Job ID = 11293653 sra ファイルのダウンロード中... Completed: 300057K bytes transferred in 9 seconds (251622K 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 14470269 spots for /home/okishinya/chipatlas/results/dm3/SRX3873734/SRR6927799.sra Written 14470269 spots for /home/okishinya/chipatlas/results/dm3/SRX3873734/SRR6927799.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: 00:03:58 14470269 reads; of these: 14470269 (100.00%) were unpaired; of these: 1508051 (10.42%) aligned 0 times 10880422 (75.19%) aligned exactly 1 time 2081796 (14.39%) aligned >1 times 89.58% overall alignment rate Time searching: 00:03:58 Overall time: 00:03:58 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] 3179024 / 12962218 = 0.2453 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 17:54:48: # Command line: callpeak -t SRX3873734.bam -f BAM -g dm -n SRX3873734.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3873734.10 # format = BAM # ChIP-seq file = ['SRX3873734.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 17:54:48: # Command line: callpeak -t SRX3873734.bam -f BAM -g dm -n SRX3873734.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3873734.20 # format = BAM # ChIP-seq file = ['SRX3873734.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 17:54:48: # Command line: callpeak -t SRX3873734.bam -f BAM -g dm -n SRX3873734.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3873734.05 # format = BAM # ChIP-seq file = ['SRX3873734.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 17:54:48: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:54:48: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:54:48: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:54:48: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:54:48: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:54:48: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:54:54: 1000000 INFO @ Sun, 04 Nov 2018 17:54:54: 1000000 INFO @ Sun, 04 Nov 2018 17:54:54: 1000000 INFO @ Sun, 04 Nov 2018 17:55:00: 2000000 INFO @ Sun, 04 Nov 2018 17:55:01: 2000000 INFO @ Sun, 04 Nov 2018 17:55:01: 2000000 INFO @ Sun, 04 Nov 2018 17:55:06: 3000000 INFO @ Sun, 04 Nov 2018 17:55:07: 3000000 INFO @ Sun, 04 Nov 2018 17:55:08: 3000000 INFO @ Sun, 04 Nov 2018 17:55:13: 4000000 INFO @ Sun, 04 Nov 2018 17:55:14: 4000000 INFO @ Sun, 04 Nov 2018 17:55:14: 4000000 INFO @ Sun, 04 Nov 2018 17:55:19: 5000000 INFO @ Sun, 04 Nov 2018 17:55:20: 5000000 INFO @ Sun, 04 Nov 2018 17:55:21: 5000000 INFO @ Sun, 04 Nov 2018 17:55:25: 6000000 INFO @ Sun, 04 Nov 2018 17:55:27: 6000000 INFO @ Sun, 04 Nov 2018 17:55:27: 6000000 INFO @ Sun, 04 Nov 2018 17:55:31: 7000000 INFO @ Sun, 04 Nov 2018 17:55:33: 7000000 INFO @ Sun, 04 Nov 2018 17:55:34: 7000000 INFO @ Sun, 04 Nov 2018 17:55:37: 8000000 INFO @ Sun, 04 Nov 2018 17:55:39: 8000000 INFO @ Sun, 04 Nov 2018 17:55:40: 8000000 INFO @ Sun, 04 Nov 2018 17:55:43: 9000000 INFO @ Sun, 04 Nov 2018 17:55:46: 9000000 INFO @ Sun, 04 Nov 2018 17:55:47: 9000000 INFO @ Sun, 04 Nov 2018 17:55:48: #1 tag size is determined as 49 bps INFO @ Sun, 04 Nov 2018 17:55:48: #1 tag size = 49 INFO @ Sun, 04 Nov 2018 17:55:48: #1 total tags in treatment: 9783194 INFO @ Sun, 04 Nov 2018 17:55:48: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 17:55:48: #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 17:55:49: #1 tags after filtering in treatment: 9783194 INFO @ Sun, 04 Nov 2018 17:55:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 17:55:49: #1 finished! INFO @ Sun, 04 Nov 2018 17:55:49: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 17:55:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 17:55:50: #2 number of paired peaks: 7755 INFO @ Sun, 04 Nov 2018 17:55:50: start model_add_line... INFO @ Sun, 04 Nov 2018 17:55:50: start X-correlation... INFO @ Sun, 04 Nov 2018 17:55:51: end of X-cor INFO @ Sun, 04 Nov 2018 17:55:51: #2 finished! INFO @ Sun, 04 Nov 2018 17:55:51: #2 predicted fragment length is 150 bps INFO @ Sun, 04 Nov 2018 17:55:51: #2 alternative fragment length(s) may be 150 bps INFO @ Sun, 04 Nov 2018 17:55:51: #2.2 Generate R script for model : SRX3873734.05_model.r INFO @ Sun, 04 Nov 2018 17:55:51: #3 Call peaks... INFO @ Sun, 04 Nov 2018 17:55:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 17:55:51: #1 tag size is determined as 49 bps INFO @ Sun, 04 Nov 2018 17:55:51: #1 tag size = 49 INFO @ Sun, 04 Nov 2018 17:55:51: #1 total tags in treatment: 9783194 INFO @ Sun, 04 Nov 2018 17:55:51: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 17:55:51: #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 17:55:51: #1 tags after filtering in treatment: 9783194 INFO @ Sun, 04 Nov 2018 17:55:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 17:55:51: #1 finished! INFO @ Sun, 04 Nov 2018 17:55:51: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 17:55:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 17:55:52: #1 tag size is determined as 49 bps INFO @ Sun, 04 Nov 2018 17:55:52: #1 tag size = 49 INFO @ Sun, 04 Nov 2018 17:55:52: #1 total tags in treatment: 9783194 INFO @ Sun, 04 Nov 2018 17:55:52: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 17:55:52: #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 17:55:52: #1 tags after filtering in treatment: 9783194 INFO @ Sun, 04 Nov 2018 17:55:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 17:55:52: #1 finished! INFO @ Sun, 04 Nov 2018 17:55:52: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 17:55:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 17:55:53: #2 number of paired peaks: 7755 INFO @ Sun, 04 Nov 2018 17:55:53: start model_add_line... INFO @ Sun, 04 Nov 2018 17:55:53: start X-correlation... INFO @ Sun, 04 Nov 2018 17:55:53: end of X-cor INFO @ Sun, 04 Nov 2018 17:55:53: #2 finished! INFO @ Sun, 04 Nov 2018 17:55:53: #2 predicted fragment length is 150 bps INFO @ Sun, 04 Nov 2018 17:55:53: #2 alternative fragment length(s) may be 150 bps INFO @ Sun, 04 Nov 2018 17:55:53: #2.2 Generate R script for model : SRX3873734.10_model.r INFO @ Sun, 04 Nov 2018 17:55:53: #3 Call peaks... INFO @ Sun, 04 Nov 2018 17:55:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 17:55:53: #2 number of paired peaks: 7755 INFO @ Sun, 04 Nov 2018 17:55:53: start model_add_line... INFO @ Sun, 04 Nov 2018 17:55:54: start X-correlation... INFO @ Sun, 04 Nov 2018 17:55:54: end of X-cor INFO @ Sun, 04 Nov 2018 17:55:54: #2 finished! INFO @ Sun, 04 Nov 2018 17:55:54: #2 predicted fragment length is 150 bps INFO @ Sun, 04 Nov 2018 17:55:54: #2 alternative fragment length(s) may be 150 bps INFO @ Sun, 04 Nov 2018 17:55:54: #2.2 Generate R script for model : SRX3873734.20_model.r INFO @ Sun, 04 Nov 2018 17:55:54: #3 Call peaks... INFO @ Sun, 04 Nov 2018 17:55:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 17:56:21: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 17:56:24: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 17:56:24: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 17:56:34: #4 Write output xls file... SRX3873734.05_peaks.xls INFO @ Sun, 04 Nov 2018 17:56:34: #4 Write peak in narrowPeak format file... SRX3873734.05_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 17:56:34: #4 Write summits bed file... SRX3873734.05_summits.bed INFO @ Sun, 04 Nov 2018 17:56:34: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (10469 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sun, 04 Nov 2018 17:56:37: #4 Write output xls file... SRX3873734.20_peaks.xls INFO @ Sun, 04 Nov 2018 17:56:37: #4 Write peak in narrowPeak format file... SRX3873734.20_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 17:56:37: #4 Write summits bed file... SRX3873734.20_summits.bed INFO @ Sun, 04 Nov 2018 17:56:37: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5821 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 04 Nov 2018 17:56:38: #4 Write output xls file... SRX3873734.10_peaks.xls INFO @ Sun, 04 Nov 2018 17:56:38: #4 Write peak in narrowPeak format file... SRX3873734.10_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 17:56:38: #4 Write summits bed file... SRX3873734.10_summits.bed INFO @ Sun, 04 Nov 2018 17:56:38: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8214 records, 4 fields): 26 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。