times ---- 4692039 pairs aligned concordantly 0 times; of these: 533892 (11.38%) aligned discordantly 1 time ---- 4158147 pairs aligned 0 times concordantly or discordantly; of these: 8316294 mates make up the pairs; of these: 7677471 (92.32%) aligned 0 times 432034 (5.20%) aligned exactly 1 time 206789 (2.49%) aligned >1 times 72.94% overall alignment rate Time searching: 00:05:55 Overall time: 00:05:55 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] 1225303 / 9845509 = 0.1245 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 19:44:01: # Command line: callpeak -t SRX2675889.bam -f BAM -g 12100000 -n SRX2675889.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2675889.10 # format = BAM # ChIP-seq file = ['SRX2675889.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 19:44:01: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:44:01: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:44:01: # Command line: callpeak -t SRX2675889.bam -f BAM -g 12100000 -n SRX2675889.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2675889.05 # format = BAM # ChIP-seq file = ['SRX2675889.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 19:44:01: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:44:01: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:44:01: # Command line: callpeak -t SRX2675889.bam -f BAM -g 12100000 -n SRX2675889.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2675889.20 # format = BAM # ChIP-seq file = ['SRX2675889.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 19:44:01: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:44:01: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:44:06: 1000000 INFO @ Sun, 03 Sep 2017 19:44:06: 1000000 INFO @ Sun, 03 Sep 2017 19:44:06: 1000000 INFO @ Sun, 03 Sep 2017 19:44:11: 2000000 INFO @ Sun, 03 Sep 2017 19:44:11: 2000000 INFO @ Sun, 03 Sep 2017 19:44:11: 2000000 INFO @ Sun, 03 Sep 2017 19:44:15: 3000000 INFO @ Sun, 03 Sep 2017 19:44:16: 3000000 INFO @ Sun, 03 Sep 2017 19:44:16: 3000000 INFO @ Sun, 03 Sep 2017 19:44:20: 4000000 INFO @ Sun, 03 Sep 2017 19:44:20: 4000000 INFO @ Sun, 03 Sep 2017 19:44:21: 4000000 INFO @ Sun, 03 Sep 2017 19:44:25: 5000000 INFO @ Sun, 03 Sep 2017 19:44:25: 5000000 INFO @ Sun, 03 Sep 2017 19:44:26: 5000000 INFO @ Sun, 03 Sep 2017 19:44:30: 6000000 INFO @ Sun, 03 Sep 2017 19:44:30: 6000000 INFO @ Sun, 03 Sep 2017 19:44:31: 6000000 INFO @ Sun, 03 Sep 2017 19:44:35: 7000000 INFO @ Sun, 03 Sep 2017 19:44:35: 7000000 INFO @ Sun, 03 Sep 2017 19:44:36: 7000000 INFO @ Sun, 03 Sep 2017 19:44:39: 8000000 INFO @ Sun, 03 Sep 2017 19:44:40: 8000000 INFO @ Sun, 03 Sep 2017 19:44:41: 8000000 INFO @ Sun, 03 Sep 2017 19:44:44: 9000000 INFO @ Sun, 03 Sep 2017 19:44:45: 9000000 INFO @ Sun, 03 Sep 2017 19:44:46: 9000000 INFO @ Sun, 03 Sep 2017 19:44:49: 10000000 INFO @ Sun, 03 Sep 2017 19:44:50: 10000000 INFO @ Sun, 03 Sep 2017 19:44:52: 10000000 INFO @ Sun, 03 Sep 2017 19:44:54: 11000000 INFO @ Sun, 03 Sep 2017 19:44:55: 11000000 INFO @ Sun, 03 Sep 2017 19:44:57: 11000000 INFO @ Sun, 03 Sep 2017 19:44:59: 12000000 INFO @ Sun, 03 Sep 2017 19:45:00: 12000000 INFO @ Sun, 03 Sep 2017 19:45:02: 12000000 INFO @ Sun, 03 Sep 2017 19:45:03: 13000000 INFO @ Sun, 03 Sep 2017 19:45:05: 13000000 INFO @ Sun, 03 Sep 2017 19:45:07: 13000000 INFO @ Sun, 03 Sep 2017 19:45:08: 14000000 INFO @ Sun, 03 Sep 2017 19:45:10: 14000000 INFO @ Sun, 03 Sep 2017 19:45:12: 14000000 INFO @ Sun, 03 Sep 2017 19:45:13: 15000000 INFO @ Sun, 03 Sep 2017 19:45:15: 15000000 INFO @ Sun, 03 Sep 2017 19:45:17: 15000000 INFO @ Sun, 03 Sep 2017 19:45:18: 16000000 INFO @ Sun, 03 Sep 2017 19:45:20: 16000000 INFO @ Sun, 03 Sep 2017 19:45:22: 17000000 INFO @ Sun, 03 Sep 2017 19:45:22: 16000000 INFO @ Sun, 03 Sep 2017 19:45:25: 17000000 INFO @ Sun, 03 Sep 2017 19:45:27: 18000000 INFO @ Sun, 03 Sep 2017 19:45:27: 17000000 INFO @ Sun, 03 Sep 2017 19:45:28: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:45:28: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:45:28: #1 total tags in treatment: 8272487 INFO @ Sun, 03 Sep 2017 19:45:28: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:45:28: #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 19:45:28: #1 tags after filtering in treatment: 4200322 INFO @ Sun, 03 Sep 2017 19:45:28: #1 Redundant rate of treatment: 0.49 INFO @ Sun, 03 Sep 2017 19:45:28: #1 finished! INFO @ Sun, 03 Sep 2017 19:45:28: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:45:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:45:29: #2 number of paired peaks: 6 WARNING @ Sun, 03 Sep 2017 19:45:29: Too few paired peaks (6) 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 19:45:29: Process for pairing-model is terminated! cat: SRX2675889.05_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): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2675889.05_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 `SRX2675889.05_*.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 `SRX2675889.05_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 19:45:30: 18000000 INFO @ Sun, 03 Sep 2017 19:45:31: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:45:31: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:45:31: #1 total tags in treatment: 8272487 INFO @ Sun, 03 Sep 2017 19:45:31: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:45:31: #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 19:45:31: #1 tags after filtering in treatment: 4200322 INFO @ Sun, 03 Sep 2017 19:45:31: #1 Redundant rate of treatment: 0.49 INFO @ Sun, 03 Sep 2017 19:45:31: #1 finished! INFO @ Sun, 03 Sep 2017 19:45:31: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:45:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:45:32: #2 number of paired peaks: 6 WARNING @ Sun, 03 Sep 2017 19:45:32: Too few paired peaks (6) 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 19:45:32: Process for pairing-model is terminated! cat: SRX2675889.20_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 `SRX2675889.20_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 `SRX2675889.20_*.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 `SRX2675889.20_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 @ Sun, 03 Sep 2017 19:45:32: 18000000 INFO @ Sun, 03 Sep 2017 19:45:34: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:45:34: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:45:34: #1 total tags in treatment: 8272487 INFO @ Sun, 03 Sep 2017 19:45:34: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:45:34: #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 19:45:34: #1 tags after filtering in treatment: 4200322 INFO @ Sun, 03 Sep 2017 19:45:34: #1 Redundant rate of treatment: 0.49 INFO @ Sun, 03 Sep 2017 19:45:34: #1 finished! INFO @ Sun, 03 Sep 2017 19:45:34: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:45:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:45:34: #2 number of paired peaks: 6 WARNING @ Sun, 03 Sep 2017 19:45:34: Too few paired peaks (6) 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 19:45:34: Process for pairing-model is terminated! cat: SRX2675889.10_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): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2675889.10_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 `SRX2675889.10_*.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 `SRX2675889.10_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。