Job ID = 9732089 sra ファイルのダウンロード中... Completed: 324649K bytes transferred in 8 seconds (317582K 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 13993454 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2675879/SRR5380656.sra Written 13993454 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: 00:05:41 13993454 reads; of these: 13993454 (100.00%) were paired; of these: 4191455 (29.95%) aligned concordantly 0 times 8702988 (62.19%) aligned concordantly exactly 1 time 1099011 (7.85%) aligned concordantly >1 times ---- 4191455 pairs aligned concordantly 0 times; of these: 462540 (11.04%) aligned discordantly 1 time ---- 3728915 pairs aligned 0 times concordantly or discordantly; of these: 7457830 mates make up the pairs; of these: 6934842 (92.99%) aligned 0 times 348093 (4.67%) aligned exactly 1 time 174895 (2.35%) aligned >1 times 75.22% overall alignment rate Time searching: 00:05:41 Overall time: 00:05:41 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] 1324347 / 10141279 = 0.1306 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 19:37:44: # Command line: callpeak -t SRX2675879.bam -f BAM -g 12100000 -n SRX2675879.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2675879.05 # format = BAM # ChIP-seq file = ['SRX2675879.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 19:37:44: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:37:44: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:37:44: # Command line: callpeak -t SRX2675879.bam -f BAM -g 12100000 -n SRX2675879.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2675879.20 # format = BAM # ChIP-seq file = ['SRX2675879.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 19:37:44: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:37:44: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:37:44: # Command line: callpeak -t SRX2675879.bam -f BAM -g 12100000 -n SRX2675879.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2675879.10 # format = BAM # ChIP-seq file = ['SRX2675879.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 19:37:44: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:37:44: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:37:49: 1000000 INFO @ Sun, 03 Sep 2017 19:37:50: 1000000 INFO @ Sun, 03 Sep 2017 19:37:50: 1000000 INFO @ Sun, 03 Sep 2017 19:37:54: 2000000 INFO @ Sun, 03 Sep 2017 19:37:55: 2000000 INFO @ Sun, 03 Sep 2017 19:37:55: 2000000 INFO @ Sun, 03 Sep 2017 19:38:00: 3000000 INFO @ Sun, 03 Sep 2017 19:38:01: 3000000 INFO @ Sun, 03 Sep 2017 19:38:01: 3000000 INFO @ Sun, 03 Sep 2017 19:38:05: 4000000 INFO @ Sun, 03 Sep 2017 19:38:07: 4000000 INFO @ Sun, 03 Sep 2017 19:38:07: 4000000 INFO @ Sun, 03 Sep 2017 19:38:10: 5000000 INFO @ Sun, 03 Sep 2017 19:38:12: 5000000 INFO @ Sun, 03 Sep 2017 19:38:12: 5000000 INFO @ Sun, 03 Sep 2017 19:38:15: 6000000 INFO @ Sun, 03 Sep 2017 19:38:18: 6000000 INFO @ Sun, 03 Sep 2017 19:38:18: 6000000 INFO @ Sun, 03 Sep 2017 19:38:21: 7000000 INFO @ Sun, 03 Sep 2017 19:38:24: 7000000 INFO @ Sun, 03 Sep 2017 19:38:24: 7000000 INFO @ Sun, 03 Sep 2017 19:38:26: 8000000 INFO @ Sun, 03 Sep 2017 19:38:30: 8000000 INFO @ Sun, 03 Sep 2017 19:38:30: 8000000 INFO @ Sun, 03 Sep 2017 19:38:31: 9000000 INFO @ Sun, 03 Sep 2017 19:38:35: 9000000 INFO @ Sun, 03 Sep 2017 19:38:35: 9000000 INFO @ Sun, 03 Sep 2017 19:38:36: 10000000 INFO @ Sun, 03 Sep 2017 19:38:41: 10000000 INFO @ Sun, 03 Sep 2017 19:38:41: 10000000 INFO @ Sun, 03 Sep 2017 19:38:41: 11000000 INFO @ Sun, 03 Sep 2017 19:38:46: 12000000 INFO @ Sun, 03 Sep 2017 19:38:47: 11000000 INFO @ Sun, 03 Sep 2017 19:38:47: 11000000 INFO @ Sun, 03 Sep 2017 19:38:52: 13000000 INFO @ Sun, 03 Sep 2017 19:38:52: 12000000 INFO @ Sun, 03 Sep 2017 19:38:52: 12000000 INFO @ Sun, 03 Sep 2017 19:38:57: 14000000 INFO @ Sun, 03 Sep 2017 19:38:58: 13000000 INFO @ Sun, 03 Sep 2017 19:38:58: 13000000 INFO @ Sun, 03 Sep 2017 19:39:02: 15000000 INFO @ Sun, 03 Sep 2017 19:39:03: 14000000 INFO @ Sun, 03 Sep 2017 19:39:04: 14000000 INFO @ Sun, 03 Sep 2017 19:39:07: 16000000 INFO @ Sun, 03 Sep 2017 19:39:09: 15000000 INFO @ Sun, 03 Sep 2017 19:39:09: 15000000 INFO @ Sun, 03 Sep 2017 19:39:12: 17000000 INFO @ Sun, 03 Sep 2017 19:39:15: 16000000 INFO @ Sun, 03 Sep 2017 19:39:15: 16000000 INFO @ Sun, 03 Sep 2017 19:39:17: 18000000 INFO @ Sun, 03 Sep 2017 19:39:19: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:39:19: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:39:19: #1 total tags in treatment: 8482012 INFO @ Sun, 03 Sep 2017 19:39:19: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:39:19: #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 19:39:20: #1 tags after filtering in treatment: 4304004 INFO @ Sun, 03 Sep 2017 19:39:20: #1 Redundant rate of treatment: 0.49 INFO @ Sun, 03 Sep 2017 19:39:20: #1 finished! INFO @ Sun, 03 Sep 2017 19:39:20: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:39:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:39:20: #2 number of paired peaks: 1 WARNING @ Sun, 03 Sep 2017 19:39:20: 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 19:39:20: Process for pairing-model is terminated! cat: SRX2675879.20_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 `SRX2675879.20_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 `SRX2675879.20_*.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 `SRX2675879.20_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 19:39:21: 17000000 INFO @ Sun, 03 Sep 2017 19:39:21: 17000000 INFO @ Sun, 03 Sep 2017 19:39:26: 18000000 INFO @ Sun, 03 Sep 2017 19:39:26: 18000000 INFO @ Sun, 03 Sep 2017 19:39:28: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:39:28: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:39:28: #1 total tags in treatment: 8482012 INFO @ Sun, 03 Sep 2017 19:39:28: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:39:28: #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 19:39:28: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:39:28: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:39:28: #1 total tags in treatment: 8482012 INFO @ Sun, 03 Sep 2017 19:39:28: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:39:28: #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 19:39:29: #1 tags after filtering in treatment: 4304004 INFO @ Sun, 03 Sep 2017 19:39:29: #1 Redundant rate of treatment: 0.49 INFO @ Sun, 03 Sep 2017 19:39:29: #1 finished! INFO @ Sun, 03 Sep 2017 19:39:29: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:39:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:39:29: #1 tags after filtering in treatment: 4304004 INFO @ Sun, 03 Sep 2017 19:39:29: #1 Redundant rate of treatment: 0.49 INFO @ Sun, 03 Sep 2017 19:39:29: #1 finished! INFO @ Sun, 03 Sep 2017 19:39:29: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:39:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:39:29: #2 number of paired peaks: 1 WARNING @ Sun, 03 Sep 2017 19:39:29: 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 19:39:29: Process for pairing-model is terminated! INFO @ Sun, 03 Sep 2017 19:39:29: #2 number of paired peaks: 1 WARNING @ Sun, 03 Sep 2017 19:39:29: 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 19:39:29: Process for pairing-model is terminated! cat: SRX2675879.05_peaks.narrowPeak: そのようなファイルやディレクトリはありません cat: SRX2675879.10_peaks.narrowPeakpass1 - making usageList (0 chroms): 2 millis : 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 `SRX2675879.05_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 `SRX2675879.05_*.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 `SRX2675879.05_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 pass1 - making usageList (0 chroms): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2675879.10_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 `SRX2675879.10_*.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 `SRX2675879.10_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。