Job ID = 9033039 sra ファイルのダウンロード中... Completed: 1406298K bytes transferred in 13 seconds (831727K 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 --:--:-- 0:00:06 --:--:-- 0 101 5455 0 5455 0 0 759 0 --:--:-- 0:00:07 --:--:-- 6835 100 33141 0 33141 0 0 4053 0 --:--:-- 0:00:08 --:--:-- 18473 100 102k 0 102k 0 0 11439 0 --:--:-- 0:00:09 --:--:-- 37580 100 109k 0 109k 0 0 12156 0 --:--:-- 0:00:09 --:--:-- 39545 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 43848249 spots for /home/okishinya/chipatlas/results/dm3/SRX886166/SRR1813780.sra Written 43848249 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: 00:11:36 43848249 reads; of these: 43848249 (100.00%) were unpaired; of these: 12925171 (29.48%) aligned 0 times 22955977 (52.35%) aligned exactly 1 time 7967101 (18.17%) aligned >1 times 70.52% overall alignment rate Time searching: 00:11:36 Overall time: 00:11:36 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 23791837 / 30923078 = 0.7694 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 @ Sun, 04 Jun 2017 00:20:33: # Command line: callpeak -t SRX886166.bam -f BAM -g dm -n SRX886166.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX886166.20 # format = BAM # ChIP-seq file = ['SRX886166.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 04 Jun 2017 00:20:33: #1 read tag files... INFO @ Sun, 04 Jun 2017 00:20:33: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 00:20:33: # Command line: callpeak -t SRX886166.bam -f BAM -g dm -n SRX886166.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX886166.05 # format = BAM # ChIP-seq file = ['SRX886166.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 04 Jun 2017 00:20:33: #1 read tag files... INFO @ Sun, 04 Jun 2017 00:20:33: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 00:20:33: # Command line: callpeak -t SRX886166.bam -f BAM -g dm -n SRX886166.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX886166.10 # format = BAM # ChIP-seq file = ['SRX886166.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 04 Jun 2017 00:20:33: #1 read tag files... INFO @ Sun, 04 Jun 2017 00:20:33: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 00:20:39: 1000000 INFO @ Sun, 04 Jun 2017 00:20:39: 1000000 INFO @ Sun, 04 Jun 2017 00:20:39: 1000000 INFO @ Sun, 04 Jun 2017 00:20:45: 2000000 INFO @ Sun, 04 Jun 2017 00:20:45: 2000000 INFO @ Sun, 04 Jun 2017 00:20:45: 2000000 INFO @ Sun, 04 Jun 2017 00:20:51: 3000000 INFO @ Sun, 04 Jun 2017 00:20:51: 3000000 INFO @ Sun, 04 Jun 2017 00:20:51: 3000000 INFO @ Sun, 04 Jun 2017 00:20:56: 4000000 INFO @ Sun, 04 Jun 2017 00:20:57: 4000000 INFO @ Sun, 04 Jun 2017 00:20:57: 4000000 INFO @ Sun, 04 Jun 2017 00:21:02: 5000000 INFO @ Sun, 04 Jun 2017 00:21:02: 5000000 INFO @ Sun, 04 Jun 2017 00:21:03: 5000000 INFO @ Sun, 04 Jun 2017 00:21:08: 6000000 INFO @ Sun, 04 Jun 2017 00:21:09: 6000000 INFO @ Sun, 04 Jun 2017 00:21:10: 6000000 INFO @ Sun, 04 Jun 2017 00:21:14: 7000000 INFO @ Sun, 04 Jun 2017 00:21:14: #1 tag size is determined as 51 bps INFO @ Sun, 04 Jun 2017 00:21:14: #1 tag size = 51 INFO @ Sun, 04 Jun 2017 00:21:14: #1 total tags in treatment: 7131241 INFO @ Sun, 04 Jun 2017 00:21:14: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 00:21:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 00:21:15: 7000000 INFO @ Sun, 04 Jun 2017 00:21:16: #1 tags after filtering in treatment: 7128444 INFO @ Sun, 04 Jun 2017 00:21:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 00:21:16: #1 finished! INFO @ Sun, 04 Jun 2017 00:21:16: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 00:21:16: #1 tag size is determined as 51 bps INFO @ Sun, 04 Jun 2017 00:21:16: #1 tag size = 51 INFO @ Sun, 04 Jun 2017 00:21:16: #1 total tags in treatment: 7131241 INFO @ Sun, 04 Jun 2017 00:21:16: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 00:21:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 00:21:17: #2 number of paired peaks: 4258 INFO @ Sun, 04 Jun 2017 00:21:17: start model_add_line... INFO @ Sun, 04 Jun 2017 00:21:17: #1 tags after filtering in treatment: 7128444 INFO @ Sun, 04 Jun 2017 00:21:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 00:21:17: #1 finished! INFO @ Sun, 04 Jun 2017 00:21:17: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 00:21:18: 7000000 INFO @ Sun, 04 Jun 2017 00:21:18: #1 tag size is determined as 51 bps INFO @ Sun, 04 Jun 2017 00:21:18: #1 tag size = 51 INFO @ Sun, 04 Jun 2017 00:21:18: #1 total tags in treatment: 7131241 INFO @ Sun, 04 Jun 2017 00:21:18: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 00:21:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 00:21:19: #2 number of paired peaks: 4258 INFO @ Sun, 04 Jun 2017 00:21:19: start model_add_line... INFO @ Sun, 04 Jun 2017 00:21:20: #1 tags after filtering in treatment: 7128444 INFO @ Sun, 04 Jun 2017 00:21:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 00:21:20: #1 finished! INFO @ Sun, 04 Jun 2017 00:21:20: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 00:21:22: #2 number of paired peaks: 4258 INFO @ Sun, 04 Jun 2017 00:21:22: start model_add_line... INFO @ Sun, 04 Jun 2017 00:21:48: start X-correlation... INFO @ Sun, 04 Jun 2017 00:21:48: end of X-cor INFO @ Sun, 04 Jun 2017 00:21:48: #2 finished! INFO @ Sun, 04 Jun 2017 00:21:48: #2 predicted fragment length is 66 bps INFO @ Sun, 04 Jun 2017 00:21:48: #2 alternative fragment length(s) may be 66 bps INFO @ Sun, 04 Jun 2017 00:21:48: #2.2 Generate R script for model : SRX886166.20_model.r WARNING @ Sun, 04 Jun 2017 00:21:48: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Jun 2017 00:21:48: #2 You may need to consider one of the other alternative d(s): 66 WARNING @ Sun, 04 Jun 2017 00:21:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 04 Jun 2017 00:21:48: #3 Call peaks... INFO @ Sun, 04 Jun 2017 00:21:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 00:21:50: start X-correlation... INFO @ Sun, 04 Jun 2017 00:21:50: end of X-cor INFO @ Sun, 04 Jun 2017 00:21:50: #2 finished! INFO @ Sun, 04 Jun 2017 00:21:50: #2 predicted fragment length is 66 bps INFO @ Sun, 04 Jun 2017 00:21:50: #2 alternative fragment length(s) may be 66 bps INFO @ Sun, 04 Jun 2017 00:21:50: #2.2 Generate R script for model : SRX886166.05_model.r WARNING @ Sun, 04 Jun 2017 00:21:50: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Jun 2017 00:21:50: #2 You may need to consider one of the other alternative d(s): 66 WARNING @ Sun, 04 Jun 2017 00:21:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 04 Jun 2017 00:21:50: #3 Call peaks... INFO @ Sun, 04 Jun 2017 00:21:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 00:21:53: start X-correlation... INFO @ Sun, 04 Jun 2017 00:21:53: end of X-cor INFO @ Sun, 04 Jun 2017 00:21:53: #2 finished! INFO @ Sun, 04 Jun 2017 00:21:53: #2 predicted fragment length is 66 bps INFO @ Sun, 04 Jun 2017 00:21:53: #2 alternative fragment length(s) may be 66 bps INFO @ Sun, 04 Jun 2017 00:21:53: #2.2 Generate R script for model : SRX886166.10_model.r WARNING @ Sun, 04 Jun 2017 00:21:53: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Jun 2017 00:21:53: #2 You may need to consider one of the other alternative d(s): 66 WARNING @ Sun, 04 Jun 2017 00:21:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 04 Jun 2017 00:21:53: #3 Call peaks... INFO @ Sun, 04 Jun 2017 00:21:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 00:22:29: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 00:22:32: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 00:22:34: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 00:23:00: #4 Write output xls file... SRX886166.20_peaks.xls INFO @ Sun, 04 Jun 2017 00:23:00: #4 Write peak in narrowPeak format file... SRX886166.20_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 00:23:00: #4 Write summits bed file... SRX886166.20_summits.bed INFO @ Sun, 04 Jun 2017 00:23:00: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (3851 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 00:23:07: #4 Write output xls file... SRX886166.10_peaks.xls INFO @ Sun, 04 Jun 2017 00:23:07: #4 Write peak in narrowPeak format file... SRX886166.10_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 00:23:07: #4 Write summits bed file... SRX886166.10_summits.bed INFO @ Sun, 04 Jun 2017 00:23:07: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6672 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 00:23:07: #4 Write output xls file... SRX886166.05_peaks.xls INFO @ Sun, 04 Jun 2017 00:23:08: #4 Write peak in narrowPeak format file... SRX886166.05_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 00:23:08: #4 Write summits bed file... SRX886166.05_summits.bed INFO @ Sun, 04 Jun 2017 00:23:08: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (10130 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。