Job ID = 3001469 sra ファイルのダウンロード中... Completed: 178679K bytes transferred in 5 seconds (281532K bits/sec), in 2 files, 3 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 6969 0 --:--:-- 0:00:02 --:--:-- 9506 100 14953 0 14953 0 0 4750 0 --:--:-- 0:00:03 --:--:-- 5806 100 14953 0 14953 0 0 3603 0 --:--:-- 0:00:04 --:--:-- 4180 100 14953 0 14953 0 0 2902 0 --:--:-- 0:00:05 --:--:-- 3265 100 14953 0 14953 0 0 2429 0 --:--:-- 0:00:06 --:--:-- 2679 100 14953 0 14953 0 0 2089 0 --:--:-- 0:00:07 --:--:-- 0 100 14953 0 14953 0 0 1833 0 --:--:-- 0:00:08 --:--:-- 0 100 14953 0 14953 0 0 1632 0 --:--:-- 0:00:09 --:--:-- 0 100 14953 0 14953 0 0 1471 0 --:--:-- 0:00:10 --:--:-- 0 100 14953 0 14953 0 0 1339 0 --:--:-- 0:00:11 --:--:-- 0 100 14953 0 14953 0 0 1229 0 --:--:-- 0:00:12 --:--:-- 0 100 14953 0 14953 0 0 1135 0 --:--:-- 0:00:13 --:--:-- 0 100 14953 0 14953 0 0 1055 0 --:--:-- 0:00:14 --:--:-- 0 100 14953 0 14953 0 0 985 0 --:--:-- 0:00:15 --:--:-- 0 100 14953 0 14953 0 0 924 0 --:--:-- 0:00:16 --:--:-- 0 100 14953 0 14953 0 0 870 0 --:--:-- 0:00:17 --:--:-- 0 100 14953 0 14953 0 0 822 0 --:--:-- 0:00:18 --:--:-- 0 100 14953 0 14953 0 0 779 0 --:--:-- 0:00:19 --:--:-- 0 100 14953 0 14953 0 0 740 0 --:--:-- 0:00:20 --:--:-- 0 100 14953 0 14953 0 0 705 0 --:--:-- 0:00:21 --:--:-- 0 100 14953 0 14953 0 0 673 0 --:--:-- 0:00:22 --:--:-- 0 100 14953 0 14953 0 0 644 0 --:--:-- 0:00:23 --:--:-- 0 100 14953 0 14953 0 0 618 0 --:--:-- 0:00:24 --:--:-- 0 100 14953 0 14953 0 0 593 0 --:--:-- 0:00:25 --:--:-- 0 100 14953 0 14953 0 0 570 0 --:--:-- 0:00:26 --:--:-- 0 100 14953 0 14953 0 0 549 0 --:--:-- 0:00:27 --:--:-- 0 100 14953 0 14953 0 0 530 0 --:--:-- 0:00:28 --:--:-- 0 100 14953 0 14953 0 0 512 0 --:--:-- 0:00:29 --:--:-- 0 100 14953 0 14953 0 0 495 0 --:--:-- 0:00:30 --:--:-- 0 100 16407 0 16407 0 0 529 0 --:--:-- 0:00:31 --:--:-- 301 100 34483 0 34483 0 0 1105 0 --:--:-- 0:00:31 --:--:-- 4871 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 5218747 spots for /home/okishinya/chipatlas/results/ce10/SRX002673/SRR013607.sra Written 5218747 spots total Written 6111726 spots for /home/okishinya/chipatlas/results/ce10/SRX002673/SRR013606.sra Written 6111726 spots total 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: 00:02:23 11330473 reads; of these: 11330473 (100.00%) were unpaired; of these: 4289722 (37.86%) aligned 0 times 5742409 (50.68%) aligned exactly 1 time 1298342 (11.46%) aligned >1 times 62.14% overall alignment rate Time searching: 00:02:23 Overall time: 00:02:23 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] 1194690 / 7040751 = 0.1697 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 18:48:37: # Command line: callpeak -t SRX002673.bam -f BAM -g ce -n SRX002673.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX002673.05 # format = BAM # ChIP-seq file = ['SRX002673.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 18:48:37: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:48:37: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:48:37: # Command line: callpeak -t SRX002673.bam -f BAM -g ce -n SRX002673.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX002673.20 # format = BAM # ChIP-seq file = ['SRX002673.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 18:48:37: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:48:37: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:48:37: # Command line: callpeak -t SRX002673.bam -f BAM -g ce -n SRX002673.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX002673.10 # format = BAM # ChIP-seq file = ['SRX002673.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 18:48:37: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:48:37: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:48:44: 1000000 INFO @ Mon, 07 Sep 2015 18:48:44: 1000000 INFO @ Mon, 07 Sep 2015 18:48:44: 1000000 INFO @ Mon, 07 Sep 2015 18:48:50: 2000000 INFO @ Mon, 07 Sep 2015 18:48:50: 2000000 INFO @ Mon, 07 Sep 2015 18:48:51: 2000000 INFO @ Mon, 07 Sep 2015 18:48:57: 3000000 INFO @ Mon, 07 Sep 2015 18:48:57: 3000000 INFO @ Mon, 07 Sep 2015 18:48:57: 3000000 INFO @ Mon, 07 Sep 2015 18:49:03: 4000000 INFO @ Mon, 07 Sep 2015 18:49:04: 4000000 INFO @ Mon, 07 Sep 2015 18:49:04: 4000000 INFO @ Mon, 07 Sep 2015 18:49:10: 5000000 INFO @ Mon, 07 Sep 2015 18:49:10: 5000000 INFO @ Mon, 07 Sep 2015 18:49:11: 5000000 INFO @ Mon, 07 Sep 2015 18:49:15: #1 tag size is determined as 27 bps INFO @ Mon, 07 Sep 2015 18:49:15: #1 tag size = 27 INFO @ Mon, 07 Sep 2015 18:49:15: #1 total tags in treatment: 5846061 INFO @ Mon, 07 Sep 2015 18:49:15: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:49:15: #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 18:49:15: #1 tag size is determined as 27 bps INFO @ Mon, 07 Sep 2015 18:49:15: #1 tag size = 27 INFO @ Mon, 07 Sep 2015 18:49:15: #1 total tags in treatment: 5846061 INFO @ Mon, 07 Sep 2015 18:49:15: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:49:15: #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 18:49:16: #1 tags after filtering in treatment: 5845984 INFO @ Mon, 07 Sep 2015 18:49:16: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:49:16: #1 finished! INFO @ Mon, 07 Sep 2015 18:49:16: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:49:16: #1 tags after filtering in treatment: 5845984 INFO @ Mon, 07 Sep 2015 18:49:16: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:49:16: #1 finished! INFO @ Mon, 07 Sep 2015 18:49:16: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:49:17: #1 tag size is determined as 27 bps INFO @ Mon, 07 Sep 2015 18:49:17: #1 tag size = 27 INFO @ Mon, 07 Sep 2015 18:49:17: #1 total tags in treatment: 5846061 INFO @ Mon, 07 Sep 2015 18:49:17: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:49:17: #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 18:49:17: #2 number of paired peaks: 485 WARNING @ Mon, 07 Sep 2015 18:49:17: Fewer paired peaks (485) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 485 pairs to build model! INFO @ Mon, 07 Sep 2015 18:49:17: start model_add_line... INFO @ Mon, 07 Sep 2015 18:49:18: #1 tags after filtering in treatment: 5845984 INFO @ Mon, 07 Sep 2015 18:49:18: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:49:18: #1 finished! INFO @ Mon, 07 Sep 2015 18:49:18: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:49:18: #2 number of paired peaks: 485 WARNING @ Mon, 07 Sep 2015 18:49:18: Fewer paired peaks (485) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 485 pairs to build model! INFO @ Mon, 07 Sep 2015 18:49:18: start model_add_line... INFO @ Mon, 07 Sep 2015 18:49:19: #2 number of paired peaks: 485 WARNING @ Mon, 07 Sep 2015 18:49:19: Fewer paired peaks (485) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 485 pairs to build model! INFO @ Mon, 07 Sep 2015 18:49:19: start model_add_line... INFO @ Mon, 07 Sep 2015 18:49:22: start X-correlation... INFO @ Mon, 07 Sep 2015 18:49:22: end of X-cor INFO @ Mon, 07 Sep 2015 18:49:22: #2 finished! INFO @ Mon, 07 Sep 2015 18:49:22: #2 predicted fragment length is 68 bps INFO @ Mon, 07 Sep 2015 18:49:22: #2 alternative fragment length(s) may be 4,68 bps INFO @ Mon, 07 Sep 2015 18:49:22: #2.2 Generate R script for model : SRX002673.10_model.r INFO @ Mon, 07 Sep 2015 18:49:22: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:49:22: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:49:22: start X-correlation... INFO @ Mon, 07 Sep 2015 18:49:22: end of X-cor INFO @ Mon, 07 Sep 2015 18:49:22: #2 finished! INFO @ Mon, 07 Sep 2015 18:49:22: #2 predicted fragment length is 68 bps INFO @ Mon, 07 Sep 2015 18:49:22: #2 alternative fragment length(s) may be 4,68 bps INFO @ Mon, 07 Sep 2015 18:49:22: #2.2 Generate R script for model : SRX002673.20_model.r INFO @ Mon, 07 Sep 2015 18:49:22: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:49:22: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:49:23: start X-correlation... INFO @ Mon, 07 Sep 2015 18:49:23: end of X-cor INFO @ Mon, 07 Sep 2015 18:49:23: #2 finished! INFO @ Mon, 07 Sep 2015 18:49:23: #2 predicted fragment length is 68 bps INFO @ Mon, 07 Sep 2015 18:49:23: #2 alternative fragment length(s) may be 4,68 bps INFO @ Mon, 07 Sep 2015 18:49:23: #2.2 Generate R script for model : SRX002673.05_model.r INFO @ Mon, 07 Sep 2015 18:49:23: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:49:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:49:55: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:49:56: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:49:57: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:50:18: #4 Write output xls file... SRX002673.20_peaks.xls INFO @ Mon, 07 Sep 2015 18:50:18: #4 Write peak in narrowPeak format file... SRX002673.20_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:50:18: #4 Write summits bed file... SRX002673.20_summits.bed INFO @ Mon, 07 Sep 2015 18:50:18: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (458 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 07 Sep 2015 18:50:22: #4 Write output xls file... SRX002673.05_peaks.xls INFO @ Mon, 07 Sep 2015 18:50:22: #4 Write peak in narrowPeak format file... SRX002673.05_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:50:22: #4 Write summits bed file... SRX002673.05_summits.bed INFO @ Mon, 07 Sep 2015 18:50:22: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3188 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 07 Sep 2015 18:50:23: #4 Write output xls file... SRX002673.10_peaks.xls INFO @ Mon, 07 Sep 2015 18:50:23: #4 Write peak in narrowPeak format file... SRX002673.10_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:50:23: #4 Write summits bed file... SRX002673.10_summits.bed INFO @ Mon, 07 Sep 2015 18:50:23: Done! pass1 - making usageList (7 chroms): 5 millis pass2 - checking and writing primary data (1513 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。