Job ID = 10480663 sra ファイルのダウンロード中... Completed: 558823K bytes transferred in 55 seconds (82208K 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... Written 16775702 spots for /home/okishinya/chipatlas/results/dm3/SRX2832099/SRR5573763.sra Written 16775702 spots total 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: 00:05:04 16775702 reads; of these: 16775702 (100.00%) were unpaired; of these: 331915 (1.98%) aligned 0 times 12954312 (77.22%) aligned exactly 1 time 3489475 (20.80%) aligned >1 times 98.02% overall alignment rate Time searching: 00:05:05 Overall time: 00:05:05 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] 4706873 / 16443787 = 0.2862 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, 16 Mar 2018 07:30:00: # Command line: callpeak -t SRX2832099.bam -f BAM -g dm -n SRX2832099.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2832099.20 # format = BAM # ChIP-seq file = ['SRX2832099.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 @ Fri, 16 Mar 2018 07:30:00: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:30:00: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:30:00: # Command line: callpeak -t SRX2832099.bam -f BAM -g dm -n SRX2832099.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2832099.10 # format = BAM # ChIP-seq file = ['SRX2832099.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 @ Fri, 16 Mar 2018 07:30:00: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:30:00: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:30:00: # Command line: callpeak -t SRX2832099.bam -f BAM -g dm -n SRX2832099.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2832099.05 # format = BAM # ChIP-seq file = ['SRX2832099.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 @ Fri, 16 Mar 2018 07:30:00: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:30:00: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:30:06: 1000000 INFO @ Fri, 16 Mar 2018 07:30:06: 1000000 INFO @ Fri, 16 Mar 2018 07:30:06: 1000000 INFO @ Fri, 16 Mar 2018 07:30:12: 2000000 INFO @ Fri, 16 Mar 2018 07:30:12: 2000000 INFO @ Fri, 16 Mar 2018 07:30:12: 2000000 INFO @ Fri, 16 Mar 2018 07:30:18: 3000000 INFO @ Fri, 16 Mar 2018 07:30:18: 3000000 INFO @ Fri, 16 Mar 2018 07:30:19: 3000000 INFO @ Fri, 16 Mar 2018 07:30:24: 4000000 INFO @ Fri, 16 Mar 2018 07:30:24: 4000000 INFO @ Fri, 16 Mar 2018 07:30:25: 4000000 INFO @ Fri, 16 Mar 2018 07:30:31: 5000000 INFO @ Fri, 16 Mar 2018 07:30:31: 5000000 INFO @ Fri, 16 Mar 2018 07:30:32: 5000000 INFO @ Fri, 16 Mar 2018 07:30:37: 6000000 INFO @ Fri, 16 Mar 2018 07:30:37: 6000000 INFO @ Fri, 16 Mar 2018 07:30:38: 6000000 INFO @ Fri, 16 Mar 2018 07:30:43: 7000000 INFO @ Fri, 16 Mar 2018 07:30:43: 7000000 INFO @ Fri, 16 Mar 2018 07:30:45: 7000000 INFO @ Fri, 16 Mar 2018 07:30:49: 8000000 INFO @ Fri, 16 Mar 2018 07:30:50: 8000000 INFO @ Fri, 16 Mar 2018 07:30:52: 8000000 INFO @ Fri, 16 Mar 2018 07:30:55: 9000000 INFO @ Fri, 16 Mar 2018 07:30:56: 9000000 INFO @ Fri, 16 Mar 2018 07:30:58: 9000000 INFO @ Fri, 16 Mar 2018 07:31:02: 10000000 INFO @ Fri, 16 Mar 2018 07:31:02: 10000000 INFO @ Fri, 16 Mar 2018 07:31:05: 10000000 INFO @ Fri, 16 Mar 2018 07:31:08: 11000000 INFO @ Fri, 16 Mar 2018 07:31:09: 11000000 INFO @ Fri, 16 Mar 2018 07:31:11: 11000000 INFO @ Fri, 16 Mar 2018 07:31:13: #1 tag size is determined as 50 bps INFO @ Fri, 16 Mar 2018 07:31:13: #1 tag size = 50 INFO @ Fri, 16 Mar 2018 07:31:13: #1 total tags in treatment: 11736914 INFO @ Fri, 16 Mar 2018 07:31:13: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:31:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 07:31:13: #1 tags after filtering in treatment: 11736914 INFO @ Fri, 16 Mar 2018 07:31:13: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:31:13: #1 finished! INFO @ Fri, 16 Mar 2018 07:31:13: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:31:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:31:14: #1 tag size is determined as 50 bps INFO @ Fri, 16 Mar 2018 07:31:14: #1 tag size = 50 INFO @ Fri, 16 Mar 2018 07:31:14: #1 total tags in treatment: 11736914 INFO @ Fri, 16 Mar 2018 07:31:14: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:31:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 07:31:14: #1 tags after filtering in treatment: 11736914 INFO @ Fri, 16 Mar 2018 07:31:14: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:31:14: #1 finished! INFO @ Fri, 16 Mar 2018 07:31:14: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:31:14: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:31:14: #2 number of paired peaks: 4508 INFO @ Fri, 16 Mar 2018 07:31:14: start model_add_line... INFO @ Fri, 16 Mar 2018 07:31:14: start X-correlation... INFO @ Fri, 16 Mar 2018 07:31:14: end of X-cor INFO @ Fri, 16 Mar 2018 07:31:14: #2 finished! INFO @ Fri, 16 Mar 2018 07:31:14: #2 predicted fragment length is 168 bps INFO @ Fri, 16 Mar 2018 07:31:14: #2 alternative fragment length(s) may be 4,168 bps INFO @ Fri, 16 Mar 2018 07:31:14: #2.2 Generate R script for model : SRX2832099.05_model.r INFO @ Fri, 16 Mar 2018 07:31:14: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:31:14: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:31:15: #2 number of paired peaks: 4508 INFO @ Fri, 16 Mar 2018 07:31:15: start model_add_line... INFO @ Fri, 16 Mar 2018 07:31:15: start X-correlation... INFO @ Fri, 16 Mar 2018 07:31:15: end of X-cor INFO @ Fri, 16 Mar 2018 07:31:15: #2 finished! INFO @ Fri, 16 Mar 2018 07:31:15: #2 predicted fragment length is 168 bps INFO @ Fri, 16 Mar 2018 07:31:15: #2 alternative fragment length(s) may be 4,168 bps INFO @ Fri, 16 Mar 2018 07:31:15: #2.2 Generate R script for model : SRX2832099.10_model.r INFO @ Fri, 16 Mar 2018 07:31:15: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:31:15: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:31:16: #1 tag size is determined as 50 bps INFO @ Fri, 16 Mar 2018 07:31:16: #1 tag size = 50 INFO @ Fri, 16 Mar 2018 07:31:16: #1 total tags in treatment: 11736914 INFO @ Fri, 16 Mar 2018 07:31:16: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:31:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 07:31:16: #1 tags after filtering in treatment: 11736914 INFO @ Fri, 16 Mar 2018 07:31:16: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:31:16: #1 finished! INFO @ Fri, 16 Mar 2018 07:31:16: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:31:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:31:18: #2 number of paired peaks: 4508 INFO @ Fri, 16 Mar 2018 07:31:18: start model_add_line... INFO @ Fri, 16 Mar 2018 07:31:18: start X-correlation... INFO @ Fri, 16 Mar 2018 07:31:18: end of X-cor INFO @ Fri, 16 Mar 2018 07:31:18: #2 finished! INFO @ Fri, 16 Mar 2018 07:31:18: #2 predicted fragment length is 168 bps INFO @ Fri, 16 Mar 2018 07:31:18: #2 alternative fragment length(s) may be 4,168 bps INFO @ Fri, 16 Mar 2018 07:31:18: #2.2 Generate R script for model : SRX2832099.20_model.r INFO @ Fri, 16 Mar 2018 07:31:18: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:31:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:31:45: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:31:46: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:31:47: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:32:00: #4 Write output xls file... SRX2832099.10_peaks.xls INFO @ Fri, 16 Mar 2018 07:32:00: #4 Write peak in narrowPeak format file... SRX2832099.10_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:32:00: #4 Write summits bed file... SRX2832099.10_summits.bed INFO @ Fri, 16 Mar 2018 07:32:00: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5489 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 07:32:02: #4 Write output xls file... SRX2832099.05_peaks.xls INFO @ Fri, 16 Mar 2018 07:32:02: #4 Write peak in narrowPeak format file... SRX2832099.05_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:32:02: #4 Write summits bed file... SRX2832099.05_summits.bed INFO @ Fri, 16 Mar 2018 07:32:02: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (10892 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 07:32:03: #4 Write output xls file... SRX2832099.20_peaks.xls INFO @ Fri, 16 Mar 2018 07:32:03: #4 Write peak in narrowPeak format file... SRX2832099.20_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:32:03: #4 Write summits bed file... SRX2832099.20_summits.bed INFO @ Fri, 16 Mar 2018 07:32:03: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1850 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。