Job ID = 10194942 sra ファイルのダウンロード中... Completed: 791219K bytes transferred in 14 seconds (442495K bits/sec), in 1 file. sra ファイルのダウンロードが完了しました。 Read layout: SINGLE fastq に変換中... Written 21447264 spots for /home/okishinya/chipatlas/results/rn6/SRX2568195/SRR5264107.sra Written 21447264 spots total rm: cannot remove `[DSE]RX*': 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 `[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: 00:00:01 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 01:00:47 21447264 reads; of these: 21447264 (100.00%) were unpaired; of these: 1065077 (4.97%) aligned 0 times 15071159 (70.27%) aligned exactly 1 time 5311028 (24.76%) aligned >1 times 95.03% overall alignment rate Time searching: 01:00:52 Overall time: 01:00:52 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 2714219 / 20382187 = 0.1332 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 @ Sat, 11 Nov 2017 01:09:46: # Command line: callpeak -t SRX2568195.bam -f BAM -g 2.15e9 -n SRX2568195.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2568195.10 # format = BAM # ChIP-seq file = ['SRX2568195.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 11 Nov 2017 01:09:46: # Command line: callpeak -t SRX2568195.bam -f BAM -g 2.15e9 -n SRX2568195.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2568195.05 # format = BAM # ChIP-seq file = ['SRX2568195.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 11 Nov 2017 01:09:46: # Command line: callpeak -t SRX2568195.bam -f BAM -g 2.15e9 -n SRX2568195.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2568195.20 # format = BAM # ChIP-seq file = ['SRX2568195.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 11 Nov 2017 01:09:46: #1 read tag files... INFO @ Sat, 11 Nov 2017 01:09:46: #1 read tag files... INFO @ Sat, 11 Nov 2017 01:09:46: #1 read tag files... INFO @ Sat, 11 Nov 2017 01:09:46: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 01:09:46: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 01:09:46: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 01:09:54: 1000000 INFO @ Sat, 11 Nov 2017 01:09:59: 1000000 INFO @ Sat, 11 Nov 2017 01:09:59: 1000000 INFO @ Sat, 11 Nov 2017 01:10:03: 2000000 INFO @ Sat, 11 Nov 2017 01:10:14: 2000000 INFO @ Sat, 11 Nov 2017 01:10:14: 2000000 INFO @ Sat, 11 Nov 2017 01:10:19: 3000000 INFO @ Sat, 11 Nov 2017 01:10:28: 3000000 INFO @ Sat, 11 Nov 2017 01:10:28: 3000000 INFO @ Sat, 11 Nov 2017 01:10:33: 4000000 INFO @ Sat, 11 Nov 2017 01:10:42: 4000000 INFO @ Sat, 11 Nov 2017 01:10:42: 4000000 INFO @ Sat, 11 Nov 2017 01:10:47: 5000000 INFO @ Sat, 11 Nov 2017 01:10:54: 5000000 INFO @ Sat, 11 Nov 2017 01:10:54: 5000000 INFO @ Sat, 11 Nov 2017 01:11:00: 6000000 INFO @ Sat, 11 Nov 2017 01:11:05: 6000000 INFO @ Sat, 11 Nov 2017 01:11:05: 6000000 INFO @ Sat, 11 Nov 2017 01:11:11: 7000000 INFO @ Sat, 11 Nov 2017 01:11:17: 7000000 INFO @ Sat, 11 Nov 2017 01:11:17: 7000000 INFO @ Sat, 11 Nov 2017 01:11:20: 8000000 INFO @ Sat, 11 Nov 2017 01:11:28: 8000000 INFO @ Sat, 11 Nov 2017 01:11:28: 8000000 INFO @ Sat, 11 Nov 2017 01:11:29: 9000000 INFO @ Sat, 11 Nov 2017 01:11:39: 9000000 INFO @ Sat, 11 Nov 2017 01:11:39: 9000000 INFO @ Sat, 11 Nov 2017 01:11:40: 10000000 INFO @ Sat, 11 Nov 2017 01:11:51: 10000000 INFO @ Sat, 11 Nov 2017 01:11:51: 10000000 INFO @ Sat, 11 Nov 2017 01:11:53: 11000000 INFO @ Sat, 11 Nov 2017 01:12:02: 11000000 INFO @ Sat, 11 Nov 2017 01:12:02: 11000000 INFO @ Sat, 11 Nov 2017 01:12:06: 12000000 INFO @ Sat, 11 Nov 2017 01:12:14: 12000000 INFO @ Sat, 11 Nov 2017 01:12:14: 12000000 INFO @ Sat, 11 Nov 2017 01:12:22: 13000000 INFO @ Sat, 11 Nov 2017 01:12:27: 13000000 INFO @ Sat, 11 Nov 2017 01:12:27: 13000000 INFO @ Sat, 11 Nov 2017 01:12:36: 14000000 INFO @ Sat, 11 Nov 2017 01:12:38: 14000000 INFO @ Sat, 11 Nov 2017 01:12:40: 14000000 INFO @ Sat, 11 Nov 2017 01:12:49: 15000000 INFO @ Sat, 11 Nov 2017 01:12:50: 15000000 INFO @ Sat, 11 Nov 2017 01:12:51: 15000000 INFO @ Sat, 11 Nov 2017 01:13:04: 16000000 INFO @ Sat, 11 Nov 2017 01:13:06: 16000000 INFO @ Sat, 11 Nov 2017 01:13:07: 16000000 INFO @ Sat, 11 Nov 2017 01:13:17: 17000000 INFO @ Sat, 11 Nov 2017 01:13:20: 17000000 INFO @ Sat, 11 Nov 2017 01:13:21: 17000000 INFO @ Sat, 11 Nov 2017 01:13:25: #1 tag size is determined as 75 bps INFO @ Sat, 11 Nov 2017 01:13:25: #1 tag size = 75 INFO @ Sat, 11 Nov 2017 01:13:25: #1 total tags in treatment: 17667968 INFO @ Sat, 11 Nov 2017 01:13:25: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 01:13:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 01:13:25: #1 tags after filtering in treatment: 17667829 INFO @ Sat, 11 Nov 2017 01:13:25: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 01:13:25: #1 finished! INFO @ Sat, 11 Nov 2017 01:13:25: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 01:13:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 01:13:28: #2 number of paired peaks: 5587 INFO @ Sat, 11 Nov 2017 01:13:28: start model_add_line... INFO @ Sat, 11 Nov 2017 01:13:28: start X-correlation... INFO @ Sat, 11 Nov 2017 01:13:28: end of X-cor INFO @ Sat, 11 Nov 2017 01:13:28: #2 finished! INFO @ Sat, 11 Nov 2017 01:13:28: #2 predicted fragment length is 76 bps INFO @ Sat, 11 Nov 2017 01:13:28: #2 alternative fragment length(s) may be 76,564 bps INFO @ Sat, 11 Nov 2017 01:13:28: #2.2 Generate R script for model : SRX2568195.20_model.r WARNING @ Sat, 11 Nov 2017 01:13:28: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 01:13:28: #2 You may need to consider one of the other alternative d(s): 76,564 WARNING @ Sat, 11 Nov 2017 01:13:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Nov 2017 01:13:28: #3 Call peaks... INFO @ Sat, 11 Nov 2017 01:13:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 01:13:28: #1 tag size is determined as 75 bps INFO @ Sat, 11 Nov 2017 01:13:28: #1 tag size = 75 INFO @ Sat, 11 Nov 2017 01:13:28: #1 total tags in treatment: 17667968 INFO @ Sat, 11 Nov 2017 01:13:28: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 01:13:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 01:13:29: #1 tag size is determined as 75 bps INFO @ Sat, 11 Nov 2017 01:13:29: #1 tag size = 75 INFO @ Sat, 11 Nov 2017 01:13:29: #1 total tags in treatment: 17667968 INFO @ Sat, 11 Nov 2017 01:13:29: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 01:13:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 01:13:29: #1 tags after filtering in treatment: 17667829 INFO @ Sat, 11 Nov 2017 01:13:29: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 01:13:29: #1 finished! INFO @ Sat, 11 Nov 2017 01:13:29: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 01:13:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 01:13:30: #1 tags after filtering in treatment: 17667829 INFO @ Sat, 11 Nov 2017 01:13:30: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 01:13:30: #1 finished! INFO @ Sat, 11 Nov 2017 01:13:30: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 01:13:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 01:13:32: #2 number of paired peaks: 5587 INFO @ Sat, 11 Nov 2017 01:13:32: start model_add_line... INFO @ Sat, 11 Nov 2017 01:13:32: start X-correlation... INFO @ Sat, 11 Nov 2017 01:13:32: end of X-cor INFO @ Sat, 11 Nov 2017 01:13:32: #2 finished! INFO @ Sat, 11 Nov 2017 01:13:32: #2 predicted fragment length is 76 bps INFO @ Sat, 11 Nov 2017 01:13:32: #2 alternative fragment length(s) may be 76,564 bps INFO @ Sat, 11 Nov 2017 01:13:32: #2.2 Generate R script for model : SRX2568195.05_model.r WARNING @ Sat, 11 Nov 2017 01:13:32: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 01:13:32: #2 You may need to consider one of the other alternative d(s): 76,564 WARNING @ Sat, 11 Nov 2017 01:13:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Nov 2017 01:13:32: #3 Call peaks... INFO @ Sat, 11 Nov 2017 01:13:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 01:13:32: #2 number of paired peaks: 5587 INFO @ Sat, 11 Nov 2017 01:13:32: start model_add_line... INFO @ Sat, 11 Nov 2017 01:13:32: start X-correlation... INFO @ Sat, 11 Nov 2017 01:13:32: end of X-cor INFO @ Sat, 11 Nov 2017 01:13:32: #2 finished! INFO @ Sat, 11 Nov 2017 01:13:32: #2 predicted fragment length is 76 bps INFO @ Sat, 11 Nov 2017 01:13:32: #2 alternative fragment length(s) may be 76,564 bps INFO @ Sat, 11 Nov 2017 01:13:32: #2.2 Generate R script for model : SRX2568195.10_model.r WARNING @ Sat, 11 Nov 2017 01:13:32: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 01:13:32: #2 You may need to consider one of the other alternative d(s): 76,564 WARNING @ Sat, 11 Nov 2017 01:13:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Nov 2017 01:13:32: #3 Call peaks... INFO @ Sat, 11 Nov 2017 01:13:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 01:14:20: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 01:14:23: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 01:14:24: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 01:14:54: #4 Write output xls file... SRX2568195.05_peaks.xls INFO @ Sat, 11 Nov 2017 01:14:54: #4 Write peak in narrowPeak format file... SRX2568195.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 01:14:54: #4 Write summits bed file... SRX2568195.05_summits.bed INFO @ Sat, 11 Nov 2017 01:14:54: Done! pass1 - making usageList (46 chroms): 2 millis pass2 - checking and writing primary data (1129 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 01:14:55: #4 Write output xls file... SRX2568195.20_peaks.xls INFO @ Sat, 11 Nov 2017 01:14:55: #4 Write peak in narrowPeak format file... SRX2568195.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 01:14:55: #4 Write summits bed file... SRX2568195.20_summits.bed INFO @ Sat, 11 Nov 2017 01:14:55: Done! pass1 - making usageList (27 chroms): 1 millis pass2 - checking and writing primary data (371 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 01:14:56: #4 Write output xls file... SRX2568195.10_peaks.xls INFO @ Sat, 11 Nov 2017 01:14:56: #4 Write peak in narrowPeak format file... SRX2568195.10_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 01:14:56: #4 Write summits bed file... SRX2568195.10_summits.bed INFO @ Sat, 11 Nov 2017 01:14:56: Done! pass1 - making usageList (39 chroms): 2 millis pass2 - checking and writing primary data (660 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。