Job ID = 9732094 sra ファイルのダウンロード中... Completed: 325285K bytes transferred in 9 seconds (287519K 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 14108961 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2675885/SRR5380661.sra Written 14108961 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: 00:06:07 14108961 reads; of these: 14108961 (100.00%) were paired; of these: 3023607 (21.43%) aligned concordantly 0 times 10214711 (72.40%) aligned concordantly exactly 1 time 870643 (6.17%) aligned concordantly >1 times ---- 3023607 pairs aligned concordantly 0 times; of these: 823003 (27.22%) aligned discordantly 1 time ---- 2200604 pairs aligned 0 times concordantly or discordantly; of these: 4401208 mates make up the pairs; of these: 3862294 (87.76%) aligned 0 times 354436 (8.05%) aligned exactly 1 time 184478 (4.19%) aligned >1 times 86.31% overall alignment rate Time searching: 00:06:07 Overall time: 00:06:07 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] 1453365 / 11855983 = 0.1226 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 19:43:33: # Command line: callpeak -t SRX2675885.bam -f BAM -g 12100000 -n SRX2675885.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2675885.20 # format = BAM # ChIP-seq file = ['SRX2675885.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 19:43:33: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:43:33: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:43:33: # Command line: callpeak -t SRX2675885.bam -f BAM -g 12100000 -n SRX2675885.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2675885.10 # format = BAM # ChIP-seq file = ['SRX2675885.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 19:43:33: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:43:33: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:43:33: # Command line: callpeak -t SRX2675885.bam -f BAM -g 12100000 -n SRX2675885.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2675885.05 # format = BAM # ChIP-seq file = ['SRX2675885.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 19:43:33: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:43:33: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:43:38: 1000000 INFO @ Sun, 03 Sep 2017 19:43:38: 1000000 INFO @ Sun, 03 Sep 2017 19:43:38: 1000000 INFO @ Sun, 03 Sep 2017 19:43:44: 2000000 INFO @ Sun, 03 Sep 2017 19:43:44: 2000000 INFO @ Sun, 03 Sep 2017 19:43:44: 2000000 INFO @ Sun, 03 Sep 2017 19:43:49: 3000000 INFO @ Sun, 03 Sep 2017 19:43:49: 3000000 INFO @ Sun, 03 Sep 2017 19:43:49: 3000000 INFO @ Sun, 03 Sep 2017 19:43:54: 4000000 INFO @ Sun, 03 Sep 2017 19:43:55: 4000000 INFO @ Sun, 03 Sep 2017 19:43:55: 4000000 INFO @ Sun, 03 Sep 2017 19:43:59: 5000000 INFO @ Sun, 03 Sep 2017 19:44:00: 5000000 INFO @ Sun, 03 Sep 2017 19:44:01: 5000000 INFO @ Sun, 03 Sep 2017 19:44:05: 6000000 INFO @ Sun, 03 Sep 2017 19:44:06: 6000000 INFO @ Sun, 03 Sep 2017 19:44:06: 6000000 INFO @ Sun, 03 Sep 2017 19:44:10: 7000000 INFO @ Sun, 03 Sep 2017 19:44:11: 7000000 INFO @ Sun, 03 Sep 2017 19:44:12: 7000000 INFO @ Sun, 03 Sep 2017 19:44:15: 8000000 INFO @ Sun, 03 Sep 2017 19:44:17: 8000000 INFO @ Sun, 03 Sep 2017 19:44:18: 8000000 INFO @ Sun, 03 Sep 2017 19:44:20: 9000000 INFO @ Sun, 03 Sep 2017 19:44:22: 9000000 INFO @ Sun, 03 Sep 2017 19:44:23: 9000000 INFO @ Sun, 03 Sep 2017 19:44:25: 10000000 INFO @ Sun, 03 Sep 2017 19:44:28: 10000000 INFO @ Sun, 03 Sep 2017 19:44:29: 10000000 INFO @ Sun, 03 Sep 2017 19:44:31: 11000000 INFO @ Sun, 03 Sep 2017 19:44:34: 11000000 INFO @ Sun, 03 Sep 2017 19:44:35: 11000000 INFO @ Sun, 03 Sep 2017 19:44:36: 12000000 INFO @ Sun, 03 Sep 2017 19:44:40: 12000000 INFO @ Sun, 03 Sep 2017 19:44:40: 12000000 INFO @ Sun, 03 Sep 2017 19:44:41: 13000000 INFO @ Sun, 03 Sep 2017 19:44:45: 13000000 INFO @ Sun, 03 Sep 2017 19:44:46: 13000000 INFO @ Sun, 03 Sep 2017 19:44:46: 14000000 INFO @ Sun, 03 Sep 2017 19:44:51: 14000000 INFO @ Sun, 03 Sep 2017 19:44:51: 15000000 INFO @ Sun, 03 Sep 2017 19:44:52: 14000000 INFO @ Sun, 03 Sep 2017 19:44:56: 15000000 INFO @ Sun, 03 Sep 2017 19:44:57: 16000000 INFO @ Sun, 03 Sep 2017 19:44:57: 15000000 INFO @ Sun, 03 Sep 2017 19:45:02: 17000000 INFO @ Sun, 03 Sep 2017 19:45:02: 16000000 INFO @ Sun, 03 Sep 2017 19:45:03: 16000000 INFO @ Sun, 03 Sep 2017 19:45:07: 18000000 INFO @ Sun, 03 Sep 2017 19:45:08: 17000000 INFO @ Sun, 03 Sep 2017 19:45:09: 17000000 INFO @ Sun, 03 Sep 2017 19:45:12: 19000000 INFO @ Sun, 03 Sep 2017 19:45:13: 18000000 INFO @ Sun, 03 Sep 2017 19:45:14: 18000000 INFO @ Sun, 03 Sep 2017 19:45:17: 20000000 INFO @ Sun, 03 Sep 2017 19:45:19: 19000000 INFO @ Sun, 03 Sep 2017 19:45:20: 19000000 INFO @ Sun, 03 Sep 2017 19:45:22: 21000000 INFO @ Sun, 03 Sep 2017 19:45:24: 20000000 INFO @ Sun, 03 Sep 2017 19:45:25: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:45:25: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:45:25: #1 total tags in treatment: 9648504 INFO @ Sun, 03 Sep 2017 19:45:25: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:45:25: #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 19:45:25: #1 tags after filtering in treatment: 4397908 INFO @ Sun, 03 Sep 2017 19:45:25: #1 Redundant rate of treatment: 0.54 INFO @ Sun, 03 Sep 2017 19:45:25: #1 finished! INFO @ Sun, 03 Sep 2017 19:45:25: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:45:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:45:25: #2 number of paired peaks: 0 WARNING @ Sun, 03 Sep 2017 19:45:25: 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 19:45:25: Process for pairing-model is terminated! cat: SRX2675885.10_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): 7 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2675885.10_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 `SRX2675885.10_*.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 `SRX2675885.10_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 19:45:26: 20000000 INFO @ Sun, 03 Sep 2017 19:45:30: 21000000 INFO @ Sun, 03 Sep 2017 19:45:31: 21000000 INFO @ Sun, 03 Sep 2017 19:45:32: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:45:32: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:45:32: #1 total tags in treatment: 9648504 INFO @ Sun, 03 Sep 2017 19:45:32: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:45:32: #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 19:45:32: #1 tags after filtering in treatment: 4397908 INFO @ Sun, 03 Sep 2017 19:45:32: #1 Redundant rate of treatment: 0.54 INFO @ Sun, 03 Sep 2017 19:45:32: #1 finished! INFO @ Sun, 03 Sep 2017 19:45:32: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:45:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:45:33: #2 number of paired peaks: 0 WARNING @ Sun, 03 Sep 2017 19:45:33: 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 19:45:33: Process for pairing-model is terminated! cat: SRX2675885.05_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): 12 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2675885.05_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 `SRX2675885.05_*.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 `SRX2675885.05_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 19:45:33: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:45:33: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:45:33: #1 total tags in treatment: 9648504 INFO @ Sun, 03 Sep 2017 19:45:33: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:45:33: #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: 4397908 INFO @ Sun, 03 Sep 2017 19:45:34: #1 Redundant rate of treatment: 0.54 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: 0 WARNING @ Sun, 03 Sep 2017 19:45:34: 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 19:45:34: Process for pairing-model is terminated! cat: SRX2675885.20_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): 10 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2675885.20_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 `SRX2675885.20_*.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 `SRX2675885.20_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。