Job ID = 8696821 sra ファイルのダウンロード中... Completed: 195945K bytes transferred in 27 seconds (59084K 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 7663 0 7663 0 0 960 0 --:--:-- 0:00:07 --:--:-- 5991 100 29619 0 29619 0 0 3347 0 --:--:-- 0:00:08 --:--:-- 13776 100 31490 0 31490 0 0 3558 0 --:--:-- 0:00:08 --:--:-- 14639 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 16794645 spots for /home/okishinya/chipatlas/results/dm3/SRX110759/SRR388341.sra Written 16794645 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: 00:14:37 16794645 reads; of these: 16794645 (100.00%) were unpaired; of these: 5285475 (31.47%) aligned 0 times 6196914 (36.90%) aligned exactly 1 time 5312256 (31.63%) aligned >1 times 68.53% overall alignment rate Time searching: 00:14:37 Overall time: 00:14:37 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] 4089209 / 11509170 = 0.3553 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 12:16:32: # Command line: callpeak -t SRX110759.bam -f BAM -g dm -n SRX110759.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX110759.05 # format = BAM # ChIP-seq file = ['SRX110759.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 12:16:32: #1 read tag files... INFO @ Fri, 10 Mar 2017 12:16:32: #1 read treatment tags... INFO @ Fri, 10 Mar 2017 12:16:32: # Command line: callpeak -t SRX110759.bam -f BAM -g dm -n SRX110759.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX110759.10 # format = BAM # ChIP-seq file = ['SRX110759.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 12:16:32: #1 read tag files... INFO @ Fri, 10 Mar 2017 12:16:32: #1 read treatment tags... INFO @ Fri, 10 Mar 2017 12:16:32: # Command line: callpeak -t SRX110759.bam -f BAM -g dm -n SRX110759.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX110759.20 # format = BAM # ChIP-seq file = ['SRX110759.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 12:16:32: #1 read tag files... INFO @ Fri, 10 Mar 2017 12:16:32: #1 read treatment tags... INFO @ Fri, 10 Mar 2017 12:16:41: 1000000 INFO @ Fri, 10 Mar 2017 12:16:49: 2000000 INFO @ Fri, 10 Mar 2017 12:16:58: 3000000 INFO @ Fri, 10 Mar 2017 12:17:00: 1000000 INFO @ Fri, 10 Mar 2017 12:17:07: 4000000 INFO @ Fri, 10 Mar 2017 12:17:16: 5000000 INFO @ Fri, 10 Mar 2017 12:17:17: 2000000 INFO @ Fri, 10 Mar 2017 12:17:19: 1000000 INFO @ Fri, 10 Mar 2017 12:17:25: 6000000 INFO @ Fri, 10 Mar 2017 12:17:33: 7000000 INFO @ Fri, 10 Mar 2017 12:17:34: 3000000 INFO @ Fri, 10 Mar 2017 12:17:37: #1 tag size is determined as 18 bps INFO @ Fri, 10 Mar 2017 12:17:37: #1 tag size = 18 INFO @ Fri, 10 Mar 2017 12:17:37: #1 total tags in treatment: 7419961 INFO @ Fri, 10 Mar 2017 12:17:37: #1 user defined the maximum tags... INFO @ Fri, 10 Mar 2017 12:17:37: #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 12:17:39: #1 tags after filtering in treatment: 7419961 INFO @ Fri, 10 Mar 2017 12:17:39: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Mar 2017 12:17:39: #1 finished! INFO @ Fri, 10 Mar 2017 12:17:39: #2 Build Peak Model... INFO @ Fri, 10 Mar 2017 12:17:41: #2 number of paired peaks: 3619 INFO @ Fri, 10 Mar 2017 12:17:41: start model_add_line... INFO @ Fri, 10 Mar 2017 12:17:52: 4000000 INFO @ Fri, 10 Mar 2017 12:18:04: 2000000 INFO @ Fri, 10 Mar 2017 12:18:08: start X-correlation... INFO @ Fri, 10 Mar 2017 12:18:08: end of X-cor INFO @ Fri, 10 Mar 2017 12:18:08: #2 finished! INFO @ Fri, 10 Mar 2017 12:18:08: #2 predicted fragment length is 80 bps INFO @ Fri, 10 Mar 2017 12:18:08: #2 alternative fragment length(s) may be 80 bps INFO @ Fri, 10 Mar 2017 12:18:08: #2.2 Generate R script for model : SRX110759.20_model.r INFO @ Fri, 10 Mar 2017 12:18:08: #3 Call peaks... INFO @ Fri, 10 Mar 2017 12:18:08: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Mar 2017 12:18:10: 5000000 INFO @ Fri, 10 Mar 2017 12:18:27: 6000000 INFO @ Fri, 10 Mar 2017 12:18:42: 7000000 INFO @ Fri, 10 Mar 2017 12:18:49: #1 tag size is determined as 18 bps INFO @ Fri, 10 Mar 2017 12:18:49: #1 tag size = 18 INFO @ Fri, 10 Mar 2017 12:18:49: #1 total tags in treatment: 7419961 INFO @ Fri, 10 Mar 2017 12:18:49: #1 user defined the maximum tags... INFO @ Fri, 10 Mar 2017 12:18:49: #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 12:18:51: #1 tags after filtering in treatment: 7419961 INFO @ Fri, 10 Mar 2017 12:18:51: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Mar 2017 12:18:51: #1 finished! INFO @ Fri, 10 Mar 2017 12:18:51: #2 Build Peak Model... INFO @ Fri, 10 Mar 2017 12:18:53: #2 number of paired peaks: 3619 INFO @ Fri, 10 Mar 2017 12:18:53: start model_add_line... INFO @ Fri, 10 Mar 2017 12:18:53: 3000000 INFO @ Fri, 10 Mar 2017 12:19:01: #3 Call peaks for each chromosome... INFO @ Fri, 10 Mar 2017 12:19:21: 4000000 INFO @ Fri, 10 Mar 2017 12:19:29: start X-correlation... INFO @ Fri, 10 Mar 2017 12:19:29: end of X-cor INFO @ Fri, 10 Mar 2017 12:19:29: #2 finished! INFO @ Fri, 10 Mar 2017 12:19:29: #2 predicted fragment length is 80 bps INFO @ Fri, 10 Mar 2017 12:19:29: #2 alternative fragment length(s) may be 80 bps INFO @ Fri, 10 Mar 2017 12:19:29: #2.2 Generate R script for model : SRX110759.05_model.r INFO @ Fri, 10 Mar 2017 12:19:29: #3 Call peaks... INFO @ Fri, 10 Mar 2017 12:19:29: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Mar 2017 12:19:39: #4 Write output xls file... SRX110759.20_peaks.xls INFO @ Fri, 10 Mar 2017 12:19:40: #4 Write peak in narrowPeak format file... SRX110759.20_peaks.narrowPeak INFO @ Fri, 10 Mar 2017 12:19:40: #4 Write summits bed file... SRX110759.20_summits.bed INFO @ Fri, 10 Mar 2017 12:19:40: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (3560 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Mar 2017 12:20:12: 5000000 BigWig に変換しました。 INFO @ Fri, 10 Mar 2017 12:20:55: #3 Call peaks for each chromosome... INFO @ Fri, 10 Mar 2017 12:21:07: 6000000 INFO @ Fri, 10 Mar 2017 12:21:53: 7000000 INFO @ Fri, 10 Mar 2017 12:22:00: #4 Write output xls file... SRX110759.05_peaks.xls INFO @ Fri, 10 Mar 2017 12:22:00: #4 Write peak in narrowPeak format file... SRX110759.05_peaks.narrowPeak INFO @ Fri, 10 Mar 2017 12:22:00: #4 Write summits bed file... SRX110759.05_summits.bed INFO @ Fri, 10 Mar 2017 12:22:00: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (7808 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Fri, 10 Mar 2017 12:22:05: #1 tag size is determined as 18 bps INFO @ Fri, 10 Mar 2017 12:22:05: #1 tag size = 18 INFO @ Fri, 10 Mar 2017 12:22:05: #1 total tags in treatment: 7419961 INFO @ Fri, 10 Mar 2017 12:22:05: #1 user defined the maximum tags... INFO @ Fri, 10 Mar 2017 12:22:05: #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 12:22:06: #1 tags after filtering in treatment: 7419961 INFO @ Fri, 10 Mar 2017 12:22:06: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Mar 2017 12:22:06: #1 finished! INFO @ Fri, 10 Mar 2017 12:22:06: #2 Build Peak Model... INFO @ Fri, 10 Mar 2017 12:22:09: #2 number of paired peaks: 3619 INFO @ Fri, 10 Mar 2017 12:22:09: start model_add_line... INFO @ Fri, 10 Mar 2017 12:22:47: start X-correlation... INFO @ Fri, 10 Mar 2017 12:22:47: end of X-cor INFO @ Fri, 10 Mar 2017 12:22:47: #2 finished! INFO @ Fri, 10 Mar 2017 12:22:47: #2 predicted fragment length is 80 bps INFO @ Fri, 10 Mar 2017 12:22:47: #2 alternative fragment length(s) may be 80 bps INFO @ Fri, 10 Mar 2017 12:22:47: #2.2 Generate R script for model : SRX110759.10_model.r INFO @ Fri, 10 Mar 2017 12:22:47: #3 Call peaks... INFO @ Fri, 10 Mar 2017 12:22:47: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Mar 2017 12:24:11: #3 Call peaks for each chromosome... INFO @ Fri, 10 Mar 2017 12:25:10: #4 Write output xls file... SRX110759.10_peaks.xls INFO @ Fri, 10 Mar 2017 12:25:10: #4 Write peak in narrowPeak format file... SRX110759.10_peaks.narrowPeak INFO @ Fri, 10 Mar 2017 12:25:10: #4 Write summits bed file... SRX110759.10_summits.bed INFO @ Fri, 10 Mar 2017 12:25:10: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (5396 records, 4 fields): 20 millis CompletedMACS2peakCalling