Job ID = 9730466 sra ファイルのダウンロード中... Completed: 616326K bytes transferred in 44 seconds (114637K 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: SINGLE fastq に変換中... Written 26735128 spots for /home/okishinya/chipatlas/results/dm3/SRX2831139/SRR5572461.sra Written 26735128 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: 00:09:50 26735128 reads; of these: 26735128 (100.00%) were unpaired; of these: 832801 (3.12%) aligned 0 times 18794413 (70.30%) aligned exactly 1 time 7107914 (26.59%) aligned >1 times 96.88% overall alignment rate Time searching: 00:09:50 Overall time: 00:09:50 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 3125827 / 25902327 = 0.1207 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 01:12:24: # Command line: callpeak -t SRX2831139.bam -f BAM -g dm -n SRX2831139.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2831139.10 # format = BAM # ChIP-seq file = ['SRX2831139.bam'] # control file = None # effective genome size = 1.20e+08 # 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 01:12:24: #1 read tag files... INFO @ Sun, 03 Sep 2017 01:12:24: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 01:12:24: # Command line: callpeak -t SRX2831139.bam -f BAM -g dm -n SRX2831139.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2831139.20 # format = BAM # ChIP-seq file = ['SRX2831139.bam'] # control file = None # effective genome size = 1.20e+08 # 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 01:12:24: #1 read tag files... INFO @ Sun, 03 Sep 2017 01:12:24: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 01:12:24: # Command line: callpeak -t SRX2831139.bam -f BAM -g dm -n SRX2831139.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2831139.05 # format = BAM # ChIP-seq file = ['SRX2831139.bam'] # control file = None # effective genome size = 1.20e+08 # 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 01:12:24: #1 read tag files... INFO @ Sun, 03 Sep 2017 01:12:24: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 01:12:32: 1000000 INFO @ Sun, 03 Sep 2017 01:12:32: 1000000 INFO @ Sun, 03 Sep 2017 01:12:33: 1000000 INFO @ Sun, 03 Sep 2017 01:12:40: 2000000 INFO @ Sun, 03 Sep 2017 01:12:40: 2000000 INFO @ Sun, 03 Sep 2017 01:12:43: 2000000 INFO @ Sun, 03 Sep 2017 01:12:47: 3000000 INFO @ Sun, 03 Sep 2017 01:12:47: 3000000 INFO @ Sun, 03 Sep 2017 01:12:52: 3000000 INFO @ Sun, 03 Sep 2017 01:12:55: 4000000 INFO @ Sun, 03 Sep 2017 01:12:55: 4000000 INFO @ Sun, 03 Sep 2017 01:13:01: 4000000 INFO @ Sun, 03 Sep 2017 01:13:02: 5000000 INFO @ Sun, 03 Sep 2017 01:13:02: 5000000 INFO @ Sun, 03 Sep 2017 01:13:09: 6000000 INFO @ Sun, 03 Sep 2017 01:13:09: 6000000 INFO @ Sun, 03 Sep 2017 01:13:11: 5000000 INFO @ Sun, 03 Sep 2017 01:13:17: 7000000 INFO @ Sun, 03 Sep 2017 01:13:17: 7000000 INFO @ Sun, 03 Sep 2017 01:13:20: 6000000 INFO @ Sun, 03 Sep 2017 01:13:24: 8000000 INFO @ Sun, 03 Sep 2017 01:13:24: 8000000 INFO @ Sun, 03 Sep 2017 01:13:29: 7000000 INFO @ Sun, 03 Sep 2017 01:13:31: 9000000 INFO @ Sun, 03 Sep 2017 01:13:31: 9000000 INFO @ Sun, 03 Sep 2017 01:13:38: 10000000 INFO @ Sun, 03 Sep 2017 01:13:38: 10000000 INFO @ Sun, 03 Sep 2017 01:13:38: 8000000 INFO @ Sun, 03 Sep 2017 01:13:46: 11000000 INFO @ Sun, 03 Sep 2017 01:13:46: 11000000 INFO @ Sun, 03 Sep 2017 01:13:48: 9000000 INFO @ Sun, 03 Sep 2017 01:13:53: 12000000 INFO @ Sun, 03 Sep 2017 01:13:53: 12000000 INFO @ Sun, 03 Sep 2017 01:13:57: 10000000 INFO @ Sun, 03 Sep 2017 01:14:01: 13000000 INFO @ Sun, 03 Sep 2017 01:14:01: 13000000 INFO @ Sun, 03 Sep 2017 01:14:06: 11000000 INFO @ Sun, 03 Sep 2017 01:14:09: 14000000 INFO @ Sun, 03 Sep 2017 01:14:09: 14000000 INFO @ Sun, 03 Sep 2017 01:14:15: 12000000 INFO @ Sun, 03 Sep 2017 01:14:17: 15000000 INFO @ Sun, 03 Sep 2017 01:14:17: 15000000 INFO @ Sun, 03 Sep 2017 01:14:24: 13000000 INFO @ Sun, 03 Sep 2017 01:14:25: 16000000 INFO @ Sun, 03 Sep 2017 01:14:25: 16000000 INFO @ Sun, 03 Sep 2017 01:14:32: 14000000 INFO @ Sun, 03 Sep 2017 01:14:33: 17000000 INFO @ Sun, 03 Sep 2017 01:14:33: 17000000 INFO @ Sun, 03 Sep 2017 01:14:39: 15000000 INFO @ Sun, 03 Sep 2017 01:14:40: 18000000 INFO @ Sun, 03 Sep 2017 01:14:40: 18000000 INFO @ Sun, 03 Sep 2017 01:14:47: 16000000 INFO @ Sun, 03 Sep 2017 01:14:47: 19000000 INFO @ Sun, 03 Sep 2017 01:14:47: 19000000 INFO @ Sun, 03 Sep 2017 01:14:54: 17000000 INFO @ Sun, 03 Sep 2017 01:14:56: 20000000 INFO @ Sun, 03 Sep 2017 01:14:56: 20000000 INFO @ Sun, 03 Sep 2017 01:15:01: 18000000 INFO @ Sun, 03 Sep 2017 01:15:03: 21000000 INFO @ Sun, 03 Sep 2017 01:15:03: 21000000 INFO @ Sun, 03 Sep 2017 01:15:08: 19000000 INFO @ Sun, 03 Sep 2017 01:15:10: 22000000 INFO @ Sun, 03 Sep 2017 01:15:10: 22000000 INFO @ Sun, 03 Sep 2017 01:15:15: 20000000 INFO @ Sun, 03 Sep 2017 01:15:16: #1 tag size is determined as 50 bps INFO @ Sun, 03 Sep 2017 01:15:16: #1 tag size = 50 INFO @ Sun, 03 Sep 2017 01:15:16: #1 total tags in treatment: 22776500 INFO @ Sun, 03 Sep 2017 01:15:16: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 01:15:16: #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 01:15:16: #1 tag size is determined as 50 bps INFO @ Sun, 03 Sep 2017 01:15:16: #1 tag size = 50 INFO @ Sun, 03 Sep 2017 01:15:16: #1 total tags in treatment: 22776500 INFO @ Sun, 03 Sep 2017 01:15:16: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 01:15:16: #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 01:15:17: #1 tags after filtering in treatment: 22776500 INFO @ Sun, 03 Sep 2017 01:15:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Sep 2017 01:15:17: #1 finished! INFO @ Sun, 03 Sep 2017 01:15:17: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 01:15:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 01:15:17: #1 tags after filtering in treatment: 22776500 INFO @ Sun, 03 Sep 2017 01:15:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Sep 2017 01:15:17: #1 finished! INFO @ Sun, 03 Sep 2017 01:15:17: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 01:15:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 01:15:18: #2 number of paired peaks: 402 WARNING @ Sun, 03 Sep 2017 01:15:18: Fewer paired peaks (402) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 402 pairs to build model! INFO @ Sun, 03 Sep 2017 01:15:18: start model_add_line... INFO @ Sun, 03 Sep 2017 01:15:18: #2 number of paired peaks: 402 WARNING @ Sun, 03 Sep 2017 01:15:18: Fewer paired peaks (402) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 402 pairs to build model! INFO @ Sun, 03 Sep 2017 01:15:18: start model_add_line... INFO @ Sun, 03 Sep 2017 01:15:18: start X-correlation... INFO @ Sun, 03 Sep 2017 01:15:18: end of X-cor INFO @ Sun, 03 Sep 2017 01:15:18: #2 finished! INFO @ Sun, 03 Sep 2017 01:15:18: #2 predicted fragment length is 43 bps INFO @ Sun, 03 Sep 2017 01:15:18: #2 alternative fragment length(s) may be 2,43 bps INFO @ Sun, 03 Sep 2017 01:15:18: #2.2 Generate R script for model : SRX2831139.20_model.r INFO @ Sun, 03 Sep 2017 01:15:18: start X-correlation... WARNING @ Sun, 03 Sep 2017 01:15:18: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Sep 2017 01:15:18: #2 You may need to consider one of the other alternative d(s): 2,43 WARNING @ Sun, 03 Sep 2017 01:15:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Sep 2017 01:15:18: #3 Call peaks... INFO @ Sun, 03 Sep 2017 01:15:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Sep 2017 01:15:18: end of X-cor INFO @ Sun, 03 Sep 2017 01:15:18: #2 finished! INFO @ Sun, 03 Sep 2017 01:15:18: #2 predicted fragment length is 43 bps INFO @ Sun, 03 Sep 2017 01:15:18: #2 alternative fragment length(s) may be 2,43 bps INFO @ Sun, 03 Sep 2017 01:15:18: #2.2 Generate R script for model : SRX2831139.10_model.r WARNING @ Sun, 03 Sep 2017 01:15:18: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Sep 2017 01:15:18: #2 You may need to consider one of the other alternative d(s): 2,43 WARNING @ Sun, 03 Sep 2017 01:15:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Sep 2017 01:15:18: #3 Call peaks... INFO @ Sun, 03 Sep 2017 01:15:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Sep 2017 01:15:22: 21000000 INFO @ Sun, 03 Sep 2017 01:15:29: 22000000 INFO @ Sun, 03 Sep 2017 01:15:35: #1 tag size is determined as 50 bps INFO @ Sun, 03 Sep 2017 01:15:35: #1 tag size = 50 INFO @ Sun, 03 Sep 2017 01:15:35: #1 total tags in treatment: 22776500 INFO @ Sun, 03 Sep 2017 01:15:35: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 01:15:35: #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 01:15:35: #1 tags after filtering in treatment: 22776500 INFO @ Sun, 03 Sep 2017 01:15:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Sep 2017 01:15:35: #1 finished! INFO @ Sun, 03 Sep 2017 01:15:35: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 01:15:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 01:15:37: #2 number of paired peaks: 402 WARNING @ Sun, 03 Sep 2017 01:15:37: Fewer paired peaks (402) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 402 pairs to build model! INFO @ Sun, 03 Sep 2017 01:15:37: start model_add_line... INFO @ Sun, 03 Sep 2017 01:15:37: start X-correlation... INFO @ Sun, 03 Sep 2017 01:15:37: end of X-cor INFO @ Sun, 03 Sep 2017 01:15:37: #2 finished! INFO @ Sun, 03 Sep 2017 01:15:37: #2 predicted fragment length is 43 bps INFO @ Sun, 03 Sep 2017 01:15:37: #2 alternative fragment length(s) may be 2,43 bps INFO @ Sun, 03 Sep 2017 01:15:37: #2.2 Generate R script for model : SRX2831139.05_model.r WARNING @ Sun, 03 Sep 2017 01:15:37: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Sep 2017 01:15:37: #2 You may need to consider one of the other alternative d(s): 2,43 WARNING @ Sun, 03 Sep 2017 01:15:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Sep 2017 01:15:37: #3 Call peaks... INFO @ Sun, 03 Sep 2017 01:15:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Sep 2017 01:16:02: #3 Call peaks for each chromosome... INFO @ Sun, 03 Sep 2017 01:16:07: #3 Call peaks for each chromosome... INFO @ Sun, 03 Sep 2017 01:16:19: #3 Call peaks for each chromosome... INFO @ Sun, 03 Sep 2017 01:16:26: #4 Write output xls file... SRX2831139.10_peaks.xls INFO @ Sun, 03 Sep 2017 01:16:26: #4 Write peak in narrowPeak format file... SRX2831139.10_peaks.narrowPeak INFO @ Sun, 03 Sep 2017 01:16:26: #4 Write summits bed file... SRX2831139.10_summits.bed INFO @ Sun, 03 Sep 2017 01:16:26: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2339 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 03 Sep 2017 01:16:38: #4 Write output xls file... SRX2831139.20_peaks.xls INFO @ Sun, 03 Sep 2017 01:16:38: #4 Write peak in narrowPeak format file... SRX2831139.20_peaks.narrowPeak INFO @ Sun, 03 Sep 2017 01:16:38: #4 Write summits bed file... SRX2831139.20_summits.bed INFO @ Sun, 03 Sep 2017 01:16:38: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (795 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 03 Sep 2017 01:16:43: #4 Write output xls file... SRX2831139.05_peaks.xls INFO @ Sun, 03 Sep 2017 01:16:43: #4 Write peak in narrowPeak format file... SRX2831139.05_peaks.narrowPeak INFO @ Sun, 03 Sep 2017 01:16:43: #4 Write summits bed file... SRX2831139.05_summits.bed INFO @ Sun, 03 Sep 2017 01:16:43: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3824 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。