Job ID = 8696822 sra ファイルのダウンロード中... Completed: 474586K bytes transferred in 42 seconds (92526K 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 14581 0 14581 0 0 1862 0 --:--:-- 0:00:07 --:--:-- 13340 100 31490 0 31490 0 0 3693 0 --:--:-- 0:00:08 --:--:-- 17592 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 39773699 spots for /home/okishinya/chipatlas/results/dm3/SRX110760/SRR388342.sra Written 39773699 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: 00:36:36 39773699 reads; of these: 39773699 (100.00%) were unpaired; of these: 11466902 (28.83%) aligned 0 times 15773447 (39.66%) aligned exactly 1 time 12533350 (31.51%) aligned >1 times 71.17% overall alignment rate Time searching: 00:36:36 Overall time: 00:36:36 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] 15641233 / 28306797 = 0.5526 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 12:42:59: # Command line: callpeak -t SRX110760.bam -f BAM -g dm -n SRX110760.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX110760.20 # format = BAM # ChIP-seq file = ['SRX110760.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 12:42:59: #1 read tag files... INFO @ Fri, 10 Mar 2017 12:42:59: #1 read treatment tags... INFO @ Fri, 10 Mar 2017 12:42:59: # Command line: callpeak -t SRX110760.bam -f BAM -g dm -n SRX110760.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX110760.10 # format = BAM # ChIP-seq file = ['SRX110760.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 12:42:59: #1 read tag files... INFO @ Fri, 10 Mar 2017 12:42:59: #1 read treatment tags... INFO @ Fri, 10 Mar 2017 12:42:59: # Command line: callpeak -t SRX110760.bam -f BAM -g dm -n SRX110760.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX110760.05 # format = BAM # ChIP-seq file = ['SRX110760.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 12:42:59: #1 read tag files... INFO @ Fri, 10 Mar 2017 12:42:59: #1 read treatment tags... INFO @ Fri, 10 Mar 2017 12:43:06: 1000000 INFO @ Fri, 10 Mar 2017 12:43:07: 1000000 INFO @ Fri, 10 Mar 2017 12:43:08: 1000000 INFO @ Fri, 10 Mar 2017 12:43:13: 2000000 INFO @ Fri, 10 Mar 2017 12:43:15: 2000000 INFO @ Fri, 10 Mar 2017 12:43:19: 3000000 INFO @ Fri, 10 Mar 2017 12:43:20: 2000000 INFO @ Fri, 10 Mar 2017 12:43:24: 3000000 INFO @ Fri, 10 Mar 2017 12:43:25: 4000000 INFO @ Fri, 10 Mar 2017 12:43:31: 5000000 INFO @ Fri, 10 Mar 2017 12:43:32: 3000000 INFO @ Fri, 10 Mar 2017 12:43:34: 4000000 INFO @ Fri, 10 Mar 2017 12:43:37: 6000000 INFO @ Fri, 10 Mar 2017 12:43:43: 5000000 INFO @ Fri, 10 Mar 2017 12:43:43: 7000000 INFO @ Fri, 10 Mar 2017 12:43:43: 4000000 INFO @ Fri, 10 Mar 2017 12:43:49: 8000000 INFO @ Fri, 10 Mar 2017 12:43:52: 6000000 INFO @ Fri, 10 Mar 2017 12:43:55: 5000000 INFO @ Fri, 10 Mar 2017 12:43:55: 9000000 INFO @ Fri, 10 Mar 2017 12:44:01: 7000000 INFO @ Fri, 10 Mar 2017 12:44:03: 10000000 INFO @ Fri, 10 Mar 2017 12:44:07: 6000000 INFO @ Fri, 10 Mar 2017 12:44:10: 11000000 INFO @ Fri, 10 Mar 2017 12:44:10: 8000000 INFO @ Fri, 10 Mar 2017 12:44:17: 12000000 INFO @ Fri, 10 Mar 2017 12:44:18: 7000000 INFO @ Fri, 10 Mar 2017 12:44:19: 9000000 INFO @ Fri, 10 Mar 2017 12:44:22: #1 tag size is determined as 18 bps INFO @ Fri, 10 Mar 2017 12:44:22: #1 tag size = 18 INFO @ Fri, 10 Mar 2017 12:44:22: #1 total tags in treatment: 12665564 INFO @ Fri, 10 Mar 2017 12:44:22: #1 user defined the maximum tags... INFO @ Fri, 10 Mar 2017 12:44:22: #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 12:44:25: #1 tags after filtering in treatment: 12665564 INFO @ Fri, 10 Mar 2017 12:44:25: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Mar 2017 12:44:25: #1 finished! INFO @ Fri, 10 Mar 2017 12:44:25: #2 Build Peak Model... INFO @ Fri, 10 Mar 2017 12:44:28: 10000000 INFO @ Fri, 10 Mar 2017 12:44:29: #2 number of paired peaks: 4824 INFO @ Fri, 10 Mar 2017 12:44:29: start model_add_line... INFO @ Fri, 10 Mar 2017 12:44:30: 8000000 INFO @ Fri, 10 Mar 2017 12:44:34: 11000000 INFO @ Fri, 10 Mar 2017 12:44:41: 9000000 INFO @ Fri, 10 Mar 2017 12:44:41: 12000000 INFO @ Fri, 10 Mar 2017 12:44:46: #1 tag size is determined as 18 bps INFO @ Fri, 10 Mar 2017 12:44:46: #1 tag size = 18 INFO @ Fri, 10 Mar 2017 12:44:46: #1 total tags in treatment: 12665564 INFO @ Fri, 10 Mar 2017 12:44:46: #1 user defined the maximum tags... INFO @ Fri, 10 Mar 2017 12:44:46: #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 12:44:49: #1 tags after filtering in treatment: 12665564 INFO @ Fri, 10 Mar 2017 12:44:49: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Mar 2017 12:44:49: #1 finished! INFO @ Fri, 10 Mar 2017 12:44:49: #2 Build Peak Model... INFO @ Fri, 10 Mar 2017 12:44:51: 10000000 INFO @ Fri, 10 Mar 2017 12:44:52: #2 number of paired peaks: 4824 INFO @ Fri, 10 Mar 2017 12:44:52: start model_add_line... INFO @ Fri, 10 Mar 2017 12:45:03: 11000000 INFO @ Fri, 10 Mar 2017 12:45:18: 12000000 INFO @ Fri, 10 Mar 2017 12:45:19: start X-correlation... INFO @ Fri, 10 Mar 2017 12:45:19: end of X-cor INFO @ Fri, 10 Mar 2017 12:45:19: #2 finished! INFO @ Fri, 10 Mar 2017 12:45:19: #2 predicted fragment length is 80 bps INFO @ Fri, 10 Mar 2017 12:45:19: #2 alternative fragment length(s) may be 80 bps INFO @ Fri, 10 Mar 2017 12:45:19: #2.2 Generate R script for model : SRX110760.10_model.r INFO @ Fri, 10 Mar 2017 12:45:19: #3 Call peaks... INFO @ Fri, 10 Mar 2017 12:45:19: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Mar 2017 12:45:27: #1 tag size is determined as 18 bps INFO @ Fri, 10 Mar 2017 12:45:27: #1 tag size = 18 INFO @ Fri, 10 Mar 2017 12:45:27: #1 total tags in treatment: 12665564 INFO @ Fri, 10 Mar 2017 12:45:27: #1 user defined the maximum tags... INFO @ Fri, 10 Mar 2017 12:45:27: #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 12:45:29: #1 tags after filtering in treatment: 12665564 INFO @ Fri, 10 Mar 2017 12:45:29: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Mar 2017 12:45:29: #1 finished! INFO @ Fri, 10 Mar 2017 12:45:29: #2 Build Peak Model... INFO @ Fri, 10 Mar 2017 12:45:33: #2 number of paired peaks: 4824 INFO @ Fri, 10 Mar 2017 12:45:33: start model_add_line... INFO @ Fri, 10 Mar 2017 12:45:43: start X-correlation... INFO @ Fri, 10 Mar 2017 12:45:43: end of X-cor INFO @ Fri, 10 Mar 2017 12:45:43: #2 finished! INFO @ Fri, 10 Mar 2017 12:45:43: #2 predicted fragment length is 80 bps INFO @ Fri, 10 Mar 2017 12:45:43: #2 alternative fragment length(s) may be 80 bps INFO @ Fri, 10 Mar 2017 12:45:43: #2.2 Generate R script for model : SRX110760.20_model.r INFO @ Fri, 10 Mar 2017 12:45:43: #3 Call peaks... INFO @ Fri, 10 Mar 2017 12:45:43: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Mar 2017 12:46:24: start X-correlation... INFO @ Fri, 10 Mar 2017 12:46:24: end of X-cor INFO @ Fri, 10 Mar 2017 12:46:24: #2 finished! INFO @ Fri, 10 Mar 2017 12:46:24: #2 predicted fragment length is 80 bps INFO @ Fri, 10 Mar 2017 12:46:24: #2 alternative fragment length(s) may be 80 bps INFO @ Fri, 10 Mar 2017 12:46:24: #2.2 Generate R script for model : SRX110760.05_model.r INFO @ Fri, 10 Mar 2017 12:46:24: #3 Call peaks... INFO @ Fri, 10 Mar 2017 12:46:24: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Mar 2017 12:46:44: #3 Call peaks for each chromosome... INFO @ Fri, 10 Mar 2017 12:47:21: #3 Call peaks for each chromosome... INFO @ Fri, 10 Mar 2017 12:47:51: #3 Call peaks for each chromosome... INFO @ Fri, 10 Mar 2017 12:47:54: #4 Write output xls file... SRX110760.10_peaks.xls INFO @ Fri, 10 Mar 2017 12:47:54: #4 Write peak in narrowPeak format file... SRX110760.10_peaks.narrowPeak INFO @ Fri, 10 Mar 2017 12:47:54: #4 Write summits bed file... SRX110760.10_summits.bed INFO @ Fri, 10 Mar 2017 12:47:54: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (9640 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Fri, 10 Mar 2017 12:48:33: #4 Write output xls file... SRX110760.20_peaks.xls INFO @ Fri, 10 Mar 2017 12:48:33: #4 Write peak in narrowPeak format file... SRX110760.20_peaks.narrowPeak INFO @ Fri, 10 Mar 2017 12:48:33: #4 Write summits bed file... SRX110760.20_summits.bed INFO @ Fri, 10 Mar 2017 12:48:33: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (6670 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Mar 2017 12:49:08: #4 Write output xls file... SRX110760.05_peaks.xls INFO @ Fri, 10 Mar 2017 12:49:08: #4 Write peak in narrowPeak format file... SRX110760.05_peaks.narrowPeak INFO @ Fri, 10 Mar 2017 12:49:08: #4 Write summits bed file... SRX110760.05_summits.bed INFO @ Fri, 10 Mar 2017 12:49:08: Done! pass1 - making usageList (14 chroms): 5 millis pass2 - checking and writing primary data (13055 records, 4 fields): 26 millis CompletedMACS2peakCalling BigWig に変換しました。