Job ID = 9041682 sra ファイルのダウンロード中... Completed: 1293462K bytes transferred in 14 seconds (715492K bits/sec), in 4 files, 5 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 --:--:-- 0 100 14324 0 14324 0 0 1955 0 --:--:-- 0:00:07 --:--:-- 14126 100 34590 0 34590 0 0 4242 0 --:--:-- 0:00:08 --:--:-- 18758 100 74612 0 74612 0 0 8267 0 --:--:-- 0:00:09 --:--:-- 27491 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 8944573 spots for /home/okishinya/chipatlas/results/dm3/SRX1308480/SRR2566772.sra Written 8944573 spots total Written 8947712 spots for /home/okishinya/chipatlas/results/dm3/SRX1308480/SRR2566771.sra Written 8947712 spots total Written 10730402 spots for /home/okishinya/chipatlas/results/dm3/SRX1308480/SRR2566774.sra Written 10730402 spots total Written 10727054 spots for /home/okishinya/chipatlas/results/dm3/SRX1308480/SRR2566773.sra Written 10727054 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: 00:06:28 39349741 reads; of these: 39349741 (100.00%) were unpaired; of these: 4200636 (10.68%) aligned 0 times 28725470 (73.00%) aligned exactly 1 time 6423635 (16.32%) aligned >1 times 89.32% overall alignment rate Time searching: 00:06:28 Overall time: 00:06:28 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] 30506288 / 35149105 = 0.8679 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, 05 Jun 2017 01:25:02: # Command line: callpeak -t SRX1308480.bam -f BAM -g dm -n SRX1308480.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1308480.05 # format = BAM # ChIP-seq file = ['SRX1308480.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 @ Mon, 05 Jun 2017 01:25:02: # Command line: callpeak -t SRX1308480.bam -f BAM -g dm -n SRX1308480.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1308480.20 # format = BAM # ChIP-seq file = ['SRX1308480.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 @ Mon, 05 Jun 2017 01:25:02: #1 read tag files... INFO @ Mon, 05 Jun 2017 01:25:02: #1 read tag files... INFO @ Mon, 05 Jun 2017 01:25:02: #1 read treatment tags... INFO @ Mon, 05 Jun 2017 01:25:02: #1 read treatment tags... INFO @ Mon, 05 Jun 2017 01:25:02: # Command line: callpeak -t SRX1308480.bam -f BAM -g dm -n SRX1308480.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1308480.10 # format = BAM # ChIP-seq file = ['SRX1308480.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 @ Mon, 05 Jun 2017 01:25:02: #1 read tag files... INFO @ Mon, 05 Jun 2017 01:25:02: #1 read treatment tags... INFO @ Mon, 05 Jun 2017 01:25:09: 1000000 INFO @ Mon, 05 Jun 2017 01:25:09: 1000000 INFO @ Mon, 05 Jun 2017 01:25:09: 1000000 INFO @ Mon, 05 Jun 2017 01:25:16: 2000000 INFO @ Mon, 05 Jun 2017 01:25:16: 2000000 INFO @ Mon, 05 Jun 2017 01:25:16: 2000000 INFO @ Mon, 05 Jun 2017 01:25:23: 3000000 INFO @ Mon, 05 Jun 2017 01:25:23: 3000000 INFO @ Mon, 05 Jun 2017 01:25:23: 3000000 INFO @ Mon, 05 Jun 2017 01:25:30: 4000000 INFO @ Mon, 05 Jun 2017 01:25:30: 4000000 INFO @ Mon, 05 Jun 2017 01:25:30: 4000000 INFO @ Mon, 05 Jun 2017 01:25:34: #1 tag size is determined as 51 bps INFO @ Mon, 05 Jun 2017 01:25:34: #1 tag size = 51 INFO @ Mon, 05 Jun 2017 01:25:34: #1 total tags in treatment: 4642817 INFO @ Mon, 05 Jun 2017 01:25:34: #1 user defined the maximum tags... INFO @ Mon, 05 Jun 2017 01:25:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 05 Jun 2017 01:25:34: #1 tag size is determined as 51 bps INFO @ Mon, 05 Jun 2017 01:25:34: #1 tag size = 51 INFO @ Mon, 05 Jun 2017 01:25:34: #1 total tags in treatment: 4642817 INFO @ Mon, 05 Jun 2017 01:25:34: #1 user defined the maximum tags... INFO @ Mon, 05 Jun 2017 01:25:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 05 Jun 2017 01:25:34: #1 tag size is determined as 51 bps INFO @ Mon, 05 Jun 2017 01:25:34: #1 tag size = 51 INFO @ Mon, 05 Jun 2017 01:25:34: #1 total tags in treatment: 4642817 INFO @ Mon, 05 Jun 2017 01:25:34: #1 user defined the maximum tags... INFO @ Mon, 05 Jun 2017 01:25:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 05 Jun 2017 01:25:35: #1 tags after filtering in treatment: 4641393 INFO @ Mon, 05 Jun 2017 01:25:35: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Jun 2017 01:25:35: #1 finished! INFO @ Mon, 05 Jun 2017 01:25:35: #2 Build Peak Model... INFO @ Mon, 05 Jun 2017 01:25:35: #1 tags after filtering in treatment: 4641393 INFO @ Mon, 05 Jun 2017 01:25:35: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Jun 2017 01:25:35: #1 finished! INFO @ Mon, 05 Jun 2017 01:25:35: #2 Build Peak Model... INFO @ Mon, 05 Jun 2017 01:25:35: #1 tags after filtering in treatment: 4641393 INFO @ Mon, 05 Jun 2017 01:25:35: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Jun 2017 01:25:35: #1 finished! INFO @ Mon, 05 Jun 2017 01:25:35: #2 Build Peak Model... INFO @ Mon, 05 Jun 2017 01:25:36: #2 number of paired peaks: 1676 INFO @ Mon, 05 Jun 2017 01:25:36: start model_add_line... INFO @ Mon, 05 Jun 2017 01:25:36: #2 number of paired peaks: 1676 INFO @ Mon, 05 Jun 2017 01:25:36: start model_add_line... INFO @ Mon, 05 Jun 2017 01:25:36: #2 number of paired peaks: 1676 INFO @ Mon, 05 Jun 2017 01:25:36: start model_add_line... INFO @ Mon, 05 Jun 2017 01:25:43: start X-correlation... INFO @ Mon, 05 Jun 2017 01:25:43: end of X-cor INFO @ Mon, 05 Jun 2017 01:25:43: #2 finished! INFO @ Mon, 05 Jun 2017 01:25:43: #2 predicted fragment length is 63 bps INFO @ Mon, 05 Jun 2017 01:25:43: #2 alternative fragment length(s) may be 63 bps INFO @ Mon, 05 Jun 2017 01:25:43: #2.2 Generate R script for model : SRX1308480.10_model.r WARNING @ Mon, 05 Jun 2017 01:25:43: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 05 Jun 2017 01:25:43: #2 You may need to consider one of the other alternative d(s): 63 WARNING @ Mon, 05 Jun 2017 01:25:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 05 Jun 2017 01:25:43: #3 Call peaks... INFO @ Mon, 05 Jun 2017 01:25:43: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 05 Jun 2017 01:25:44: start X-correlation... INFO @ Mon, 05 Jun 2017 01:25:44: end of X-cor INFO @ Mon, 05 Jun 2017 01:25:44: #2 finished! INFO @ Mon, 05 Jun 2017 01:25:44: #2 predicted fragment length is 63 bps INFO @ Mon, 05 Jun 2017 01:25:44: #2 alternative fragment length(s) may be 63 bps INFO @ Mon, 05 Jun 2017 01:25:44: #2.2 Generate R script for model : SRX1308480.20_model.r WARNING @ Mon, 05 Jun 2017 01:25:44: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 05 Jun 2017 01:25:44: #2 You may need to consider one of the other alternative d(s): 63 WARNING @ Mon, 05 Jun 2017 01:25:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 05 Jun 2017 01:25:44: #3 Call peaks... INFO @ Mon, 05 Jun 2017 01:25:44: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 05 Jun 2017 01:25:44: start X-correlation... INFO @ Mon, 05 Jun 2017 01:25:44: end of X-cor INFO @ Mon, 05 Jun 2017 01:25:44: #2 finished! INFO @ Mon, 05 Jun 2017 01:25:44: #2 predicted fragment length is 63 bps INFO @ Mon, 05 Jun 2017 01:25:44: #2 alternative fragment length(s) may be 63 bps INFO @ Mon, 05 Jun 2017 01:25:44: #2.2 Generate R script for model : SRX1308480.05_model.r WARNING @ Mon, 05 Jun 2017 01:25:44: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 05 Jun 2017 01:25:44: #2 You may need to consider one of the other alternative d(s): 63 WARNING @ Mon, 05 Jun 2017 01:25:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 05 Jun 2017 01:25:44: #3 Call peaks... INFO @ Mon, 05 Jun 2017 01:25:44: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 05 Jun 2017 01:26:09: #3 Call peaks for each chromosome... INFO @ Mon, 05 Jun 2017 01:26:10: #3 Call peaks for each chromosome... INFO @ Mon, 05 Jun 2017 01:26:11: #3 Call peaks for each chromosome... INFO @ Mon, 05 Jun 2017 01:26:30: #4 Write output xls file... SRX1308480.10_peaks.xls INFO @ Mon, 05 Jun 2017 01:26:30: #4 Write peak in narrowPeak format file... SRX1308480.10_peaks.narrowPeak INFO @ Mon, 05 Jun 2017 01:26:30: #4 Write summits bed file... SRX1308480.10_summits.bed INFO @ Mon, 05 Jun 2017 01:26:30: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2465 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 05 Jun 2017 01:26:31: #4 Write output xls file... SRX1308480.20_peaks.xls INFO @ Mon, 05 Jun 2017 01:26:31: #4 Write peak in narrowPeak format file... SRX1308480.20_peaks.narrowPeak INFO @ Mon, 05 Jun 2017 01:26:31: #4 Write summits bed file... SRX1308480.20_summits.bed INFO @ Mon, 05 Jun 2017 01:26:31: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1330 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 05 Jun 2017 01:26:31: #4 Write output xls file... SRX1308480.05_peaks.xls INFO @ Mon, 05 Jun 2017 01:26:31: #4 Write peak in narrowPeak format file... SRX1308480.05_peaks.narrowPeak INFO @ Mon, 05 Jun 2017 01:26:31: #4 Write summits bed file... SRX1308480.05_summits.bed INFO @ Mon, 05 Jun 2017 01:26:31: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5220 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。