Job ID = 9732054 sra ファイルのダウンロード中... Completed: 330037K bytes transferred in 12 seconds (220006K 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 15064506 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2675855/SRR5380631.sra Written 15064506 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: 00:07:15 15064506 reads; of these: 15064506 (100.00%) were paired; of these: 4793389 (31.82%) aligned concordantly 0 times 9186235 (60.98%) aligned concordantly exactly 1 time 1084882 (7.20%) aligned concordantly >1 times ---- 4793389 pairs aligned concordantly 0 times; of these: 951010 (19.84%) aligned discordantly 1 time ---- 3842379 pairs aligned 0 times concordantly or discordantly; of these: 7684758 mates make up the pairs; of these: 6922526 (90.08%) aligned 0 times 465797 (6.06%) aligned exactly 1 time 296435 (3.86%) aligned >1 times 77.02% overall alignment rate Time searching: 00:07:15 Overall time: 00:07:15 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] 1592011 / 11136410 = 0.1430 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 19:26:08: # Command line: callpeak -t SRX2675855.bam -f BAM -g 12100000 -n SRX2675855.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2675855.20 # format = BAM # ChIP-seq file = ['SRX2675855.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 19:26:08: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:26:08: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:26:08: # Command line: callpeak -t SRX2675855.bam -f BAM -g 12100000 -n SRX2675855.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2675855.05 # format = BAM # ChIP-seq file = ['SRX2675855.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 19:26:08: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:26:08: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:26:08: # Command line: callpeak -t SRX2675855.bam -f BAM -g 12100000 -n SRX2675855.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2675855.10 # format = BAM # ChIP-seq file = ['SRX2675855.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 19:26:08: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:26:08: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:26:13: 1000000 INFO @ Sun, 03 Sep 2017 19:26:14: 1000000 INFO @ Sun, 03 Sep 2017 19:26:14: 1000000 INFO @ Sun, 03 Sep 2017 19:26:19: 2000000 INFO @ Sun, 03 Sep 2017 19:26:19: 2000000 INFO @ Sun, 03 Sep 2017 19:26:19: 2000000 INFO @ Sun, 03 Sep 2017 19:26:24: 3000000 INFO @ Sun, 03 Sep 2017 19:26:24: 3000000 INFO @ Sun, 03 Sep 2017 19:26:24: 3000000 INFO @ Sun, 03 Sep 2017 19:26:29: 4000000 INFO @ Sun, 03 Sep 2017 19:26:30: 4000000 INFO @ Sun, 03 Sep 2017 19:26:30: 4000000 INFO @ Sun, 03 Sep 2017 19:26:34: 5000000 INFO @ Sun, 03 Sep 2017 19:26:35: 5000000 INFO @ Sun, 03 Sep 2017 19:26:35: 5000000 INFO @ Sun, 03 Sep 2017 19:26:39: 6000000 INFO @ Sun, 03 Sep 2017 19:26:41: 6000000 INFO @ Sun, 03 Sep 2017 19:26:41: 6000000 INFO @ Sun, 03 Sep 2017 19:26:44: 7000000 INFO @ Sun, 03 Sep 2017 19:26:46: 7000000 INFO @ Sun, 03 Sep 2017 19:26:46: 7000000 INFO @ Sun, 03 Sep 2017 19:26:49: 8000000 INFO @ Sun, 03 Sep 2017 19:26:51: 8000000 INFO @ Sun, 03 Sep 2017 19:26:51: 8000000 INFO @ Sun, 03 Sep 2017 19:26:55: 9000000 INFO @ Sun, 03 Sep 2017 19:26:57: 9000000 INFO @ Sun, 03 Sep 2017 19:26:57: 9000000 INFO @ Sun, 03 Sep 2017 19:27:00: 10000000 INFO @ Sun, 03 Sep 2017 19:27:02: 10000000 INFO @ Sun, 03 Sep 2017 19:27:02: 10000000 INFO @ Sun, 03 Sep 2017 19:27:05: 11000000 INFO @ Sun, 03 Sep 2017 19:27:07: 11000000 INFO @ Sun, 03 Sep 2017 19:27:07: 11000000 INFO @ Sun, 03 Sep 2017 19:27:10: 12000000 INFO @ Sun, 03 Sep 2017 19:27:12: 12000000 INFO @ Sun, 03 Sep 2017 19:27:12: 12000000 INFO @ Sun, 03 Sep 2017 19:27:15: 13000000 INFO @ Sun, 03 Sep 2017 19:27:18: 13000000 INFO @ Sun, 03 Sep 2017 19:27:18: 13000000 INFO @ Sun, 03 Sep 2017 19:27:20: 14000000 INFO @ Sun, 03 Sep 2017 19:27:23: 14000000 INFO @ Sun, 03 Sep 2017 19:27:23: 14000000 INFO @ Sun, 03 Sep 2017 19:27:25: 15000000 INFO @ Sun, 03 Sep 2017 19:27:28: 15000000 INFO @ Sun, 03 Sep 2017 19:27:28: 15000000 INFO @ Sun, 03 Sep 2017 19:27:31: 16000000 INFO @ Sun, 03 Sep 2017 19:27:33: 16000000 INFO @ Sun, 03 Sep 2017 19:27:33: 16000000 INFO @ Sun, 03 Sep 2017 19:27:36: 17000000 INFO @ Sun, 03 Sep 2017 19:27:39: 17000000 INFO @ Sun, 03 Sep 2017 19:27:39: 17000000 INFO @ Sun, 03 Sep 2017 19:27:41: 18000000 INFO @ Sun, 03 Sep 2017 19:27:44: 18000000 INFO @ Sun, 03 Sep 2017 19:27:44: 18000000 INFO @ Sun, 03 Sep 2017 19:27:46: 19000000 INFO @ Sun, 03 Sep 2017 19:27:49: 19000000 INFO @ Sun, 03 Sep 2017 19:27:49: 19000000 INFO @ Sun, 03 Sep 2017 19:27:51: 20000000 INFO @ Sun, 03 Sep 2017 19:27:51: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:27:51: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:27:51: #1 total tags in treatment: 8713559 INFO @ Sun, 03 Sep 2017 19:27:51: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:27:51: #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 19:27:51: #1 tags after filtering in treatment: 4029365 INFO @ Sun, 03 Sep 2017 19:27:51: #1 Redundant rate of treatment: 0.54 INFO @ Sun, 03 Sep 2017 19:27:51: #1 finished! INFO @ Sun, 03 Sep 2017 19:27:51: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:27:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:27:52: #2 number of paired peaks: 5 WARNING @ Sun, 03 Sep 2017 19:27:52: Too few paired peaks (5) 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 19:27:52: Process for pairing-model is terminated! cat: SRX2675855.10_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): 11 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2675855.10_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 `SRX2675855.10_*.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 `SRX2675855.10_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 19:27:54: 20000000 INFO @ Sun, 03 Sep 2017 19:27:54: 20000000 INFO @ Sun, 03 Sep 2017 19:27:54: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:27:54: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:27:54: #1 total tags in treatment: 8713559 INFO @ Sun, 03 Sep 2017 19:27:54: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:27:54: #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 19:27:54: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:27:54: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:27:54: #1 total tags in treatment: 8713559 INFO @ Sun, 03 Sep 2017 19:27:54: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:27:54: #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 19:27:55: #1 tags after filtering in treatment: 4029365 INFO @ Sun, 03 Sep 2017 19:27:55: #1 Redundant rate of treatment: 0.54 INFO @ Sun, 03 Sep 2017 19:27:55: #1 finished! INFO @ Sun, 03 Sep 2017 19:27:55: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:27:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:27:55: #1 tags after filtering in treatment: 4029365 INFO @ Sun, 03 Sep 2017 19:27:55: #1 Redundant rate of treatment: 0.54 INFO @ Sun, 03 Sep 2017 19:27:55: #1 finished! INFO @ Sun, 03 Sep 2017 19:27:55: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:27:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:27:55: #2 number of paired peaks: 5 WARNING @ Sun, 03 Sep 2017 19:27:55: Too few paired peaks (5) 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 19:27:55: Process for pairing-model is terminated! cat: SRX2675855.05_peaks.narrowPeak: そのようなファイルやディレクトリはありません INFO @ Sun, 03 Sep 2017 19:27:55: #2 number of paired peaks: 5 WARNING @ Sun, 03 Sep 2017 19:27:55: Too few paired peaks (5) 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 19:27:55: Process for pairing-model is terminated! pass1 - making usageList (0 chroms): 11 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) cat: SRX2675855.20_peaks.narrowPeak: そのようなファイルやディレクトリはありません rm: cannot remove `SRX2675855.05_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 `SRX2675855.05_*.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 `SRX2675855.05_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): 9 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2675855.20_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 `SRX2675855.20_*.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 `SRX2675855.20_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。