Job ID = 9157960 sra ファイルのダウンロード中... Completed: 539623K bytes transferred in 14 seconds (304483K bits/sec), in 1 file, 2 directories. 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 31600235 spots for /home/okishinya/chipatlas/results/dm3/SRX2734367/SRR5445344.sra Written 31600235 spots total 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: 00:08:00 31600235 reads; of these: 31600235 (100.00%) were unpaired; of these: 3250924 (10.29%) aligned 0 times 24837962 (78.60%) aligned exactly 1 time 3511349 (11.11%) aligned >1 times 89.71% overall alignment rate Time searching: 00:08:00 Overall time: 00:08:00 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] 9121726 / 28349311 = 0.3218 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 @ Tue, 27 Jun 2017 14:28:19: # Command line: callpeak -t SRX2734367.bam -f BAM -g dm -n SRX2734367.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2734367.20 # format = BAM # ChIP-seq file = ['SRX2734367.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 @ Tue, 27 Jun 2017 14:28:19: #1 read tag files... INFO @ Tue, 27 Jun 2017 14:28:19: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 14:28:19: # Command line: callpeak -t SRX2734367.bam -f BAM -g dm -n SRX2734367.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2734367.05 # format = BAM # ChIP-seq file = ['SRX2734367.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 @ Tue, 27 Jun 2017 14:28:19: #1 read tag files... INFO @ Tue, 27 Jun 2017 14:28:19: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 14:28:19: # Command line: callpeak -t SRX2734367.bam -f BAM -g dm -n SRX2734367.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2734367.10 # format = BAM # ChIP-seq file = ['SRX2734367.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 @ Tue, 27 Jun 2017 14:28:19: #1 read tag files... INFO @ Tue, 27 Jun 2017 14:28:19: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 14:28:26: 1000000 INFO @ Tue, 27 Jun 2017 14:28:26: 1000000 INFO @ Tue, 27 Jun 2017 14:28:27: 1000000 INFO @ Tue, 27 Jun 2017 14:28:34: 2000000 INFO @ Tue, 27 Jun 2017 14:28:34: 2000000 INFO @ Tue, 27 Jun 2017 14:28:35: 2000000 INFO @ Tue, 27 Jun 2017 14:28:42: 3000000 INFO @ Tue, 27 Jun 2017 14:28:42: 3000000 INFO @ Tue, 27 Jun 2017 14:28:42: 3000000 INFO @ Tue, 27 Jun 2017 14:28:49: 4000000 INFO @ Tue, 27 Jun 2017 14:28:49: 4000000 INFO @ Tue, 27 Jun 2017 14:28:50: 4000000 INFO @ Tue, 27 Jun 2017 14:28:56: 5000000 INFO @ Tue, 27 Jun 2017 14:28:56: 5000000 INFO @ Tue, 27 Jun 2017 14:28:58: 5000000 INFO @ Tue, 27 Jun 2017 14:29:04: 6000000 INFO @ Tue, 27 Jun 2017 14:29:04: 6000000 INFO @ Tue, 27 Jun 2017 14:29:06: 6000000 INFO @ Tue, 27 Jun 2017 14:29:11: 7000000 INFO @ Tue, 27 Jun 2017 14:29:11: 7000000 INFO @ Tue, 27 Jun 2017 14:29:14: 7000000 INFO @ Tue, 27 Jun 2017 14:29:19: 8000000 INFO @ Tue, 27 Jun 2017 14:29:19: 8000000 INFO @ Tue, 27 Jun 2017 14:29:21: 8000000 INFO @ Tue, 27 Jun 2017 14:29:26: 9000000 INFO @ Tue, 27 Jun 2017 14:29:26: 9000000 INFO @ Tue, 27 Jun 2017 14:29:29: 9000000 INFO @ Tue, 27 Jun 2017 14:29:33: 10000000 INFO @ Tue, 27 Jun 2017 14:29:33: 10000000 INFO @ Tue, 27 Jun 2017 14:29:37: 10000000 INFO @ Tue, 27 Jun 2017 14:29:41: 11000000 INFO @ Tue, 27 Jun 2017 14:29:41: 11000000 INFO @ Tue, 27 Jun 2017 14:29:45: 11000000 INFO @ Tue, 27 Jun 2017 14:29:48: 12000000 INFO @ Tue, 27 Jun 2017 14:29:48: 12000000 INFO @ Tue, 27 Jun 2017 14:29:53: 12000000 INFO @ Tue, 27 Jun 2017 14:29:55: 13000000 INFO @ Tue, 27 Jun 2017 14:29:55: 13000000 INFO @ Tue, 27 Jun 2017 14:30:01: 13000000 INFO @ Tue, 27 Jun 2017 14:30:03: 14000000 INFO @ Tue, 27 Jun 2017 14:30:03: 14000000 INFO @ Tue, 27 Jun 2017 14:30:08: 14000000 INFO @ Tue, 27 Jun 2017 14:30:10: 15000000 INFO @ Tue, 27 Jun 2017 14:30:10: 15000000 INFO @ Tue, 27 Jun 2017 14:30:16: 15000000 INFO @ Tue, 27 Jun 2017 14:30:17: 16000000 INFO @ Tue, 27 Jun 2017 14:30:17: 16000000 INFO @ Tue, 27 Jun 2017 14:30:24: 16000000 INFO @ Tue, 27 Jun 2017 14:30:25: 17000000 INFO @ Tue, 27 Jun 2017 14:30:25: 17000000 INFO @ Tue, 27 Jun 2017 14:30:32: 17000000 INFO @ Tue, 27 Jun 2017 14:30:32: 18000000 INFO @ Tue, 27 Jun 2017 14:30:32: 18000000 INFO @ Tue, 27 Jun 2017 14:30:39: 18000000 INFO @ Tue, 27 Jun 2017 14:30:39: 19000000 INFO @ Tue, 27 Jun 2017 14:30:39: 19000000 INFO @ Tue, 27 Jun 2017 14:30:41: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 14:30:41: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 14:30:41: #1 total tags in treatment: 19227585 INFO @ Tue, 27 Jun 2017 14:30:41: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 14:30:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 14:30:41: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 14:30:41: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 14:30:41: #1 total tags in treatment: 19227585 INFO @ Tue, 27 Jun 2017 14:30:41: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 14:30:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 14:30:41: #1 tags after filtering in treatment: 19227585 INFO @ Tue, 27 Jun 2017 14:30:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 14:30:41: #1 finished! INFO @ Tue, 27 Jun 2017 14:30:41: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 14:30:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 14:30:41: #1 tags after filtering in treatment: 19227585 INFO @ Tue, 27 Jun 2017 14:30:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 14:30:41: #1 finished! INFO @ Tue, 27 Jun 2017 14:30:41: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 14:30:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 14:30:43: #2 number of paired peaks: 2890 INFO @ Tue, 27 Jun 2017 14:30:43: start model_add_line... INFO @ Tue, 27 Jun 2017 14:30:43: #2 number of paired peaks: 2890 INFO @ Tue, 27 Jun 2017 14:30:43: start model_add_line... INFO @ Tue, 27 Jun 2017 14:30:43: start X-correlation... INFO @ Tue, 27 Jun 2017 14:30:43: end of X-cor INFO @ Tue, 27 Jun 2017 14:30:43: #2 finished! INFO @ Tue, 27 Jun 2017 14:30:43: #2 predicted fragment length is 202 bps INFO @ Tue, 27 Jun 2017 14:30:43: #2 alternative fragment length(s) may be 202 bps INFO @ Tue, 27 Jun 2017 14:30:43: #2.2 Generate R script for model : SRX2734367.20_model.r INFO @ Tue, 27 Jun 2017 14:30:43: #3 Call peaks... INFO @ Tue, 27 Jun 2017 14:30:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 14:30:43: start X-correlation... INFO @ Tue, 27 Jun 2017 14:30:43: end of X-cor INFO @ Tue, 27 Jun 2017 14:30:43: #2 finished! INFO @ Tue, 27 Jun 2017 14:30:43: #2 predicted fragment length is 202 bps INFO @ Tue, 27 Jun 2017 14:30:43: #2 alternative fragment length(s) may be 202 bps INFO @ Tue, 27 Jun 2017 14:30:43: #2.2 Generate R script for model : SRX2734367.05_model.r INFO @ Tue, 27 Jun 2017 14:30:43: #3 Call peaks... INFO @ Tue, 27 Jun 2017 14:30:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 14:30:46: 19000000 INFO @ Tue, 27 Jun 2017 14:30:47: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 14:30:47: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 14:30:47: #1 total tags in treatment: 19227585 INFO @ Tue, 27 Jun 2017 14:30:47: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 14:30:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 14:30:48: #1 tags after filtering in treatment: 19227585 INFO @ Tue, 27 Jun 2017 14:30:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 14:30:48: #1 finished! INFO @ Tue, 27 Jun 2017 14:30:48: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 14:30:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 14:30:49: #2 number of paired peaks: 2890 INFO @ Tue, 27 Jun 2017 14:30:49: start model_add_line... INFO @ Tue, 27 Jun 2017 14:30:50: start X-correlation... INFO @ Tue, 27 Jun 2017 14:30:50: end of X-cor INFO @ Tue, 27 Jun 2017 14:30:50: #2 finished! INFO @ Tue, 27 Jun 2017 14:30:50: #2 predicted fragment length is 202 bps INFO @ Tue, 27 Jun 2017 14:30:50: #2 alternative fragment length(s) may be 202 bps INFO @ Tue, 27 Jun 2017 14:30:50: #2.2 Generate R script for model : SRX2734367.10_model.r INFO @ Tue, 27 Jun 2017 14:30:50: #3 Call peaks... INFO @ Tue, 27 Jun 2017 14:30:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 14:31:44: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 14:31:44: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 14:31:47: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 14:32:10: #4 Write output xls file... SRX2734367.20_peaks.xls INFO @ Tue, 27 Jun 2017 14:32:10: #4 Write peak in narrowPeak format file... SRX2734367.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 14:32:10: #4 Write summits bed file... SRX2734367.20_summits.bed INFO @ Tue, 27 Jun 2017 14:32:10: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4809 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 14:32:11: #4 Write output xls file... SRX2734367.10_peaks.xls INFO @ Tue, 27 Jun 2017 14:32:11: #4 Write peak in narrowPeak format file... SRX2734367.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 14:32:11: #4 Write summits bed file... SRX2734367.10_summits.bed INFO @ Tue, 27 Jun 2017 14:32:11: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (6225 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 14:32:12: #4 Write output xls file... SRX2734367.05_peaks.xls INFO @ Tue, 27 Jun 2017 14:32:12: #4 Write peak in narrowPeak format file... SRX2734367.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 14:32:12: #4 Write summits bed file... SRX2734367.05_summits.bed INFO @ Tue, 27 Jun 2017 14:32:12: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7331 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。