Job ID = 11632692 sra ファイルのダウンロード中... Completed: 296756K bytes transferred in 6 seconds (396879K 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 11707113 spots for /home/okishinya/chipatlas/results/rn6/SRX3782451/SRR6826269.sra Written 11707113 spots for /home/okishinya/chipatlas/results/rn6/SRX3782451/SRR6826269.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:46 11707113 reads; of these: 11707113 (100.00%) were unpaired; of these: 1338609 (11.43%) aligned 0 times 8736676 (74.63%) aligned exactly 1 time 1631828 (13.94%) aligned >1 times 88.57% overall alignment rate Time searching: 00:05:47 Overall time: 00:05:47 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_rmdupse_core] 1325571 / 10368504 = 0.1278 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 @ Fri, 15 Feb 2019 06:32:06: # Command line: callpeak -t SRX3782451.bam -f BAM -g 2.15e9 -n SRX3782451.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3782451.05 # format = BAM # ChIP-seq file = ['SRX3782451.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Fri, 15 Feb 2019 06:32:06: #1 read tag files... INFO @ Fri, 15 Feb 2019 06:32:06: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 06:32:06: # Command line: callpeak -t SRX3782451.bam -f BAM -g 2.15e9 -n SRX3782451.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3782451.20 # format = BAM # ChIP-seq file = ['SRX3782451.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Fri, 15 Feb 2019 06:32:06: #1 read tag files... INFO @ Fri, 15 Feb 2019 06:32:06: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 06:32:06: # Command line: callpeak -t SRX3782451.bam -f BAM -g 2.15e9 -n SRX3782451.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3782451.10 # format = BAM # ChIP-seq file = ['SRX3782451.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Fri, 15 Feb 2019 06:32:06: #1 read tag files... INFO @ Fri, 15 Feb 2019 06:32:06: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 06:32:13: 1000000 INFO @ Fri, 15 Feb 2019 06:32:13: 1000000 INFO @ Fri, 15 Feb 2019 06:32:13: 1000000 INFO @ Fri, 15 Feb 2019 06:32:19: 2000000 INFO @ Fri, 15 Feb 2019 06:32:19: 2000000 INFO @ Fri, 15 Feb 2019 06:32:20: 2000000 INFO @ Fri, 15 Feb 2019 06:32:26: 3000000 INFO @ Fri, 15 Feb 2019 06:32:26: 3000000 INFO @ Fri, 15 Feb 2019 06:32:27: 3000000 INFO @ Fri, 15 Feb 2019 06:32:33: 4000000 INFO @ Fri, 15 Feb 2019 06:32:33: 4000000 INFO @ Fri, 15 Feb 2019 06:32:34: 4000000 INFO @ Fri, 15 Feb 2019 06:32:39: 5000000 INFO @ Fri, 15 Feb 2019 06:32:40: 5000000 INFO @ Fri, 15 Feb 2019 06:32:42: 5000000 INFO @ Fri, 15 Feb 2019 06:32:46: 6000000 INFO @ Fri, 15 Feb 2019 06:32:47: 6000000 INFO @ Fri, 15 Feb 2019 06:32:49: 6000000 INFO @ Fri, 15 Feb 2019 06:32:52: 7000000 INFO @ Fri, 15 Feb 2019 06:32:53: 7000000 INFO @ Fri, 15 Feb 2019 06:32:56: 7000000 INFO @ Fri, 15 Feb 2019 06:32:59: 8000000 INFO @ Fri, 15 Feb 2019 06:33:00: 8000000 INFO @ Fri, 15 Feb 2019 06:33:03: 8000000 INFO @ Fri, 15 Feb 2019 06:33:06: 9000000 INFO @ Fri, 15 Feb 2019 06:33:06: #1 tag size is determined as 46 bps INFO @ Fri, 15 Feb 2019 06:33:06: #1 tag size = 46 INFO @ Fri, 15 Feb 2019 06:33:06: #1 total tags in treatment: 9042933 INFO @ Fri, 15 Feb 2019 06:33:06: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 06:33:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 06:33:06: #1 tags after filtering in treatment: 9042676 INFO @ Fri, 15 Feb 2019 06:33:06: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 06:33:06: #1 finished! INFO @ Fri, 15 Feb 2019 06:33:06: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 06:33:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 06:33:07: 9000000 INFO @ Fri, 15 Feb 2019 06:33:08: #1 tag size is determined as 46 bps INFO @ Fri, 15 Feb 2019 06:33:08: #1 tag size = 46 INFO @ Fri, 15 Feb 2019 06:33:08: #1 total tags in treatment: 9042933 INFO @ Fri, 15 Feb 2019 06:33:08: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 06:33:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 06:33:08: #1 tags after filtering in treatment: 9042676 INFO @ Fri, 15 Feb 2019 06:33:08: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 06:33:08: #1 finished! INFO @ Fri, 15 Feb 2019 06:33:08: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 06:33:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 06:33:10: 9000000 INFO @ Fri, 15 Feb 2019 06:33:11: #1 tag size is determined as 46 bps INFO @ Fri, 15 Feb 2019 06:33:11: #1 tag size = 46 INFO @ Fri, 15 Feb 2019 06:33:11: #1 total tags in treatment: 9042933 INFO @ Fri, 15 Feb 2019 06:33:11: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 06:33:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 06:33:11: #2 number of paired peaks: 100582 INFO @ Fri, 15 Feb 2019 06:33:11: start model_add_line... INFO @ Fri, 15 Feb 2019 06:33:11: #1 tags after filtering in treatment: 9042676 INFO @ Fri, 15 Feb 2019 06:33:11: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 06:33:11: #1 finished! INFO @ Fri, 15 Feb 2019 06:33:11: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 06:33:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 06:33:11: start X-correlation... INFO @ Fri, 15 Feb 2019 06:33:11: end of X-cor INFO @ Fri, 15 Feb 2019 06:33:11: #2 finished! INFO @ Fri, 15 Feb 2019 06:33:11: #2 predicted fragment length is 217 bps INFO @ Fri, 15 Feb 2019 06:33:11: #2 alternative fragment length(s) may be 217 bps INFO @ Fri, 15 Feb 2019 06:33:11: #2.2 Generate R script for model : SRX3782451.10_model.r INFO @ Fri, 15 Feb 2019 06:33:11: #3 Call peaks... INFO @ Fri, 15 Feb 2019 06:33:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 06:33:12: #2 number of paired peaks: 100582 INFO @ Fri, 15 Feb 2019 06:33:12: start model_add_line... INFO @ Fri, 15 Feb 2019 06:33:12: start X-correlation... INFO @ Fri, 15 Feb 2019 06:33:12: end of X-cor INFO @ Fri, 15 Feb 2019 06:33:12: #2 finished! INFO @ Fri, 15 Feb 2019 06:33:12: #2 predicted fragment length is 217 bps INFO @ Fri, 15 Feb 2019 06:33:12: #2 alternative fragment length(s) may be 217 bps INFO @ Fri, 15 Feb 2019 06:33:12: #2.2 Generate R script for model : SRX3782451.20_model.r INFO @ Fri, 15 Feb 2019 06:33:12: #3 Call peaks... INFO @ Fri, 15 Feb 2019 06:33:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 06:33:15: #2 number of paired peaks: 100582 INFO @ Fri, 15 Feb 2019 06:33:15: start model_add_line... INFO @ Fri, 15 Feb 2019 06:33:15: start X-correlation... INFO @ Fri, 15 Feb 2019 06:33:15: end of X-cor INFO @ Fri, 15 Feb 2019 06:33:15: #2 finished! INFO @ Fri, 15 Feb 2019 06:33:15: #2 predicted fragment length is 217 bps INFO @ Fri, 15 Feb 2019 06:33:15: #2 alternative fragment length(s) may be 217 bps INFO @ Fri, 15 Feb 2019 06:33:15: #2.2 Generate R script for model : SRX3782451.05_model.r INFO @ Fri, 15 Feb 2019 06:33:15: #3 Call peaks... INFO @ Fri, 15 Feb 2019 06:33:15: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 06:33:34: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 06:33:35: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 06:33:37: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 06:33:48: #4 Write output xls file... SRX3782451.20_peaks.xls INFO @ Fri, 15 Feb 2019 06:33:48: #4 Write peak in narrowPeak format file... SRX3782451.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 06:33:48: #4 Write summits bed file... SRX3782451.20_summits.bed INFO @ Fri, 15 Feb 2019 06:33:48: Done! pass1 - making usageList (17 chroms): 2 millis pass2 - checking and writing primary data (110 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 06:33:49: #4 Write output xls file... SRX3782451.10_peaks.xls INFO @ Fri, 15 Feb 2019 06:33:49: #4 Write peak in narrowPeak format file... SRX3782451.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 06:33:49: #4 Write summits bed file... SRX3782451.10_summits.bed INFO @ Fri, 15 Feb 2019 06:33:49: Done! pass1 - making usageList (30 chroms): 2 millis pass2 - checking and writing primary data (2929 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 06:33:50: #4 Write output xls file... SRX3782451.05_peaks.xls INFO @ Fri, 15 Feb 2019 06:33:51: #4 Write peak in narrowPeak format file... SRX3782451.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 06:33:51: #4 Write summits bed file... SRX3782451.05_summits.bed INFO @ Fri, 15 Feb 2019 06:33:51: Done! pass1 - making usageList (64 chroms): 5 millis pass2 - checking and writing primary data (13870 records, 4 fields): 19 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。