Job ID = 3001498 sra ファイルのダウンロード中... Completed: 69933K bytes transferred in 4 seconds (116985K 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 8489 0 --:--:-- 0:00:01 --:--:-- 9524 100 14953 0 14953 0 0 5411 0 --:--:-- 0:00:02 --:--:-- 5813 100 14953 0 14953 0 0 3972 0 --:--:-- 0:00:03 --:--:-- 4184 100 14953 0 14953 0 0 3137 0 --:--:-- 0:00:04 --:--:-- 3268 100 14953 0 14953 0 0 2592 0 --:--:-- 0:00:05 --:--:-- 2681 100 14953 0 14953 0 0 2208 0 --:--:-- 0:00:06 --:--:-- 0 100 14953 0 14953 0 0 1924 0 --:--:-- 0:00:07 --:--:-- 0 100 14953 0 14953 0 0 1704 0 --:--:-- 0:00:08 --:--:-- 0 100 14953 0 14953 0 0 1529 0 --:--:-- 0:00:09 --:--:-- 0 100 14953 0 14953 0 0 1387 0 --:--:-- 0:00:10 --:--:-- 0 100 14953 0 14953 0 0 1269 0 --:--:-- 0:00:11 --:--:-- 0 100 14953 0 14953 0 0 1170 0 --:--:-- 0:00:12 --:--:-- 0 100 14953 0 14953 0 0 1084 0 --:--:-- 0:00:13 --:--:-- 0 100 14953 0 14953 0 0 1011 0 --:--:-- 0:00:14 --:--:-- 0 100 14953 0 14953 0 0 947 0 --:--:-- 0:00:15 --:--:-- 0 100 14953 0 14953 0 0 890 0 --:--:-- 0:00:16 --:--:-- 0 100 14953 0 14953 0 0 840 0 --:--:-- 0:00:17 --:--:-- 0 100 14953 0 14953 0 0 795 0 --:--:-- 0:00:18 --:--:-- 0 100 14953 0 14953 0 0 755 0 --:--:-- 0:00:19 --:--:-- 0 100 14953 0 14953 0 0 719 0 --:--:-- 0:00:20 --:--:-- 0 100 14953 0 14953 0 0 686 0 --:--:-- 0:00:21 --:--:-- 0 100 14953 0 14953 0 0 655 0 --:--:-- 0:00:22 --:--:-- 0 100 14953 0 14953 0 0 628 0 --:--:-- 0:00:23 --:--:-- 0 100 14953 0 14953 0 0 602 0 --:--:-- 0:00:24 --:--:-- 0 100 14953 0 14953 0 0 579 0 --:--:-- 0:00:25 --:--:-- 0 100 14953 0 14953 0 0 557 0 --:--:-- 0:00:26 --:--:-- 0 100 14953 0 14953 0 0 537 0 --:--:-- 0:00:27 --:--:-- 0 100 14953 0 14953 0 0 519 0 --:--:-- 0:00:28 --:--:-- 0 100 14953 0 14953 0 0 501 0 --:--:-- 0:00:29 --:--:-- 0 100 17849 0 17849 0 0 582 0 --:--:-- 0:00:30 --:--:-- 601 100 34613 0 34613 0 0 1123 0 --:--:-- 0:00:30 --:--:-- 4911 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 4652073 spots for /home/okishinya/chipatlas/results/ce10/SRX005632/SRR017601.sra Written 4652073 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: 00:00:26 4652073 reads; of these: 4652073 (100.00%) were unpaired; of these: 3449549 (74.15%) aligned 0 times 944706 (20.31%) aligned exactly 1 time 257818 (5.54%) aligned >1 times 25.85% overall alignment rate Time searching: 00:00:26 Overall time: 00:00:26 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] 190384 / 1202524 = 0.1583 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 18:46:05: # Command line: callpeak -t SRX005632.bam -f BAM -g ce -n SRX005632.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX005632.05 # format = BAM # ChIP-seq file = ['SRX005632.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 18:46:05: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:46:05: # Command line: callpeak -t SRX005632.bam -f BAM -g ce -n SRX005632.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX005632.10 # format = BAM # ChIP-seq file = ['SRX005632.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 18:46:05: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:46:05: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:46:05: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:46:05: # Command line: callpeak -t SRX005632.bam -f BAM -g ce -n SRX005632.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX005632.20 # format = BAM # ChIP-seq file = ['SRX005632.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 18:46:05: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:46:05: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:46:09: 1000000 INFO @ Mon, 07 Sep 2015 18:46:09: 1000000 INFO @ Mon, 07 Sep 2015 18:46:09: 1000000 INFO @ Mon, 07 Sep 2015 18:46:09: #1 tag size is determined as 27 bps INFO @ Mon, 07 Sep 2015 18:46:09: #1 tag size = 27 INFO @ Mon, 07 Sep 2015 18:46:09: #1 total tags in treatment: 1012140 INFO @ Mon, 07 Sep 2015 18:46:09: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:46:09: #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 18:46:09: #1 tag size is determined as 27 bps INFO @ Mon, 07 Sep 2015 18:46:09: #1 tag size = 27 INFO @ Mon, 07 Sep 2015 18:46:09: #1 total tags in treatment: 1012140 INFO @ Mon, 07 Sep 2015 18:46:09: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:46:09: #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 18:46:09: #1 tag size is determined as 27 bps INFO @ Mon, 07 Sep 2015 18:46:09: #1 tag size = 27 INFO @ Mon, 07 Sep 2015 18:46:09: #1 total tags in treatment: 1012140 INFO @ Mon, 07 Sep 2015 18:46:09: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:46:09: #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 18:46:10: #1 tags after filtering in treatment: 1012135 INFO @ Mon, 07 Sep 2015 18:46:10: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:46:10: #1 finished! INFO @ Mon, 07 Sep 2015 18:46:10: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:46:10: #1 tags after filtering in treatment: 1012135 INFO @ Mon, 07 Sep 2015 18:46:10: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:46:10: #1 finished! INFO @ Mon, 07 Sep 2015 18:46:10: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:46:10: #1 tags after filtering in treatment: 1012135 INFO @ Mon, 07 Sep 2015 18:46:10: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:46:10: #1 finished! INFO @ Mon, 07 Sep 2015 18:46:10: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:46:10: #2 number of paired peaks: 1049 INFO @ Mon, 07 Sep 2015 18:46:10: start model_add_line... INFO @ Mon, 07 Sep 2015 18:46:10: #2 number of paired peaks: 1049 INFO @ Mon, 07 Sep 2015 18:46:10: start model_add_line... INFO @ Mon, 07 Sep 2015 18:46:10: #2 number of paired peaks: 1049 INFO @ Mon, 07 Sep 2015 18:46:10: start model_add_line... INFO @ Mon, 07 Sep 2015 18:46:11: start X-correlation... INFO @ Mon, 07 Sep 2015 18:46:11: end of X-cor INFO @ Mon, 07 Sep 2015 18:46:11: #2 finished! INFO @ Mon, 07 Sep 2015 18:46:11: #2 predicted fragment length is 93 bps INFO @ Mon, 07 Sep 2015 18:46:11: #2 alternative fragment length(s) may be 93,548 bps INFO @ Mon, 07 Sep 2015 18:46:11: #2.2 Generate R script for model : SRX005632.10_model.r INFO @ Mon, 07 Sep 2015 18:46:11: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:46:11: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:46:11: start X-correlation... INFO @ Mon, 07 Sep 2015 18:46:11: end of X-cor INFO @ Mon, 07 Sep 2015 18:46:11: #2 finished! INFO @ Mon, 07 Sep 2015 18:46:11: #2 predicted fragment length is 93 bps INFO @ Mon, 07 Sep 2015 18:46:11: #2 alternative fragment length(s) may be 93,548 bps INFO @ Mon, 07 Sep 2015 18:46:11: #2.2 Generate R script for model : SRX005632.05_model.r INFO @ Mon, 07 Sep 2015 18:46:11: start X-correlation... INFO @ Mon, 07 Sep 2015 18:46:11: end of X-cor INFO @ Mon, 07 Sep 2015 18:46:11: #2 finished! INFO @ Mon, 07 Sep 2015 18:46:11: #2 predicted fragment length is 93 bps INFO @ Mon, 07 Sep 2015 18:46:11: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:46:11: #2 alternative fragment length(s) may be 93,548 bps INFO @ Mon, 07 Sep 2015 18:46:11: #2.2 Generate R script for model : SRX005632.20_model.r INFO @ Mon, 07 Sep 2015 18:46:11: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:46:11: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:46:11: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:46:18: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:46:18: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:46:18: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:46:22: #4 Write output xls file... SRX005632.10_peaks.xls INFO @ Mon, 07 Sep 2015 18:46:22: #4 Write peak in narrowPeak format file... SRX005632.10_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:46:22: #4 Write summits bed file... SRX005632.10_summits.bed INFO @ Mon, 07 Sep 2015 18:46:22: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (293 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 07 Sep 2015 18:46:22: #4 Write output xls file... SRX005632.20_peaks.xls INFO @ Mon, 07 Sep 2015 18:46:22: #4 Write peak in narrowPeak format file... SRX005632.20_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:46:22: #4 Write summits bed file... SRX005632.20_summits.bed INFO @ Mon, 07 Sep 2015 18:46:22: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (81 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 07 Sep 2015 18:46:23: #4 Write output xls file... SRX005632.05_peaks.xls INFO @ Mon, 07 Sep 2015 18:46:23: #4 Write peak in narrowPeak format file... SRX005632.05_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:46:23: #4 Write summits bed file... SRX005632.05_summits.bed INFO @ Mon, 07 Sep 2015 18:46:23: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1045 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。