Job ID = 10175247 sra ファイルのダウンロード中... Completed: 474185K bytes transferred in 21 seconds (184547K 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 26739492 spots for /home/okishinya/chipatlas/results/dm3/SRX2804225/SRR5534653.sra Written 26739492 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: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:11:14 26739492 reads; of these: 26739492 (100.00%) were unpaired; of these: 4036461 (15.10%) aligned 0 times 15346847 (57.39%) aligned exactly 1 time 7356184 (27.51%) aligned >1 times 84.90% overall alignment rate Time searching: 00:11:15 Overall time: 00:11:15 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 2838642 / 22703031 = 0.1250 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 @ Mon, 06 Nov 2017 12:08:25: # Command line: callpeak -t SRX2804225.bam -f BAM -g dm -n SRX2804225.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2804225.05 # format = BAM # ChIP-seq file = ['SRX2804225.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 @ Mon, 06 Nov 2017 12:08:25: #1 read tag files... INFO @ Mon, 06 Nov 2017 12:08:25: #1 read treatment tags... INFO @ Mon, 06 Nov 2017 12:08:25: # Command line: callpeak -t SRX2804225.bam -f BAM -g dm -n SRX2804225.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2804225.20 # format = BAM # ChIP-seq file = ['SRX2804225.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 @ Mon, 06 Nov 2017 12:08:25: #1 read tag files... INFO @ Mon, 06 Nov 2017 12:08:25: #1 read treatment tags... INFO @ Mon, 06 Nov 2017 12:08:25: # Command line: callpeak -t SRX2804225.bam -f BAM -g dm -n SRX2804225.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2804225.10 # format = BAM # ChIP-seq file = ['SRX2804225.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 @ Mon, 06 Nov 2017 12:08:25: #1 read tag files... INFO @ Mon, 06 Nov 2017 12:08:25: #1 read treatment tags... INFO @ Mon, 06 Nov 2017 12:08:34: 1000000 INFO @ Mon, 06 Nov 2017 12:08:34: 1000000 INFO @ Mon, 06 Nov 2017 12:08:34: 1000000 INFO @ Mon, 06 Nov 2017 12:08:42: 2000000 INFO @ Mon, 06 Nov 2017 12:08:42: 2000000 INFO @ Mon, 06 Nov 2017 12:08:43: 2000000 INFO @ Mon, 06 Nov 2017 12:08:51: 3000000 INFO @ Mon, 06 Nov 2017 12:08:51: 3000000 INFO @ Mon, 06 Nov 2017 12:08:51: 3000000 INFO @ Mon, 06 Nov 2017 12:08:58: 4000000 INFO @ Mon, 06 Nov 2017 12:08:58: 4000000 INFO @ Mon, 06 Nov 2017 12:08:58: 4000000 INFO @ Mon, 06 Nov 2017 12:09:06: 5000000 INFO @ Mon, 06 Nov 2017 12:09:06: 5000000 INFO @ Mon, 06 Nov 2017 12:09:06: 5000000 INFO @ Mon, 06 Nov 2017 12:09:13: 6000000 INFO @ Mon, 06 Nov 2017 12:09:13: 6000000 INFO @ Mon, 06 Nov 2017 12:09:13: 6000000 INFO @ Mon, 06 Nov 2017 12:09:20: 7000000 INFO @ Mon, 06 Nov 2017 12:09:21: 7000000 INFO @ Mon, 06 Nov 2017 12:09:21: 7000000 INFO @ Mon, 06 Nov 2017 12:09:27: 8000000 INFO @ Mon, 06 Nov 2017 12:09:27: 8000000 INFO @ Mon, 06 Nov 2017 12:09:27: 8000000 INFO @ Mon, 06 Nov 2017 12:09:34: 9000000 INFO @ Mon, 06 Nov 2017 12:09:34: 9000000 INFO @ Mon, 06 Nov 2017 12:09:34: 9000000 INFO @ Mon, 06 Nov 2017 12:09:41: 10000000 INFO @ Mon, 06 Nov 2017 12:09:41: 10000000 INFO @ Mon, 06 Nov 2017 12:09:41: 10000000 INFO @ Mon, 06 Nov 2017 12:09:47: 11000000 INFO @ Mon, 06 Nov 2017 12:09:48: 11000000 INFO @ Mon, 06 Nov 2017 12:09:49: 11000000 INFO @ Mon, 06 Nov 2017 12:09:53: 12000000 INFO @ Mon, 06 Nov 2017 12:09:55: 12000000 INFO @ Mon, 06 Nov 2017 12:09:56: 12000000 INFO @ Mon, 06 Nov 2017 12:10:00: 13000000 INFO @ Mon, 06 Nov 2017 12:10:02: 13000000 INFO @ Mon, 06 Nov 2017 12:10:03: 13000000 INFO @ Mon, 06 Nov 2017 12:10:06: 14000000 INFO @ Mon, 06 Nov 2017 12:10:09: 14000000 INFO @ Mon, 06 Nov 2017 12:10:10: 14000000 INFO @ Mon, 06 Nov 2017 12:10:13: 15000000 INFO @ Mon, 06 Nov 2017 12:10:17: 15000000 INFO @ Mon, 06 Nov 2017 12:10:18: 15000000 INFO @ Mon, 06 Nov 2017 12:10:19: 16000000 INFO @ Mon, 06 Nov 2017 12:10:24: 16000000 INFO @ Mon, 06 Nov 2017 12:10:25: 16000000 INFO @ Mon, 06 Nov 2017 12:10:26: 17000000 INFO @ Mon, 06 Nov 2017 12:10:31: 17000000 INFO @ Mon, 06 Nov 2017 12:10:32: 18000000 INFO @ Mon, 06 Nov 2017 12:10:33: 17000000 INFO @ Mon, 06 Nov 2017 12:10:38: 18000000 INFO @ Mon, 06 Nov 2017 12:10:39: 19000000 INFO @ Mon, 06 Nov 2017 12:10:40: 18000000 INFO @ Mon, 06 Nov 2017 12:10:44: #1 tag size is determined as 51 bps INFO @ Mon, 06 Nov 2017 12:10:44: #1 tag size = 51 INFO @ Mon, 06 Nov 2017 12:10:44: #1 total tags in treatment: 19864389 INFO @ Mon, 06 Nov 2017 12:10:44: #1 user defined the maximum tags... INFO @ Mon, 06 Nov 2017 12:10:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Nov 2017 12:10:45: #1 tags after filtering in treatment: 19864389 INFO @ Mon, 06 Nov 2017 12:10:45: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Nov 2017 12:10:45: #1 finished! INFO @ Mon, 06 Nov 2017 12:10:45: #2 Build Peak Model... INFO @ Mon, 06 Nov 2017 12:10:45: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Nov 2017 12:10:45: 19000000 INFO @ Mon, 06 Nov 2017 12:10:46: #2 number of paired peaks: 121 WARNING @ Mon, 06 Nov 2017 12:10:46: Fewer paired peaks (121) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 121 pairs to build model! INFO @ Mon, 06 Nov 2017 12:10:46: start model_add_line... INFO @ Mon, 06 Nov 2017 12:10:46: start X-correlation... INFO @ Mon, 06 Nov 2017 12:10:46: end of X-cor INFO @ Mon, 06 Nov 2017 12:10:46: #2 finished! INFO @ Mon, 06 Nov 2017 12:10:46: #2 predicted fragment length is 54 bps INFO @ Mon, 06 Nov 2017 12:10:46: #2 alternative fragment length(s) may be 54 bps INFO @ Mon, 06 Nov 2017 12:10:46: #2.2 Generate R script for model : SRX2804225.10_model.r WARNING @ Mon, 06 Nov 2017 12:10:46: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 06 Nov 2017 12:10:46: #2 You may need to consider one of the other alternative d(s): 54 WARNING @ Mon, 06 Nov 2017 12:10:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 06 Nov 2017 12:10:46: #3 Call peaks... INFO @ Mon, 06 Nov 2017 12:10:46: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Nov 2017 12:10:47: 19000000 INFO @ Mon, 06 Nov 2017 12:10:51: #1 tag size is determined as 51 bps INFO @ Mon, 06 Nov 2017 12:10:51: #1 tag size = 51 INFO @ Mon, 06 Nov 2017 12:10:51: #1 total tags in treatment: 19864389 INFO @ Mon, 06 Nov 2017 12:10:51: #1 user defined the maximum tags... INFO @ Mon, 06 Nov 2017 12:10:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Nov 2017 12:10:51: #1 tags after filtering in treatment: 19864389 INFO @ Mon, 06 Nov 2017 12:10:51: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Nov 2017 12:10:51: #1 finished! INFO @ Mon, 06 Nov 2017 12:10:51: #2 Build Peak Model... INFO @ Mon, 06 Nov 2017 12:10:51: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Nov 2017 12:10:53: #2 number of paired peaks: 121 WARNING @ Mon, 06 Nov 2017 12:10:53: Fewer paired peaks (121) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 121 pairs to build model! INFO @ Mon, 06 Nov 2017 12:10:53: start model_add_line... INFO @ Mon, 06 Nov 2017 12:10:53: start X-correlation... INFO @ Mon, 06 Nov 2017 12:10:53: end of X-cor INFO @ Mon, 06 Nov 2017 12:10:53: #2 finished! INFO @ Mon, 06 Nov 2017 12:10:53: #2 predicted fragment length is 54 bps INFO @ Mon, 06 Nov 2017 12:10:53: #2 alternative fragment length(s) may be 54 bps INFO @ Mon, 06 Nov 2017 12:10:53: #2.2 Generate R script for model : SRX2804225.05_model.r WARNING @ Mon, 06 Nov 2017 12:10:53: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 06 Nov 2017 12:10:53: #2 You may need to consider one of the other alternative d(s): 54 WARNING @ Mon, 06 Nov 2017 12:10:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 06 Nov 2017 12:10:53: #3 Call peaks... INFO @ Mon, 06 Nov 2017 12:10:53: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Nov 2017 12:10:53: #1 tag size is determined as 51 bps INFO @ Mon, 06 Nov 2017 12:10:53: #1 tag size = 51 INFO @ Mon, 06 Nov 2017 12:10:53: #1 total tags in treatment: 19864389 INFO @ Mon, 06 Nov 2017 12:10:53: #1 user defined the maximum tags... INFO @ Mon, 06 Nov 2017 12:10:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Nov 2017 12:10:53: #1 tags after filtering in treatment: 19864389 INFO @ Mon, 06 Nov 2017 12:10:53: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Nov 2017 12:10:53: #1 finished! INFO @ Mon, 06 Nov 2017 12:10:53: #2 Build Peak Model... INFO @ Mon, 06 Nov 2017 12:10:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Nov 2017 12:10:55: #2 number of paired peaks: 121 WARNING @ Mon, 06 Nov 2017 12:10:55: Fewer paired peaks (121) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 121 pairs to build model! INFO @ Mon, 06 Nov 2017 12:10:55: start model_add_line... INFO @ Mon, 06 Nov 2017 12:10:55: start X-correlation... INFO @ Mon, 06 Nov 2017 12:10:55: end of X-cor INFO @ Mon, 06 Nov 2017 12:10:55: #2 finished! INFO @ Mon, 06 Nov 2017 12:10:55: #2 predicted fragment length is 54 bps INFO @ Mon, 06 Nov 2017 12:10:55: #2 alternative fragment length(s) may be 54 bps INFO @ Mon, 06 Nov 2017 12:10:55: #2.2 Generate R script for model : SRX2804225.20_model.r WARNING @ Mon, 06 Nov 2017 12:10:55: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 06 Nov 2017 12:10:55: #2 You may need to consider one of the other alternative d(s): 54 WARNING @ Mon, 06 Nov 2017 12:10:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 06 Nov 2017 12:10:55: #3 Call peaks... INFO @ Mon, 06 Nov 2017 12:10:55: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Nov 2017 12:11:27: #3 Call peaks for each chromosome... INFO @ Mon, 06 Nov 2017 12:11:33: #3 Call peaks for each chromosome... INFO @ Mon, 06 Nov 2017 12:11:34: #3 Call peaks for each chromosome... INFO @ Mon, 06 Nov 2017 12:11:47: #4 Write output xls file... SRX2804225.10_peaks.xls INFO @ Mon, 06 Nov 2017 12:11:48: #4 Write peak in narrowPeak format file... SRX2804225.10_peaks.narrowPeak INFO @ Mon, 06 Nov 2017 12:11:48: #4 Write summits bed file... SRX2804225.10_summits.bed INFO @ Mon, 06 Nov 2017 12:11:48: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1868 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 06 Nov 2017 12:11:55: #4 Write output xls file... SRX2804225.20_peaks.xls INFO @ Mon, 06 Nov 2017 12:11:55: #4 Write peak in narrowPeak format file... SRX2804225.20_peaks.narrowPeak INFO @ Mon, 06 Nov 2017 12:11:55: #4 Write summits bed file... SRX2804225.20_summits.bed INFO @ Mon, 06 Nov 2017 12:11:55: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (1002 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 06 Nov 2017 12:11:56: #4 Write output xls file... SRX2804225.05_peaks.xls INFO @ Mon, 06 Nov 2017 12:11:56: #4 Write peak in narrowPeak format file... SRX2804225.05_peaks.narrowPeak INFO @ Mon, 06 Nov 2017 12:11:56: #4 Write summits bed file... SRX2804225.05_summits.bed INFO @ Mon, 06 Nov 2017 12:11:56: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3785 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。