Job ID = 8696843 sra ファイルのダウンロード中... Completed: 470850K bytes transferred in 15 seconds (255476K 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 2728 0 --:--:-- 0:00:08 --:--:-- 15029 100 31424 0 31424 0 0 3644 0 --:--:-- 0:00:08 --:--:-- 16976 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 40013592 spots for /home/okishinya/chipatlas/results/dm3/SRX110781/SRR388363.sra Written 40013592 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: 00:34:16 40013592 reads; of these: 40013592 (100.00%) were unpaired; of these: 5981445 (14.95%) aligned 0 times 16703536 (41.74%) aligned exactly 1 time 17328611 (43.31%) aligned >1 times 85.05% overall alignment rate Time searching: 00:34:16 Overall time: 00:34:16 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 12 files... [bam_rmdupse_core] 13319694 / 34032147 = 0.3914 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 13:05:03: # Command line: callpeak -t SRX110781.bam -f BAM -g dm -n SRX110781.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX110781.20 # format = BAM # ChIP-seq file = ['SRX110781.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 13:05:03: #1 read tag files... INFO @ Fri, 10 Mar 2017 13:05:03: #1 read treatment tags... INFO @ Fri, 10 Mar 2017 13:05:03: # Command line: callpeak -t SRX110781.bam -f BAM -g dm -n SRX110781.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX110781.10 # format = BAM # ChIP-seq file = ['SRX110781.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 13:05:03: #1 read tag files... INFO @ Fri, 10 Mar 2017 13:05:03: #1 read treatment tags... INFO @ Fri, 10 Mar 2017 13:05:03: # Command line: callpeak -t SRX110781.bam -f BAM -g dm -n SRX110781.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX110781.05 # format = BAM # ChIP-seq file = ['SRX110781.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 13:05:03: #1 read tag files... INFO @ Fri, 10 Mar 2017 13:05:03: #1 read treatment tags... INFO @ Fri, 10 Mar 2017 13:05:11: 1000000 INFO @ Fri, 10 Mar 2017 13:05:13: 1000000 INFO @ Fri, 10 Mar 2017 13:05:17: 1000000 INFO @ Fri, 10 Mar 2017 13:05:18: 2000000 INFO @ Fri, 10 Mar 2017 13:05:21: 2000000 INFO @ Fri, 10 Mar 2017 13:05:25: 3000000 INFO @ Fri, 10 Mar 2017 13:05:30: 2000000 INFO @ Fri, 10 Mar 2017 13:05:30: 3000000 INFO @ Fri, 10 Mar 2017 13:05:32: 4000000 INFO @ Fri, 10 Mar 2017 13:05:38: 4000000 INFO @ Fri, 10 Mar 2017 13:05:39: 5000000 INFO @ Fri, 10 Mar 2017 13:05:42: 3000000 INFO @ Fri, 10 Mar 2017 13:05:46: 6000000 INFO @ Fri, 10 Mar 2017 13:05:47: 5000000 INFO @ Fri, 10 Mar 2017 13:05:52: 4000000 INFO @ Fri, 10 Mar 2017 13:05:54: 7000000 INFO @ Fri, 10 Mar 2017 13:05:55: 6000000 INFO @ Fri, 10 Mar 2017 13:06:01: 5000000 INFO @ Fri, 10 Mar 2017 13:06:01: 8000000 INFO @ Fri, 10 Mar 2017 13:06:04: 7000000 INFO @ Fri, 10 Mar 2017 13:06:09: 9000000 INFO @ Fri, 10 Mar 2017 13:06:09: 6000000 INFO @ Fri, 10 Mar 2017 13:06:12: 8000000 INFO @ Fri, 10 Mar 2017 13:06:16: 7000000 INFO @ Fri, 10 Mar 2017 13:06:16: 10000000 INFO @ Fri, 10 Mar 2017 13:06:21: 9000000 INFO @ Fri, 10 Mar 2017 13:06:23: 8000000 INFO @ Fri, 10 Mar 2017 13:06:23: 11000000 INFO @ Fri, 10 Mar 2017 13:06:30: 10000000 INFO @ Fri, 10 Mar 2017 13:06:31: 9000000 INFO @ Fri, 10 Mar 2017 13:06:33: 12000000 INFO @ Fri, 10 Mar 2017 13:06:38: 11000000 INFO @ Fri, 10 Mar 2017 13:06:42: 10000000 INFO @ Fri, 10 Mar 2017 13:06:43: 13000000 INFO @ Fri, 10 Mar 2017 13:06:47: 12000000 INFO @ Fri, 10 Mar 2017 13:06:52: 11000000 INFO @ Fri, 10 Mar 2017 13:06:53: 14000000 INFO @ Fri, 10 Mar 2017 13:06:55: 13000000 INFO @ Fri, 10 Mar 2017 13:07:02: 12000000 INFO @ Fri, 10 Mar 2017 13:07:04: 15000000 INFO @ Fri, 10 Mar 2017 13:07:04: 14000000 INFO @ Fri, 10 Mar 2017 13:07:12: 15000000 INFO @ Fri, 10 Mar 2017 13:07:15: 13000000 INFO @ Fri, 10 Mar 2017 13:07:17: 16000000 INFO @ Fri, 10 Mar 2017 13:07:20: 16000000 INFO @ Fri, 10 Mar 2017 13:07:27: 14000000 INFO @ Fri, 10 Mar 2017 13:07:28: 17000000 INFO @ Fri, 10 Mar 2017 13:07:29: 17000000 INFO @ Fri, 10 Mar 2017 13:07:37: 15000000 INFO @ Fri, 10 Mar 2017 13:07:38: 18000000 INFO @ Fri, 10 Mar 2017 13:07:38: 18000000 INFO @ Fri, 10 Mar 2017 13:07:46: 19000000 INFO @ Fri, 10 Mar 2017 13:07:47: 16000000 INFO @ Fri, 10 Mar 2017 13:07:49: 19000000 INFO @ Fri, 10 Mar 2017 13:07:55: 20000000 INFO @ Fri, 10 Mar 2017 13:07:58: 17000000 INFO @ Fri, 10 Mar 2017 13:07:59: 20000000 INFO @ Fri, 10 Mar 2017 13:08:01: #1 tag size is determined as 18 bps INFO @ Fri, 10 Mar 2017 13:08:01: #1 tag size = 18 INFO @ Fri, 10 Mar 2017 13:08:01: #1 total tags in treatment: 20712453 INFO @ Fri, 10 Mar 2017 13:08:01: #1 user defined the maximum tags... INFO @ Fri, 10 Mar 2017 13:08:01: #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 13:08:06: #1 tags after filtering in treatment: 20712453 INFO @ Fri, 10 Mar 2017 13:08:06: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Mar 2017 13:08:06: #1 finished! INFO @ Fri, 10 Mar 2017 13:08:06: #2 Build Peak Model... INFO @ Fri, 10 Mar 2017 13:08:06: #1 tag size is determined as 18 bps INFO @ Fri, 10 Mar 2017 13:08:06: #1 tag size = 18 INFO @ Fri, 10 Mar 2017 13:08:06: #1 total tags in treatment: 20712453 INFO @ Fri, 10 Mar 2017 13:08:06: #1 user defined the maximum tags... INFO @ Fri, 10 Mar 2017 13:08:06: #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 13:08:06: 18000000 INFO @ Fri, 10 Mar 2017 13:08:10: #2 number of paired peaks: 736 WARNING @ Fri, 10 Mar 2017 13:08:10: Fewer paired peaks (736) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 736 pairs to build model! INFO @ Fri, 10 Mar 2017 13:08:10: start model_add_line... INFO @ Fri, 10 Mar 2017 13:08:11: #1 tags after filtering in treatment: 20712453 INFO @ Fri, 10 Mar 2017 13:08:11: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Mar 2017 13:08:11: #1 finished! INFO @ Fri, 10 Mar 2017 13:08:11: #2 Build Peak Model... INFO @ Fri, 10 Mar 2017 13:08:13: 19000000 INFO @ Fri, 10 Mar 2017 13:08:15: #2 number of paired peaks: 736 WARNING @ Fri, 10 Mar 2017 13:08:15: Fewer paired peaks (736) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 736 pairs to build model! INFO @ Fri, 10 Mar 2017 13:08:15: start model_add_line... INFO @ Fri, 10 Mar 2017 13:08:19: 20000000 INFO @ Fri, 10 Mar 2017 13:08:24: start X-correlation... INFO @ Fri, 10 Mar 2017 13:08:24: end of X-cor INFO @ Fri, 10 Mar 2017 13:08:24: #2 finished! INFO @ Fri, 10 Mar 2017 13:08:24: #2 predicted fragment length is 320 bps INFO @ Fri, 10 Mar 2017 13:08:24: #2 alternative fragment length(s) may be 4,320 bps INFO @ Fri, 10 Mar 2017 13:08:24: #2.2 Generate R script for model : SRX110781.10_model.r INFO @ Fri, 10 Mar 2017 13:08:24: #3 Call peaks... INFO @ Fri, 10 Mar 2017 13:08:24: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Mar 2017 13:08:28: start X-correlation... INFO @ Fri, 10 Mar 2017 13:08:28: end of X-cor INFO @ Fri, 10 Mar 2017 13:08:28: #2 finished! INFO @ Fri, 10 Mar 2017 13:08:28: #2 predicted fragment length is 320 bps INFO @ Fri, 10 Mar 2017 13:08:28: #2 alternative fragment length(s) may be 4,320 bps INFO @ Fri, 10 Mar 2017 13:08:28: #2.2 Generate R script for model : SRX110781.20_model.r INFO @ Fri, 10 Mar 2017 13:08:28: #3 Call peaks... INFO @ Fri, 10 Mar 2017 13:08:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Mar 2017 13:08:29: #1 tag size is determined as 18 bps INFO @ Fri, 10 Mar 2017 13:08:29: #1 tag size = 18 INFO @ Fri, 10 Mar 2017 13:08:29: #1 total tags in treatment: 20712453 INFO @ Fri, 10 Mar 2017 13:08:29: #1 user defined the maximum tags... INFO @ Fri, 10 Mar 2017 13:08:29: #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 13:08:34: #1 tags after filtering in treatment: 20712453 INFO @ Fri, 10 Mar 2017 13:08:34: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Mar 2017 13:08:34: #1 finished! INFO @ Fri, 10 Mar 2017 13:08:34: #2 Build Peak Model... INFO @ Fri, 10 Mar 2017 13:08:38: #2 number of paired peaks: 736 WARNING @ Fri, 10 Mar 2017 13:08:38: Fewer paired peaks (736) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 736 pairs to build model! INFO @ Fri, 10 Mar 2017 13:08:38: start model_add_line... INFO @ Fri, 10 Mar 2017 13:08:50: start X-correlation... INFO @ Fri, 10 Mar 2017 13:08:50: end of X-cor INFO @ Fri, 10 Mar 2017 13:08:50: #2 finished! INFO @ Fri, 10 Mar 2017 13:08:50: #2 predicted fragment length is 320 bps INFO @ Fri, 10 Mar 2017 13:08:50: #2 alternative fragment length(s) may be 4,320 bps INFO @ Fri, 10 Mar 2017 13:08:50: #2.2 Generate R script for model : SRX110781.05_model.r INFO @ Fri, 10 Mar 2017 13:08:50: #3 Call peaks... INFO @ Fri, 10 Mar 2017 13:08:50: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Mar 2017 13:10:58: #3 Call peaks for each chromosome... INFO @ Fri, 10 Mar 2017 13:11:04: #3 Call peaks for each chromosome... INFO @ Fri, 10 Mar 2017 13:11:16: #3 Call peaks for each chromosome... INFO @ Fri, 10 Mar 2017 13:12:32: #4 Write output xls file... SRX110781.20_peaks.xls INFO @ Fri, 10 Mar 2017 13:12:32: #4 Write peak in narrowPeak format file... SRX110781.20_peaks.narrowPeak INFO @ Fri, 10 Mar 2017 13:12:32: #4 Write summits bed file... SRX110781.20_summits.bed INFO @ Fri, 10 Mar 2017 13:12:32: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (697 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 10 Mar 2017 13:12:56: #4 Write output xls file... SRX110781.05_peaks.xls INFO @ Fri, 10 Mar 2017 13:12:56: #4 Write peak in narrowPeak format file... SRX110781.05_peaks.narrowPeak INFO @ Fri, 10 Mar 2017 13:12:56: #4 Write summits bed file... SRX110781.05_summits.bed INFO @ Fri, 10 Mar 2017 13:12:56: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1967 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 10 Mar 2017 13:13:06: #4 Write output xls file... SRX110781.10_peaks.xls INFO @ Fri, 10 Mar 2017 13:13:06: #4 Write peak in narrowPeak format file... SRX110781.10_peaks.narrowPeak INFO @ Fri, 10 Mar 2017 13:13:06: #4 Write summits bed file... SRX110781.10_summits.bed INFO @ Fri, 10 Mar 2017 13:13:06: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (1251 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。