Job ID = 11171383 sra ファイルのダウンロード中... Completed: 493694K bytes transferred in 7 seconds (546937K 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... Read 36923199 spots for /home/okishinya/chipatlas/results/dm3/SRX4315054/SRR7444515.sra Written 36923199 spots for /home/okishinya/chipatlas/results/dm3/SRX4315054/SRR7444515.sra 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: 00:10:22 36923199 reads; of these: 36923199 (100.00%) were unpaired; of these: 2735 (0.01%) aligned 0 times 34064888 (92.26%) aligned exactly 1 time 2855576 (7.73%) aligned >1 times 99.99% overall alignment rate Time searching: 00:10:22 Overall time: 00:10:22 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 16 files... [bam_rmdupse_core] 9399756 / 36920464 = 0.2546 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, 08 Sep 2018 14:27:16: # Command line: callpeak -t SRX4315054.bam -f BAM -g dm -n SRX4315054.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4315054.10 # format = BAM # ChIP-seq file = ['SRX4315054.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 @ Sat, 08 Sep 2018 14:27:16: #1 read tag files... INFO @ Sat, 08 Sep 2018 14:27:16: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 14:27:16: # Command line: callpeak -t SRX4315054.bam -f BAM -g dm -n SRX4315054.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4315054.05 # format = BAM # ChIP-seq file = ['SRX4315054.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 @ Sat, 08 Sep 2018 14:27:16: #1 read tag files... INFO @ Sat, 08 Sep 2018 14:27:16: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 14:27:16: # Command line: callpeak -t SRX4315054.bam -f BAM -g dm -n SRX4315054.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4315054.20 # format = BAM # ChIP-seq file = ['SRX4315054.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 @ Sat, 08 Sep 2018 14:27:16: #1 read tag files... INFO @ Sat, 08 Sep 2018 14:27:16: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 14:27:23: 1000000 INFO @ Sat, 08 Sep 2018 14:27:24: 1000000 INFO @ Sat, 08 Sep 2018 14:27:24: 1000000 INFO @ Sat, 08 Sep 2018 14:27:30: 2000000 INFO @ Sat, 08 Sep 2018 14:27:32: 2000000 INFO @ Sat, 08 Sep 2018 14:27:32: 2000000 INFO @ Sat, 08 Sep 2018 14:27:37: 3000000 INFO @ Sat, 08 Sep 2018 14:27:40: 3000000 INFO @ Sat, 08 Sep 2018 14:27:40: 3000000 INFO @ Sat, 08 Sep 2018 14:27:44: 4000000 INFO @ Sat, 08 Sep 2018 14:27:47: 4000000 INFO @ Sat, 08 Sep 2018 14:27:47: 4000000 INFO @ Sat, 08 Sep 2018 14:27:51: 5000000 INFO @ Sat, 08 Sep 2018 14:27:55: 5000000 INFO @ Sat, 08 Sep 2018 14:27:55: 5000000 INFO @ Sat, 08 Sep 2018 14:27:58: 6000000 INFO @ Sat, 08 Sep 2018 14:28:03: 6000000 INFO @ Sat, 08 Sep 2018 14:28:03: 6000000 INFO @ Sat, 08 Sep 2018 14:28:05: 7000000 INFO @ Sat, 08 Sep 2018 14:28:10: 7000000 INFO @ Sat, 08 Sep 2018 14:28:10: 7000000 INFO @ Sat, 08 Sep 2018 14:28:11: 8000000 INFO @ Sat, 08 Sep 2018 14:28:18: 8000000 INFO @ Sat, 08 Sep 2018 14:28:18: 8000000 INFO @ Sat, 08 Sep 2018 14:28:18: 9000000 INFO @ Sat, 08 Sep 2018 14:28:25: 10000000 INFO @ Sat, 08 Sep 2018 14:28:26: 9000000 INFO @ Sat, 08 Sep 2018 14:28:26: 9000000 INFO @ Sat, 08 Sep 2018 14:28:32: 11000000 INFO @ Sat, 08 Sep 2018 14:28:34: 10000000 INFO @ Sat, 08 Sep 2018 14:28:34: 10000000 INFO @ Sat, 08 Sep 2018 14:28:39: 12000000 INFO @ Sat, 08 Sep 2018 14:28:41: 11000000 INFO @ Sat, 08 Sep 2018 14:28:41: 11000000 INFO @ Sat, 08 Sep 2018 14:28:46: 13000000 INFO @ Sat, 08 Sep 2018 14:28:49: 12000000 INFO @ Sat, 08 Sep 2018 14:28:49: 12000000 INFO @ Sat, 08 Sep 2018 14:28:53: 14000000 INFO @ Sat, 08 Sep 2018 14:28:57: 13000000 INFO @ Sat, 08 Sep 2018 14:28:57: 13000000 INFO @ Sat, 08 Sep 2018 14:28:59: 15000000 INFO @ Sat, 08 Sep 2018 14:29:04: 14000000 INFO @ Sat, 08 Sep 2018 14:29:04: 14000000 INFO @ Sat, 08 Sep 2018 14:29:06: 16000000 INFO @ Sat, 08 Sep 2018 14:29:12: 15000000 INFO @ Sat, 08 Sep 2018 14:29:12: 15000000 INFO @ Sat, 08 Sep 2018 14:29:13: 17000000 INFO @ Sat, 08 Sep 2018 14:29:19: 16000000 INFO @ Sat, 08 Sep 2018 14:29:19: 16000000 INFO @ Sat, 08 Sep 2018 14:29:20: 18000000 INFO @ Sat, 08 Sep 2018 14:29:27: 19000000 INFO @ Sat, 08 Sep 2018 14:29:27: 17000000 INFO @ Sat, 08 Sep 2018 14:29:27: 17000000 INFO @ Sat, 08 Sep 2018 14:29:33: 20000000 INFO @ Sat, 08 Sep 2018 14:29:35: 18000000 INFO @ Sat, 08 Sep 2018 14:29:35: 18000000 INFO @ Sat, 08 Sep 2018 14:29:40: 21000000 INFO @ Sat, 08 Sep 2018 14:29:42: 19000000 INFO @ Sat, 08 Sep 2018 14:29:42: 19000000 INFO @ Sat, 08 Sep 2018 14:29:47: 22000000 INFO @ Sat, 08 Sep 2018 14:29:50: 20000000 INFO @ Sat, 08 Sep 2018 14:29:50: 20000000 INFO @ Sat, 08 Sep 2018 14:29:54: 23000000 INFO @ Sat, 08 Sep 2018 14:29:58: 21000000 INFO @ Sat, 08 Sep 2018 14:29:58: 21000000 INFO @ Sat, 08 Sep 2018 14:30:01: 24000000 INFO @ Sat, 08 Sep 2018 14:30:06: 22000000 INFO @ Sat, 08 Sep 2018 14:30:06: 22000000 INFO @ Sat, 08 Sep 2018 14:30:08: 25000000 INFO @ Sat, 08 Sep 2018 14:30:13: 23000000 INFO @ Sat, 08 Sep 2018 14:30:13: 23000000 INFO @ Sat, 08 Sep 2018 14:30:15: 26000000 INFO @ Sat, 08 Sep 2018 14:30:21: 24000000 INFO @ Sat, 08 Sep 2018 14:30:21: 24000000 INFO @ Sat, 08 Sep 2018 14:30:22: 27000000 INFO @ Sat, 08 Sep 2018 14:30:25: #1 tag size is determined as 73 bps INFO @ Sat, 08 Sep 2018 14:30:25: #1 tag size = 73 INFO @ Sat, 08 Sep 2018 14:30:25: #1 total tags in treatment: 27520708 INFO @ Sat, 08 Sep 2018 14:30:25: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 14:30:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 14:30:26: #1 tags after filtering in treatment: 27520708 INFO @ Sat, 08 Sep 2018 14:30:26: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 14:30:26: #1 finished! INFO @ Sat, 08 Sep 2018 14:30:26: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 14:30:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 14:30:28: #2 number of paired peaks: 3361 INFO @ Sat, 08 Sep 2018 14:30:28: start model_add_line... INFO @ Sat, 08 Sep 2018 14:30:28: 25000000 INFO @ Sat, 08 Sep 2018 14:30:28: 25000000 INFO @ Sat, 08 Sep 2018 14:30:29: start X-correlation... INFO @ Sat, 08 Sep 2018 14:30:29: end of X-cor INFO @ Sat, 08 Sep 2018 14:30:29: #2 finished! INFO @ Sat, 08 Sep 2018 14:30:29: #2 predicted fragment length is 119 bps INFO @ Sat, 08 Sep 2018 14:30:29: #2 alternative fragment length(s) may be 119 bps INFO @ Sat, 08 Sep 2018 14:30:29: #2.2 Generate R script for model : SRX4315054.10_model.r WARNING @ Sat, 08 Sep 2018 14:30:29: #2 Since the d (119) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 14:30:29: #2 You may need to consider one of the other alternative d(s): 119 WARNING @ Sat, 08 Sep 2018 14:30:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 14:30:29: #3 Call peaks... INFO @ Sat, 08 Sep 2018 14:30:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 14:30:36: 26000000 INFO @ Sat, 08 Sep 2018 14:30:36: 26000000 INFO @ Sat, 08 Sep 2018 14:30:43: 27000000 INFO @ Sat, 08 Sep 2018 14:30:43: 27000000 INFO @ Sat, 08 Sep 2018 14:30:47: #1 tag size is determined as 73 bps INFO @ Sat, 08 Sep 2018 14:30:47: #1 tag size = 73 INFO @ Sat, 08 Sep 2018 14:30:47: #1 total tags in treatment: 27520708 INFO @ Sat, 08 Sep 2018 14:30:47: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 14:30:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 14:30:47: #1 tag size is determined as 73 bps INFO @ Sat, 08 Sep 2018 14:30:47: #1 tag size = 73 INFO @ Sat, 08 Sep 2018 14:30:47: #1 total tags in treatment: 27520708 INFO @ Sat, 08 Sep 2018 14:30:47: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 14:30:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 14:30:48: #1 tags after filtering in treatment: 27520708 INFO @ Sat, 08 Sep 2018 14:30:48: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 14:30:48: #1 finished! INFO @ Sat, 08 Sep 2018 14:30:48: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 14:30:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 14:30:48: #1 tags after filtering in treatment: 27520708 INFO @ Sat, 08 Sep 2018 14:30:48: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 14:30:48: #1 finished! INFO @ Sat, 08 Sep 2018 14:30:48: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 14:30:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 14:30:50: #2 number of paired peaks: 3361 INFO @ Sat, 08 Sep 2018 14:30:50: start model_add_line... INFO @ Sat, 08 Sep 2018 14:30:50: #2 number of paired peaks: 3361 INFO @ Sat, 08 Sep 2018 14:30:50: start model_add_line... INFO @ Sat, 08 Sep 2018 14:30:50: start X-correlation... INFO @ Sat, 08 Sep 2018 14:30:50: end of X-cor INFO @ Sat, 08 Sep 2018 14:30:50: #2 finished! INFO @ Sat, 08 Sep 2018 14:30:50: #2 predicted fragment length is 119 bps INFO @ Sat, 08 Sep 2018 14:30:50: #2 alternative fragment length(s) may be 119 bps INFO @ Sat, 08 Sep 2018 14:30:50: #2.2 Generate R script for model : SRX4315054.05_model.r WARNING @ Sat, 08 Sep 2018 14:30:50: #2 Since the d (119) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 14:30:50: #2 You may need to consider one of the other alternative d(s): 119 WARNING @ Sat, 08 Sep 2018 14:30:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 14:30:50: #3 Call peaks... INFO @ Sat, 08 Sep 2018 14:30:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 14:30:51: start X-correlation... INFO @ Sat, 08 Sep 2018 14:30:51: end of X-cor INFO @ Sat, 08 Sep 2018 14:30:51: #2 finished! INFO @ Sat, 08 Sep 2018 14:30:51: #2 predicted fragment length is 119 bps INFO @ Sat, 08 Sep 2018 14:30:51: #2 alternative fragment length(s) may be 119 bps INFO @ Sat, 08 Sep 2018 14:30:51: #2.2 Generate R script for model : SRX4315054.20_model.r WARNING @ Sat, 08 Sep 2018 14:30:51: #2 Since the d (119) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 14:30:51: #2 You may need to consider one of the other alternative d(s): 119 WARNING @ Sat, 08 Sep 2018 14:30:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 14:30:51: #3 Call peaks... INFO @ Sat, 08 Sep 2018 14:30:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 14:31:32: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 14:31:53: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 14:31:55: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 14:32:02: #4 Write output xls file... SRX4315054.10_peaks.xls INFO @ Sat, 08 Sep 2018 14:32:02: #4 Write peak in narrowPeak format file... SRX4315054.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 14:32:02: #4 Write summits bed file... SRX4315054.10_summits.bed INFO @ Sat, 08 Sep 2018 14:32:02: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (12034 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 14:32:24: #4 Write output xls file... SRX4315054.20_peaks.xls INFO @ Sat, 08 Sep 2018 14:32:24: #4 Write peak in narrowPeak format file... SRX4315054.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 14:32:24: #4 Write summits bed file... SRX4315054.20_summits.bed INFO @ Sat, 08 Sep 2018 14:32:24: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (8745 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 14:32:25: #4 Write output xls file... SRX4315054.05_peaks.xls INFO @ Sat, 08 Sep 2018 14:32:25: #4 Write peak in narrowPeak format file... SRX4315054.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 14:32:25: #4 Write summits bed file... SRX4315054.05_summits.bed INFO @ Sat, 08 Sep 2018 14:32:25: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (14752 records, 4 fields): 18 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。