Job ID = 9732040 sra ファイルのダウンロード中... Completed: 315737K bytes transferred in 9 seconds (263376K 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 14359962 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2675843/SRR5380620.sra Written 14359962 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: 00:06:50 14359962 reads; of these: 14359962 (100.00%) were paired; of these: 3090427 (21.52%) aligned concordantly 0 times 10379026 (72.28%) aligned concordantly exactly 1 time 890509 (6.20%) aligned concordantly >1 times ---- 3090427 pairs aligned concordantly 0 times; of these: 995045 (32.20%) aligned discordantly 1 time ---- 2095382 pairs aligned 0 times concordantly or discordantly; of these: 4190764 mates make up the pairs; of these: 3561856 (84.99%) aligned 0 times 404377 (9.65%) aligned exactly 1 time 224531 (5.36%) aligned >1 times 87.60% overall alignment rate Time searching: 00:06:50 Overall time: 00:06:50 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] 1391143 / 12193096 = 0.1141 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 19:14:35: # Command line: callpeak -t SRX2675843.bam -f BAM -g 12100000 -n SRX2675843.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2675843.05 # format = BAM # ChIP-seq file = ['SRX2675843.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 19:14:35: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:14:35: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:14:35: # Command line: callpeak -t SRX2675843.bam -f BAM -g 12100000 -n SRX2675843.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2675843.10 # format = BAM # ChIP-seq file = ['SRX2675843.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 19:14:35: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:14:35: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:14:35: # Command line: callpeak -t SRX2675843.bam -f BAM -g 12100000 -n SRX2675843.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2675843.20 # format = BAM # ChIP-seq file = ['SRX2675843.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 19:14:35: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:14:35: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:14:41: 1000000 INFO @ Sun, 03 Sep 2017 19:14:41: 1000000 INFO @ Sun, 03 Sep 2017 19:14:41: 1000000 INFO @ Sun, 03 Sep 2017 19:14:46: 2000000 INFO @ Sun, 03 Sep 2017 19:14:46: 2000000 INFO @ Sun, 03 Sep 2017 19:14:47: 2000000 INFO @ Sun, 03 Sep 2017 19:14:51: 3000000 INFO @ Sun, 03 Sep 2017 19:14:52: 3000000 INFO @ Sun, 03 Sep 2017 19:14:53: 3000000 INFO @ Sun, 03 Sep 2017 19:14:56: 4000000 INFO @ Sun, 03 Sep 2017 19:14:57: 4000000 INFO @ Sun, 03 Sep 2017 19:14:59: 4000000 INFO @ Sun, 03 Sep 2017 19:15:01: 5000000 INFO @ Sun, 03 Sep 2017 19:15:03: 5000000 INFO @ Sun, 03 Sep 2017 19:15:05: 5000000 INFO @ Sun, 03 Sep 2017 19:15:06: 6000000 INFO @ Sun, 03 Sep 2017 19:15:09: 6000000 INFO @ Sun, 03 Sep 2017 19:15:11: 6000000 INFO @ Sun, 03 Sep 2017 19:15:11: 7000000 INFO @ Sun, 03 Sep 2017 19:15:14: 7000000 INFO @ Sun, 03 Sep 2017 19:15:16: 8000000 INFO @ Sun, 03 Sep 2017 19:15:17: 7000000 INFO @ Sun, 03 Sep 2017 19:15:20: 8000000 INFO @ Sun, 03 Sep 2017 19:15:21: 9000000 INFO @ Sun, 03 Sep 2017 19:15:23: 8000000 INFO @ Sun, 03 Sep 2017 19:15:25: 9000000 INFO @ Sun, 03 Sep 2017 19:15:27: 10000000 INFO @ Sun, 03 Sep 2017 19:15:29: 9000000 INFO @ Sun, 03 Sep 2017 19:15:31: 10000000 INFO @ Sun, 03 Sep 2017 19:15:32: 11000000 INFO @ Sun, 03 Sep 2017 19:15:35: 10000000 INFO @ Sun, 03 Sep 2017 19:15:36: 11000000 INFO @ Sun, 03 Sep 2017 19:15:37: 12000000 INFO @ Sun, 03 Sep 2017 19:15:41: 11000000 INFO @ Sun, 03 Sep 2017 19:15:42: 12000000 INFO @ Sun, 03 Sep 2017 19:15:42: 13000000 INFO @ Sun, 03 Sep 2017 19:15:47: 14000000 INFO @ Sun, 03 Sep 2017 19:15:47: 12000000 INFO @ Sun, 03 Sep 2017 19:15:47: 13000000 INFO @ Sun, 03 Sep 2017 19:15:52: 15000000 INFO @ Sun, 03 Sep 2017 19:15:53: 14000000 INFO @ Sun, 03 Sep 2017 19:15:53: 13000000 INFO @ Sun, 03 Sep 2017 19:15:58: 16000000 INFO @ Sun, 03 Sep 2017 19:15:59: 15000000 INFO @ Sun, 03 Sep 2017 19:16:00: 14000000 INFO @ Sun, 03 Sep 2017 19:16:03: 17000000 INFO @ Sun, 03 Sep 2017 19:16:04: 16000000 INFO @ Sun, 03 Sep 2017 19:16:06: 15000000 INFO @ Sun, 03 Sep 2017 19:16:08: 18000000 INFO @ Sun, 03 Sep 2017 19:16:09: 17000000 INFO @ Sun, 03 Sep 2017 19:16:11: 16000000 INFO @ Sun, 03 Sep 2017 19:16:14: 19000000 INFO @ Sun, 03 Sep 2017 19:16:15: 18000000 INFO @ Sun, 03 Sep 2017 19:16:18: 17000000 INFO @ Sun, 03 Sep 2017 19:16:19: 20000000 INFO @ Sun, 03 Sep 2017 19:16:20: 19000000 INFO @ Sun, 03 Sep 2017 19:16:23: 18000000 INFO @ Sun, 03 Sep 2017 19:16:25: 21000000 INFO @ Sun, 03 Sep 2017 19:16:25: 20000000 INFO @ Sun, 03 Sep 2017 19:16:29: 19000000 INFO @ Sun, 03 Sep 2017 19:16:30: 22000000 INFO @ Sun, 03 Sep 2017 19:16:30: 21000000 INFO @ Sun, 03 Sep 2017 19:16:32: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:16:32: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:16:32: #1 total tags in treatment: 9895534 INFO @ Sun, 03 Sep 2017 19:16:32: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:16:32: #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 19:16:32: #1 tags after filtering in treatment: 4455215 INFO @ Sun, 03 Sep 2017 19:16:32: #1 Redundant rate of treatment: 0.55 INFO @ Sun, 03 Sep 2017 19:16:32: #1 finished! INFO @ Sun, 03 Sep 2017 19:16:32: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:16:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:16:32: #2 number of paired peaks: 0 WARNING @ Sun, 03 Sep 2017 19:16:32: 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 @ Sun, 03 Sep 2017 19:16:32: Process for pairing-model is terminated! cat: SRX2675843.10_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): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2675843.10_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 `SRX2675843.10_*.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 `SRX2675843.10_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 @ Sun, 03 Sep 2017 19:16:35: 20000000 INFO @ Sun, 03 Sep 2017 19:16:36: 22000000 INFO @ Sun, 03 Sep 2017 19:16:38: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:16:38: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:16:38: #1 total tags in treatment: 9895534 INFO @ Sun, 03 Sep 2017 19:16:38: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:16:38: #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 19:16:38: #1 tags after filtering in treatment: 4455215 INFO @ Sun, 03 Sep 2017 19:16:38: #1 Redundant rate of treatment: 0.55 INFO @ Sun, 03 Sep 2017 19:16:38: #1 finished! INFO @ Sun, 03 Sep 2017 19:16:38: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:16:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:16:39: #2 number of paired peaks: 0 WARNING @ Sun, 03 Sep 2017 19:16:39: 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 @ Sun, 03 Sep 2017 19:16:39: Process for pairing-model is terminated! cat: SRX2675843.05_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 `SRX2675843.05_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 `SRX2675843.05_*.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 `SRX2675843.05_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 19:16:40: 21000000 INFO @ Sun, 03 Sep 2017 19:16:45: 22000000 INFO @ Sun, 03 Sep 2017 19:16:47: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:16:47: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:16:47: #1 total tags in treatment: 9895534 INFO @ Sun, 03 Sep 2017 19:16:47: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:16:47: #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 19:16:47: #1 tags after filtering in treatment: 4455215 INFO @ Sun, 03 Sep 2017 19:16:47: #1 Redundant rate of treatment: 0.55 INFO @ Sun, 03 Sep 2017 19:16:47: #1 finished! INFO @ Sun, 03 Sep 2017 19:16:47: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:16:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:16:47: #2 number of paired peaks: 0 WARNING @ Sun, 03 Sep 2017 19:16:47: 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 @ Sun, 03 Sep 2017 19:16:47: Process for pairing-model is terminated! cat: SRX2675843.20_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 `SRX2675843.20_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 `SRX2675843.20_*.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 `SRX2675843.20_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。