Job ID = 11293698 sra ファイルのダウンロード中... Completed: 826118K bytes transferred in 30 seconds (219168K 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 25060642 spots for /home/okishinya/chipatlas/results/dm3/SRX4375859/SRR7506513.sra Written 25060642 spots for /home/okishinya/chipatlas/results/dm3/SRX4375859/SRR7506513.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: 00:06:45 25060642 reads; of these: 25060642 (100.00%) were unpaired; of these: 7131029 (28.46%) aligned 0 times 14818573 (59.13%) aligned exactly 1 time 3111040 (12.41%) aligned >1 times 71.54% overall alignment rate Time searching: 00:06:45 Overall time: 00:06:45 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] 5318558 / 17929613 = 0.2966 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 18:00:50: # Command line: callpeak -t SRX4375859.bam -f BAM -g dm -n SRX4375859.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4375859.10 # format = BAM # ChIP-seq file = ['SRX4375859.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 18:00:50: # Command line: callpeak -t SRX4375859.bam -f BAM -g dm -n SRX4375859.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4375859.05 # format = BAM # ChIP-seq file = ['SRX4375859.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 18:00:50: #1 read tag files... INFO @ Sun, 04 Nov 2018 18:00:50: #1 read tag files... INFO @ Sun, 04 Nov 2018 18:00:50: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 18:00:50: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 18:00:50: # Command line: callpeak -t SRX4375859.bam -f BAM -g dm -n SRX4375859.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4375859.20 # format = BAM # ChIP-seq file = ['SRX4375859.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 18:00:50: #1 read tag files... INFO @ Sun, 04 Nov 2018 18:00:50: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 18:00:57: 1000000 INFO @ Sun, 04 Nov 2018 18:00:57: 1000000 INFO @ Sun, 04 Nov 2018 18:00:57: 1000000 INFO @ Sun, 04 Nov 2018 18:01:03: 2000000 INFO @ Sun, 04 Nov 2018 18:01:03: 2000000 INFO @ Sun, 04 Nov 2018 18:01:03: 2000000 INFO @ Sun, 04 Nov 2018 18:01:09: 3000000 INFO @ Sun, 04 Nov 2018 18:01:10: 3000000 INFO @ Sun, 04 Nov 2018 18:01:10: 3000000 INFO @ Sun, 04 Nov 2018 18:01:15: 4000000 INFO @ Sun, 04 Nov 2018 18:01:16: 4000000 INFO @ Sun, 04 Nov 2018 18:01:16: 4000000 INFO @ Sun, 04 Nov 2018 18:01:22: 5000000 INFO @ Sun, 04 Nov 2018 18:01:22: 5000000 INFO @ Sun, 04 Nov 2018 18:01:23: 5000000 INFO @ Sun, 04 Nov 2018 18:01:28: 6000000 INFO @ Sun, 04 Nov 2018 18:01:29: 6000000 INFO @ Sun, 04 Nov 2018 18:01:29: 6000000 INFO @ Sun, 04 Nov 2018 18:01:34: 7000000 INFO @ Sun, 04 Nov 2018 18:01:36: 7000000 INFO @ Sun, 04 Nov 2018 18:01:36: 7000000 INFO @ Sun, 04 Nov 2018 18:01:40: 8000000 INFO @ Sun, 04 Nov 2018 18:01:42: 8000000 INFO @ Sun, 04 Nov 2018 18:01:43: 8000000 INFO @ Sun, 04 Nov 2018 18:01:46: 9000000 INFO @ Sun, 04 Nov 2018 18:01:49: 9000000 INFO @ Sun, 04 Nov 2018 18:01:49: 9000000 INFO @ Sun, 04 Nov 2018 18:01:52: 10000000 INFO @ Sun, 04 Nov 2018 18:01:56: 10000000 INFO @ Sun, 04 Nov 2018 18:01:56: 10000000 INFO @ Sun, 04 Nov 2018 18:01:59: 11000000 INFO @ Sun, 04 Nov 2018 18:02:02: 11000000 INFO @ Sun, 04 Nov 2018 18:02:03: 11000000 INFO @ Sun, 04 Nov 2018 18:02:05: 12000000 INFO @ Sun, 04 Nov 2018 18:02:09: #1 tag size is determined as 51 bps INFO @ Sun, 04 Nov 2018 18:02:09: #1 tag size = 51 INFO @ Sun, 04 Nov 2018 18:02:09: #1 total tags in treatment: 12611055 INFO @ Sun, 04 Nov 2018 18:02:09: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 18:02:09: #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 18:02:09: #1 tags after filtering in treatment: 12611055 INFO @ Sun, 04 Nov 2018 18:02:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 18:02:09: #1 finished! INFO @ Sun, 04 Nov 2018 18:02:09: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 18:02:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 18:02:09: 12000000 INFO @ Sun, 04 Nov 2018 18:02:10: 12000000 INFO @ Sun, 04 Nov 2018 18:02:10: #2 number of paired peaks: 7257 INFO @ Sun, 04 Nov 2018 18:02:10: start model_add_line... INFO @ Sun, 04 Nov 2018 18:02:11: start X-correlation... INFO @ Sun, 04 Nov 2018 18:02:11: end of X-cor INFO @ Sun, 04 Nov 2018 18:02:11: #2 finished! INFO @ Sun, 04 Nov 2018 18:02:11: #2 predicted fragment length is 198 bps INFO @ Sun, 04 Nov 2018 18:02:11: #2 alternative fragment length(s) may be 198 bps INFO @ Sun, 04 Nov 2018 18:02:11: #2.2 Generate R script for model : SRX4375859.10_model.r INFO @ Sun, 04 Nov 2018 18:02:11: #3 Call peaks... INFO @ Sun, 04 Nov 2018 18:02:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 18:02:13: #1 tag size is determined as 51 bps INFO @ Sun, 04 Nov 2018 18:02:13: #1 tag size = 51 INFO @ Sun, 04 Nov 2018 18:02:13: #1 total tags in treatment: 12611055 INFO @ Sun, 04 Nov 2018 18:02:13: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 18:02:13: #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 18:02:13: #1 tags after filtering in treatment: 12611055 INFO @ Sun, 04 Nov 2018 18:02:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 18:02:13: #1 finished! INFO @ Sun, 04 Nov 2018 18:02:13: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 18:02:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 18:02:14: #1 tag size is determined as 51 bps INFO @ Sun, 04 Nov 2018 18:02:14: #1 tag size = 51 INFO @ Sun, 04 Nov 2018 18:02:14: #1 total tags in treatment: 12611055 INFO @ Sun, 04 Nov 2018 18:02:14: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 18:02:14: #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 18:02:14: #1 tags after filtering in treatment: 12611055 INFO @ Sun, 04 Nov 2018 18:02:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 18:02:14: #1 finished! INFO @ Sun, 04 Nov 2018 18:02:14: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 18:02:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 18:02:15: #2 number of paired peaks: 7257 INFO @ Sun, 04 Nov 2018 18:02:15: start model_add_line... INFO @ Sun, 04 Nov 2018 18:02:15: start X-correlation... INFO @ Sun, 04 Nov 2018 18:02:15: end of X-cor INFO @ Sun, 04 Nov 2018 18:02:15: #2 finished! INFO @ Sun, 04 Nov 2018 18:02:15: #2 predicted fragment length is 198 bps INFO @ Sun, 04 Nov 2018 18:02:15: #2 alternative fragment length(s) may be 198 bps INFO @ Sun, 04 Nov 2018 18:02:15: #2.2 Generate R script for model : SRX4375859.20_model.r INFO @ Sun, 04 Nov 2018 18:02:15: #3 Call peaks... INFO @ Sun, 04 Nov 2018 18:02:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 18:02:16: #2 number of paired peaks: 7257 INFO @ Sun, 04 Nov 2018 18:02:16: start model_add_line... INFO @ Sun, 04 Nov 2018 18:02:16: start X-correlation... INFO @ Sun, 04 Nov 2018 18:02:16: end of X-cor INFO @ Sun, 04 Nov 2018 18:02:16: #2 finished! INFO @ Sun, 04 Nov 2018 18:02:16: #2 predicted fragment length is 198 bps INFO @ Sun, 04 Nov 2018 18:02:16: #2 alternative fragment length(s) may be 198 bps INFO @ Sun, 04 Nov 2018 18:02:16: #2.2 Generate R script for model : SRX4375859.05_model.r INFO @ Sun, 04 Nov 2018 18:02:16: #3 Call peaks... INFO @ Sun, 04 Nov 2018 18:02:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 18:02:55: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 18:03:00: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 18:03:02: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 18:03:12: #4 Write output xls file... SRX4375859.10_peaks.xls INFO @ Sun, 04 Nov 2018 18:03:12: #4 Write peak in narrowPeak format file... SRX4375859.10_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 18:03:12: #4 Write summits bed file... SRX4375859.10_summits.bed INFO @ Sun, 04 Nov 2018 18:03:12: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (8784 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 04 Nov 2018 18:03:21: #4 Write output xls file... SRX4375859.05_peaks.xls INFO @ Sun, 04 Nov 2018 18:03:21: #4 Write peak in narrowPeak format file... SRX4375859.05_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 18:03:21: #4 Write summits bed file... SRX4375859.05_summits.bed INFO @ Sun, 04 Nov 2018 18:03:21: Done! INFO @ Sun, 04 Nov 2018 18:03:21: #4 Write output xls file... SRX4375859.20_peaks.xls INFO @ Sun, 04 Nov 2018 18:03:21: #4 Write peak in narrowPeak format file... SRX4375859.20_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 18:03:21: #4 Write summits bed file... SRX4375859.20_summits.bed pass1 - making usageList (15 chroms): 3 millis INFO @ Sun, 04 Nov 2018 18:03:21: Done! pass2 - checking and writing primary data (11175 records, 4 fields): 15 millis CompletedMACS2peakCalling pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (6369 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。