Job ID = 3001476 sra ファイルのダウンロード中... Completed: 336624K bytes transferred in 11 seconds (237362K 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 --:--:-- --:--:-- --:--:-- 0 100 13468 0 13468 0 0 18534 0 --:--:-- --:--:-- --:--:-- 25220 100 14953 0 14953 0 0 7765 0 --:--:-- 0:00:01 --:--:-- 8628 100 14953 0 14953 0 0 5109 0 --:--:-- 0:00:02 --:--:-- 5469 100 14953 0 14953 0 0 3807 0 --:--:-- 0:00:03 --:--:-- 4003 100 14953 0 14953 0 0 3033 0 --:--:-- 0:00:04 --:--:-- 3156 100 14953 0 14953 0 0 2521 0 --:--:-- 0:00:05 --:--:-- 285 100 14953 0 14953 0 0 2156 0 --:--:-- 0:00:06 --:--:-- 0 100 14953 0 14953 0 0 1884 0 --:--:-- 0:00:07 --:--:-- 0 100 14953 0 14953 0 0 1673 0 --:--:-- 0:00:08 --:--:-- 0 100 14953 0 14953 0 0 1504 0 --:--:-- 0:00:09 --:--:-- 0 100 14953 0 14953 0 0 1366 0 --:--:-- 0:00:10 --:--:-- 0 100 14953 0 14953 0 0 1252 0 --:--:-- 0:00:11 --:--:-- 0 100 14953 0 14953 0 0 1155 0 --:--:-- 0:00:12 --:--:-- 0 100 14953 0 14953 0 0 1072 0 --:--:-- 0:00:13 --:--:-- 0 100 14953 0 14953 0 0 1000 0 --:--:-- 0:00:14 --:--:-- 0 100 14953 0 14953 0 0 937 0 --:--:-- 0:00:15 --:--:-- 0 100 14953 0 14953 0 0 882 0 --:--:-- 0:00:16 --:--:-- 0 100 14953 0 14953 0 0 832 0 --:--:-- 0:00:17 --:--:-- 0 100 14953 0 14953 0 0 788 0 --:--:-- 0:00:18 --:--:-- 0 100 14953 0 14953 0 0 749 0 --:--:-- 0:00:19 --:--:-- 0 100 14953 0 14953 0 0 713 0 --:--:-- 0:00:20 --:--:-- 0 100 14953 0 14953 0 0 680 0 --:--:-- 0:00:21 --:--:-- 0 100 14953 0 14953 0 0 651 0 --:--:-- 0:00:22 --:--:-- 0 100 14953 0 14953 0 0 624 0 --:--:-- 0:00:23 --:--:-- 0 100 14953 0 14953 0 0 599 0 --:--:-- 0:00:24 --:--:-- 0 100 14953 0 14953 0 0 575 0 --:--:-- 0:00:25 --:--:-- 0 100 14953 0 14953 0 0 554 0 --:--:-- 0:00:26 --:--:-- 0 100 14953 0 14953 0 0 534 0 --:--:-- 0:00:27 --:--:-- 0 100 14953 0 14953 0 0 516 0 --:--:-- 0:00:28 --:--:-- 0 100 14953 0 14953 0 0 498 0 --:--:-- 0:00:29 --:--:-- 0 100 17867 0 17867 0 0 584 0 --:--:-- 0:00:30 --:--:-- 630 100 40356 0 40356 0 0 1303 0 --:--:-- 0:00:30 --:--:-- 6357 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 1427608 spots for /home/okishinya/chipatlas/results/ce10/SRX003819/SRR015059.sra Written 1427608 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:00:09 1427608 reads; of these: 1427608 (100.00%) were unpaired; of these: 926535 (64.90%) aligned 0 times 438341 (30.70%) aligned exactly 1 time 62732 (4.39%) aligned >1 times 35.10% overall alignment rate Time searching: 00:00:11 Overall time: 00:00:11 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 18277 / 501073 = 0.0365 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 @ Mon, 07 Sep 2015 18:45:09: # Command line: callpeak -t SRX003819.bam -f BAM -g ce -n SRX003819.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX003819.20 # format = BAM # ChIP-seq file = ['SRX003819.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Mon, 07 Sep 2015 18:45:09: # Command line: callpeak -t SRX003819.bam -f BAM -g ce -n SRX003819.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX003819.05 # format = BAM # ChIP-seq file = ['SRX003819.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Mon, 07 Sep 2015 18:45:09: # Command line: callpeak -t SRX003819.bam -f BAM -g ce -n SRX003819.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX003819.10 # format = BAM # ChIP-seq file = ['SRX003819.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Mon, 07 Sep 2015 18:45:09: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:45:09: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:45:09: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:45:09: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:45:09: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:45:09: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:45:11: #1 tag size is determined as 36 bps INFO @ Mon, 07 Sep 2015 18:45:11: #1 tag size = 36 INFO @ Mon, 07 Sep 2015 18:45:11: #1 total tags in treatment: 482796 INFO @ Mon, 07 Sep 2015 18:45:11: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:45:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 07 Sep 2015 18:45:11: #1 tag size is determined as 36 bps INFO @ Mon, 07 Sep 2015 18:45:11: #1 tag size = 36 INFO @ Mon, 07 Sep 2015 18:45:11: #1 total tags in treatment: 482796 INFO @ Mon, 07 Sep 2015 18:45:11: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:45:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 07 Sep 2015 18:45:11: #1 tag size is determined as 36 bps INFO @ Mon, 07 Sep 2015 18:45:11: #1 tag size = 36 INFO @ Mon, 07 Sep 2015 18:45:11: #1 total tags in treatment: 482796 INFO @ Mon, 07 Sep 2015 18:45:11: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:45:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 07 Sep 2015 18:45:11: #1 tags after filtering in treatment: 482772 INFO @ Mon, 07 Sep 2015 18:45:11: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:45:11: #1 finished! INFO @ Mon, 07 Sep 2015 18:45:11: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:45:11: #1 tags after filtering in treatment: 482772 INFO @ Mon, 07 Sep 2015 18:45:11: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:45:11: #1 finished! INFO @ Mon, 07 Sep 2015 18:45:11: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:45:11: #1 tags after filtering in treatment: 482772 INFO @ Mon, 07 Sep 2015 18:45:11: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:45:11: #1 finished! INFO @ Mon, 07 Sep 2015 18:45:11: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:45:12: #2 number of paired peaks: 3308 INFO @ Mon, 07 Sep 2015 18:45:12: start model_add_line... INFO @ Mon, 07 Sep 2015 18:45:12: #2 number of paired peaks: 3308 INFO @ Mon, 07 Sep 2015 18:45:12: start model_add_line... INFO @ Mon, 07 Sep 2015 18:45:12: #2 number of paired peaks: 3308 INFO @ Mon, 07 Sep 2015 18:45:12: start model_add_line... INFO @ Mon, 07 Sep 2015 18:45:13: start X-correlation... INFO @ Mon, 07 Sep 2015 18:45:13: start X-correlation... INFO @ Mon, 07 Sep 2015 18:45:13: start X-correlation... INFO @ Mon, 07 Sep 2015 18:45:13: end of X-cor INFO @ Mon, 07 Sep 2015 18:45:13: end of X-cor INFO @ Mon, 07 Sep 2015 18:45:13: #2 finished! INFO @ Mon, 07 Sep 2015 18:45:13: #2 finished! INFO @ Mon, 07 Sep 2015 18:45:13: end of X-cor INFO @ Mon, 07 Sep 2015 18:45:13: #2 finished! INFO @ Mon, 07 Sep 2015 18:45:13: #2 predicted fragment length is 90 bps INFO @ Mon, 07 Sep 2015 18:45:13: #2 predicted fragment length is 90 bps INFO @ Mon, 07 Sep 2015 18:45:13: #2 predicted fragment length is 90 bps INFO @ Mon, 07 Sep 2015 18:45:13: #2 alternative fragment length(s) may be 90 bps INFO @ Mon, 07 Sep 2015 18:45:13: #2 alternative fragment length(s) may be 90 bps INFO @ Mon, 07 Sep 2015 18:45:13: #2 alternative fragment length(s) may be 90 bps INFO @ Mon, 07 Sep 2015 18:45:13: #2.2 Generate R script for model : SRX003819.05_model.r INFO @ Mon, 07 Sep 2015 18:45:13: #2.2 Generate R script for model : SRX003819.10_model.r INFO @ Mon, 07 Sep 2015 18:45:13: #2.2 Generate R script for model : SRX003819.20_model.r INFO @ Mon, 07 Sep 2015 18:45:13: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:45:13: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:45:13: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:45:13: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:45:13: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:45:13: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:45:16: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:45:17: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:45:17: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:45:19: #4 Write output xls file... SRX003819.20_peaks.xls INFO @ Mon, 07 Sep 2015 18:45:19: #4 Write peak in narrowPeak format file... SRX003819.20_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:45:19: #4 Write summits bed file... SRX003819.20_summits.bed INFO @ Mon, 07 Sep 2015 18:45:19: Done! INFO @ Mon, 07 Sep 2015 18:45:19: #4 Write output xls file... SRX003819.10_peaks.xls pass1 - making usageList (6 chroms): 5 millis pass2 - checking and writing primary data (192 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 07 Sep 2015 18:45:19: #4 Write peak in narrowPeak format file... SRX003819.10_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:45:19: #4 Write summits bed file... SRX003819.10_summits.bed INFO @ Mon, 07 Sep 2015 18:45:19: #4 Write output xls file... SRX003819.05_peaks.xls INFO @ Mon, 07 Sep 2015 18:45:19: #4 Write peak in narrowPeak format file... SRX003819.05_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:45:19: Done! pass1 - making usageList (6 chroms): 4 millis BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 07 Sep 2015 18:45:20: #4 Write summits bed file... SRX003819.05_summits.bed pass2 - checking and writing primary data (655 records, 4 fields): 346 millis CompletedMACS2peakCalling INFO @ Mon, 07 Sep 2015 18:45:20: Done! BigWig に変換しました。 pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1457 records, 4 fields): 3 millis CompletedMACS2peakCalling