Job ID = 9730470 sra ファイルのダウンロード中... Completed: 532706K bytes transferred in 37 seconds (116790K 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 22226714 spots for /home/okishinya/chipatlas/results/dm3/SRX2831143/SRR5572465.sra Written 22226714 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: 00:08:46 22226714 reads; of these: 22226714 (100.00%) were unpaired; of these: 1111932 (5.00%) aligned 0 times 14743000 (66.33%) aligned exactly 1 time 6371782 (28.67%) aligned >1 times 95.00% overall alignment rate Time searching: 00:08:46 Overall time: 00:08:46 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] 3039683 / 21114782 = 0.1440 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 01:10:09: # Command line: callpeak -t SRX2831143.bam -f BAM -g dm -n SRX2831143.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2831143.05 # format = BAM # ChIP-seq file = ['SRX2831143.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 01:10:09: # Command line: callpeak -t SRX2831143.bam -f BAM -g dm -n SRX2831143.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2831143.10 # format = BAM # ChIP-seq file = ['SRX2831143.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 01:10:09: # Command line: callpeak -t SRX2831143.bam -f BAM -g dm -n SRX2831143.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2831143.20 # format = BAM # ChIP-seq file = ['SRX2831143.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 01:10:09: #1 read tag files... INFO @ Sun, 03 Sep 2017 01:10:09: #1 read tag files... INFO @ Sun, 03 Sep 2017 01:10:09: #1 read tag files... INFO @ Sun, 03 Sep 2017 01:10:09: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 01:10:09: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 01:10:09: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 01:10:16: 1000000 INFO @ Sun, 03 Sep 2017 01:10:16: 1000000 INFO @ Sun, 03 Sep 2017 01:10:16: 1000000 INFO @ Sun, 03 Sep 2017 01:10:23: 2000000 INFO @ Sun, 03 Sep 2017 01:10:23: 2000000 INFO @ Sun, 03 Sep 2017 01:10:24: 2000000 INFO @ Sun, 03 Sep 2017 01:10:30: 3000000 INFO @ Sun, 03 Sep 2017 01:10:31: 3000000 INFO @ Sun, 03 Sep 2017 01:10:31: 3000000 INFO @ Sun, 03 Sep 2017 01:10:37: 4000000 INFO @ Sun, 03 Sep 2017 01:10:38: 4000000 INFO @ Sun, 03 Sep 2017 01:10:38: 4000000 INFO @ Sun, 03 Sep 2017 01:10:44: 5000000 INFO @ Sun, 03 Sep 2017 01:10:45: 5000000 INFO @ Sun, 03 Sep 2017 01:10:46: 5000000 INFO @ Sun, 03 Sep 2017 01:10:51: 6000000 INFO @ Sun, 03 Sep 2017 01:10:52: 6000000 INFO @ Sun, 03 Sep 2017 01:10:53: 6000000 INFO @ Sun, 03 Sep 2017 01:10:58: 7000000 INFO @ Sun, 03 Sep 2017 01:10:59: 7000000 INFO @ Sun, 03 Sep 2017 01:11:01: 7000000 INFO @ Sun, 03 Sep 2017 01:11:05: 8000000 INFO @ Sun, 03 Sep 2017 01:11:07: 8000000 INFO @ Sun, 03 Sep 2017 01:11:08: 8000000 INFO @ Sun, 03 Sep 2017 01:11:11: 9000000 INFO @ Sun, 03 Sep 2017 01:11:14: 9000000 INFO @ Sun, 03 Sep 2017 01:11:15: 9000000 INFO @ Sun, 03 Sep 2017 01:11:18: 10000000 INFO @ Sun, 03 Sep 2017 01:11:21: 10000000 INFO @ Sun, 03 Sep 2017 01:11:23: 10000000 INFO @ Sun, 03 Sep 2017 01:11:25: 11000000 INFO @ Sun, 03 Sep 2017 01:11:28: 11000000 INFO @ Sun, 03 Sep 2017 01:11:30: 11000000 INFO @ Sun, 03 Sep 2017 01:11:33: 12000000 INFO @ Sun, 03 Sep 2017 01:11:36: 12000000 INFO @ Sun, 03 Sep 2017 01:11:37: 12000000 INFO @ Sun, 03 Sep 2017 01:11:41: 13000000 INFO @ Sun, 03 Sep 2017 01:11:44: 13000000 INFO @ Sun, 03 Sep 2017 01:11:44: 13000000 INFO @ Sun, 03 Sep 2017 01:11:48: 14000000 INFO @ Sun, 03 Sep 2017 01:11:51: 14000000 INFO @ Sun, 03 Sep 2017 01:11:52: 14000000 INFO @ Sun, 03 Sep 2017 01:11:56: 15000000 INFO @ Sun, 03 Sep 2017 01:11:59: 15000000 INFO @ Sun, 03 Sep 2017 01:11:59: 15000000 INFO @ Sun, 03 Sep 2017 01:12:03: 16000000 INFO @ Sun, 03 Sep 2017 01:12:06: 16000000 INFO @ Sun, 03 Sep 2017 01:12:06: 16000000 INFO @ Sun, 03 Sep 2017 01:12:10: 17000000 INFO @ Sun, 03 Sep 2017 01:12:13: 17000000 INFO @ Sun, 03 Sep 2017 01:12:14: 17000000 INFO @ Sun, 03 Sep 2017 01:12:18: 18000000 INFO @ Sun, 03 Sep 2017 01:12:18: #1 tag size is determined as 50 bps INFO @ Sun, 03 Sep 2017 01:12:18: #1 tag size = 50 INFO @ Sun, 03 Sep 2017 01:12:18: #1 total tags in treatment: 18075099 INFO @ Sun, 03 Sep 2017 01:12:18: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 01:12:18: #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 01:12:19: #1 tags after filtering in treatment: 18075099 INFO @ Sun, 03 Sep 2017 01:12:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Sep 2017 01:12:19: #1 finished! INFO @ Sun, 03 Sep 2017 01:12:19: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 01:12:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 01:12:19: 18000000 INFO @ Sun, 03 Sep 2017 01:12:20: #2 number of paired peaks: 484 WARNING @ Sun, 03 Sep 2017 01:12:20: Fewer paired peaks (484) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 484 pairs to build model! INFO @ Sun, 03 Sep 2017 01:12:20: start model_add_line... INFO @ Sun, 03 Sep 2017 01:12:20: #1 tag size is determined as 50 bps INFO @ Sun, 03 Sep 2017 01:12:20: #1 tag size = 50 INFO @ Sun, 03 Sep 2017 01:12:20: #1 total tags in treatment: 18075099 INFO @ Sun, 03 Sep 2017 01:12:20: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 01:12:20: #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 01:12:20: start X-correlation... INFO @ Sun, 03 Sep 2017 01:12:20: end of X-cor INFO @ Sun, 03 Sep 2017 01:12:20: #2 finished! INFO @ Sun, 03 Sep 2017 01:12:20: #2 predicted fragment length is 45 bps INFO @ Sun, 03 Sep 2017 01:12:20: #2 alternative fragment length(s) may be 2,45,584 bps INFO @ Sun, 03 Sep 2017 01:12:20: #2.2 Generate R script for model : SRX2831143.20_model.r WARNING @ Sun, 03 Sep 2017 01:12:20: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Sep 2017 01:12:20: #2 You may need to consider one of the other alternative d(s): 2,45,584 WARNING @ Sun, 03 Sep 2017 01:12:20: #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 01:12:20: #3 Call peaks... INFO @ Sun, 03 Sep 2017 01:12:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Sep 2017 01:12:20: #1 tags after filtering in treatment: 18075099 INFO @ Sun, 03 Sep 2017 01:12:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Sep 2017 01:12:20: #1 finished! INFO @ Sun, 03 Sep 2017 01:12:20: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 01:12:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 01:12:21: 18000000 INFO @ Sun, 03 Sep 2017 01:12:22: #2 number of paired peaks: 484 WARNING @ Sun, 03 Sep 2017 01:12:22: Fewer paired peaks (484) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 484 pairs to build model! INFO @ Sun, 03 Sep 2017 01:12:22: start model_add_line... INFO @ Sun, 03 Sep 2017 01:12:22: #1 tag size is determined as 50 bps INFO @ Sun, 03 Sep 2017 01:12:22: #1 tag size = 50 INFO @ Sun, 03 Sep 2017 01:12:22: #1 total tags in treatment: 18075099 INFO @ Sun, 03 Sep 2017 01:12:22: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 01:12:22: #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 01:12:22: start X-correlation... INFO @ Sun, 03 Sep 2017 01:12:22: end of X-cor INFO @ Sun, 03 Sep 2017 01:12:22: #2 finished! INFO @ Sun, 03 Sep 2017 01:12:22: #2 predicted fragment length is 45 bps INFO @ Sun, 03 Sep 2017 01:12:22: #2 alternative fragment length(s) may be 2,45,584 bps INFO @ Sun, 03 Sep 2017 01:12:22: #2.2 Generate R script for model : SRX2831143.05_model.r WARNING @ Sun, 03 Sep 2017 01:12:22: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Sep 2017 01:12:22: #2 You may need to consider one of the other alternative d(s): 2,45,584 WARNING @ Sun, 03 Sep 2017 01:12:22: #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 01:12:22: #3 Call peaks... INFO @ Sun, 03 Sep 2017 01:12:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Sep 2017 01:12:22: #1 tags after filtering in treatment: 18075099 INFO @ Sun, 03 Sep 2017 01:12:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Sep 2017 01:12:22: #1 finished! INFO @ Sun, 03 Sep 2017 01:12:22: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 01:12:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 01:12:23: #2 number of paired peaks: 484 WARNING @ Sun, 03 Sep 2017 01:12:23: Fewer paired peaks (484) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 484 pairs to build model! INFO @ Sun, 03 Sep 2017 01:12:23: start model_add_line... INFO @ Sun, 03 Sep 2017 01:12:24: start X-correlation... INFO @ Sun, 03 Sep 2017 01:12:24: end of X-cor INFO @ Sun, 03 Sep 2017 01:12:24: #2 finished! INFO @ Sun, 03 Sep 2017 01:12:24: #2 predicted fragment length is 45 bps INFO @ Sun, 03 Sep 2017 01:12:24: #2 alternative fragment length(s) may be 2,45,584 bps INFO @ Sun, 03 Sep 2017 01:12:24: #2.2 Generate R script for model : SRX2831143.10_model.r WARNING @ Sun, 03 Sep 2017 01:12:24: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Sep 2017 01:12:24: #2 You may need to consider one of the other alternative d(s): 2,45,584 WARNING @ Sun, 03 Sep 2017 01:12:24: #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 01:12:24: #3 Call peaks... INFO @ Sun, 03 Sep 2017 01:12:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Sep 2017 01:12:57: #3 Call peaks for each chromosome... INFO @ Sun, 03 Sep 2017 01:12:58: #3 Call peaks for each chromosome... INFO @ Sun, 03 Sep 2017 01:12:59: #3 Call peaks for each chromosome... INFO @ Sun, 03 Sep 2017 01:13:18: #4 Write output xls file... SRX2831143.20_peaks.xls INFO @ Sun, 03 Sep 2017 01:13:18: #4 Write peak in narrowPeak format file... SRX2831143.20_peaks.narrowPeak INFO @ Sun, 03 Sep 2017 01:13:18: #4 Write summits bed file... SRX2831143.20_summits.bed INFO @ Sun, 03 Sep 2017 01:13:18: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1146 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 03 Sep 2017 01:13:20: #4 Write output xls file... SRX2831143.05_peaks.xls INFO @ Sun, 03 Sep 2017 01:13:20: #4 Write peak in narrowPeak format file... SRX2831143.05_peaks.narrowPeak INFO @ Sun, 03 Sep 2017 01:13:20: #4 Write summits bed file... SRX2831143.05_summits.bed INFO @ Sun, 03 Sep 2017 01:13:20: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3654 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 03 Sep 2017 01:13:21: #4 Write output xls file... SRX2831143.10_peaks.xls INFO @ Sun, 03 Sep 2017 01:13:21: #4 Write peak in narrowPeak format file... SRX2831143.10_peaks.narrowPeak INFO @ Sun, 03 Sep 2017 01:13:21: #4 Write summits bed file... SRX2831143.10_summits.bed INFO @ Sun, 03 Sep 2017 01:13:21: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2271 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。