Job ID = 10175249 sra ファイルのダウンロード中... Completed: 611019K bytes transferred in 23 seconds (213547K 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 35532007 spots for /home/okishinya/chipatlas/results/dm3/SRX2804227/SRR5534655.sra Written 35532007 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:14:08 35532007 reads; of these: 35532007 (100.00%) were unpaired; of these: 8701469 (24.49%) aligned 0 times 17635741 (49.63%) aligned exactly 1 time 9194797 (25.88%) aligned >1 times 75.51% overall alignment rate Time searching: 00:14:08 Overall time: 00:14:08 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] 3964918 / 26830538 = 0.1478 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 12:13:50: # Command line: callpeak -t SRX2804227.bam -f BAM -g dm -n SRX2804227.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2804227.05 # format = BAM # ChIP-seq file = ['SRX2804227.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 12:13:50: #1 read tag files... INFO @ Mon, 06 Nov 2017 12:13:50: #1 read treatment tags... INFO @ Mon, 06 Nov 2017 12:13:50: # Command line: callpeak -t SRX2804227.bam -f BAM -g dm -n SRX2804227.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2804227.10 # format = BAM # ChIP-seq file = ['SRX2804227.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 12:13:50: #1 read tag files... INFO @ Mon, 06 Nov 2017 12:13:50: #1 read treatment tags... INFO @ Mon, 06 Nov 2017 12:13:50: # Command line: callpeak -t SRX2804227.bam -f BAM -g dm -n SRX2804227.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2804227.20 # format = BAM # ChIP-seq file = ['SRX2804227.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 12:13:50: #1 read tag files... INFO @ Mon, 06 Nov 2017 12:13:50: #1 read treatment tags... INFO @ Mon, 06 Nov 2017 12:13:56: 1000000 INFO @ Mon, 06 Nov 2017 12:13:56: 1000000 INFO @ Mon, 06 Nov 2017 12:13:56: 1000000 INFO @ Mon, 06 Nov 2017 12:14:02: 2000000 INFO @ Mon, 06 Nov 2017 12:14:03: 2000000 INFO @ Mon, 06 Nov 2017 12:14:03: 2000000 INFO @ Mon, 06 Nov 2017 12:14:09: 3000000 INFO @ Mon, 06 Nov 2017 12:14:10: 3000000 INFO @ Mon, 06 Nov 2017 12:14:10: 3000000 INFO @ Mon, 06 Nov 2017 12:14:15: 4000000 INFO @ Mon, 06 Nov 2017 12:14:16: 4000000 INFO @ Mon, 06 Nov 2017 12:14:16: 4000000 INFO @ Mon, 06 Nov 2017 12:14:21: 5000000 INFO @ Mon, 06 Nov 2017 12:14:23: 5000000 INFO @ Mon, 06 Nov 2017 12:14:23: 5000000 INFO @ Mon, 06 Nov 2017 12:14:27: 6000000 INFO @ Mon, 06 Nov 2017 12:14:30: 6000000 INFO @ Mon, 06 Nov 2017 12:14:30: 6000000 INFO @ Mon, 06 Nov 2017 12:14:34: 7000000 INFO @ Mon, 06 Nov 2017 12:14:37: 7000000 INFO @ Mon, 06 Nov 2017 12:14:37: 7000000 INFO @ Mon, 06 Nov 2017 12:14:40: 8000000 INFO @ Mon, 06 Nov 2017 12:14:43: 8000000 INFO @ Mon, 06 Nov 2017 12:14:43: 8000000 INFO @ Mon, 06 Nov 2017 12:14:46: 9000000 INFO @ Mon, 06 Nov 2017 12:14:50: 9000000 INFO @ Mon, 06 Nov 2017 12:14:50: 9000000 INFO @ Mon, 06 Nov 2017 12:14:52: 10000000 INFO @ Mon, 06 Nov 2017 12:14:56: 10000000 INFO @ Mon, 06 Nov 2017 12:14:56: 10000000 INFO @ Mon, 06 Nov 2017 12:14:59: 11000000 INFO @ Mon, 06 Nov 2017 12:15:03: 11000000 INFO @ Mon, 06 Nov 2017 12:15:03: 11000000 INFO @ Mon, 06 Nov 2017 12:15:05: 12000000 INFO @ Mon, 06 Nov 2017 12:15:09: 12000000 INFO @ Mon, 06 Nov 2017 12:15:09: 12000000 INFO @ Mon, 06 Nov 2017 12:15:11: 13000000 INFO @ Mon, 06 Nov 2017 12:15:16: 13000000 INFO @ Mon, 06 Nov 2017 12:15:16: 13000000 INFO @ Mon, 06 Nov 2017 12:15:17: 14000000 INFO @ Mon, 06 Nov 2017 12:15:23: 14000000 INFO @ Mon, 06 Nov 2017 12:15:23: 14000000 INFO @ Mon, 06 Nov 2017 12:15:23: 15000000 INFO @ Mon, 06 Nov 2017 12:15:29: 15000000 INFO @ Mon, 06 Nov 2017 12:15:29: 15000000 INFO @ Mon, 06 Nov 2017 12:15:30: 16000000 INFO @ Mon, 06 Nov 2017 12:15:36: 17000000 INFO @ Mon, 06 Nov 2017 12:15:36: 16000000 INFO @ Mon, 06 Nov 2017 12:15:36: 16000000 INFO @ Mon, 06 Nov 2017 12:15:42: 18000000 INFO @ Mon, 06 Nov 2017 12:15:43: 17000000 INFO @ Mon, 06 Nov 2017 12:15:43: 17000000 INFO @ Mon, 06 Nov 2017 12:15:48: 19000000 INFO @ Mon, 06 Nov 2017 12:15:50: 18000000 INFO @ Mon, 06 Nov 2017 12:15:50: 18000000 INFO @ Mon, 06 Nov 2017 12:15:55: 20000000 INFO @ Mon, 06 Nov 2017 12:15:56: 19000000 INFO @ Mon, 06 Nov 2017 12:15:56: 19000000 INFO @ Mon, 06 Nov 2017 12:16:01: 21000000 INFO @ Mon, 06 Nov 2017 12:16:03: 20000000 INFO @ Mon, 06 Nov 2017 12:16:03: 20000000 INFO @ Mon, 06 Nov 2017 12:16:07: 22000000 INFO @ Mon, 06 Nov 2017 12:16:10: 21000000 INFO @ Mon, 06 Nov 2017 12:16:10: 21000000 INFO @ Mon, 06 Nov 2017 12:16:12: #1 tag size is determined as 51 bps INFO @ Mon, 06 Nov 2017 12:16:12: #1 tag size = 51 INFO @ Mon, 06 Nov 2017 12:16:12: #1 total tags in treatment: 22865620 INFO @ Mon, 06 Nov 2017 12:16:12: #1 user defined the maximum tags... INFO @ Mon, 06 Nov 2017 12:16:12: #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 12:16:13: #1 tags after filtering in treatment: 22865620 INFO @ Mon, 06 Nov 2017 12:16:13: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Nov 2017 12:16:13: #1 finished! INFO @ Mon, 06 Nov 2017 12:16:13: #2 Build Peak Model... INFO @ Mon, 06 Nov 2017 12:16:13: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Nov 2017 12:16:14: #2 number of paired peaks: 129 WARNING @ Mon, 06 Nov 2017 12:16:14: Fewer paired peaks (129) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 129 pairs to build model! INFO @ Mon, 06 Nov 2017 12:16:14: start model_add_line... INFO @ Mon, 06 Nov 2017 12:16:15: start X-correlation... INFO @ Mon, 06 Nov 2017 12:16:15: end of X-cor INFO @ Mon, 06 Nov 2017 12:16:15: #2 finished! INFO @ Mon, 06 Nov 2017 12:16:15: #2 predicted fragment length is 96 bps INFO @ Mon, 06 Nov 2017 12:16:15: #2 alternative fragment length(s) may be 96,550 bps INFO @ Mon, 06 Nov 2017 12:16:15: #2.2 Generate R script for model : SRX2804227.05_model.r WARNING @ Mon, 06 Nov 2017 12:16:15: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 06 Nov 2017 12:16:15: #2 You may need to consider one of the other alternative d(s): 96,550 WARNING @ Mon, 06 Nov 2017 12:16:15: #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 12:16:15: #3 Call peaks... INFO @ Mon, 06 Nov 2017 12:16:15: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Nov 2017 12:16:17: 22000000 INFO @ Mon, 06 Nov 2017 12:16:17: 22000000 INFO @ Mon, 06 Nov 2017 12:16:22: #1 tag size is determined as 51 bps INFO @ Mon, 06 Nov 2017 12:16:22: #1 tag size is determined as 51 bps INFO @ Mon, 06 Nov 2017 12:16:22: #1 tag size = 51 INFO @ Mon, 06 Nov 2017 12:16:22: #1 tag size = 51 INFO @ Mon, 06 Nov 2017 12:16:22: #1 total tags in treatment: 22865620 INFO @ Mon, 06 Nov 2017 12:16:22: #1 total tags in treatment: 22865620 INFO @ Mon, 06 Nov 2017 12:16:22: #1 user defined the maximum tags... INFO @ Mon, 06 Nov 2017 12:16:22: #1 user defined the maximum tags... INFO @ Mon, 06 Nov 2017 12:16:22: #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 12:16:22: #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 12:16:23: #1 tags after filtering in treatment: 22865620 INFO @ Mon, 06 Nov 2017 12:16:23: #1 tags after filtering in treatment: 22865620 INFO @ Mon, 06 Nov 2017 12:16:23: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Nov 2017 12:16:23: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Nov 2017 12:16:23: #1 finished! INFO @ Mon, 06 Nov 2017 12:16:23: #1 finished! INFO @ Mon, 06 Nov 2017 12:16:23: #2 Build Peak Model... INFO @ Mon, 06 Nov 2017 12:16:23: #2 Build Peak Model... INFO @ Mon, 06 Nov 2017 12:16:23: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Nov 2017 12:16:23: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Nov 2017 12:16:24: #2 number of paired peaks: 129 WARNING @ Mon, 06 Nov 2017 12:16:24: Fewer paired peaks (129) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 129 pairs to build model! INFO @ Mon, 06 Nov 2017 12:16:24: start model_add_line... INFO @ Mon, 06 Nov 2017 12:16:24: #2 number of paired peaks: 129 WARNING @ Mon, 06 Nov 2017 12:16:24: Fewer paired peaks (129) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 129 pairs to build model! INFO @ Mon, 06 Nov 2017 12:16:24: start model_add_line... INFO @ Mon, 06 Nov 2017 12:16:25: start X-correlation... INFO @ Mon, 06 Nov 2017 12:16:25: end of X-cor INFO @ Mon, 06 Nov 2017 12:16:25: #2 finished! INFO @ Mon, 06 Nov 2017 12:16:25: #2 predicted fragment length is 96 bps INFO @ Mon, 06 Nov 2017 12:16:25: #2 alternative fragment length(s) may be 96,550 bps INFO @ Mon, 06 Nov 2017 12:16:25: #2.2 Generate R script for model : SRX2804227.20_model.r INFO @ Mon, 06 Nov 2017 12:16:25: start X-correlation... INFO @ Mon, 06 Nov 2017 12:16:25: end of X-cor INFO @ Mon, 06 Nov 2017 12:16:25: #2 finished! INFO @ Mon, 06 Nov 2017 12:16:25: #2 predicted fragment length is 96 bps INFO @ Mon, 06 Nov 2017 12:16:25: #2 alternative fragment length(s) may be 96,550 bps INFO @ Mon, 06 Nov 2017 12:16:25: #2.2 Generate R script for model : SRX2804227.10_model.r WARNING @ Mon, 06 Nov 2017 12:16:25: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 06 Nov 2017 12:16:25: #2 You may need to consider one of the other alternative d(s): 96,550 WARNING @ Mon, 06 Nov 2017 12:16:25: #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 12:16:25: #3 Call peaks... INFO @ Mon, 06 Nov 2017 12:16:25: #3 Pre-compute pvalue-qvalue table... WARNING @ Mon, 06 Nov 2017 12:16:25: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 06 Nov 2017 12:16:25: #2 You may need to consider one of the other alternative d(s): 96,550 WARNING @ Mon, 06 Nov 2017 12:16:25: #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 12:16:25: #3 Call peaks... INFO @ Mon, 06 Nov 2017 12:16:25: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Nov 2017 12:17:00: #3 Call peaks for each chromosome... INFO @ Mon, 06 Nov 2017 12:17:10: #3 Call peaks for each chromosome... INFO @ Mon, 06 Nov 2017 12:17:11: #3 Call peaks for each chromosome... INFO @ Mon, 06 Nov 2017 12:17:25: #4 Write output xls file... SRX2804227.05_peaks.xls INFO @ Mon, 06 Nov 2017 12:17:25: #4 Write peak in narrowPeak format file... SRX2804227.05_peaks.narrowPeak INFO @ Mon, 06 Nov 2017 12:17:25: #4 Write summits bed file... SRX2804227.05_summits.bed INFO @ Mon, 06 Nov 2017 12:17:25: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7385 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 06 Nov 2017 12:17:34: #4 Write output xls file... SRX2804227.20_peaks.xls INFO @ Mon, 06 Nov 2017 12:17:34: #4 Write peak in narrowPeak format file... SRX2804227.20_peaks.narrowPeak INFO @ Mon, 06 Nov 2017 12:17:34: #4 Write summits bed file... SRX2804227.20_summits.bed INFO @ Mon, 06 Nov 2017 12:17:34: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2728 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 06 Nov 2017 12:17:35: #4 Write output xls file... SRX2804227.10_peaks.xls INFO @ Mon, 06 Nov 2017 12:17:35: #4 Write peak in narrowPeak format file... SRX2804227.10_peaks.narrowPeak INFO @ Mon, 06 Nov 2017 12:17:35: #4 Write summits bed file... SRX2804227.10_summits.bed INFO @ Mon, 06 Nov 2017 12:17:35: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4559 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。