Job ID = 9029489 sra ファイルのダウンロード中... Completed: 284708K bytes transferred in 5 seconds (424800K 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 --:--:-- 0 100 14324 0 14324 0 0 1910 0 --:--:-- 0:00:07 --:--:-- 14210 100 52529 0 52529 0 0 6306 0 --:--:-- 0:00:08 --:--:-- 28579 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 11209710 spots for /home/okishinya/chipatlas/results/dm3/SRX1794243/SRR3575287.sra Written 11209710 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: 00:03:44 11209710 reads; of these: 11209710 (100.00%) were unpaired; of these: 330523 (2.95%) aligned 0 times 8897523 (79.37%) aligned exactly 1 time 1981664 (17.68%) aligned >1 times 97.05% overall alignment rate Time searching: 00:03:44 Overall time: 00:03:44 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] 751531 / 10879187 = 0.0691 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 @ Sat, 03 Jun 2017 14:01:25: # Command line: callpeak -t SRX1794243.bam -f BAM -g dm -n SRX1794243.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1794243.05 # format = BAM # ChIP-seq file = ['SRX1794243.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 @ Sat, 03 Jun 2017 14:01:25: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:01:25: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:01:25: # Command line: callpeak -t SRX1794243.bam -f BAM -g dm -n SRX1794243.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1794243.10 # format = BAM # ChIP-seq file = ['SRX1794243.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 @ Sat, 03 Jun 2017 14:01:25: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:01:25: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:01:25: # Command line: callpeak -t SRX1794243.bam -f BAM -g dm -n SRX1794243.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1794243.20 # format = BAM # ChIP-seq file = ['SRX1794243.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 @ Sat, 03 Jun 2017 14:01:25: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:01:25: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:01:33: 1000000 INFO @ Sat, 03 Jun 2017 14:01:34: 1000000 INFO @ Sat, 03 Jun 2017 14:01:34: 1000000 INFO @ Sat, 03 Jun 2017 14:01:40: 2000000 INFO @ Sat, 03 Jun 2017 14:01:43: 2000000 INFO @ Sat, 03 Jun 2017 14:01:43: 2000000 INFO @ Sat, 03 Jun 2017 14:01:48: 3000000 INFO @ Sat, 03 Jun 2017 14:01:52: 3000000 INFO @ Sat, 03 Jun 2017 14:01:52: 3000000 INFO @ Sat, 03 Jun 2017 14:01:56: 4000000 INFO @ Sat, 03 Jun 2017 14:02:02: 4000000 INFO @ Sat, 03 Jun 2017 14:02:02: 4000000 INFO @ Sat, 03 Jun 2017 14:02:03: 5000000 INFO @ Sat, 03 Jun 2017 14:02:11: 5000000 INFO @ Sat, 03 Jun 2017 14:02:11: 5000000 INFO @ Sat, 03 Jun 2017 14:02:11: 6000000 INFO @ Sat, 03 Jun 2017 14:02:18: 7000000 INFO @ Sat, 03 Jun 2017 14:02:20: 6000000 INFO @ Sat, 03 Jun 2017 14:02:20: 6000000 INFO @ Sat, 03 Jun 2017 14:02:26: 8000000 INFO @ Sat, 03 Jun 2017 14:02:29: 7000000 INFO @ Sat, 03 Jun 2017 14:02:29: 7000000 INFO @ Sat, 03 Jun 2017 14:02:34: 9000000 INFO @ Sat, 03 Jun 2017 14:02:37: 8000000 INFO @ Sat, 03 Jun 2017 14:02:38: 8000000 INFO @ Sat, 03 Jun 2017 14:02:42: 10000000 INFO @ Sat, 03 Jun 2017 14:02:43: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 14:02:43: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 14:02:43: #1 total tags in treatment: 10127656 INFO @ Sat, 03 Jun 2017 14:02:43: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:02:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 14:02:45: #1 tags after filtering in treatment: 10125741 INFO @ Sat, 03 Jun 2017 14:02:45: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:02:45: #1 finished! INFO @ Sat, 03 Jun 2017 14:02:45: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:02:46: 9000000 INFO @ Sat, 03 Jun 2017 14:02:47: #2 number of paired peaks: 2424 INFO @ Sat, 03 Jun 2017 14:02:47: start model_add_line... INFO @ Sat, 03 Jun 2017 14:02:48: 9000000 INFO @ Sat, 03 Jun 2017 14:02:55: 10000000 INFO @ Sat, 03 Jun 2017 14:02:56: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 14:02:56: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 14:02:56: #1 total tags in treatment: 10127656 INFO @ Sat, 03 Jun 2017 14:02:56: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:02:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 14:02:58: 10000000 INFO @ Sat, 03 Jun 2017 14:02:59: #1 tags after filtering in treatment: 10125741 INFO @ Sat, 03 Jun 2017 14:02:59: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:02:59: #1 finished! INFO @ Sat, 03 Jun 2017 14:02:59: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:02:59: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 14:02:59: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 14:02:59: #1 total tags in treatment: 10127656 INFO @ Sat, 03 Jun 2017 14:02:59: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:02:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 14:03:01: #2 number of paired peaks: 2424 INFO @ Sat, 03 Jun 2017 14:03:01: start model_add_line... INFO @ Sat, 03 Jun 2017 14:03:01: #1 tags after filtering in treatment: 10125741 INFO @ Sat, 03 Jun 2017 14:03:01: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:03:01: #1 finished! INFO @ Sat, 03 Jun 2017 14:03:01: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:03:03: #2 number of paired peaks: 2424 INFO @ Sat, 03 Jun 2017 14:03:03: start model_add_line... INFO @ Sat, 03 Jun 2017 14:03:03: start X-correlation... INFO @ Sat, 03 Jun 2017 14:03:03: end of X-cor INFO @ Sat, 03 Jun 2017 14:03:03: #2 finished! INFO @ Sat, 03 Jun 2017 14:03:03: #2 predicted fragment length is 136 bps INFO @ Sat, 03 Jun 2017 14:03:03: #2 alternative fragment length(s) may be 4,136,146 bps INFO @ Sat, 03 Jun 2017 14:03:03: #2.2 Generate R script for model : SRX1794243.05_model.r INFO @ Sat, 03 Jun 2017 14:03:03: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:03:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:03:18: start X-correlation... INFO @ Sat, 03 Jun 2017 14:03:18: end of X-cor INFO @ Sat, 03 Jun 2017 14:03:18: #2 finished! INFO @ Sat, 03 Jun 2017 14:03:18: #2 predicted fragment length is 136 bps INFO @ Sat, 03 Jun 2017 14:03:18: #2 alternative fragment length(s) may be 4,136,146 bps INFO @ Sat, 03 Jun 2017 14:03:18: #2.2 Generate R script for model : SRX1794243.20_model.r INFO @ Sat, 03 Jun 2017 14:03:18: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:03:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:03:20: start X-correlation... INFO @ Sat, 03 Jun 2017 14:03:20: end of X-cor INFO @ Sat, 03 Jun 2017 14:03:20: #2 finished! INFO @ Sat, 03 Jun 2017 14:03:20: #2 predicted fragment length is 136 bps INFO @ Sat, 03 Jun 2017 14:03:20: #2 alternative fragment length(s) may be 4,136,146 bps INFO @ Sat, 03 Jun 2017 14:03:20: #2.2 Generate R script for model : SRX1794243.10_model.r INFO @ Sat, 03 Jun 2017 14:03:20: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:03:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:04:01: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:04:18: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:04:19: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:04:48: #4 Write output xls file... SRX1794243.05_peaks.xls INFO @ Sat, 03 Jun 2017 14:04:48: #4 Write peak in narrowPeak format file... SRX1794243.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:04:48: #4 Write summits bed file... SRX1794243.05_summits.bed INFO @ Sat, 03 Jun 2017 14:04:48: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6919 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 14:04:57: #4 Write output xls file... SRX1794243.20_peaks.xls INFO @ Sat, 03 Jun 2017 14:04:57: #4 Write peak in narrowPeak format file... SRX1794243.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:04:57: #4 Write summits bed file... SRX1794243.20_summits.bed INFO @ Sat, 03 Jun 2017 14:04:57: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (707 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 14:05:01: #4 Write output xls file... SRX1794243.10_peaks.xls INFO @ Sat, 03 Jun 2017 14:05:01: #4 Write peak in narrowPeak format file... SRX1794243.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:05:01: #4 Write summits bed file... SRX1794243.10_summits.bed INFO @ Sat, 03 Jun 2017 14:05:01: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2558 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。