Job ID = 11597978 sra ファイルのダウンロード中... Completed: 584444K bytes transferred in 14 seconds (328228K 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 24537737 spots for /home/okishinya/chipatlas/results/dm3/SRX4664645/SRR7813072.sra Written 24537737 spots for /home/okishinya/chipatlas/results/dm3/SRX4664645/SRR7813072.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:09:33 24537737 reads; of these: 24537737 (100.00%) were unpaired; of these: 617649 (2.52%) aligned 0 times 17445824 (71.10%) aligned exactly 1 time 6474264 (26.38%) aligned >1 times 97.48% overall alignment rate Time searching: 00:09:34 Overall time: 00:09:34 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] 4541734 / 23920088 = 0.1899 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 @ Wed, 30 Jan 2019 16:54:35: # Command line: callpeak -t SRX4664645.bam -f BAM -g dm -n SRX4664645.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4664645.10 # format = BAM # ChIP-seq file = ['SRX4664645.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 @ Wed, 30 Jan 2019 16:54:35: #1 read tag files... INFO @ Wed, 30 Jan 2019 16:54:35: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 16:54:35: # Command line: callpeak -t SRX4664645.bam -f BAM -g dm -n SRX4664645.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4664645.20 # format = BAM # ChIP-seq file = ['SRX4664645.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 @ Wed, 30 Jan 2019 16:54:35: #1 read tag files... INFO @ Wed, 30 Jan 2019 16:54:35: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 16:54:35: # Command line: callpeak -t SRX4664645.bam -f BAM -g dm -n SRX4664645.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4664645.05 # format = BAM # ChIP-seq file = ['SRX4664645.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 @ Wed, 30 Jan 2019 16:54:35: #1 read tag files... INFO @ Wed, 30 Jan 2019 16:54:35: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 16:54:42: 1000000 INFO @ Wed, 30 Jan 2019 16:54:42: 1000000 INFO @ Wed, 30 Jan 2019 16:54:42: 1000000 INFO @ Wed, 30 Jan 2019 16:54:48: 2000000 INFO @ Wed, 30 Jan 2019 16:54:48: 2000000 INFO @ Wed, 30 Jan 2019 16:54:48: 2000000 INFO @ Wed, 30 Jan 2019 16:54:54: 3000000 INFO @ Wed, 30 Jan 2019 16:54:54: 3000000 INFO @ Wed, 30 Jan 2019 16:54:55: 3000000 INFO @ Wed, 30 Jan 2019 16:55:00: 4000000 INFO @ Wed, 30 Jan 2019 16:55:01: 4000000 INFO @ Wed, 30 Jan 2019 16:55:01: 4000000 INFO @ Wed, 30 Jan 2019 16:55:06: 5000000 INFO @ Wed, 30 Jan 2019 16:55:07: 5000000 INFO @ Wed, 30 Jan 2019 16:55:07: 5000000 INFO @ Wed, 30 Jan 2019 16:55:13: 6000000 INFO @ Wed, 30 Jan 2019 16:55:13: 6000000 INFO @ Wed, 30 Jan 2019 16:55:14: 6000000 INFO @ Wed, 30 Jan 2019 16:55:19: 7000000 INFO @ Wed, 30 Jan 2019 16:55:20: 7000000 INFO @ Wed, 30 Jan 2019 16:55:20: 7000000 INFO @ Wed, 30 Jan 2019 16:55:25: 8000000 INFO @ Wed, 30 Jan 2019 16:55:26: 8000000 INFO @ Wed, 30 Jan 2019 16:55:26: 8000000 INFO @ Wed, 30 Jan 2019 16:55:32: 9000000 INFO @ Wed, 30 Jan 2019 16:55:33: 9000000 INFO @ Wed, 30 Jan 2019 16:55:33: 9000000 INFO @ Wed, 30 Jan 2019 16:55:38: 10000000 INFO @ Wed, 30 Jan 2019 16:55:39: 10000000 INFO @ Wed, 30 Jan 2019 16:55:39: 10000000 INFO @ Wed, 30 Jan 2019 16:55:45: 11000000 INFO @ Wed, 30 Jan 2019 16:55:45: 11000000 INFO @ Wed, 30 Jan 2019 16:55:46: 11000000 INFO @ Wed, 30 Jan 2019 16:55:51: 12000000 INFO @ Wed, 30 Jan 2019 16:55:52: 12000000 INFO @ Wed, 30 Jan 2019 16:55:52: 12000000 INFO @ Wed, 30 Jan 2019 16:55:57: 13000000 INFO @ Wed, 30 Jan 2019 16:55:58: 13000000 INFO @ Wed, 30 Jan 2019 16:55:59: 13000000 INFO @ Wed, 30 Jan 2019 16:56:04: 14000000 INFO @ Wed, 30 Jan 2019 16:56:04: 14000000 INFO @ Wed, 30 Jan 2019 16:56:05: 14000000 INFO @ Wed, 30 Jan 2019 16:56:10: 15000000 INFO @ Wed, 30 Jan 2019 16:56:11: 15000000 INFO @ Wed, 30 Jan 2019 16:56:12: 15000000 INFO @ Wed, 30 Jan 2019 16:56:16: 16000000 INFO @ Wed, 30 Jan 2019 16:56:17: 16000000 INFO @ Wed, 30 Jan 2019 16:56:18: 16000000 INFO @ Wed, 30 Jan 2019 16:56:23: 17000000 INFO @ Wed, 30 Jan 2019 16:56:23: 17000000 INFO @ Wed, 30 Jan 2019 16:56:25: 17000000 INFO @ Wed, 30 Jan 2019 16:56:29: 18000000 INFO @ Wed, 30 Jan 2019 16:56:30: 18000000 INFO @ Wed, 30 Jan 2019 16:56:31: 18000000 INFO @ Wed, 30 Jan 2019 16:56:36: 19000000 INFO @ Wed, 30 Jan 2019 16:56:36: 19000000 INFO @ Wed, 30 Jan 2019 16:56:38: 19000000 INFO @ Wed, 30 Jan 2019 16:56:38: #1 tag size is determined as 50 bps INFO @ Wed, 30 Jan 2019 16:56:38: #1 tag size = 50 INFO @ Wed, 30 Jan 2019 16:56:38: #1 total tags in treatment: 19378354 INFO @ Wed, 30 Jan 2019 16:56:38: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 16:56:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 30 Jan 2019 16:56:39: #1 tags after filtering in treatment: 19378354 INFO @ Wed, 30 Jan 2019 16:56:39: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 16:56:39: #1 finished! INFO @ Wed, 30 Jan 2019 16:56:39: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 16:56:39: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 16:56:39: #1 tag size is determined as 50 bps INFO @ Wed, 30 Jan 2019 16:56:39: #1 tag size = 50 INFO @ Wed, 30 Jan 2019 16:56:39: #1 total tags in treatment: 19378354 INFO @ Wed, 30 Jan 2019 16:56:39: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 16:56:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 30 Jan 2019 16:56:39: #1 tags after filtering in treatment: 19378354 INFO @ Wed, 30 Jan 2019 16:56:39: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 16:56:39: #1 finished! INFO @ Wed, 30 Jan 2019 16:56:39: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 16:56:39: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 16:56:40: #1 tag size is determined as 50 bps INFO @ Wed, 30 Jan 2019 16:56:40: #1 tag size = 50 INFO @ Wed, 30 Jan 2019 16:56:40: #1 total tags in treatment: 19378354 INFO @ Wed, 30 Jan 2019 16:56:40: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 16:56:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 30 Jan 2019 16:56:40: #2 number of paired peaks: 1475 INFO @ Wed, 30 Jan 2019 16:56:40: start model_add_line... INFO @ Wed, 30 Jan 2019 16:56:40: start X-correlation... INFO @ Wed, 30 Jan 2019 16:56:40: end of X-cor INFO @ Wed, 30 Jan 2019 16:56:40: #2 finished! INFO @ Wed, 30 Jan 2019 16:56:40: #2 predicted fragment length is 130 bps INFO @ Wed, 30 Jan 2019 16:56:40: #2 alternative fragment length(s) may be 130 bps INFO @ Wed, 30 Jan 2019 16:56:40: #2.2 Generate R script for model : SRX4664645.20_model.r INFO @ Wed, 30 Jan 2019 16:56:40: #3 Call peaks... INFO @ Wed, 30 Jan 2019 16:56:40: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 16:56:41: #2 number of paired peaks: 1475 INFO @ Wed, 30 Jan 2019 16:56:41: start model_add_line... INFO @ Wed, 30 Jan 2019 16:56:41: #1 tags after filtering in treatment: 19378354 INFO @ Wed, 30 Jan 2019 16:56:41: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 16:56:41: #1 finished! INFO @ Wed, 30 Jan 2019 16:56:41: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 16:56:41: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 16:56:41: start X-correlation... INFO @ Wed, 30 Jan 2019 16:56:41: end of X-cor INFO @ Wed, 30 Jan 2019 16:56:41: #2 finished! INFO @ Wed, 30 Jan 2019 16:56:41: #2 predicted fragment length is 130 bps INFO @ Wed, 30 Jan 2019 16:56:41: #2 alternative fragment length(s) may be 130 bps INFO @ Wed, 30 Jan 2019 16:56:41: #2.2 Generate R script for model : SRX4664645.10_model.r INFO @ Wed, 30 Jan 2019 16:56:41: #3 Call peaks... INFO @ Wed, 30 Jan 2019 16:56:41: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 16:56:42: #2 number of paired peaks: 1475 INFO @ Wed, 30 Jan 2019 16:56:42: start model_add_line... INFO @ Wed, 30 Jan 2019 16:56:42: start X-correlation... INFO @ Wed, 30 Jan 2019 16:56:42: end of X-cor INFO @ Wed, 30 Jan 2019 16:56:42: #2 finished! INFO @ Wed, 30 Jan 2019 16:56:42: #2 predicted fragment length is 130 bps INFO @ Wed, 30 Jan 2019 16:56:42: #2 alternative fragment length(s) may be 130 bps INFO @ Wed, 30 Jan 2019 16:56:42: #2.2 Generate R script for model : SRX4664645.05_model.r INFO @ Wed, 30 Jan 2019 16:56:42: #3 Call peaks... INFO @ Wed, 30 Jan 2019 16:56:42: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 16:57:24: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 16:57:25: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 16:57:26: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 16:57:47: #4 Write output xls file... SRX4664645.20_peaks.xls INFO @ Wed, 30 Jan 2019 16:57:47: #4 Write peak in narrowPeak format file... SRX4664645.20_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 16:57:47: #4 Write summits bed file... SRX4664645.20_summits.bed INFO @ Wed, 30 Jan 2019 16:57:47: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5254 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Wed, 30 Jan 2019 16:57:49: #4 Write output xls file... SRX4664645.10_peaks.xls INFO @ Wed, 30 Jan 2019 16:57:49: #4 Write peak in narrowPeak format file... SRX4664645.10_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 16:57:49: #4 Write summits bed file... SRX4664645.10_summits.bed INFO @ Wed, 30 Jan 2019 16:57:50: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8192 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Wed, 30 Jan 2019 16:57:51: #4 Write output xls file... SRX4664645.05_peaks.xls INFO @ Wed, 30 Jan 2019 16:57:51: #4 Write peak in narrowPeak format file... SRX4664645.05_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 16:57:51: #4 Write summits bed file... SRX4664645.05_summits.bed INFO @ Wed, 30 Jan 2019 16:57:51: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (11142 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。