Job ID = 9029603 sra ファイルのダウンロード中... Completed: 1635611K bytes transferred in 19 seconds (687948K 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 1884 0 --:--:-- 0:00:07 --:--:-- 13603 100 50517 0 50517 0 0 5993 0 --:--:-- 0:00:08 --:--:-- 26827 100 122k 0 122k 0 0 13291 0 --:--:-- 0:00:09 --:--:-- 43511 100 148k 0 148k 0 0 15585 0 --:--:-- 0:00:09 --:--:-- 47367 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 52116026 spots for /home/okishinya/chipatlas/results/dm3/SRX1872292/SRR3712753.sra Written 52116026 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: 00:16:22 52116026 reads; of these: 52116026 (100.00%) were unpaired; of these: 18529611 (35.55%) aligned 0 times 24796361 (47.58%) aligned exactly 1 time 8790054 (16.87%) aligned >1 times 64.45% overall alignment rate Time searching: 00:16:22 Overall time: 00:16:22 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 16 files... [bam_rmdupse_core] 27032084 / 33586415 = 0.8049 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 14:46:35: # Command line: callpeak -t SRX1872292.bam -f BAM -g dm -n SRX1872292.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1872292.05 # format = BAM # ChIP-seq file = ['SRX1872292.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 14:46:35: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:46:35: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:46:35: # Command line: callpeak -t SRX1872292.bam -f BAM -g dm -n SRX1872292.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1872292.10 # format = BAM # ChIP-seq file = ['SRX1872292.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 14:46:35: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:46:35: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:46:35: # Command line: callpeak -t SRX1872292.bam -f BAM -g dm -n SRX1872292.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1872292.20 # format = BAM # ChIP-seq file = ['SRX1872292.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 14:46:35: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:46:35: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:46:41: 1000000 INFO @ Sat, 03 Jun 2017 14:46:41: 1000000 INFO @ Sat, 03 Jun 2017 14:46:42: 1000000 INFO @ Sat, 03 Jun 2017 14:46:47: 2000000 INFO @ Sat, 03 Jun 2017 14:46:48: 2000000 INFO @ Sat, 03 Jun 2017 14:46:49: 2000000 INFO @ Sat, 03 Jun 2017 14:46:53: 3000000 INFO @ Sat, 03 Jun 2017 14:46:54: 3000000 INFO @ Sat, 03 Jun 2017 14:46:56: 3000000 INFO @ Sat, 03 Jun 2017 14:47:00: 4000000 INFO @ Sat, 03 Jun 2017 14:47:01: 4000000 INFO @ Sat, 03 Jun 2017 14:47:03: 4000000 INFO @ Sat, 03 Jun 2017 14:47:06: 5000000 INFO @ Sat, 03 Jun 2017 14:47:07: 5000000 INFO @ Sat, 03 Jun 2017 14:47:10: 5000000 INFO @ Sat, 03 Jun 2017 14:47:12: 6000000 INFO @ Sat, 03 Jun 2017 14:47:14: 6000000 INFO @ Sat, 03 Jun 2017 14:47:16: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 14:47:16: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 14:47:16: #1 total tags in treatment: 6554331 INFO @ Sat, 03 Jun 2017 14:47:16: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:47:16: #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 14:47:17: 6000000 INFO @ Sat, 03 Jun 2017 14:47:17: #1 tags after filtering in treatment: 6548422 INFO @ Sat, 03 Jun 2017 14:47:17: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:47:17: #1 finished! INFO @ Sat, 03 Jun 2017 14:47:17: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:47:18: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 14:47:18: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 14:47:18: #1 total tags in treatment: 6554331 INFO @ Sat, 03 Jun 2017 14:47:18: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:47:18: #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 14:47:18: #2 number of paired peaks: 1708 INFO @ Sat, 03 Jun 2017 14:47:18: start model_add_line... INFO @ Sat, 03 Jun 2017 14:47:19: #1 tags after filtering in treatment: 6548422 INFO @ Sat, 03 Jun 2017 14:47:19: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:47:19: #1 finished! INFO @ Sat, 03 Jun 2017 14:47:19: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:47:20: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 14:47:20: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 14:47:20: #1 total tags in treatment: 6554331 INFO @ Sat, 03 Jun 2017 14:47:20: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:47:20: #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 14:47:21: #2 number of paired peaks: 1708 INFO @ Sat, 03 Jun 2017 14:47:21: start model_add_line... INFO @ Sat, 03 Jun 2017 14:47:22: #1 tags after filtering in treatment: 6548422 INFO @ Sat, 03 Jun 2017 14:47:22: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:47:22: #1 finished! INFO @ Sat, 03 Jun 2017 14:47:22: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:47:23: #2 number of paired peaks: 1708 INFO @ Sat, 03 Jun 2017 14:47:23: start model_add_line... INFO @ Sat, 03 Jun 2017 14:47:29: start X-correlation... INFO @ Sat, 03 Jun 2017 14:47:29: end of X-cor INFO @ Sat, 03 Jun 2017 14:47:29: #2 finished! INFO @ Sat, 03 Jun 2017 14:47:29: #2 predicted fragment length is 146 bps INFO @ Sat, 03 Jun 2017 14:47:29: #2 alternative fragment length(s) may be 146 bps INFO @ Sat, 03 Jun 2017 14:47:29: #2.2 Generate R script for model : SRX1872292.10_model.r INFO @ Sat, 03 Jun 2017 14:47:29: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:47:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:47:31: start X-correlation... INFO @ Sat, 03 Jun 2017 14:47:31: end of X-cor INFO @ Sat, 03 Jun 2017 14:47:31: #2 finished! INFO @ Sat, 03 Jun 2017 14:47:31: #2 predicted fragment length is 146 bps INFO @ Sat, 03 Jun 2017 14:47:31: #2 alternative fragment length(s) may be 146 bps INFO @ Sat, 03 Jun 2017 14:47:31: #2.2 Generate R script for model : SRX1872292.20_model.r INFO @ Sat, 03 Jun 2017 14:47:31: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:47:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:47:34: start X-correlation... INFO @ Sat, 03 Jun 2017 14:47:34: end of X-cor INFO @ Sat, 03 Jun 2017 14:47:34: #2 finished! INFO @ Sat, 03 Jun 2017 14:47:34: #2 predicted fragment length is 146 bps INFO @ Sat, 03 Jun 2017 14:47:34: #2 alternative fragment length(s) may be 146 bps INFO @ Sat, 03 Jun 2017 14:47:34: #2.2 Generate R script for model : SRX1872292.05_model.r INFO @ Sat, 03 Jun 2017 14:47:34: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:47:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:48:08: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:48:10: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:48:11: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:48:36: #4 Write output xls file... SRX1872292.10_peaks.xls INFO @ Sat, 03 Jun 2017 14:48:36: #4 Write peak in narrowPeak format file... SRX1872292.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:48:36: #4 Write summits bed file... SRX1872292.10_summits.bed INFO @ Sat, 03 Jun 2017 14:48:36: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2384 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 14:48:40: #4 Write output xls file... SRX1872292.20_peaks.xls INFO @ Sat, 03 Jun 2017 14:48:40: #4 Write peak in narrowPeak format file... SRX1872292.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:48:40: #4 Write summits bed file... SRX1872292.20_summits.bed INFO @ Sat, 03 Jun 2017 14:48:40: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1612 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 14:48:43: #4 Write output xls file... SRX1872292.05_peaks.xls INFO @ Sat, 03 Jun 2017 14:48:43: #4 Write peak in narrowPeak format file... SRX1872292.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:48:43: #4 Write summits bed file... SRX1872292.05_summits.bed INFO @ Sat, 03 Jun 2017 14:48:43: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3799 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。