Job ID = 11293681 sra ファイルのダウンロード中... Completed: 686460K bytes transferred in 28 seconds (197996K 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 20273408 spots for /home/okishinya/chipatlas/results/dm3/SRX4375843/SRR7506497.sra Written 20273408 spots for /home/okishinya/chipatlas/results/dm3/SRX4375843/SRR7506497.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: 00:05:37 20273408 reads; of these: 20273408 (100.00%) were unpaired; of these: 3523661 (17.38%) aligned 0 times 13532893 (66.75%) aligned exactly 1 time 3216854 (15.87%) aligned >1 times 82.62% overall alignment rate Time searching: 00:05:37 Overall time: 00:05:37 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] 5033687 / 16749747 = 0.3005 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 17:58:36: # Command line: callpeak -t SRX4375843.bam -f BAM -g dm -n SRX4375843.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4375843.05 # format = BAM # ChIP-seq file = ['SRX4375843.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 17:58:36: # Command line: callpeak -t SRX4375843.bam -f BAM -g dm -n SRX4375843.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4375843.20 # format = BAM # ChIP-seq file = ['SRX4375843.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 17:58:36: # Command line: callpeak -t SRX4375843.bam -f BAM -g dm -n SRX4375843.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4375843.10 # format = BAM # ChIP-seq file = ['SRX4375843.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 17:58:36: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:58:36: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:58:36: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:58:36: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:58:36: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:58:36: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:58:42: 1000000 INFO @ Sun, 04 Nov 2018 17:58:42: 1000000 INFO @ Sun, 04 Nov 2018 17:58:43: 1000000 INFO @ Sun, 04 Nov 2018 17:58:48: 2000000 INFO @ Sun, 04 Nov 2018 17:58:48: 2000000 INFO @ Sun, 04 Nov 2018 17:58:49: 2000000 INFO @ Sun, 04 Nov 2018 17:58:55: 3000000 INFO @ Sun, 04 Nov 2018 17:58:55: 3000000 INFO @ Sun, 04 Nov 2018 17:58:56: 3000000 INFO @ Sun, 04 Nov 2018 17:59:01: 4000000 INFO @ Sun, 04 Nov 2018 17:59:01: 4000000 INFO @ Sun, 04 Nov 2018 17:59:03: 4000000 INFO @ Sun, 04 Nov 2018 17:59:07: 5000000 INFO @ Sun, 04 Nov 2018 17:59:07: 5000000 INFO @ Sun, 04 Nov 2018 17:59:09: 5000000 INFO @ Sun, 04 Nov 2018 17:59:13: 6000000 INFO @ Sun, 04 Nov 2018 17:59:13: 6000000 INFO @ Sun, 04 Nov 2018 17:59:16: 6000000 INFO @ Sun, 04 Nov 2018 17:59:20: 7000000 INFO @ Sun, 04 Nov 2018 17:59:20: 7000000 INFO @ Sun, 04 Nov 2018 17:59:23: 7000000 INFO @ Sun, 04 Nov 2018 17:59:26: 8000000 INFO @ Sun, 04 Nov 2018 17:59:26: 8000000 INFO @ Sun, 04 Nov 2018 17:59:30: 8000000 INFO @ Sun, 04 Nov 2018 17:59:32: 9000000 INFO @ Sun, 04 Nov 2018 17:59:32: 9000000 INFO @ Sun, 04 Nov 2018 17:59:36: 9000000 INFO @ Sun, 04 Nov 2018 17:59:38: 10000000 INFO @ Sun, 04 Nov 2018 17:59:38: 10000000 INFO @ Sun, 04 Nov 2018 17:59:43: 10000000 INFO @ Sun, 04 Nov 2018 17:59:45: 11000000 INFO @ Sun, 04 Nov 2018 17:59:45: 11000000 INFO @ Sun, 04 Nov 2018 17:59:49: #1 tag size is determined as 51 bps INFO @ Sun, 04 Nov 2018 17:59:49: #1 tag size = 51 INFO @ Sun, 04 Nov 2018 17:59:49: #1 total tags in treatment: 11716060 INFO @ Sun, 04 Nov 2018 17:59:49: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 17:59:49: #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 17:59:49: #1 tag size is determined as 51 bps INFO @ Sun, 04 Nov 2018 17:59:49: #1 tag size = 51 INFO @ Sun, 04 Nov 2018 17:59:49: #1 total tags in treatment: 11716060 INFO @ Sun, 04 Nov 2018 17:59:49: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 17:59:49: #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 17:59:49: #1 tags after filtering in treatment: 11716060 INFO @ Sun, 04 Nov 2018 17:59:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 17:59:49: #1 finished! INFO @ Sun, 04 Nov 2018 17:59:49: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 17:59:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 17:59:49: #1 tags after filtering in treatment: 11716060 INFO @ Sun, 04 Nov 2018 17:59:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 17:59:49: #1 finished! INFO @ Sun, 04 Nov 2018 17:59:49: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 17:59:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 17:59:50: 11000000 INFO @ Sun, 04 Nov 2018 17:59:51: #2 number of paired peaks: 7932 INFO @ Sun, 04 Nov 2018 17:59:51: start model_add_line... INFO @ Sun, 04 Nov 2018 17:59:51: #2 number of paired peaks: 7932 INFO @ Sun, 04 Nov 2018 17:59:51: start model_add_line... INFO @ Sun, 04 Nov 2018 17:59:51: start X-correlation... INFO @ Sun, 04 Nov 2018 17:59:51: start X-correlation... INFO @ Sun, 04 Nov 2018 17:59:51: end of X-cor INFO @ Sun, 04 Nov 2018 17:59:51: end of X-cor INFO @ Sun, 04 Nov 2018 17:59:51: #2 finished! INFO @ Sun, 04 Nov 2018 17:59:51: #2 finished! INFO @ Sun, 04 Nov 2018 17:59:51: #2 predicted fragment length is 182 bps INFO @ Sun, 04 Nov 2018 17:59:51: #2 predicted fragment length is 182 bps INFO @ Sun, 04 Nov 2018 17:59:51: #2 alternative fragment length(s) may be 182 bps INFO @ Sun, 04 Nov 2018 17:59:51: #2 alternative fragment length(s) may be 182 bps INFO @ Sun, 04 Nov 2018 17:59:51: #2.2 Generate R script for model : SRX4375843.10_model.r INFO @ Sun, 04 Nov 2018 17:59:51: #2.2 Generate R script for model : SRX4375843.20_model.r INFO @ Sun, 04 Nov 2018 17:59:51: #3 Call peaks... INFO @ Sun, 04 Nov 2018 17:59:51: #3 Call peaks... INFO @ Sun, 04 Nov 2018 17:59:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 17:59:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 17:59:54: #1 tag size is determined as 51 bps INFO @ Sun, 04 Nov 2018 17:59:54: #1 tag size = 51 INFO @ Sun, 04 Nov 2018 17:59:54: #1 total tags in treatment: 11716060 INFO @ Sun, 04 Nov 2018 17:59:54: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 17:59:54: #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 17:59:55: #1 tags after filtering in treatment: 11716060 INFO @ Sun, 04 Nov 2018 17:59:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 17:59:55: #1 finished! INFO @ Sun, 04 Nov 2018 17:59:55: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 17:59:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 17:59:56: #2 number of paired peaks: 7932 INFO @ Sun, 04 Nov 2018 17:59:56: start model_add_line... INFO @ Sun, 04 Nov 2018 17:59:57: start X-correlation... INFO @ Sun, 04 Nov 2018 17:59:57: end of X-cor INFO @ Sun, 04 Nov 2018 17:59:57: #2 finished! INFO @ Sun, 04 Nov 2018 17:59:57: #2 predicted fragment length is 182 bps INFO @ Sun, 04 Nov 2018 17:59:57: #2 alternative fragment length(s) may be 182 bps INFO @ Sun, 04 Nov 2018 17:59:57: #2.2 Generate R script for model : SRX4375843.05_model.r INFO @ Sun, 04 Nov 2018 17:59:57: #3 Call peaks... INFO @ Sun, 04 Nov 2018 17:59:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 18:00:33: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 18:00:35: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 18:00:36: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 18:00:51: #4 Write output xls file... SRX4375843.20_peaks.xls INFO @ Sun, 04 Nov 2018 18:00:51: #4 Write peak in narrowPeak format file... SRX4375843.20_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 18:00:51: #4 Write summits bed file... SRX4375843.20_summits.bed INFO @ Sun, 04 Nov 2018 18:00:51: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6385 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 04 Nov 2018 18:00:52: #4 Write output xls file... SRX4375843.10_peaks.xls INFO @ Sun, 04 Nov 2018 18:00:52: #4 Write peak in narrowPeak format file... SRX4375843.10_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 18:00:52: #4 Write summits bed file... SRX4375843.10_summits.bed INFO @ Sun, 04 Nov 2018 18:00:52: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (9264 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 04 Nov 2018 18:00:53: #4 Write output xls file... SRX4375843.05_peaks.xls INFO @ Sun, 04 Nov 2018 18:00:54: #4 Write peak in narrowPeak format file... SRX4375843.05_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 18:00:54: #4 Write summits bed file... SRX4375843.05_summits.bed INFO @ Sun, 04 Nov 2018 18:00:54: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (12233 records, 4 fields): 16 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。