Job ID = 11240758 sra ファイルのダウンロード中... Completed: 135782K bytes transferred in 6 seconds (167909K 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 8954892 spots for /home/okishinya/chipatlas/results/dm3/SRX4669042/SRR7817567.sra Written 8954892 spots for /home/okishinya/chipatlas/results/dm3/SRX4669042/SRR7817567.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: 00:03:29 8954892 reads; of these: 8954892 (100.00%) were unpaired; of these: 369240 (4.12%) aligned 0 times 5311668 (59.32%) aligned exactly 1 time 3273984 (36.56%) aligned >1 times 95.88% overall alignment rate Time searching: 00:03:29 Overall time: 00:03:29 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_rmdupse_core] 1896759 / 8585652 = 0.2209 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, 07 Oct 2018 20:34:55: # Command line: callpeak -t SRX4669042.bam -f BAM -g dm -n SRX4669042.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4669042.10 # format = BAM # ChIP-seq file = ['SRX4669042.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, 07 Oct 2018 20:34:55: # Command line: callpeak -t SRX4669042.bam -f BAM -g dm -n SRX4669042.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4669042.20 # format = BAM # ChIP-seq file = ['SRX4669042.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, 07 Oct 2018 20:34:55: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:34:55: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:34:55: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:34:55: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:34:55: # Command line: callpeak -t SRX4669042.bam -f BAM -g dm -n SRX4669042.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4669042.05 # format = BAM # ChIP-seq file = ['SRX4669042.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, 07 Oct 2018 20:34:55: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:34:55: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:35:02: 1000000 INFO @ Sun, 07 Oct 2018 20:35:03: 1000000 INFO @ Sun, 07 Oct 2018 20:35:03: 1000000 INFO @ Sun, 07 Oct 2018 20:35:09: 2000000 INFO @ Sun, 07 Oct 2018 20:35:12: 2000000 INFO @ Sun, 07 Oct 2018 20:35:12: 2000000 INFO @ Sun, 07 Oct 2018 20:35:16: 3000000 INFO @ Sun, 07 Oct 2018 20:35:20: 3000000 INFO @ Sun, 07 Oct 2018 20:35:20: 3000000 INFO @ Sun, 07 Oct 2018 20:35:23: 4000000 INFO @ Sun, 07 Oct 2018 20:35:29: 4000000 INFO @ Sun, 07 Oct 2018 20:35:29: 4000000 INFO @ Sun, 07 Oct 2018 20:35:30: 5000000 INFO @ Sun, 07 Oct 2018 20:35:37: 6000000 INFO @ Sun, 07 Oct 2018 20:35:37: 5000000 INFO @ Sun, 07 Oct 2018 20:35:37: 5000000 INFO @ Sun, 07 Oct 2018 20:35:42: #1 tag size is determined as 50 bps INFO @ Sun, 07 Oct 2018 20:35:42: #1 tag size = 50 INFO @ Sun, 07 Oct 2018 20:35:42: #1 total tags in treatment: 6688893 INFO @ Sun, 07 Oct 2018 20:35:42: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:35:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 20:35:42: #1 tags after filtering in treatment: 6688893 INFO @ Sun, 07 Oct 2018 20:35:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:35:42: #1 finished! INFO @ Sun, 07 Oct 2018 20:35:42: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:35:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:35:43: #2 number of paired peaks: 1410 INFO @ Sun, 07 Oct 2018 20:35:43: start model_add_line... INFO @ Sun, 07 Oct 2018 20:35:43: start X-correlation... INFO @ Sun, 07 Oct 2018 20:35:43: end of X-cor INFO @ Sun, 07 Oct 2018 20:35:43: #2 finished! INFO @ Sun, 07 Oct 2018 20:35:43: #2 predicted fragment length is 112 bps INFO @ Sun, 07 Oct 2018 20:35:43: #2 alternative fragment length(s) may be 112 bps INFO @ Sun, 07 Oct 2018 20:35:43: #2.2 Generate R script for model : SRX4669042.20_model.r INFO @ Sun, 07 Oct 2018 20:35:43: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:35:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:35:46: 6000000 INFO @ Sun, 07 Oct 2018 20:35:46: 6000000 INFO @ Sun, 07 Oct 2018 20:35:52: #1 tag size is determined as 50 bps INFO @ Sun, 07 Oct 2018 20:35:52: #1 tag size = 50 INFO @ Sun, 07 Oct 2018 20:35:52: #1 total tags in treatment: 6688893 INFO @ Sun, 07 Oct 2018 20:35:52: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:35:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 20:35:52: #1 tag size is determined as 50 bps INFO @ Sun, 07 Oct 2018 20:35:52: #1 tag size = 50 INFO @ Sun, 07 Oct 2018 20:35:52: #1 total tags in treatment: 6688893 INFO @ Sun, 07 Oct 2018 20:35:52: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:35:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 20:35:52: #1 tags after filtering in treatment: 6688893 INFO @ Sun, 07 Oct 2018 20:35:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:35:52: #1 finished! INFO @ Sun, 07 Oct 2018 20:35:52: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:35:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:35:52: #1 tags after filtering in treatment: 6688893 INFO @ Sun, 07 Oct 2018 20:35:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:35:52: #1 finished! INFO @ Sun, 07 Oct 2018 20:35:52: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:35:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:35:53: #2 number of paired peaks: 1410 INFO @ Sun, 07 Oct 2018 20:35:53: start model_add_line... INFO @ Sun, 07 Oct 2018 20:35:53: #2 number of paired peaks: 1410 INFO @ Sun, 07 Oct 2018 20:35:53: start model_add_line... INFO @ Sun, 07 Oct 2018 20:35:53: start X-correlation... INFO @ Sun, 07 Oct 2018 20:35:53: end of X-cor INFO @ Sun, 07 Oct 2018 20:35:53: #2 finished! INFO @ Sun, 07 Oct 2018 20:35:53: #2 predicted fragment length is 112 bps INFO @ Sun, 07 Oct 2018 20:35:53: #2 alternative fragment length(s) may be 112 bps INFO @ Sun, 07 Oct 2018 20:35:53: #2.2 Generate R script for model : SRX4669042.05_model.r INFO @ Sun, 07 Oct 2018 20:35:53: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:35:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:35:53: start X-correlation... INFO @ Sun, 07 Oct 2018 20:35:53: end of X-cor INFO @ Sun, 07 Oct 2018 20:35:53: #2 finished! INFO @ Sun, 07 Oct 2018 20:35:53: #2 predicted fragment length is 112 bps INFO @ Sun, 07 Oct 2018 20:35:53: #2 alternative fragment length(s) may be 112 bps INFO @ Sun, 07 Oct 2018 20:35:53: #2.2 Generate R script for model : SRX4669042.10_model.r INFO @ Sun, 07 Oct 2018 20:35:53: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:35:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:36:00: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:36:10: #4 Write output xls file... SRX4669042.20_peaks.xls INFO @ Sun, 07 Oct 2018 20:36:10: #4 Write peak in narrowPeak format file... SRX4669042.20_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:36:10: #4 Write summits bed file... SRX4669042.20_summits.bed INFO @ Sun, 07 Oct 2018 20:36:10: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (560 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 07 Oct 2018 20:36:10: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:36:10: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:36:20: #4 Write output xls file... SRX4669042.10_peaks.xls INFO @ Sun, 07 Oct 2018 20:36:20: #4 Write peak in narrowPeak format file... SRX4669042.10_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:36:20: #4 Write summits bed file... SRX4669042.10_summits.bed INFO @ Sun, 07 Oct 2018 20:36:20: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1929 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 07 Oct 2018 20:36:20: #4 Write output xls file... SRX4669042.05_peaks.xls INFO @ Sun, 07 Oct 2018 20:36:20: #4 Write peak in narrowPeak format file... SRX4669042.05_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:36:20: #4 Write summits bed file... SRX4669042.05_summits.bed INFO @ Sun, 07 Oct 2018 20:36:20: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5477 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。