Job ID = 3001506 sra ファイルのダウンロード中... Completed: 64801K bytes transferred in 4 seconds (109607K 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 8823 0 --:--:-- 0:00:01 --:--:-- 9948 100 14953 0 14953 0 0 5545 0 --:--:-- 0:00:02 --:--:-- 5969 100 14953 0 14953 0 0 4044 0 --:--:-- 0:00:03 --:--:-- 4264 100 14953 0 14953 0 0 3182 0 --:--:-- 0:00:04 --:--:-- 3316 100 14953 0 14953 0 0 2622 0 --:--:-- 0:00:05 --:--:-- 2713 100 14953 0 14953 0 0 2230 0 --:--:-- 0:00:06 --:--:-- 0 100 14953 0 14953 0 0 1940 0 --:--:-- 0:00:07 --:--:-- 0 100 14953 0 14953 0 0 1717 0 --:--:-- 0:00:08 --:--:-- 0 100 14953 0 14953 0 0 1540 0 --:--:-- 0:00:09 --:--:-- 0 100 14953 0 14953 0 0 1396 0 --:--:-- 0:00:10 --:--:-- 0 100 14953 0 14953 0 0 1276 0 --:--:-- 0:00:11 --:--:-- 0 100 14953 0 14953 0 0 1176 0 --:--:-- 0:00:12 --:--:-- 0 100 14953 0 14953 0 0 1090 0 --:--:-- 0:00:13 --:--:-- 0 100 14953 0 14953 0 0 1016 0 --:--:-- 0:00:14 --:--:-- 0 100 14953 0 14953 0 0 951 0 --:--:-- 0:00:15 --:--:-- 0 100 14953 0 14953 0 0 894 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 0 758 0 --:--:-- 0:00:19 --:--:-- 0 100 14953 0 14953 0 0 721 0 --:--:-- 0:00:20 --:--:-- 0 100 14953 0 14953 0 0 688 0 --:--:-- 0:00:21 --:--:-- 0 100 14953 0 14953 0 0 657 0 --:--:-- 0:00:22 --:--:-- 0 100 14953 0 14953 0 0 630 0 --:--:-- 0:00:23 --:--:-- 0 100 14953 0 14953 0 0 604 0 --:--:-- 0:00:24 --:--:-- 0 100 14953 0 14953 0 0 581 0 --:--:-- 0:00:25 --:--:-- 0 100 14953 0 14953 0 0 559 0 --:--:-- 0:00:26 --:--:-- 0 100 14953 0 14953 0 0 539 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 27979 0 27979 0 0 915 0 --:--:-- 0:00:30 --:--:-- 2703 100 34549 0 34549 0 0 1123 0 --:--:-- 0:00:30 --:--:-- 4891 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 4001586 spots for /home/okishinya/chipatlas/results/ce10/SRX005640/SRR017609.sra Written 4001586 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: 00:00:31 4001586 reads; of these: 4001586 (100.00%) were unpaired; of these: 1813978 (45.33%) aligned 0 times 1839015 (45.96%) aligned exactly 1 time 348593 (8.71%) aligned >1 times 54.67% overall alignment rate Time searching: 00:00:31 Overall time: 00:00:31 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] 85464 / 2187608 = 0.0391 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 18:46:25: # Command line: callpeak -t SRX005640.bam -f BAM -g ce -n SRX005640.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX005640.05 # format = BAM # ChIP-seq file = ['SRX005640.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 18:46:25: # Command line: callpeak -t SRX005640.bam -f BAM -g ce -n SRX005640.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX005640.10 # format = BAM # ChIP-seq file = ['SRX005640.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 18:46:25: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:46:25: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:46:25: # Command line: callpeak -t SRX005640.bam -f BAM -g ce -n SRX005640.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX005640.20 # format = BAM # ChIP-seq file = ['SRX005640.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 18:46:25: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:46:25: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:46:25: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:46:25: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:46:30: 1000000 INFO @ Mon, 07 Sep 2015 18:46:30: 1000000 INFO @ Mon, 07 Sep 2015 18:46:31: 1000000 INFO @ Mon, 07 Sep 2015 18:46:36: 2000000 INFO @ Mon, 07 Sep 2015 18:46:36: 2000000 INFO @ Mon, 07 Sep 2015 18:46:36: #1 tag size is determined as 27 bps INFO @ Mon, 07 Sep 2015 18:46:36: #1 tag size = 27 INFO @ Mon, 07 Sep 2015 18:46:36: #1 total tags in treatment: 2102144 INFO @ Mon, 07 Sep 2015 18:46:36: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:46:36: #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 18:46:36: #1 tag size is determined as 27 bps INFO @ Mon, 07 Sep 2015 18:46:36: #1 tag size = 27 INFO @ Mon, 07 Sep 2015 18:46:36: #1 total tags in treatment: 2102144 INFO @ Mon, 07 Sep 2015 18:46:36: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:46:36: #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 18:46:37: #1 tags after filtering in treatment: 2102135 INFO @ Mon, 07 Sep 2015 18:46:37: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:46:37: #1 finished! INFO @ Mon, 07 Sep 2015 18:46:37: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:46:37: #1 tags after filtering in treatment: 2102135 INFO @ Mon, 07 Sep 2015 18:46:37: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:46:37: #1 finished! INFO @ Mon, 07 Sep 2015 18:46:37: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:46:37: #2 number of paired peaks: 184 WARNING @ Mon, 07 Sep 2015 18:46:37: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Mon, 07 Sep 2015 18:46:37: start model_add_line... INFO @ Mon, 07 Sep 2015 18:46:37: #2 number of paired peaks: 184 WARNING @ Mon, 07 Sep 2015 18:46:37: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Mon, 07 Sep 2015 18:46:37: start model_add_line... INFO @ Mon, 07 Sep 2015 18:46:37: 2000000 INFO @ Mon, 07 Sep 2015 18:46:38: start X-correlation... INFO @ Mon, 07 Sep 2015 18:46:38: #1 tag size is determined as 27 bps INFO @ Mon, 07 Sep 2015 18:46:38: #1 tag size = 27 INFO @ Mon, 07 Sep 2015 18:46:38: #1 total tags in treatment: 2102144 INFO @ Mon, 07 Sep 2015 18:46:38: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:46:38: #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 18:46:38: end of X-cor INFO @ Mon, 07 Sep 2015 18:46:38: #2 finished! INFO @ Mon, 07 Sep 2015 18:46:38: #2 predicted fragment length is 24 bps INFO @ Mon, 07 Sep 2015 18:46:38: #2 alternative fragment length(s) may be 24,61,431,475,530,575 bps INFO @ Mon, 07 Sep 2015 18:46:38: #2.2 Generate R script for model : SRX005640.05_model.r WARNING @ Mon, 07 Sep 2015 18:46:38: #2 Since the d (24) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 07 Sep 2015 18:46:38: #2 You may need to consider one of the other alternative d(s): 24,61,431,475,530,575 WARNING @ Mon, 07 Sep 2015 18:46:38: #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 18:46:38: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:46:38: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:46:38: start X-correlation... INFO @ Mon, 07 Sep 2015 18:46:38: end of X-cor INFO @ Mon, 07 Sep 2015 18:46:38: #2 finished! INFO @ Mon, 07 Sep 2015 18:46:38: #2 predicted fragment length is 24 bps INFO @ Mon, 07 Sep 2015 18:46:38: #2 alternative fragment length(s) may be 24,61,431,475,530,575 bps INFO @ Mon, 07 Sep 2015 18:46:38: #2.2 Generate R script for model : SRX005640.20_model.r WARNING @ Mon, 07 Sep 2015 18:46:38: #2 Since the d (24) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 07 Sep 2015 18:46:38: #2 You may need to consider one of the other alternative d(s): 24,61,431,475,530,575 WARNING @ Mon, 07 Sep 2015 18:46:38: #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 18:46:38: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:46:38: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:46:38: #1 tags after filtering in treatment: 2102135 INFO @ Mon, 07 Sep 2015 18:46:38: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:46:38: #1 finished! INFO @ Mon, 07 Sep 2015 18:46:38: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:46:39: #2 number of paired peaks: 184 WARNING @ Mon, 07 Sep 2015 18:46:39: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Mon, 07 Sep 2015 18:46:39: start model_add_line... INFO @ Mon, 07 Sep 2015 18:46:40: start X-correlation... INFO @ Mon, 07 Sep 2015 18:46:40: end of X-cor INFO @ Mon, 07 Sep 2015 18:46:40: #2 finished! INFO @ Mon, 07 Sep 2015 18:46:40: #2 predicted fragment length is 24 bps INFO @ Mon, 07 Sep 2015 18:46:40: #2 alternative fragment length(s) may be 24,61,431,475,530,575 bps INFO @ Mon, 07 Sep 2015 18:46:40: #2.2 Generate R script for model : SRX005640.10_model.r WARNING @ Mon, 07 Sep 2015 18:46:40: #2 Since the d (24) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 07 Sep 2015 18:46:40: #2 You may need to consider one of the other alternative d(s): 24,61,431,475,530,575 WARNING @ Mon, 07 Sep 2015 18:46:40: #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 18:46:40: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:46:40: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:46:50: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:46:51: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:46:53: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:46:59: #4 Write output xls file... SRX005640.05_peaks.xls INFO @ Mon, 07 Sep 2015 18:46:59: #4 Write peak in narrowPeak format file... SRX005640.05_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:46:59: #4 Write summits bed file... SRX005640.05_summits.bed INFO @ Mon, 07 Sep 2015 18:46:59: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (149 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 07 Sep 2015 18:46:59: #4 Write output xls file... SRX005640.20_peaks.xls INFO @ Mon, 07 Sep 2015 18:46:59: #4 Write peak in narrowPeak format file... SRX005640.20_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:46:59: #4 Write summits bed file... SRX005640.20_summits.bed INFO @ Mon, 07 Sep 2015 18:47:00: Done! pass1 - making usageList (5 chroms): 5 millis pass2 - checking and writing primary data (8 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Mon, 07 Sep 2015 18:47:02: #4 Write output xls file... SRX005640.10_peaks.xls INFO @ Mon, 07 Sep 2015 18:47:02: #4 Write peak in narrowPeak format file... SRX005640.10_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:47:02: #4 Write summits bed file... SRX005640.10_summits.bed INFO @ Mon, 07 Sep 2015 18:47:02: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (42 records, 4 fields): 270 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。