Job ID = 8696844 sra ファイルのダウンロード中... Completed: 448861K bytes transferred in 7 seconds (479413K bits/sec), in 1 file, 2 directories. % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- 0:00:06 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:07 --:--:-- 0 100 22575 0 22575 0 0 2621 0 --:--:-- 0:00:08 --:--:-- 11648 100 31434 0 31434 0 0 3577 0 --:--:-- 0:00:08 --:--:-- 14890 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 38793541 spots for /home/okishinya/chipatlas/results/dm3/SRX110782/SRR388364.sra Written 38793541 spots total 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: 00:34:25 38793541 reads; of these: 38793541 (100.00%) were unpaired; of these: 9713231 (25.04%) aligned 0 times 14152732 (36.48%) aligned exactly 1 time 14927578 (38.48%) aligned >1 times 74.96% overall alignment rate Time searching: 00:34:25 Overall time: 00:34:25 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] 22065178 / 29080310 = 0.7588 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, 10 Mar 2017 13:02:04: # Command line: callpeak -t SRX110782.bam -f BAM -g dm -n SRX110782.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX110782.05 # format = BAM # ChIP-seq file = ['SRX110782.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 INFO @ Fri, 10 Mar 2017 13:02:04: #1 read tag files... INFO @ Fri, 10 Mar 2017 13:02:04: #1 read treatment tags... INFO @ Fri, 10 Mar 2017 13:02:04: # Command line: callpeak -t SRX110782.bam -f BAM -g dm -n SRX110782.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX110782.20 # format = BAM # ChIP-seq file = ['SRX110782.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 INFO @ Fri, 10 Mar 2017 13:02:04: #1 read tag files... INFO @ Fri, 10 Mar 2017 13:02:04: #1 read treatment tags... INFO @ Fri, 10 Mar 2017 13:02:04: # Command line: callpeak -t SRX110782.bam -f BAM -g dm -n SRX110782.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX110782.10 # format = BAM # ChIP-seq file = ['SRX110782.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 INFO @ Fri, 10 Mar 2017 13:02:04: #1 read tag files... INFO @ Fri, 10 Mar 2017 13:02:04: #1 read treatment tags... INFO @ Fri, 10 Mar 2017 13:02:11: 1000000 INFO @ Fri, 10 Mar 2017 13:02:12: 1000000 INFO @ Fri, 10 Mar 2017 13:02:13: 1000000 INFO @ Fri, 10 Mar 2017 13:02:18: 2000000 INFO @ Fri, 10 Mar 2017 13:02:19: 2000000 INFO @ Fri, 10 Mar 2017 13:02:23: 2000000 INFO @ Fri, 10 Mar 2017 13:02:24: 3000000 INFO @ Fri, 10 Mar 2017 13:02:26: 3000000 INFO @ Fri, 10 Mar 2017 13:02:31: 4000000 INFO @ Fri, 10 Mar 2017 13:02:31: 3000000 INFO @ Fri, 10 Mar 2017 13:02:33: 4000000 INFO @ Fri, 10 Mar 2017 13:02:38: 5000000 INFO @ Fri, 10 Mar 2017 13:02:39: 4000000 INFO @ Fri, 10 Mar 2017 13:02:40: 5000000 INFO @ Fri, 10 Mar 2017 13:02:45: 6000000 INFO @ Fri, 10 Mar 2017 13:02:47: 5000000 INFO @ Fri, 10 Mar 2017 13:02:48: 6000000 INFO @ Fri, 10 Mar 2017 13:02:52: 7000000 INFO @ Fri, 10 Mar 2017 13:02:53: #1 tag size is determined as 18 bps INFO @ Fri, 10 Mar 2017 13:02:53: #1 tag size = 18 INFO @ Fri, 10 Mar 2017 13:02:53: #1 total tags in treatment: 7015132 INFO @ Fri, 10 Mar 2017 13:02:53: #1 user defined the maximum tags... INFO @ Fri, 10 Mar 2017 13:02:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Mar 2017 13:02:53: 6000000 INFO @ Fri, 10 Mar 2017 13:02:54: #1 tags after filtering in treatment: 7015132 INFO @ Fri, 10 Mar 2017 13:02:54: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Mar 2017 13:02:54: #1 finished! INFO @ Fri, 10 Mar 2017 13:02:54: #2 Build Peak Model... INFO @ Fri, 10 Mar 2017 13:02:55: 7000000 INFO @ Fri, 10 Mar 2017 13:02:56: #1 tag size is determined as 18 bps INFO @ Fri, 10 Mar 2017 13:02:56: #1 tag size = 18 INFO @ Fri, 10 Mar 2017 13:02:56: #1 total tags in treatment: 7015132 INFO @ Fri, 10 Mar 2017 13:02:56: #1 user defined the maximum tags... INFO @ Fri, 10 Mar 2017 13:02:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Mar 2017 13:02:56: #2 number of paired peaks: 1487 INFO @ Fri, 10 Mar 2017 13:02:56: start model_add_line... INFO @ Fri, 10 Mar 2017 13:02:57: #1 tags after filtering in treatment: 7015132 INFO @ Fri, 10 Mar 2017 13:02:57: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Mar 2017 13:02:57: #1 finished! INFO @ Fri, 10 Mar 2017 13:02:57: #2 Build Peak Model... INFO @ Fri, 10 Mar 2017 13:02:59: #2 number of paired peaks: 1487 INFO @ Fri, 10 Mar 2017 13:02:59: start model_add_line... INFO @ Fri, 10 Mar 2017 13:03:00: 7000000 INFO @ Fri, 10 Mar 2017 13:03:00: #1 tag size is determined as 18 bps INFO @ Fri, 10 Mar 2017 13:03:00: #1 tag size = 18 INFO @ Fri, 10 Mar 2017 13:03:00: #1 total tags in treatment: 7015132 INFO @ Fri, 10 Mar 2017 13:03:00: #1 user defined the maximum tags... INFO @ Fri, 10 Mar 2017 13:03:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Mar 2017 13:03:02: #1 tags after filtering in treatment: 7015132 INFO @ Fri, 10 Mar 2017 13:03:02: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Mar 2017 13:03:02: #1 finished! INFO @ Fri, 10 Mar 2017 13:03:02: #2 Build Peak Model... INFO @ Fri, 10 Mar 2017 13:03:04: #2 number of paired peaks: 1487 INFO @ Fri, 10 Mar 2017 13:03:04: start model_add_line... INFO @ Fri, 10 Mar 2017 13:03:08: start X-correlation... INFO @ Fri, 10 Mar 2017 13:03:08: end of X-cor INFO @ Fri, 10 Mar 2017 13:03:08: #2 finished! INFO @ Fri, 10 Mar 2017 13:03:08: #2 predicted fragment length is 156 bps INFO @ Fri, 10 Mar 2017 13:03:08: #2 alternative fragment length(s) may be 156 bps INFO @ Fri, 10 Mar 2017 13:03:08: #2.2 Generate R script for model : SRX110782.20_model.r INFO @ Fri, 10 Mar 2017 13:03:08: #3 Call peaks... INFO @ Fri, 10 Mar 2017 13:03:08: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Mar 2017 13:03:11: start X-correlation... INFO @ Fri, 10 Mar 2017 13:03:11: end of X-cor INFO @ Fri, 10 Mar 2017 13:03:11: #2 finished! INFO @ Fri, 10 Mar 2017 13:03:11: #2 predicted fragment length is 156 bps INFO @ Fri, 10 Mar 2017 13:03:11: #2 alternative fragment length(s) may be 156 bps INFO @ Fri, 10 Mar 2017 13:03:11: #2.2 Generate R script for model : SRX110782.05_model.r INFO @ Fri, 10 Mar 2017 13:03:11: #3 Call peaks... INFO @ Fri, 10 Mar 2017 13:03:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Mar 2017 13:03:17: start X-correlation... INFO @ Fri, 10 Mar 2017 13:03:17: end of X-cor INFO @ Fri, 10 Mar 2017 13:03:17: #2 finished! INFO @ Fri, 10 Mar 2017 13:03:17: #2 predicted fragment length is 156 bps INFO @ Fri, 10 Mar 2017 13:03:17: #2 alternative fragment length(s) may be 156 bps INFO @ Fri, 10 Mar 2017 13:03:17: #2.2 Generate R script for model : SRX110782.10_model.r INFO @ Fri, 10 Mar 2017 13:03:17: #3 Call peaks... INFO @ Fri, 10 Mar 2017 13:03:17: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Mar 2017 13:04:01: #3 Call peaks for each chromosome... INFO @ Fri, 10 Mar 2017 13:04:01: #3 Call peaks for each chromosome... INFO @ Fri, 10 Mar 2017 13:04:07: #3 Call peaks for each chromosome... INFO @ Fri, 10 Mar 2017 13:04:41: #4 Write output xls file... SRX110782.20_peaks.xls INFO @ Fri, 10 Mar 2017 13:04:41: #4 Write peak in narrowPeak format file... SRX110782.20_peaks.narrowPeak INFO @ Fri, 10 Mar 2017 13:04:41: #4 Write summits bed file... SRX110782.20_summits.bed INFO @ Fri, 10 Mar 2017 13:04:41: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1165 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 10 Mar 2017 13:04:42: #4 Write output xls file... SRX110782.05_peaks.xls INFO @ Fri, 10 Mar 2017 13:04:42: #4 Write peak in narrowPeak format file... SRX110782.05_peaks.narrowPeak INFO @ Fri, 10 Mar 2017 13:04:42: #4 Write summits bed file... SRX110782.05_summits.bed INFO @ Fri, 10 Mar 2017 13:04:42: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2748 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 10 Mar 2017 13:04:52: #4 Write output xls file... SRX110782.10_peaks.xls INFO @ Fri, 10 Mar 2017 13:04:52: #4 Write peak in narrowPeak format file... SRX110782.10_peaks.narrowPeak INFO @ Fri, 10 Mar 2017 13:04:52: #4 Write summits bed file... SRX110782.10_summits.bed INFO @ Fri, 10 Mar 2017 13:04:52: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1732 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。