Job ID = 3001487 sra ファイルのダウンロード中... Completed: 65369K bytes transferred in 5 seconds (102146K 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 8379 0 8379 0 0 14900 0 --:--:-- --:--:-- --:--:-- 23082 100 11299 0 11299 0 0 7223 0 --:--:-- 0:00:01 --:--:-- 8277 100 14953 0 14953 0 0 5999 0 --:--:-- 0:00:02 --:--:-- 6521 100 14953 0 14953 0 0 4279 0 --:--:-- 0:00:03 --:--:-- 4538 100 14953 0 14953 0 0 3325 0 --:--:-- 0:00:04 --:--:-- 3479 100 14953 0 14953 0 0 2720 0 --:--:-- 0:00:05 --:--:-- 1332 100 14953 0 14953 0 0 2300 0 --:--:-- 0:00:06 --:--:-- 740 100 14953 0 14953 0 0 1993 0 --:--:-- 0:00:07 --:--:-- 0 100 14953 0 14953 0 0 1758 0 --:--:-- 0:00:08 --:--:-- 0 100 14953 0 14953 0 0 1573 0 --:--:-- 0:00:09 --:--:-- 0 100 14953 0 14953 0 0 1423 0 --:--:-- 0:00:10 --:--:-- 0 100 14953 0 14953 0 0 1299 0 --:--:-- 0:00:11 --:--:-- 0 100 14953 0 14953 0 0 1195 0 --:--:-- 0:00:12 --:--:-- 0 100 14953 0 14953 0 0 1106 0 --:--:-- 0:00:13 --:--:-- 0 100 14953 0 14953 0 0 1030 0 --:--:-- 0:00:14 --:--:-- 0 100 14953 0 14953 0 0 963 0 --:--:-- 0:00:15 --:--:-- 0 100 14953 0 14953 0 0 905 0 --:--:-- 0:00:16 --:--:-- 0 100 14953 0 14953 0 0 853 0 --:--:-- 0:00:17 --:--:-- 0 100 14953 0 14953 0 0 807 0 --:--:-- 0:00:18 --:--:-- 0 100 14953 0 14953 0 0 766 0 --:--:-- 0:00:19 --:--:-- 0 100 14953 0 14953 0 0 728 0 --:--:-- 0:00:20 --:--:-- 0 100 14953 0 14953 0 0 694 0 --:--:-- 0:00:21 --:--:-- 0 100 14953 0 14953 0 0 663 0 --:--:-- 0:00:22 --:--:-- 0 100 14953 0 14953 0 0 635 0 --:--:-- 0:00:23 --:--:-- 0 100 14953 0 14953 0 0 609 0 --:--:-- 0:00:24 --:--:-- 0 100 14953 0 14953 0 0 585 0 --:--:-- 0:00:25 --:--:-- 0 100 14953 0 14953 0 0 563 0 --:--:-- 0:00:26 --:--:-- 0 100 14953 0 14953 0 0 543 0 --:--:-- 0:00:27 --:--:-- 0 100 14953 0 14953 0 0 524 0 --:--:-- 0:00:28 --:--:-- 0 100 14953 0 14953 0 0 506 0 --:--:-- 0:00:29 --:--:-- 0 100 14953 0 14953 0 0 489 0 --:--:-- 0:00:30 --:--:-- 0 100 33905 0 33905 0 0 1080 0 --:--:-- 0:00:31 --:--:-- 3916 100 34514 0 34514 0 0 1100 0 --:--:-- 0:00:31 --:--:-- 5096 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 3085377 spots for /home/okishinya/chipatlas/results/ce10/SRX003830/SRR015070.sra Written 3085377 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: 00:00:18 3085377 reads; of these: 3085377 (100.00%) were unpaired; of these: 2546000 (82.52%) aligned 0 times 442160 (14.33%) aligned exactly 1 time 97217 (3.15%) aligned >1 times 17.48% overall alignment rate Time searching: 00:00:18 Overall time: 00:00:18 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] 44554 / 539377 = 0.0826 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 18:45:30: # Command line: callpeak -t SRX003830.bam -f BAM -g ce -n SRX003830.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX003830.10 # format = BAM # ChIP-seq file = ['SRX003830.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 18:45:30: # Command line: callpeak -t SRX003830.bam -f BAM -g ce -n SRX003830.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX003830.05 # format = BAM # ChIP-seq file = ['SRX003830.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 18:45:30: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:45:30: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:45:30: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:45:30: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:45:30: # Command line: callpeak -t SRX003830.bam -f BAM -g ce -n SRX003830.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX003830.20 # format = BAM # ChIP-seq file = ['SRX003830.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 18:45:30: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:45:30: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:45:33: #1 tag size is determined as 27 bps INFO @ Mon, 07 Sep 2015 18:45:33: #1 tag size = 27 INFO @ Mon, 07 Sep 2015 18:45:33: #1 total tags in treatment: 494823 INFO @ Mon, 07 Sep 2015 18:45:33: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:45:33: #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 18:45:33: #1 tag size is determined as 27 bps INFO @ Mon, 07 Sep 2015 18:45:33: #1 tag size = 27 INFO @ Mon, 07 Sep 2015 18:45:33: #1 total tags in treatment: 494823 INFO @ Mon, 07 Sep 2015 18:45:33: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:45:33: #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 18:45:33: #1 tags after filtering in treatment: 494785 INFO @ Mon, 07 Sep 2015 18:45:33: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:45:33: #1 finished! INFO @ Mon, 07 Sep 2015 18:45:33: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:45:33: #1 tags after filtering in treatment: 494785 INFO @ Mon, 07 Sep 2015 18:45:33: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:45:33: #1 finished! INFO @ Mon, 07 Sep 2015 18:45:33: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:45:33: #2 number of paired peaks: 346 WARNING @ Mon, 07 Sep 2015 18:45:33: Fewer paired peaks (346) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 346 pairs to build model! INFO @ Mon, 07 Sep 2015 18:45:33: start model_add_line... INFO @ Mon, 07 Sep 2015 18:45:33: #2 number of paired peaks: 346 WARNING @ Mon, 07 Sep 2015 18:45:33: Fewer paired peaks (346) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 346 pairs to build model! INFO @ Mon, 07 Sep 2015 18:45:33: start model_add_line... INFO @ Mon, 07 Sep 2015 18:45:33: #1 tag size is determined as 27 bps INFO @ Mon, 07 Sep 2015 18:45:33: #1 tag size = 27 INFO @ Mon, 07 Sep 2015 18:45:33: #1 total tags in treatment: 494823 INFO @ Mon, 07 Sep 2015 18:45:33: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:45:33: #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 18:45:33: start X-correlation... INFO @ Mon, 07 Sep 2015 18:45:33: #1 tags after filtering in treatment: 494785 INFO @ Mon, 07 Sep 2015 18:45:33: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:45:33: #1 finished! INFO @ Mon, 07 Sep 2015 18:45:33: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:45:33: start X-correlation... INFO @ Mon, 07 Sep 2015 18:45:33: end of X-cor INFO @ Mon, 07 Sep 2015 18:45:33: end of X-cor INFO @ Mon, 07 Sep 2015 18:45:33: #2 finished! INFO @ Mon, 07 Sep 2015 18:45:33: #2 finished! INFO @ Mon, 07 Sep 2015 18:45:33: #2 predicted fragment length is 85 bps INFO @ Mon, 07 Sep 2015 18:45:33: #2 predicted fragment length is 85 bps INFO @ Mon, 07 Sep 2015 18:45:33: #2 alternative fragment length(s) may be 85,581 bps INFO @ Mon, 07 Sep 2015 18:45:33: #2 alternative fragment length(s) may be 85,581 bps INFO @ Mon, 07 Sep 2015 18:45:33: #2.2 Generate R script for model : SRX003830.05_model.r INFO @ Mon, 07 Sep 2015 18:45:33: #2.2 Generate R script for model : SRX003830.10_model.r INFO @ Mon, 07 Sep 2015 18:45:33: #2 number of paired peaks: 346 WARNING @ Mon, 07 Sep 2015 18:45:33: Fewer paired peaks (346) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 346 pairs to build model! INFO @ Mon, 07 Sep 2015 18:45:33: start model_add_line... INFO @ Mon, 07 Sep 2015 18:45:33: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:45:33: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:45:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:45:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:45:34: start X-correlation... INFO @ Mon, 07 Sep 2015 18:45:34: end of X-cor INFO @ Mon, 07 Sep 2015 18:45:34: #2 finished! INFO @ Mon, 07 Sep 2015 18:45:34: #2 predicted fragment length is 85 bps INFO @ Mon, 07 Sep 2015 18:45:34: #2 alternative fragment length(s) may be 85,581 bps INFO @ Mon, 07 Sep 2015 18:45:34: #2.2 Generate R script for model : SRX003830.20_model.r INFO @ Mon, 07 Sep 2015 18:45:34: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:45:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:45:36: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:45:36: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:45:37: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:45:38: #4 Write output xls file... SRX003830.10_peaks.xls INFO @ Mon, 07 Sep 2015 18:45:38: #4 Write peak in narrowPeak format file... SRX003830.10_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:45:38: #4 Write summits bed file... SRX003830.10_summits.bed INFO @ Mon, 07 Sep 2015 18:45:38: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (55 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 07 Sep 2015 18:45:39: #4 Write output xls file... SRX003830.05_peaks.xls INFO @ Mon, 07 Sep 2015 18:45:39: #4 Write peak in narrowPeak format file... SRX003830.05_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:45:39: #4 Write summits bed file... SRX003830.05_summits.bed INFO @ Mon, 07 Sep 2015 18:45:39: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (147 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 07 Sep 2015 18:45:39: #4 Write output xls file... SRX003830.20_peaks.xls INFO @ Mon, 07 Sep 2015 18:45:39: #4 Write peak in narrowPeak format file... SRX003830.20_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:45:39: #4 Write summits bed file... SRX003830.20_summits.bed INFO @ Mon, 07 Sep 2015 18:45:39: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (16 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。