Job ID = 9033124 sra ファイルのダウンロード中... Completed: 638819K bytes transferred in 8 seconds (585443K 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 --:--:-- 0:00:06 --:--:-- 0 100 22318 0 22318 0 0 2795 0 --:--:-- 0:00:07 --:--:-- 14161 100 54318 0 54318 0 0 5940 0 --:--:-- 0:00:09 --:--:-- 19838 100 69656 0 69656 0 0 7481 0 --:--:-- 0:00:09 --:--:-- 23986 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 23148683 spots for /home/okishinya/chipatlas/results/dm3/SRX914956/SRR1873266.sra Written 23148683 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: 00:04:33 23148683 reads; of these: 23148683 (100.00%) were unpaired; of these: 2378331 (10.27%) aligned 0 times 18324128 (79.16%) aligned exactly 1 time 2446224 (10.57%) aligned >1 times 89.73% overall alignment rate Time searching: 00:04:33 Overall time: 00:04:33 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] 11852353 / 20770352 = 0.5706 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 @ Sun, 04 Jun 2017 00:12:15: # Command line: callpeak -t SRX914956.bam -f BAM -g dm -n SRX914956.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX914956.20 # format = BAM # ChIP-seq file = ['SRX914956.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 @ Sun, 04 Jun 2017 00:12:15: # Command line: callpeak -t SRX914956.bam -f BAM -g dm -n SRX914956.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX914956.05 # format = BAM # ChIP-seq file = ['SRX914956.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 @ Sun, 04 Jun 2017 00:12:15: #1 read tag files... INFO @ Sun, 04 Jun 2017 00:12:15: #1 read tag files... INFO @ Sun, 04 Jun 2017 00:12:15: # Command line: callpeak -t SRX914956.bam -f BAM -g dm -n SRX914956.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX914956.10 # format = BAM # ChIP-seq file = ['SRX914956.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 @ Sun, 04 Jun 2017 00:12:15: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 00:12:15: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 00:12:15: #1 read tag files... INFO @ Sun, 04 Jun 2017 00:12:15: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 00:12:21: 1000000 INFO @ Sun, 04 Jun 2017 00:12:21: 1000000 INFO @ Sun, 04 Jun 2017 00:12:21: 1000000 INFO @ Sun, 04 Jun 2017 00:12:27: 2000000 INFO @ Sun, 04 Jun 2017 00:12:27: 2000000 INFO @ Sun, 04 Jun 2017 00:12:27: 2000000 INFO @ Sun, 04 Jun 2017 00:12:33: 3000000 INFO @ Sun, 04 Jun 2017 00:12:33: 3000000 INFO @ Sun, 04 Jun 2017 00:12:33: 3000000 INFO @ Sun, 04 Jun 2017 00:12:39: 4000000 INFO @ Sun, 04 Jun 2017 00:12:39: 4000000 INFO @ Sun, 04 Jun 2017 00:12:39: 4000000 INFO @ Sun, 04 Jun 2017 00:12:45: 5000000 INFO @ Sun, 04 Jun 2017 00:12:45: 5000000 INFO @ Sun, 04 Jun 2017 00:12:45: 5000000 INFO @ Sun, 04 Jun 2017 00:12:51: 6000000 INFO @ Sun, 04 Jun 2017 00:12:51: 6000000 INFO @ Sun, 04 Jun 2017 00:12:51: 6000000 INFO @ Sun, 04 Jun 2017 00:12:57: 7000000 INFO @ Sun, 04 Jun 2017 00:12:57: 7000000 INFO @ Sun, 04 Jun 2017 00:12:57: 7000000 INFO @ Sun, 04 Jun 2017 00:13:03: 8000000 INFO @ Sun, 04 Jun 2017 00:13:03: 8000000 INFO @ Sun, 04 Jun 2017 00:13:03: 8000000 INFO @ Sun, 04 Jun 2017 00:13:08: #1 tag size is determined as 40 bps INFO @ Sun, 04 Jun 2017 00:13:08: #1 tag size = 40 INFO @ Sun, 04 Jun 2017 00:13:08: #1 total tags in treatment: 8917999 INFO @ Sun, 04 Jun 2017 00:13:08: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 00:13:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 00:13:09: #1 tag size is determined as 40 bps INFO @ Sun, 04 Jun 2017 00:13:09: #1 tag size = 40 INFO @ Sun, 04 Jun 2017 00:13:09: #1 total tags in treatment: 8917999 INFO @ Sun, 04 Jun 2017 00:13:09: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 00:13:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 00:13:09: #1 tag size is determined as 40 bps INFO @ Sun, 04 Jun 2017 00:13:09: #1 tag size = 40 INFO @ Sun, 04 Jun 2017 00:13:09: #1 total tags in treatment: 8917999 INFO @ Sun, 04 Jun 2017 00:13:09: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 00:13:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 00:13:10: #1 tags after filtering in treatment: 8914867 INFO @ Sun, 04 Jun 2017 00:13:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 00:13:10: #1 finished! INFO @ Sun, 04 Jun 2017 00:13:10: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 00:13:10: #1 tags after filtering in treatment: 8914867 INFO @ Sun, 04 Jun 2017 00:13:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 00:13:10: #1 finished! INFO @ Sun, 04 Jun 2017 00:13:10: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 00:13:10: #1 tags after filtering in treatment: 8914867 INFO @ Sun, 04 Jun 2017 00:13:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 00:13:10: #1 finished! INFO @ Sun, 04 Jun 2017 00:13:10: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 00:13:12: #2 number of paired peaks: 1367 INFO @ Sun, 04 Jun 2017 00:13:12: start model_add_line... INFO @ Sun, 04 Jun 2017 00:13:12: #2 number of paired peaks: 1367 INFO @ Sun, 04 Jun 2017 00:13:12: start model_add_line... INFO @ Sun, 04 Jun 2017 00:13:12: #2 number of paired peaks: 1367 INFO @ Sun, 04 Jun 2017 00:13:12: start model_add_line... INFO @ Sun, 04 Jun 2017 00:13:27: start X-correlation... INFO @ Sun, 04 Jun 2017 00:13:27: end of X-cor INFO @ Sun, 04 Jun 2017 00:13:27: #2 finished! INFO @ Sun, 04 Jun 2017 00:13:27: #2 predicted fragment length is 184 bps INFO @ Sun, 04 Jun 2017 00:13:27: #2 alternative fragment length(s) may be 2,184 bps INFO @ Sun, 04 Jun 2017 00:13:27: #2.2 Generate R script for model : SRX914956.10_model.r INFO @ Sun, 04 Jun 2017 00:13:27: #3 Call peaks... INFO @ Sun, 04 Jun 2017 00:13:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 00:13:27: start X-correlation... INFO @ Sun, 04 Jun 2017 00:13:27: end of X-cor INFO @ Sun, 04 Jun 2017 00:13:27: #2 finished! INFO @ Sun, 04 Jun 2017 00:13:27: #2 predicted fragment length is 184 bps INFO @ Sun, 04 Jun 2017 00:13:27: #2 alternative fragment length(s) may be 2,184 bps INFO @ Sun, 04 Jun 2017 00:13:27: #2.2 Generate R script for model : SRX914956.05_model.r INFO @ Sun, 04 Jun 2017 00:13:27: #3 Call peaks... INFO @ Sun, 04 Jun 2017 00:13:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 00:13:27: start X-correlation... INFO @ Sun, 04 Jun 2017 00:13:27: end of X-cor INFO @ Sun, 04 Jun 2017 00:13:27: #2 finished! INFO @ Sun, 04 Jun 2017 00:13:27: #2 predicted fragment length is 184 bps INFO @ Sun, 04 Jun 2017 00:13:27: #2 alternative fragment length(s) may be 2,184 bps INFO @ Sun, 04 Jun 2017 00:13:27: #2.2 Generate R script for model : SRX914956.20_model.r INFO @ Sun, 04 Jun 2017 00:13:27: #3 Call peaks... INFO @ Sun, 04 Jun 2017 00:13:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 00:14:21: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 00:14:22: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 00:14:26: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 00:14:55: #4 Write output xls file... SRX914956.20_peaks.xls INFO @ Sun, 04 Jun 2017 00:14:55: #4 Write peak in narrowPeak format file... SRX914956.20_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 00:14:55: #4 Write summits bed file... SRX914956.20_summits.bed INFO @ Sun, 04 Jun 2017 00:14:55: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (429 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 00:15:03: #4 Write output xls file... SRX914956.10_peaks.xls INFO @ Sun, 04 Jun 2017 00:15:03: #4 Write peak in narrowPeak format file... SRX914956.10_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 00:15:03: #4 Write summits bed file... SRX914956.10_summits.bed INFO @ Sun, 04 Jun 2017 00:15:03: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1703 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 00:15:05: #4 Write output xls file... SRX914956.05_peaks.xls INFO @ Sun, 04 Jun 2017 00:15:05: #4 Write peak in narrowPeak format file... SRX914956.05_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 00:15:05: #4 Write summits bed file... SRX914956.05_summits.bed INFO @ Sun, 04 Jun 2017 00:15:05: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4240 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。