Job ID = 3001489 sra ファイルのダウンロード中... Completed: 30735K bytes transferred in 5 seconds (47205K 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 8764 0 --:--:-- 0:00:01 --:--:-- 9876 100 14953 0 14953 0 0 5521 0 --:--:-- 0:00:02 --:--:-- 5943 100 14953 0 14953 0 0 4030 0 --:--:-- 0:00:03 --:--:-- 4250 100 14953 0 14953 0 0 3173 0 --:--:-- 0:00:04 --:--:-- 3308 100 14953 0 14953 0 0 2617 0 --:--:-- 0:00:05 --:--:-- 2708 100 14953 0 14953 0 0 2226 0 --:--:-- 0:00:06 --:--:-- 0 100 14953 0 14953 0 0 1937 0 --:--:-- 0:00:07 --:--:-- 0 100 14953 0 14953 0 0 1714 0 --:--:-- 0:00:08 --:--:-- 0 100 14953 0 14953 0 0 1538 0 --:--:-- 0:00:09 --:--:-- 0 100 14953 0 14953 0 0 1394 0 --:--:-- 0:00:10 --:--:-- 0 100 14953 0 14953 0 0 1275 0 --:--:-- 0:00:11 --:--:-- 0 100 14953 0 14953 0 0 1175 0 --:--:-- 0:00:12 --:--:-- 0 100 14953 0 14953 0 0 1089 0 --:--:-- 0:00:13 --:--:-- 0 100 14953 0 14953 0 0 1015 0 --:--:-- 0:00:14 --:--:-- 0 100 14953 0 14953 0 0 950 0 --:--:-- 0:00:15 --:--:-- 0 100 14953 0 14953 0 0 893 0 --:--:-- 0:00:16 --:--:-- 0 100 14953 0 14953 0 0 843 0 --:--:-- 0:00:17 --:--:-- 0 100 14953 0 14953 0 0 798 0 --:--:-- 0:00:18 --:--:-- 0 100 14953 0 14953 0 0 757 0 --:--:-- 0:00:19 --:--:-- 0 100 14953 0 14953 0 0 721 0 --:--:-- 0:00:20 --:--:-- 0 100 14953 0 14953 0 0 687 0 --:--:-- 0:00:21 --:--:-- 0 100 14953 0 14953 0 0 657 0 --:--:-- 0:00:22 --:--:-- 0 100 14953 0 14953 0 0 629 0 --:--:-- 0:00:23 --:--:-- 0 100 14953 0 14953 0 0 604 0 --:--:-- 0:00:24 --:--:-- 0 100 14953 0 14953 0 0 580 0 --:--:-- 0:00:25 --:--:-- 0 100 14953 0 14953 0 0 559 0 --:--:-- 0:00:26 --:--:-- 0 100 14953 0 14953 0 0 538 0 --:--:-- 0:00:27 --:--:-- 0 100 14953 0 14953 0 0 520 0 --:--:-- 0:00:28 --:--:-- 0 100 14953 0 14953 0 0 502 0 --:--:-- 0:00:29 --:--:-- 0 100 16407 0 16407 0 0 536 0 --:--:-- 0:00:30 --:--:-- 301 100 34063 0 34063 0 0 1107 0 --:--:-- 0:00:30 --:--:-- 4770 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 1465710 spots for /home/okishinya/chipatlas/results/ce10/SRX003832/SRR015072.sra Written 1465710 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: 00:00:14 1465710 reads; of these: 1465710 (100.00%) were unpaired; of these: 431858 (29.46%) aligned 0 times 830144 (56.64%) aligned exactly 1 time 203708 (13.90%) aligned >1 times 70.54% overall alignment rate Time searching: 00:00:14 Overall time: 00:00:14 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] 142900 / 1033852 = 0.1382 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 18:45:28: # Command line: callpeak -t SRX003832.bam -f BAM -g ce -n SRX003832.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX003832.20 # format = BAM # ChIP-seq file = ['SRX003832.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 18:45:28: # Command line: callpeak -t SRX003832.bam -f BAM -g ce -n SRX003832.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX003832.10 # format = BAM # ChIP-seq file = ['SRX003832.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 18:45:28: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:45:28: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:45:28: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:45:28: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:45:28: # Command line: callpeak -t SRX003832.bam -f BAM -g ce -n SRX003832.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX003832.05 # format = BAM # ChIP-seq file = ['SRX003832.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 18:45:28: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:45:28: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:45:33: #1 tag size is determined as 34 bps INFO @ Mon, 07 Sep 2015 18:45:33: #1 tag size = 34 INFO @ Mon, 07 Sep 2015 18:45:33: #1 total tags in treatment: 890952 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 34 bps INFO @ Mon, 07 Sep 2015 18:45:33: #1 tag size = 34 INFO @ Mon, 07 Sep 2015 18:45:33: #1 total tags in treatment: 890952 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: 890927 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: 890927 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 18:45:34: #2 number of paired peaks: 293 WARNING @ Mon, 07 Sep 2015 18:45:34: Fewer paired peaks (293) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 293 pairs to build model! INFO @ Mon, 07 Sep 2015 18:45:34: start model_add_line... INFO @ Mon, 07 Sep 2015 18:45:34: #1 tag size is determined as 34 bps INFO @ Mon, 07 Sep 2015 18:45:34: #1 tag size = 34 INFO @ Mon, 07 Sep 2015 18:45:34: #1 total tags in treatment: 890952 INFO @ Mon, 07 Sep 2015 18:45:34: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:45:34: #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 18:45:34: #2 number of paired peaks: 293 WARNING @ Mon, 07 Sep 2015 18:45:34: Fewer paired peaks (293) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 293 pairs to build model! INFO @ Mon, 07 Sep 2015 18:45:34: start model_add_line... INFO @ Mon, 07 Sep 2015 18:45:34: #1 tags after filtering in treatment: 890927 INFO @ Mon, 07 Sep 2015 18:45:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:45:34: #1 finished! INFO @ Mon, 07 Sep 2015 18:45:34: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:45:34: #2 number of paired peaks: 293 WARNING @ Mon, 07 Sep 2015 18:45:34: Fewer paired peaks (293) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 293 pairs to build model! INFO @ Mon, 07 Sep 2015 18:45:34: start model_add_line... INFO @ Mon, 07 Sep 2015 18:45:34: start X-correlation... 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 60 bps INFO @ Mon, 07 Sep 2015 18:45:34: #2 alternative fragment length(s) may be 60,503,568 bps INFO @ Mon, 07 Sep 2015 18:45:34: #2.2 Generate R script for model : SRX003832.20_model.r 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 60 bps INFO @ Mon, 07 Sep 2015 18:45:34: #2 alternative fragment length(s) may be 60,503,568 bps INFO @ Mon, 07 Sep 2015 18:45:34: #2.2 Generate R script for model : SRX003832.10_model.r WARNING @ Mon, 07 Sep 2015 18:45:34: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 07 Sep 2015 18:45:34: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 07 Sep 2015 18:45:34: #2 You may need to consider one of the other alternative d(s): 60,503,568 WARNING @ Mon, 07 Sep 2015 18:45:34: #2 You may need to consider one of the other alternative d(s): 60,503,568 WARNING @ Mon, 07 Sep 2015 18:45:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. WARNING @ Mon, 07 Sep 2015 18:45:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 07 Sep 2015 18:45:34: #3 Call peaks... 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 18:45:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:45:35: start X-correlation... INFO @ Mon, 07 Sep 2015 18:45:35: end of X-cor INFO @ Mon, 07 Sep 2015 18:45:35: #2 finished! INFO @ Mon, 07 Sep 2015 18:45:35: #2 predicted fragment length is 60 bps INFO @ Mon, 07 Sep 2015 18:45:35: #2 alternative fragment length(s) may be 60,503,568 bps INFO @ Mon, 07 Sep 2015 18:45:35: #2.2 Generate R script for model : SRX003832.05_model.r WARNING @ Mon, 07 Sep 2015 18:45:35: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 07 Sep 2015 18:45:35: #2 You may need to consider one of the other alternative d(s): 60,503,568 WARNING @ Mon, 07 Sep 2015 18:45:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 07 Sep 2015 18:45:35: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:45:35: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:45:39: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:45:40: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:45:40: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:45:43: #4 Write output xls file... SRX003832.20_peaks.xls INFO @ Mon, 07 Sep 2015 18:45:43: #4 Write peak in narrowPeak format file... SRX003832.20_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:45:43: #4 Write summits bed file... SRX003832.20_summits.bed INFO @ Mon, 07 Sep 2015 18:45:43: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (46 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 07 Sep 2015 18:45:44: #4 Write output xls file... SRX003832.10_peaks.xls INFO @ Mon, 07 Sep 2015 18:45:44: #4 Write peak in narrowPeak format file... SRX003832.10_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:45:44: #4 Write summits bed file... SRX003832.10_summits.bed INFO @ Mon, 07 Sep 2015 18:45:44: Done! INFO @ Mon, 07 Sep 2015 18:45:44: #4 Write output xls file... SRX003832.05_peaks.xls INFO @ Mon, 07 Sep 2015 18:45:44: #4 Write peak in narrowPeak format file... SRX003832.05_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:45:44: #4 Write summits bed file... SRX003832.05_summits.bed INFO @ Mon, 07 Sep 2015 18:45:44: Done! pass1 - making usageList (6 chroms): 1 millis pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (114 records, 4 fields): 2 millis CompletedMACS2peakCalling pass2 - checking and writing primary data (232 records, 4 fields): 717 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。