Job ID = 10175238 sra ファイルのダウンロード中... Completed: 426408K bytes transferred in 21 seconds (163125K 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 24057199 spots for /home/okishinya/chipatlas/results/dm3/SRX2804216/SRR5534644.sra Written 24057199 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: 00:05:44 24057199 reads; of these: 24057199 (100.00%) were unpaired; of these: 12083915 (50.23%) aligned 0 times 9282855 (38.59%) aligned exactly 1 time 2690429 (11.18%) aligned >1 times 49.77% overall alignment rate Time searching: 00:05:44 Overall time: 00:05:44 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 8 files... [bam_rmdupse_core] 2290550 / 11973284 = 0.1913 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 11:52:20: # Command line: callpeak -t SRX2804216.bam -f BAM -g dm -n SRX2804216.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2804216.05 # format = BAM # ChIP-seq file = ['SRX2804216.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 11:52:20: # Command line: callpeak -t SRX2804216.bam -f BAM -g dm -n SRX2804216.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2804216.10 # format = BAM # ChIP-seq file = ['SRX2804216.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 11:52:20: # Command line: callpeak -t SRX2804216.bam -f BAM -g dm -n SRX2804216.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2804216.20 # format = BAM # ChIP-seq file = ['SRX2804216.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 11:52:20: #1 read tag files... INFO @ Mon, 06 Nov 2017 11:52:20: #1 read tag files... INFO @ Mon, 06 Nov 2017 11:52:20: #1 read tag files... INFO @ Mon, 06 Nov 2017 11:52:20: #1 read treatment tags... INFO @ Mon, 06 Nov 2017 11:52:20: #1 read treatment tags... INFO @ Mon, 06 Nov 2017 11:52:20: #1 read treatment tags... INFO @ Mon, 06 Nov 2017 11:52:26: 1000000 INFO @ Mon, 06 Nov 2017 11:52:26: 1000000 INFO @ Mon, 06 Nov 2017 11:52:26: 1000000 INFO @ Mon, 06 Nov 2017 11:52:32: 2000000 INFO @ Mon, 06 Nov 2017 11:52:32: 2000000 INFO @ Mon, 06 Nov 2017 11:52:32: 2000000 INFO @ Mon, 06 Nov 2017 11:52:38: 3000000 INFO @ Mon, 06 Nov 2017 11:52:39: 3000000 INFO @ Mon, 06 Nov 2017 11:52:39: 3000000 INFO @ Mon, 06 Nov 2017 11:52:45: 4000000 INFO @ Mon, 06 Nov 2017 11:52:45: 4000000 INFO @ Mon, 06 Nov 2017 11:52:45: 4000000 INFO @ Mon, 06 Nov 2017 11:52:51: 5000000 INFO @ Mon, 06 Nov 2017 11:52:51: 5000000 INFO @ Mon, 06 Nov 2017 11:52:51: 5000000 INFO @ Mon, 06 Nov 2017 11:52:57: 6000000 INFO @ Mon, 06 Nov 2017 11:52:57: 6000000 INFO @ Mon, 06 Nov 2017 11:52:57: 6000000 INFO @ Mon, 06 Nov 2017 11:53:03: 7000000 INFO @ Mon, 06 Nov 2017 11:53:03: 7000000 INFO @ Mon, 06 Nov 2017 11:53:04: 7000000 INFO @ Mon, 06 Nov 2017 11:53:09: 8000000 INFO @ Mon, 06 Nov 2017 11:53:10: 8000000 INFO @ Mon, 06 Nov 2017 11:53:10: 8000000 INFO @ Mon, 06 Nov 2017 11:53:16: 9000000 INFO @ Mon, 06 Nov 2017 11:53:16: 9000000 INFO @ Mon, 06 Nov 2017 11:53:17: 9000000 INFO @ Mon, 06 Nov 2017 11:53:20: #1 tag size is determined as 51 bps INFO @ Mon, 06 Nov 2017 11:53:20: #1 tag size = 51 INFO @ Mon, 06 Nov 2017 11:53:20: #1 total tags in treatment: 9682734 INFO @ Mon, 06 Nov 2017 11:53:20: #1 user defined the maximum tags... INFO @ Mon, 06 Nov 2017 11:53:20: #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 11:53:20: #1 tags after filtering in treatment: 9682734 INFO @ Mon, 06 Nov 2017 11:53:20: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Nov 2017 11:53:20: #1 finished! INFO @ Mon, 06 Nov 2017 11:53:20: #2 Build Peak Model... INFO @ Mon, 06 Nov 2017 11:53:20: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Nov 2017 11:53:20: #1 tag size is determined as 51 bps INFO @ Mon, 06 Nov 2017 11:53:20: #1 tag size = 51 INFO @ Mon, 06 Nov 2017 11:53:20: #1 total tags in treatment: 9682734 INFO @ Mon, 06 Nov 2017 11:53:20: #1 user defined the maximum tags... INFO @ Mon, 06 Nov 2017 11:53:20: #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 11:53:21: #1 tags after filtering in treatment: 9682734 INFO @ Mon, 06 Nov 2017 11:53:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Nov 2017 11:53:21: #1 finished! INFO @ Mon, 06 Nov 2017 11:53:21: #2 Build Peak Model... INFO @ Mon, 06 Nov 2017 11:53:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Nov 2017 11:53:21: #2 number of paired peaks: 1081 INFO @ Mon, 06 Nov 2017 11:53:21: start model_add_line... INFO @ Mon, 06 Nov 2017 11:53:21: start X-correlation... INFO @ Mon, 06 Nov 2017 11:53:21: end of X-cor INFO @ Mon, 06 Nov 2017 11:53:21: #2 finished! INFO @ Mon, 06 Nov 2017 11:53:21: #2 predicted fragment length is 158 bps INFO @ Mon, 06 Nov 2017 11:53:21: #2 alternative fragment length(s) may be 158 bps INFO @ Mon, 06 Nov 2017 11:53:21: #2.2 Generate R script for model : SRX2804216.10_model.r INFO @ Mon, 06 Nov 2017 11:53:21: #3 Call peaks... INFO @ Mon, 06 Nov 2017 11:53:21: #1 tag size is determined as 51 bps INFO @ Mon, 06 Nov 2017 11:53:21: #1 tag size = 51 INFO @ Mon, 06 Nov 2017 11:53:21: #1 total tags in treatment: 9682734 INFO @ Mon, 06 Nov 2017 11:53:21: #1 user defined the maximum tags... INFO @ Mon, 06 Nov 2017 11:53:21: #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 11:53:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Nov 2017 11:53:21: #1 tags after filtering in treatment: 9682734 INFO @ Mon, 06 Nov 2017 11:53:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Nov 2017 11:53:21: #1 finished! INFO @ Mon, 06 Nov 2017 11:53:21: #2 Build Peak Model... INFO @ Mon, 06 Nov 2017 11:53:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Nov 2017 11:53:21: #2 number of paired peaks: 1081 INFO @ Mon, 06 Nov 2017 11:53:21: start model_add_line... INFO @ Mon, 06 Nov 2017 11:53:22: start X-correlation... INFO @ Mon, 06 Nov 2017 11:53:22: end of X-cor INFO @ Mon, 06 Nov 2017 11:53:22: #2 finished! INFO @ Mon, 06 Nov 2017 11:53:22: #2 predicted fragment length is 158 bps INFO @ Mon, 06 Nov 2017 11:53:22: #2 alternative fragment length(s) may be 158 bps INFO @ Mon, 06 Nov 2017 11:53:22: #2.2 Generate R script for model : SRX2804216.05_model.r INFO @ Mon, 06 Nov 2017 11:53:22: #3 Call peaks... INFO @ Mon, 06 Nov 2017 11:53:22: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Nov 2017 11:53:22: #2 number of paired peaks: 1081 INFO @ Mon, 06 Nov 2017 11:53:22: start model_add_line... INFO @ Mon, 06 Nov 2017 11:53:22: start X-correlation... INFO @ Mon, 06 Nov 2017 11:53:22: end of X-cor INFO @ Mon, 06 Nov 2017 11:53:22: #2 finished! INFO @ Mon, 06 Nov 2017 11:53:22: #2 predicted fragment length is 158 bps INFO @ Mon, 06 Nov 2017 11:53:22: #2 alternative fragment length(s) may be 158 bps INFO @ Mon, 06 Nov 2017 11:53:22: #2.2 Generate R script for model : SRX2804216.20_model.r INFO @ Mon, 06 Nov 2017 11:53:22: #3 Call peaks... INFO @ Mon, 06 Nov 2017 11:53:22: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Nov 2017 11:53:44: #3 Call peaks for each chromosome... INFO @ Mon, 06 Nov 2017 11:53:44: #3 Call peaks for each chromosome... INFO @ Mon, 06 Nov 2017 11:53:46: #3 Call peaks for each chromosome... INFO @ Mon, 06 Nov 2017 11:53:55: #4 Write output xls file... SRX2804216.10_peaks.xls INFO @ Mon, 06 Nov 2017 11:53:55: #4 Write peak in narrowPeak format file... SRX2804216.10_peaks.narrowPeak INFO @ Mon, 06 Nov 2017 11:53:55: #4 Write summits bed file... SRX2804216.10_summits.bed INFO @ Mon, 06 Nov 2017 11:53:55: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4238 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 06 Nov 2017 11:53:56: #4 Write output xls file... SRX2804216.20_peaks.xls INFO @ Mon, 06 Nov 2017 11:53:56: #4 Write peak in narrowPeak format file... SRX2804216.20_peaks.narrowPeak INFO @ Mon, 06 Nov 2017 11:53:56: #4 Write summits bed file... SRX2804216.20_summits.bed INFO @ Mon, 06 Nov 2017 11:53:56: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2875 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Mon, 06 Nov 2017 11:53:57: #4 Write output xls file... SRX2804216.05_peaks.xls INFO @ Mon, 06 Nov 2017 11:53:57: #4 Write peak in narrowPeak format file... SRX2804216.05_peaks.narrowPeak INFO @ Mon, 06 Nov 2017 11:53:57: #4 Write summits bed file... SRX2804216.05_summits.bed INFO @ Mon, 06 Nov 2017 11:53:57: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5984 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。