Job ID = 10175223 sra ファイルのダウンロード中... Completed: 539427K bytes transferred in 8 seconds (505885K 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 17876925 spots for /home/okishinya/chipatlas/results/dm3/SRX2458926/SRR5140275.sra Written 17876925 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: 00:07:17 17876925 reads; of these: 17876925 (100.00%) were unpaired; of these: 1225017 (6.85%) aligned 0 times 11539242 (64.55%) aligned exactly 1 time 5112666 (28.60%) aligned >1 times 93.15% overall alignment rate Time searching: 00:07:17 Overall time: 00:07:17 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] 2713496 / 16651908 = 0.1630 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 11:54:07: # Command line: callpeak -t SRX2458926.bam -f BAM -g dm -n SRX2458926.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2458926.10 # format = BAM # ChIP-seq file = ['SRX2458926.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 11:54:07: #1 read tag files... INFO @ Mon, 06 Nov 2017 11:54:07: #1 read treatment tags... INFO @ Mon, 06 Nov 2017 11:54:07: # Command line: callpeak -t SRX2458926.bam -f BAM -g dm -n SRX2458926.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2458926.05 # format = BAM # ChIP-seq file = ['SRX2458926.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 11:54:07: #1 read tag files... INFO @ Mon, 06 Nov 2017 11:54:07: # Command line: callpeak -t SRX2458926.bam -f BAM -g dm -n SRX2458926.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2458926.20 # format = BAM # ChIP-seq file = ['SRX2458926.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 11:54:07: #1 read treatment tags... INFO @ Mon, 06 Nov 2017 11:54:07: #1 read tag files... INFO @ Mon, 06 Nov 2017 11:54:07: #1 read treatment tags... INFO @ Mon, 06 Nov 2017 11:54:14: 1000000 INFO @ Mon, 06 Nov 2017 11:54:14: 1000000 INFO @ Mon, 06 Nov 2017 11:54:14: 1000000 INFO @ Mon, 06 Nov 2017 11:54:21: 2000000 INFO @ Mon, 06 Nov 2017 11:54:21: 2000000 INFO @ Mon, 06 Nov 2017 11:54:22: 2000000 INFO @ Mon, 06 Nov 2017 11:54:28: 3000000 INFO @ Mon, 06 Nov 2017 11:54:28: 3000000 INFO @ Mon, 06 Nov 2017 11:54:30: 3000000 INFO @ Mon, 06 Nov 2017 11:54:35: 4000000 INFO @ Mon, 06 Nov 2017 11:54:36: 4000000 INFO @ Mon, 06 Nov 2017 11:54:37: 4000000 INFO @ Mon, 06 Nov 2017 11:54:42: 5000000 INFO @ Mon, 06 Nov 2017 11:54:43: 5000000 INFO @ Mon, 06 Nov 2017 11:54:45: 5000000 INFO @ Mon, 06 Nov 2017 11:54:49: 6000000 INFO @ Mon, 06 Nov 2017 11:54:50: 6000000 INFO @ Mon, 06 Nov 2017 11:54:52: 6000000 INFO @ Mon, 06 Nov 2017 11:54:56: 7000000 INFO @ Mon, 06 Nov 2017 11:54:56: 7000000 INFO @ Mon, 06 Nov 2017 11:54:58: 7000000 INFO @ Mon, 06 Nov 2017 11:55:03: 8000000 INFO @ Mon, 06 Nov 2017 11:55:03: 8000000 INFO @ Mon, 06 Nov 2017 11:55:05: 8000000 INFO @ Mon, 06 Nov 2017 11:55:10: 9000000 INFO @ Mon, 06 Nov 2017 11:55:11: 9000000 INFO @ Mon, 06 Nov 2017 11:55:13: 9000000 INFO @ Mon, 06 Nov 2017 11:55:18: 10000000 INFO @ Mon, 06 Nov 2017 11:55:19: 10000000 INFO @ Mon, 06 Nov 2017 11:55:22: 10000000 INFO @ Mon, 06 Nov 2017 11:55:26: 11000000 INFO @ Mon, 06 Nov 2017 11:55:26: 11000000 INFO @ Mon, 06 Nov 2017 11:55:30: 11000000 INFO @ Mon, 06 Nov 2017 11:55:34: 12000000 INFO @ Mon, 06 Nov 2017 11:55:34: 12000000 INFO @ Mon, 06 Nov 2017 11:55:39: 12000000 INFO @ Mon, 06 Nov 2017 11:55:41: 13000000 INFO @ Mon, 06 Nov 2017 11:55:42: 13000000 INFO @ Mon, 06 Nov 2017 11:55:47: 13000000 INFO @ Mon, 06 Nov 2017 11:55:49: #1 tag size is determined as 49 bps INFO @ Mon, 06 Nov 2017 11:55:49: #1 tag size = 49 INFO @ Mon, 06 Nov 2017 11:55:49: #1 total tags in treatment: 13938412 INFO @ Mon, 06 Nov 2017 11:55:49: #1 user defined the maximum tags... INFO @ Mon, 06 Nov 2017 11:55:49: #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 11:55:49: #1 tag size is determined as 49 bps INFO @ Mon, 06 Nov 2017 11:55:49: #1 tag size = 49 INFO @ Mon, 06 Nov 2017 11:55:49: #1 total tags in treatment: 13938412 INFO @ Mon, 06 Nov 2017 11:55:49: #1 user defined the maximum tags... INFO @ Mon, 06 Nov 2017 11:55:49: #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 11:55:49: #1 tags after filtering in treatment: 13938412 INFO @ Mon, 06 Nov 2017 11:55:49: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Nov 2017 11:55:49: #1 finished! INFO @ Mon, 06 Nov 2017 11:55:49: #2 Build Peak Model... INFO @ Mon, 06 Nov 2017 11:55:49: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Nov 2017 11:55:49: #1 tags after filtering in treatment: 13938412 INFO @ Mon, 06 Nov 2017 11:55:49: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Nov 2017 11:55:49: #1 finished! INFO @ Mon, 06 Nov 2017 11:55:49: #2 Build Peak Model... INFO @ Mon, 06 Nov 2017 11:55:49: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Nov 2017 11:55:50: #2 number of paired peaks: 1405 INFO @ Mon, 06 Nov 2017 11:55:50: start model_add_line... INFO @ Mon, 06 Nov 2017 11:55:50: #2 number of paired peaks: 1405 INFO @ Mon, 06 Nov 2017 11:55:50: start model_add_line... INFO @ Mon, 06 Nov 2017 11:55:50: start X-correlation... INFO @ Mon, 06 Nov 2017 11:55:50: end of X-cor INFO @ Mon, 06 Nov 2017 11:55:50: #2 finished! INFO @ Mon, 06 Nov 2017 11:55:50: #2 predicted fragment length is 115 bps INFO @ Mon, 06 Nov 2017 11:55:50: #2 alternative fragment length(s) may be 2,115 bps INFO @ Mon, 06 Nov 2017 11:55:50: #2.2 Generate R script for model : SRX2458926.20_model.r INFO @ Mon, 06 Nov 2017 11:55:50: #3 Call peaks... INFO @ Mon, 06 Nov 2017 11:55:50: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Nov 2017 11:55:50: start X-correlation... INFO @ Mon, 06 Nov 2017 11:55:50: end of X-cor INFO @ Mon, 06 Nov 2017 11:55:50: #2 finished! INFO @ Mon, 06 Nov 2017 11:55:50: #2 predicted fragment length is 115 bps INFO @ Mon, 06 Nov 2017 11:55:50: #2 alternative fragment length(s) may be 2,115 bps INFO @ Mon, 06 Nov 2017 11:55:50: #2.2 Generate R script for model : SRX2458926.05_model.r INFO @ Mon, 06 Nov 2017 11:55:50: #3 Call peaks... INFO @ Mon, 06 Nov 2017 11:55:50: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Nov 2017 11:55:55: #1 tag size is determined as 49 bps INFO @ Mon, 06 Nov 2017 11:55:55: #1 tag size = 49 INFO @ Mon, 06 Nov 2017 11:55:55: #1 total tags in treatment: 13938412 INFO @ Mon, 06 Nov 2017 11:55:55: #1 user defined the maximum tags... INFO @ Mon, 06 Nov 2017 11:55:55: #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 11:55:55: #1 tags after filtering in treatment: 13938412 INFO @ Mon, 06 Nov 2017 11:55:55: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Nov 2017 11:55:55: #1 finished! INFO @ Mon, 06 Nov 2017 11:55:55: #2 Build Peak Model... INFO @ Mon, 06 Nov 2017 11:55:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Nov 2017 11:55:56: #2 number of paired peaks: 1405 INFO @ Mon, 06 Nov 2017 11:55:56: start model_add_line... INFO @ Mon, 06 Nov 2017 11:55:57: start X-correlation... INFO @ Mon, 06 Nov 2017 11:55:57: end of X-cor INFO @ Mon, 06 Nov 2017 11:55:57: #2 finished! INFO @ Mon, 06 Nov 2017 11:55:57: #2 predicted fragment length is 115 bps INFO @ Mon, 06 Nov 2017 11:55:57: #2 alternative fragment length(s) may be 2,115 bps INFO @ Mon, 06 Nov 2017 11:55:57: #2.2 Generate R script for model : SRX2458926.10_model.r INFO @ Mon, 06 Nov 2017 11:55:57: #3 Call peaks... INFO @ Mon, 06 Nov 2017 11:55:57: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Nov 2017 11:56:25: #3 Call peaks for each chromosome... INFO @ Mon, 06 Nov 2017 11:56:25: #3 Call peaks for each chromosome... INFO @ Mon, 06 Nov 2017 11:56:30: #3 Call peaks for each chromosome... INFO @ Mon, 06 Nov 2017 11:56:41: #4 Write output xls file... SRX2458926.05_peaks.xls INFO @ Mon, 06 Nov 2017 11:56:41: #4 Write peak in narrowPeak format file... SRX2458926.05_peaks.narrowPeak INFO @ Mon, 06 Nov 2017 11:56:42: #4 Write summits bed file... SRX2458926.05_summits.bed INFO @ Mon, 06 Nov 2017 11:56:42: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2562 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 06 Nov 2017 11:56:43: #4 Write output xls file... SRX2458926.20_peaks.xls INFO @ Mon, 06 Nov 2017 11:56:43: #4 Write peak in narrowPeak format file... SRX2458926.20_peaks.narrowPeak INFO @ Mon, 06 Nov 2017 11:56:43: #4 Write summits bed file... SRX2458926.20_summits.bed INFO @ Mon, 06 Nov 2017 11:56:43: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (909 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 06 Nov 2017 11:56:48: #4 Write output xls file... SRX2458926.10_peaks.xls INFO @ Mon, 06 Nov 2017 11:56:48: #4 Write peak in narrowPeak format file... SRX2458926.10_peaks.narrowPeak INFO @ Mon, 06 Nov 2017 11:56:48: #4 Write summits bed file... SRX2458926.10_summits.bed INFO @ Mon, 06 Nov 2017 11:56:48: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1476 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。