Job ID = 9029329 sra ファイルのダウンロード中... Completed: 331531K bytes transferred in 5 seconds (488538K 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 7663 0 7663 0 0 1036 0 --:--:-- 0:00:07 --:--:-- 9602 100 30246 0 30246 0 0 3604 0 --:--:-- 0:00:08 --:--:-- 16859 100 66412 0 66412 0 0 7073 0 --:--:-- 0:00:09 --:--:-- 23795 100 68283 0 68283 0 0 7271 0 --:--:-- 0:00:09 --:--:-- 24456 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 13307401 spots for /home/okishinya/chipatlas/results/dm3/SRX1571733/SRR3162499.sra Written 13307401 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: 00:03:34 13307401 reads; of these: 13307401 (100.00%) were unpaired; of these: 2344725 (17.62%) aligned 0 times 9843005 (73.97%) aligned exactly 1 time 1119671 (8.41%) aligned >1 times 82.38% overall alignment rate Time searching: 00:03:34 Overall time: 00:03:34 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] 4202639 / 10962676 = 0.3834 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 13:21:22: # Command line: callpeak -t SRX1571733.bam -f BAM -g dm -n SRX1571733.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1571733.20 # format = BAM # ChIP-seq file = ['SRX1571733.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 13:21:22: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:21:22: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:21:22: # Command line: callpeak -t SRX1571733.bam -f BAM -g dm -n SRX1571733.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1571733.10 # format = BAM # ChIP-seq file = ['SRX1571733.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 13:21:22: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:21:22: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:21:22: # Command line: callpeak -t SRX1571733.bam -f BAM -g dm -n SRX1571733.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1571733.05 # format = BAM # ChIP-seq file = ['SRX1571733.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 13:21:22: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:21:22: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:21:29: 1000000 INFO @ Sat, 03 Jun 2017 13:21:30: 1000000 INFO @ Sat, 03 Jun 2017 13:21:30: 1000000 INFO @ Sat, 03 Jun 2017 13:21:36: 2000000 INFO @ Sat, 03 Jun 2017 13:21:37: 2000000 INFO @ Sat, 03 Jun 2017 13:21:37: 2000000 INFO @ Sat, 03 Jun 2017 13:21:43: 3000000 INFO @ Sat, 03 Jun 2017 13:21:44: 3000000 INFO @ Sat, 03 Jun 2017 13:21:46: 3000000 INFO @ Sat, 03 Jun 2017 13:21:50: 4000000 INFO @ Sat, 03 Jun 2017 13:21:52: 4000000 INFO @ Sat, 03 Jun 2017 13:21:55: 4000000 INFO @ Sat, 03 Jun 2017 13:21:57: 5000000 INFO @ Sat, 03 Jun 2017 13:22:00: 5000000 INFO @ Sat, 03 Jun 2017 13:22:03: 5000000 INFO @ Sat, 03 Jun 2017 13:22:04: 6000000 INFO @ Sat, 03 Jun 2017 13:22:08: 6000000 INFO @ Sat, 03 Jun 2017 13:22:09: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:22:09: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:22:09: #1 total tags in treatment: 6760037 INFO @ Sat, 03 Jun 2017 13:22:09: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:22:09: #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 13:22:10: #1 tags after filtering in treatment: 6756508 INFO @ Sat, 03 Jun 2017 13:22:10: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:22:10: #1 finished! INFO @ Sat, 03 Jun 2017 13:22:10: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:22:12: 6000000 INFO @ Sat, 03 Jun 2017 13:22:12: #2 number of paired peaks: 9444 INFO @ Sat, 03 Jun 2017 13:22:12: start model_add_line... INFO @ Sat, 03 Jun 2017 13:22:14: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:22:14: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:22:14: #1 total tags in treatment: 6760037 INFO @ Sat, 03 Jun 2017 13:22:14: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:22:14: #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 13:22:15: #1 tags after filtering in treatment: 6756508 INFO @ Sat, 03 Jun 2017 13:22:15: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:22:15: #1 finished! INFO @ Sat, 03 Jun 2017 13:22:15: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:22:17: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:22:17: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:22:17: #1 total tags in treatment: 6760037 INFO @ Sat, 03 Jun 2017 13:22:17: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:22:17: #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 13:22:18: #2 number of paired peaks: 9444 INFO @ Sat, 03 Jun 2017 13:22:18: start model_add_line... INFO @ Sat, 03 Jun 2017 13:22:19: #1 tags after filtering in treatment: 6756508 INFO @ Sat, 03 Jun 2017 13:22:19: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:22:19: #1 finished! INFO @ Sat, 03 Jun 2017 13:22:19: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:22:21: #2 number of paired peaks: 9444 INFO @ Sat, 03 Jun 2017 13:22:21: start model_add_line... INFO @ Sat, 03 Jun 2017 13:23:01: start X-correlation... INFO @ Sat, 03 Jun 2017 13:23:01: end of X-cor INFO @ Sat, 03 Jun 2017 13:23:01: #2 finished! INFO @ Sat, 03 Jun 2017 13:23:01: #2 predicted fragment length is 279 bps INFO @ Sat, 03 Jun 2017 13:23:01: #2 alternative fragment length(s) may be 279 bps INFO @ Sat, 03 Jun 2017 13:23:01: #2.2 Generate R script for model : SRX1571733.20_model.r INFO @ Sat, 03 Jun 2017 13:23:01: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:23:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:23:08: start X-correlation... INFO @ Sat, 03 Jun 2017 13:23:08: end of X-cor INFO @ Sat, 03 Jun 2017 13:23:08: #2 finished! INFO @ Sat, 03 Jun 2017 13:23:08: #2 predicted fragment length is 279 bps INFO @ Sat, 03 Jun 2017 13:23:08: #2 alternative fragment length(s) may be 279 bps INFO @ Sat, 03 Jun 2017 13:23:08: #2.2 Generate R script for model : SRX1571733.05_model.r INFO @ Sat, 03 Jun 2017 13:23:08: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:23:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:23:11: start X-correlation... INFO @ Sat, 03 Jun 2017 13:23:11: end of X-cor INFO @ Sat, 03 Jun 2017 13:23:11: #2 finished! INFO @ Sat, 03 Jun 2017 13:23:11: #2 predicted fragment length is 279 bps INFO @ Sat, 03 Jun 2017 13:23:11: #2 alternative fragment length(s) may be 279 bps INFO @ Sat, 03 Jun 2017 13:23:11: #2.2 Generate R script for model : SRX1571733.10_model.r INFO @ Sat, 03 Jun 2017 13:23:11: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:23:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:23:44: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Jun 2017 13:23:54: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:23:55: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 03 Jun 2017 13:24:24: #4 Write output xls file... SRX1571733.20_peaks.xls INFO @ Sat, 03 Jun 2017 13:24:24: #4 Write peak in narrowPeak format file... SRX1571733.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:24:24: #4 Write summits bed file... SRX1571733.20_summits.bed INFO @ Sat, 03 Jun 2017 13:24:24: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (5561 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:24:40: #4 Write output xls file... SRX1571733.10_peaks.xls INFO @ Sat, 03 Jun 2017 13:24:40: #4 Write peak in narrowPeak format file... SRX1571733.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:24:40: #4 Write summits bed file... SRX1571733.10_summits.bed INFO @ Sat, 03 Jun 2017 13:24:40: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (6509 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:24:42: #4 Write output xls file... SRX1571733.05_peaks.xls INFO @ Sat, 03 Jun 2017 13:24:42: #4 Write peak in narrowPeak format file... SRX1571733.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:24:42: #4 Write summits bed file... SRX1571733.05_summits.bed INFO @ Sat, 03 Jun 2017 13:24:42: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (7148 records, 4 fields): 10 millis CompletedMACS2peakCalling