Job ID = 3001488 sra ファイルのダウンロード中... Completed: 72368K bytes transferred in 5 seconds (115636K 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 14953 0 14953 0 0 8214 0 --:--:-- 0:00:01 --:--:-- 9179 100 14953 0 14953 0 0 5298 0 --:--:-- 0:00:02 --:--:-- 5685 100 14953 0 14953 0 0 3911 0 --:--:-- 0:00:03 --:--:-- 4118 100 14953 0 14953 0 0 3098 0 --:--:-- 0:00:04 --:--:-- 3227 100 14953 0 14953 0 0 2566 0 --:--:-- 0:00:05 --:--:-- 2653 100 14953 0 14953 0 0 2189 0 --:--:-- 0:00:06 --:--:-- 0 100 14953 0 14953 0 0 1909 0 --:--:-- 0:00:07 --:--:-- 0 100 14953 0 14953 0 0 1693 0 --:--:-- 0:00:08 --:--:-- 0 100 14953 0 14953 0 0 1520 0 --:--:-- 0:00:09 --:--:-- 0 100 14953 0 14953 0 0 1379 0 --:--:-- 0:00:10 --:--:-- 0 100 14953 0 14953 0 0 1263 0 --:--:-- 0:00:11 --:--:-- 0 100 14953 0 14953 0 0 1164 0 --:--:-- 0:00:12 --:--:-- 0 100 14953 0 14953 0 0 1080 0 --:--:-- 0:00:13 --:--:-- 0 100 14953 0 14953 0 0 1007 0 --:--:-- 0:00:14 --:--:-- 0 100 14953 0 14953 0 0 943 0 --:--:-- 0:00:15 --:--:-- 0 100 14953 0 14953 0 0 887 0 --:--:-- 0:00:16 --:--:-- 0 100 14953 0 14953 0 0 837 0 --:--:-- 0:00:17 --:--:-- 0 100 14953 0 14953 0 0 793 0 --:--:-- 0:00:18 --:--:-- 0 100 14953 0 14953 0 0 753 0 --:--:-- 0:00:19 --:--:-- 0 100 14953 0 14953 0 0 717 0 --:--:-- 0:00:20 --:--:-- 0 100 14953 0 14953 0 0 684 0 --:--:-- 0:00:21 --:--:-- 0 100 14953 0 14953 0 0 654 0 --:--:-- 0:00:22 --:--:-- 0 100 14953 0 14953 0 0 626 0 --:--:-- 0:00:23 --:--:-- 0 100 14953 0 14953 0 0 601 0 --:--:-- 0:00:24 --:--:-- 0 100 14953 0 14953 0 0 578 0 --:--:-- 0:00:25 --:--:-- 0 100 14953 0 14953 0 0 556 0 --:--:-- 0:00:26 --:--:-- 0 100 14953 0 14953 0 0 536 0 --:--:-- 0:00:27 --:--:-- 0 100 14953 0 14953 0 0 517 0 --:--:-- 0:00:28 --:--:-- 0 100 14953 0 14953 0 0 500 0 --:--:-- 0:00:29 --:--:-- 0 100 17867 0 17867 0 0 582 0 --:--:-- 0:00:30 --:--:-- 604 100 34513 0 34513 0 0 1118 0 --:--:-- 0:00:30 --:--:-- 4885 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 4969623 spots for /home/okishinya/chipatlas/results/ce10/SRX003831/SRR015071.sra Written 4969623 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: 00:00:48 4969623 reads; of these: 4969623 (100.00%) were unpaired; of these: 165262 (3.33%) aligned 0 times 3835825 (77.19%) aligned exactly 1 time 968536 (19.49%) aligned >1 times 96.67% overall alignment rate Time searching: 00:00:49 Overall time: 00:00:49 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] 355547 / 4804361 = 0.0740 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 18:46:51: # Command line: callpeak -t SRX003831.bam -f BAM -g ce -n SRX003831.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX003831.20 # format = BAM # ChIP-seq file = ['SRX003831.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 18:46:51: # Command line: callpeak -t SRX003831.bam -f BAM -g ce -n SRX003831.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX003831.10 # format = BAM # ChIP-seq file = ['SRX003831.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 18:46:51: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:46:51: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:46:51: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:46:51: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:46:51: # Command line: callpeak -t SRX003831.bam -f BAM -g ce -n SRX003831.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX003831.05 # format = BAM # ChIP-seq file = ['SRX003831.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 18:46:51: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:46:51: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:46:57: 1000000 INFO @ Mon, 07 Sep 2015 18:46:57: 1000000 INFO @ Mon, 07 Sep 2015 18:46:58: 1000000 INFO @ Mon, 07 Sep 2015 18:47:04: 2000000 INFO @ Mon, 07 Sep 2015 18:47:04: 2000000 INFO @ Mon, 07 Sep 2015 18:47:04: 2000000 INFO @ Mon, 07 Sep 2015 18:47:10: 3000000 INFO @ Mon, 07 Sep 2015 18:47:10: 3000000 INFO @ Mon, 07 Sep 2015 18:47:10: 3000000 INFO @ Mon, 07 Sep 2015 18:47:17: 4000000 INFO @ Mon, 07 Sep 2015 18:47:17: 4000000 INFO @ Mon, 07 Sep 2015 18:47:17: 4000000 INFO @ Mon, 07 Sep 2015 18:47:20: #1 tag size is determined as 27 bps INFO @ Mon, 07 Sep 2015 18:47:20: #1 tag size = 27 INFO @ Mon, 07 Sep 2015 18:47:20: #1 total tags in treatment: 4448814 INFO @ Mon, 07 Sep 2015 18:47:20: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:47:20: #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 18:47:20: #1 tag size is determined as 27 bps INFO @ Mon, 07 Sep 2015 18:47:20: #1 tag size = 27 INFO @ Mon, 07 Sep 2015 18:47:20: #1 total tags in treatment: 4448814 INFO @ Mon, 07 Sep 2015 18:47:20: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:47:20: #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 18:47:20: #1 tag size is determined as 27 bps INFO @ Mon, 07 Sep 2015 18:47:20: #1 tag size = 27 INFO @ Mon, 07 Sep 2015 18:47:20: #1 total tags in treatment: 4448814 INFO @ Mon, 07 Sep 2015 18:47:20: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:47:20: #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 18:47:20: #1 tags after filtering in treatment: 4448776 INFO @ Mon, 07 Sep 2015 18:47:20: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:47:20: #1 finished! INFO @ Mon, 07 Sep 2015 18:47:20: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:47:20: #1 tags after filtering in treatment: 4448776 INFO @ Mon, 07 Sep 2015 18:47:20: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:47:20: #1 finished! INFO @ Mon, 07 Sep 2015 18:47:20: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:47:20: #1 tags after filtering in treatment: 4448776 INFO @ Mon, 07 Sep 2015 18:47:20: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:47:20: #1 finished! INFO @ Mon, 07 Sep 2015 18:47:20: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:47:21: #2 number of paired peaks: 327 WARNING @ Mon, 07 Sep 2015 18:47:21: Fewer paired peaks (327) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 327 pairs to build model! INFO @ Mon, 07 Sep 2015 18:47:21: start model_add_line... INFO @ Mon, 07 Sep 2015 18:47:21: #2 number of paired peaks: 327 WARNING @ Mon, 07 Sep 2015 18:47:21: Fewer paired peaks (327) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 327 pairs to build model! INFO @ Mon, 07 Sep 2015 18:47:21: start model_add_line... INFO @ Mon, 07 Sep 2015 18:47:21: #2 number of paired peaks: 327 WARNING @ Mon, 07 Sep 2015 18:47:21: Fewer paired peaks (327) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 327 pairs to build model! INFO @ Mon, 07 Sep 2015 18:47:21: start model_add_line... INFO @ Mon, 07 Sep 2015 18:47:24: start X-correlation... INFO @ Mon, 07 Sep 2015 18:47:24: end of X-cor INFO @ Mon, 07 Sep 2015 18:47:24: #2 finished! INFO @ Mon, 07 Sep 2015 18:47:24: #2 predicted fragment length is 77 bps INFO @ Mon, 07 Sep 2015 18:47:24: #2 alternative fragment length(s) may be 4,77 bps INFO @ Mon, 07 Sep 2015 18:47:24: #2.2 Generate R script for model : SRX003831.20_model.r INFO @ Mon, 07 Sep 2015 18:47:24: start X-correlation... INFO @ Mon, 07 Sep 2015 18:47:24: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:47:24: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:47:24: end of X-cor INFO @ Mon, 07 Sep 2015 18:47:24: #2 finished! INFO @ Mon, 07 Sep 2015 18:47:24: #2 predicted fragment length is 77 bps INFO @ Mon, 07 Sep 2015 18:47:24: #2 alternative fragment length(s) may be 4,77 bps INFO @ Mon, 07 Sep 2015 18:47:24: #2.2 Generate R script for model : SRX003831.05_model.r INFO @ Mon, 07 Sep 2015 18:47:24: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:47:24: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:47:24: start X-correlation... INFO @ Mon, 07 Sep 2015 18:47:24: end of X-cor INFO @ Mon, 07 Sep 2015 18:47:24: #2 finished! INFO @ Mon, 07 Sep 2015 18:47:24: #2 predicted fragment length is 77 bps INFO @ Mon, 07 Sep 2015 18:47:24: #2 alternative fragment length(s) may be 4,77 bps INFO @ Mon, 07 Sep 2015 18:47:24: #2.2 Generate R script for model : SRX003831.10_model.r INFO @ Mon, 07 Sep 2015 18:47:24: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:47:24: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:47:49: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:47:50: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:47:51: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:48:07: #4 Write output xls file... SRX003831.20_peaks.xls INFO @ Mon, 07 Sep 2015 18:48:07: #4 Write peak in narrowPeak format file... SRX003831.20_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:48:07: #4 Write summits bed file... SRX003831.20_summits.bed INFO @ Mon, 07 Sep 2015 18:48:07: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (111 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 07 Sep 2015 18:48:09: #4 Write output xls file... SRX003831.05_peaks.xls INFO @ Mon, 07 Sep 2015 18:48:09: #4 Write peak in narrowPeak format file... SRX003831.05_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:48:09: #4 Write summits bed file... SRX003831.05_summits.bed INFO @ Mon, 07 Sep 2015 18:48:09: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (826 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 07 Sep 2015 18:48:09: #4 Write output xls file... SRX003831.10_peaks.xls INFO @ Mon, 07 Sep 2015 18:48:09: #4 Write peak in narrowPeak format file... SRX003831.10_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:48:09: #4 Write summits bed file... SRX003831.10_summits.bed INFO @ Mon, 07 Sep 2015 18:48:09: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (243 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。