Job ID = 11293680 sra ファイルのダウンロード中... Completed: 740915K bytes transferred in 29 seconds (208506K 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 21971273 spots for /home/okishinya/chipatlas/results/dm3/SRX4375842/SRR7506496.sra Written 21971273 spots for /home/okishinya/chipatlas/results/dm3/SRX4375842/SRR7506496.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: 00:06:12 21971273 reads; of these: 21971273 (100.00%) were unpaired; of these: 1706366 (7.77%) aligned 0 times 16696804 (75.99%) aligned exactly 1 time 3568103 (16.24%) aligned >1 times 92.23% overall alignment rate Time searching: 00:06:12 Overall time: 00:06:13 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] 7112216 / 20264907 = 0.3510 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 @ Sun, 04 Nov 2018 18:00:00: # Command line: callpeak -t SRX4375842.bam -f BAM -g dm -n SRX4375842.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4375842.10 # format = BAM # ChIP-seq file = ['SRX4375842.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 @ Sun, 04 Nov 2018 18:00:00: # Command line: callpeak -t SRX4375842.bam -f BAM -g dm -n SRX4375842.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4375842.05 # format = BAM # ChIP-seq file = ['SRX4375842.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 @ Sun, 04 Nov 2018 18:00:00: # Command line: callpeak -t SRX4375842.bam -f BAM -g dm -n SRX4375842.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4375842.20 # format = BAM # ChIP-seq file = ['SRX4375842.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 @ Sun, 04 Nov 2018 18:00:00: #1 read tag files... INFO @ Sun, 04 Nov 2018 18:00:00: #1 read tag files... INFO @ Sun, 04 Nov 2018 18:00:00: #1 read tag files... INFO @ Sun, 04 Nov 2018 18:00:00: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 18:00:00: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 18:00:00: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 18:00:07: 1000000 INFO @ Sun, 04 Nov 2018 18:00:07: 1000000 INFO @ Sun, 04 Nov 2018 18:00:07: 1000000 INFO @ Sun, 04 Nov 2018 18:00:14: 2000000 INFO @ Sun, 04 Nov 2018 18:00:14: 2000000 INFO @ Sun, 04 Nov 2018 18:00:14: 2000000 INFO @ Sun, 04 Nov 2018 18:00:21: 3000000 INFO @ Sun, 04 Nov 2018 18:00:21: 3000000 INFO @ Sun, 04 Nov 2018 18:00:21: 3000000 INFO @ Sun, 04 Nov 2018 18:00:27: 4000000 INFO @ Sun, 04 Nov 2018 18:00:28: 4000000 INFO @ Sun, 04 Nov 2018 18:00:28: 4000000 INFO @ Sun, 04 Nov 2018 18:00:34: 5000000 INFO @ Sun, 04 Nov 2018 18:00:35: 5000000 INFO @ Sun, 04 Nov 2018 18:00:35: 5000000 INFO @ Sun, 04 Nov 2018 18:00:41: 6000000 INFO @ Sun, 04 Nov 2018 18:00:42: 6000000 INFO @ Sun, 04 Nov 2018 18:00:42: 6000000 INFO @ Sun, 04 Nov 2018 18:00:48: 7000000 INFO @ Sun, 04 Nov 2018 18:00:49: 7000000 INFO @ Sun, 04 Nov 2018 18:00:49: 7000000 INFO @ Sun, 04 Nov 2018 18:00:55: 8000000 INFO @ Sun, 04 Nov 2018 18:00:56: 8000000 INFO @ Sun, 04 Nov 2018 18:00:56: 8000000 INFO @ Sun, 04 Nov 2018 18:01:01: 9000000 INFO @ Sun, 04 Nov 2018 18:01:03: 9000000 INFO @ Sun, 04 Nov 2018 18:01:03: 9000000 INFO @ Sun, 04 Nov 2018 18:01:09: 10000000 INFO @ Sun, 04 Nov 2018 18:01:10: 10000000 INFO @ Sun, 04 Nov 2018 18:01:11: 10000000 INFO @ Sun, 04 Nov 2018 18:01:16: 11000000 INFO @ Sun, 04 Nov 2018 18:01:17: 11000000 INFO @ Sun, 04 Nov 2018 18:01:18: 11000000 INFO @ Sun, 04 Nov 2018 18:01:22: 12000000 INFO @ Sun, 04 Nov 2018 18:01:24: 12000000 INFO @ Sun, 04 Nov 2018 18:01:25: 12000000 INFO @ Sun, 04 Nov 2018 18:01:29: 13000000 INFO @ Sun, 04 Nov 2018 18:01:30: #1 tag size is determined as 51 bps INFO @ Sun, 04 Nov 2018 18:01:30: #1 tag size = 51 INFO @ Sun, 04 Nov 2018 18:01:30: #1 total tags in treatment: 13152691 INFO @ Sun, 04 Nov 2018 18:01:30: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 18:01:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Nov 2018 18:01:31: #1 tags after filtering in treatment: 13152691 INFO @ Sun, 04 Nov 2018 18:01:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 18:01:31: #1 finished! INFO @ Sun, 04 Nov 2018 18:01:31: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 18:01:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 18:01:31: 13000000 INFO @ Sun, 04 Nov 2018 18:01:32: 13000000 INFO @ Sun, 04 Nov 2018 18:01:32: #1 tag size is determined as 51 bps INFO @ Sun, 04 Nov 2018 18:01:32: #1 tag size = 51 INFO @ Sun, 04 Nov 2018 18:01:32: #1 total tags in treatment: 13152691 INFO @ Sun, 04 Nov 2018 18:01:32: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 18:01:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Nov 2018 18:01:32: #2 number of paired peaks: 8398 INFO @ Sun, 04 Nov 2018 18:01:32: start model_add_line... INFO @ Sun, 04 Nov 2018 18:01:33: #1 tags after filtering in treatment: 13152691 INFO @ Sun, 04 Nov 2018 18:01:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 18:01:33: #1 finished! INFO @ Sun, 04 Nov 2018 18:01:33: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 18:01:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 18:01:33: #1 tag size is determined as 51 bps INFO @ Sun, 04 Nov 2018 18:01:33: #1 tag size = 51 INFO @ Sun, 04 Nov 2018 18:01:33: #1 total tags in treatment: 13152691 INFO @ Sun, 04 Nov 2018 18:01:33: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 18:01:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Nov 2018 18:01:33: start X-correlation... INFO @ Sun, 04 Nov 2018 18:01:33: #1 tags after filtering in treatment: 13152691 INFO @ Sun, 04 Nov 2018 18:01:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 18:01:33: #1 finished! INFO @ Sun, 04 Nov 2018 18:01:33: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 18:01:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 18:01:33: end of X-cor INFO @ Sun, 04 Nov 2018 18:01:33: #2 finished! INFO @ Sun, 04 Nov 2018 18:01:33: #2 predicted fragment length is 189 bps INFO @ Sun, 04 Nov 2018 18:01:33: #2 alternative fragment length(s) may be 189 bps INFO @ Sun, 04 Nov 2018 18:01:33: #2.2 Generate R script for model : SRX4375842.10_model.r INFO @ Sun, 04 Nov 2018 18:01:33: #3 Call peaks... INFO @ Sun, 04 Nov 2018 18:01:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 18:01:35: #2 number of paired peaks: 8398 INFO @ Sun, 04 Nov 2018 18:01:35: start model_add_line... INFO @ Sun, 04 Nov 2018 18:01:35: #2 number of paired peaks: 8398 INFO @ Sun, 04 Nov 2018 18:01:35: start model_add_line... INFO @ Sun, 04 Nov 2018 18:01:35: start X-correlation... INFO @ Sun, 04 Nov 2018 18:01:35: end of X-cor INFO @ Sun, 04 Nov 2018 18:01:35: #2 finished! INFO @ Sun, 04 Nov 2018 18:01:35: #2 predicted fragment length is 189 bps INFO @ Sun, 04 Nov 2018 18:01:35: #2 alternative fragment length(s) may be 189 bps INFO @ Sun, 04 Nov 2018 18:01:35: #2.2 Generate R script for model : SRX4375842.05_model.r INFO @ Sun, 04 Nov 2018 18:01:35: #3 Call peaks... INFO @ Sun, 04 Nov 2018 18:01:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 18:01:35: start X-correlation... INFO @ Sun, 04 Nov 2018 18:01:35: end of X-cor INFO @ Sun, 04 Nov 2018 18:01:35: #2 finished! INFO @ Sun, 04 Nov 2018 18:01:35: #2 predicted fragment length is 189 bps INFO @ Sun, 04 Nov 2018 18:01:35: #2 alternative fragment length(s) may be 189 bps INFO @ Sun, 04 Nov 2018 18:01:35: #2.2 Generate R script for model : SRX4375842.20_model.r INFO @ Sun, 04 Nov 2018 18:01:35: #3 Call peaks... INFO @ Sun, 04 Nov 2018 18:01:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 18:02:20: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 18:02:23: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 18:02:23: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 18:02:37: #4 Write output xls file... SRX4375842.10_peaks.xls INFO @ Sun, 04 Nov 2018 18:02:38: #4 Write peak in narrowPeak format file... SRX4375842.10_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 18:02:38: #4 Write summits bed file... SRX4375842.10_summits.bed INFO @ Sun, 04 Nov 2018 18:02:38: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (9323 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 04 Nov 2018 18:02:41: #4 Write output xls file... SRX4375842.20_peaks.xls INFO @ Sun, 04 Nov 2018 18:02:41: #4 Write peak in narrowPeak format file... SRX4375842.20_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 18:02:41: #4 Write summits bed file... SRX4375842.20_summits.bed INFO @ Sun, 04 Nov 2018 18:02:41: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (6543 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 04 Nov 2018 18:02:43: #4 Write output xls file... SRX4375842.05_peaks.xls INFO @ Sun, 04 Nov 2018 18:02:43: #4 Write peak in narrowPeak format file... SRX4375842.05_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 18:02:43: #4 Write summits bed file... SRX4375842.05_summits.bed INFO @ Sun, 04 Nov 2018 18:02:43: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (12047 records, 4 fields): 20 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。