Job ID = 9031594 sra ファイルのダウンロード中... Completed: 1596201K bytes transferred in 25 seconds (522687K bits/sec), in 13 files, 14 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 0 0 0 0 0 0 0 0 --:--:-- 0:00:06 --:--:-- 0 100 21558 0 21558 0 0 2759 0 --:--:-- 0:00:07 --:--:-- 16750 100 53489 0 53489 0 0 6311 0 --:--:-- 0:00:08 --:--:-- 27416 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 842901 spots for /home/okishinya/chipatlas/results/dm3/SRX475420/SRR1175590.sra Written 842901 spots total Written 4000000 spots for /home/okishinya/chipatlas/results/dm3/SRX475420/SRR1175588.sra Written 4000000 spots total Written 4000000 spots for /home/okishinya/chipatlas/results/dm3/SRX475420/SRR1175586.sra Written 4000000 spots total Written 4000000 spots for /home/okishinya/chipatlas/results/dm3/SRX475420/SRR1175591.sra Written 4000000 spots total Written 4000000 spots for /home/okishinya/chipatlas/results/dm3/SRX475420/SRR1175592.sra Written 4000000 spots total Written 4000000 spots for /home/okishinya/chipatlas/results/dm3/SRX475420/SRR1175596.sra Written 4000000 spots total Written 4000000 spots for /home/okishinya/chipatlas/results/dm3/SRX475420/SRR1175594.sra Written 4000000 spots for /home/okishinya/chipatlas/results/dm3/SRX475420/SRR1175595.sra Written 4000000 spots total Written 4000000 spots for /home/okishinya/chipatlas/results/dm3/SRX475420/SRR1175593.sra Written 4000000 spots total Written 4000000 spots total Written 4000000 spots for /home/okishinya/chipatlas/results/dm3/SRX475420/SRR1175589.sra Written 4000000 spots total Written 4000000 spots for /home/okishinya/chipatlas/results/dm3/SRX475420/SRR1175597.sra Written 4000000 spots total Written 4000000 spots for /home/okishinya/chipatlas/results/dm3/SRX475420/SRR1175598.sra Written 4000000 spots total Written 4000000 spots for /home/okishinya/chipatlas/results/dm3/SRX475420/SRR1175587.sra Written 4000000 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: 00:18:41 48842901 reads; of these: 48842901 (100.00%) were unpaired; of these: 2602597 (5.33%) aligned 0 times 32623404 (66.79%) aligned exactly 1 time 13616900 (27.88%) aligned >1 times 94.67% overall alignment rate Time searching: 00:18:41 Overall time: 00:18:41 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 20 files... [bam_rmdupse_core] 26421805 / 46240304 = 0.5714 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 @ Sat, 03 Jun 2017 20:48:29: # Command line: callpeak -t SRX475420.bam -f BAM -g dm -n SRX475420.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX475420.10 # format = BAM # ChIP-seq file = ['SRX475420.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 @ Sat, 03 Jun 2017 20:48:29: #1 read tag files... INFO @ Sat, 03 Jun 2017 20:48:29: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 20:48:29: # Command line: callpeak -t SRX475420.bam -f BAM -g dm -n SRX475420.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX475420.05 # format = BAM # ChIP-seq file = ['SRX475420.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 @ Sat, 03 Jun 2017 20:48:29: #1 read tag files... INFO @ Sat, 03 Jun 2017 20:48:29: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 20:48:29: # Command line: callpeak -t SRX475420.bam -f BAM -g dm -n SRX475420.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX475420.20 # format = BAM # ChIP-seq file = ['SRX475420.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 @ Sat, 03 Jun 2017 20:48:29: #1 read tag files... INFO @ Sat, 03 Jun 2017 20:48:29: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 20:48:36: 1000000 INFO @ Sat, 03 Jun 2017 20:48:36: 1000000 INFO @ Sat, 03 Jun 2017 20:48:36: 1000000 INFO @ Sat, 03 Jun 2017 20:48:43: 2000000 INFO @ Sat, 03 Jun 2017 20:48:43: 2000000 INFO @ Sat, 03 Jun 2017 20:48:43: 2000000 INFO @ Sat, 03 Jun 2017 20:48:50: 3000000 INFO @ Sat, 03 Jun 2017 20:48:50: 3000000 INFO @ Sat, 03 Jun 2017 20:48:50: 3000000 INFO @ Sat, 03 Jun 2017 20:48:57: 4000000 INFO @ Sat, 03 Jun 2017 20:48:57: 4000000 INFO @ Sat, 03 Jun 2017 20:48:57: 4000000 INFO @ Sat, 03 Jun 2017 20:49:04: 5000000 INFO @ Sat, 03 Jun 2017 20:49:04: 5000000 INFO @ Sat, 03 Jun 2017 20:49:04: 5000000 INFO @ Sat, 03 Jun 2017 20:49:11: 6000000 INFO @ Sat, 03 Jun 2017 20:49:11: 6000000 INFO @ Sat, 03 Jun 2017 20:49:11: 6000000 INFO @ Sat, 03 Jun 2017 20:49:18: 7000000 INFO @ Sat, 03 Jun 2017 20:49:18: 7000000 INFO @ Sat, 03 Jun 2017 20:49:18: 7000000 INFO @ Sat, 03 Jun 2017 20:49:26: 8000000 INFO @ Sat, 03 Jun 2017 20:49:26: 8000000 INFO @ Sat, 03 Jun 2017 20:49:26: 8000000 INFO @ Sat, 03 Jun 2017 20:49:33: 9000000 INFO @ Sat, 03 Jun 2017 20:49:33: 9000000 INFO @ Sat, 03 Jun 2017 20:49:33: 9000000 INFO @ Sat, 03 Jun 2017 20:49:40: 10000000 INFO @ Sat, 03 Jun 2017 20:49:40: 10000000 INFO @ Sat, 03 Jun 2017 20:49:40: 10000000 INFO @ Sat, 03 Jun 2017 20:49:47: 11000000 INFO @ Sat, 03 Jun 2017 20:49:47: 11000000 INFO @ Sat, 03 Jun 2017 20:49:47: 11000000 INFO @ Sat, 03 Jun 2017 20:49:54: 12000000 INFO @ Sat, 03 Jun 2017 20:49:54: 12000000 INFO @ Sat, 03 Jun 2017 20:49:54: 12000000 INFO @ Sat, 03 Jun 2017 20:50:01: 13000000 INFO @ Sat, 03 Jun 2017 20:50:01: 13000000 INFO @ Sat, 03 Jun 2017 20:50:01: 13000000 INFO @ Sat, 03 Jun 2017 20:50:08: 14000000 INFO @ Sat, 03 Jun 2017 20:50:08: 14000000 INFO @ Sat, 03 Jun 2017 20:50:08: 14000000 INFO @ Sat, 03 Jun 2017 20:50:14: 15000000 INFO @ Sat, 03 Jun 2017 20:50:14: 15000000 INFO @ Sat, 03 Jun 2017 20:50:14: 15000000 INFO @ Sat, 03 Jun 2017 20:50:20: 16000000 INFO @ Sat, 03 Jun 2017 20:50:21: 16000000 INFO @ Sat, 03 Jun 2017 20:50:21: 16000000 INFO @ Sat, 03 Jun 2017 20:50:27: 17000000 INFO @ Sat, 03 Jun 2017 20:50:28: 17000000 INFO @ Sat, 03 Jun 2017 20:50:28: 17000000 INFO @ Sat, 03 Jun 2017 20:50:33: 18000000 INFO @ Sat, 03 Jun 2017 20:50:34: 18000000 INFO @ Sat, 03 Jun 2017 20:50:35: 18000000 INFO @ Sat, 03 Jun 2017 20:50:39: 19000000 INFO @ Sat, 03 Jun 2017 20:50:41: 19000000 INFO @ Sat, 03 Jun 2017 20:50:42: 19000000 INFO @ Sat, 03 Jun 2017 20:50:45: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 20:50:45: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 20:50:45: #1 total tags in treatment: 19818499 INFO @ Sat, 03 Jun 2017 20:50:45: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 20:50:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 20:50:47: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 20:50:47: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 20:50:47: #1 total tags in treatment: 19818499 INFO @ Sat, 03 Jun 2017 20:50:47: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 20:50:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 20:50:47: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 20:50:47: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 20:50:47: #1 total tags in treatment: 19818499 INFO @ Sat, 03 Jun 2017 20:50:47: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 20:50:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 20:50:48: #1 tags after filtering in treatment: 19810673 INFO @ Sat, 03 Jun 2017 20:50:48: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 20:50:48: #1 finished! INFO @ Sat, 03 Jun 2017 20:50:48: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 20:50:50: #1 tags after filtering in treatment: 19810673 INFO @ Sat, 03 Jun 2017 20:50:50: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 20:50:50: #1 finished! INFO @ Sat, 03 Jun 2017 20:50:50: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 20:50:51: #1 tags after filtering in treatment: 19810673 INFO @ Sat, 03 Jun 2017 20:50:51: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 20:50:51: #1 finished! INFO @ Sat, 03 Jun 2017 20:50:51: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 20:50:52: #2 number of paired peaks: 2659 INFO @ Sat, 03 Jun 2017 20:50:52: start model_add_line... INFO @ Sat, 03 Jun 2017 20:50:54: #2 number of paired peaks: 2659 INFO @ Sat, 03 Jun 2017 20:50:54: start model_add_line... INFO @ Sat, 03 Jun 2017 20:50:55: #2 number of paired peaks: 2659 INFO @ Sat, 03 Jun 2017 20:50:55: start model_add_line... INFO @ Sat, 03 Jun 2017 20:51:25: start X-correlation... INFO @ Sat, 03 Jun 2017 20:51:25: end of X-cor INFO @ Sat, 03 Jun 2017 20:51:25: #2 finished! INFO @ Sat, 03 Jun 2017 20:51:25: #2 predicted fragment length is 92 bps INFO @ Sat, 03 Jun 2017 20:51:25: #2 alternative fragment length(s) may be 4,92 bps INFO @ Sat, 03 Jun 2017 20:51:25: #2.2 Generate R script for model : SRX475420.20_model.r WARNING @ Sat, 03 Jun 2017 20:51:25: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 20:51:25: #2 You may need to consider one of the other alternative d(s): 4,92 WARNING @ Sat, 03 Jun 2017 20:51:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 20:51:25: #3 Call peaks... INFO @ Sat, 03 Jun 2017 20:51:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 20:51:28: start X-correlation... INFO @ Sat, 03 Jun 2017 20:51:28: end of X-cor INFO @ Sat, 03 Jun 2017 20:51:28: #2 finished! INFO @ Sat, 03 Jun 2017 20:51:28: #2 predicted fragment length is 92 bps INFO @ Sat, 03 Jun 2017 20:51:28: #2 alternative fragment length(s) may be 4,92 bps INFO @ Sat, 03 Jun 2017 20:51:28: #2.2 Generate R script for model : SRX475420.05_model.r WARNING @ Sat, 03 Jun 2017 20:51:28: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 20:51:28: #2 You may need to consider one of the other alternative d(s): 4,92 WARNING @ Sat, 03 Jun 2017 20:51:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 20:51:28: #3 Call peaks... INFO @ Sat, 03 Jun 2017 20:51:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 20:51:28: start X-correlation... INFO @ Sat, 03 Jun 2017 20:51:28: end of X-cor INFO @ Sat, 03 Jun 2017 20:51:28: #2 finished! INFO @ Sat, 03 Jun 2017 20:51:28: #2 predicted fragment length is 92 bps INFO @ Sat, 03 Jun 2017 20:51:28: #2 alternative fragment length(s) may be 4,92 bps INFO @ Sat, 03 Jun 2017 20:51:28: #2.2 Generate R script for model : SRX475420.10_model.r WARNING @ Sat, 03 Jun 2017 20:51:28: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 20:51:28: #2 You may need to consider one of the other alternative d(s): 4,92 WARNING @ Sat, 03 Jun 2017 20:51:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 20:51:28: #3 Call peaks... INFO @ Sat, 03 Jun 2017 20:51:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 20:53:02: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 20:53:04: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 20:53:14: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 20:54:17: #4 Write output xls file... SRX475420.20_peaks.xls INFO @ Sat, 03 Jun 2017 20:54:17: #4 Write peak in narrowPeak format file... SRX475420.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 20:54:17: #4 Write summits bed file... SRX475420.20_summits.bed INFO @ Sat, 03 Jun 2017 20:54:17: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5539 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 20:54:22: #4 Write output xls file... SRX475420.10_peaks.xls INFO @ Sat, 03 Jun 2017 20:54:22: #4 Write peak in narrowPeak format file... SRX475420.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 20:54:22: #4 Write summits bed file... SRX475420.10_summits.bed INFO @ Sat, 03 Jun 2017 20:54:22: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (10672 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 20:54:40: #4 Write output xls file... SRX475420.05_peaks.xls INFO @ Sat, 03 Jun 2017 20:54:41: #4 Write peak in narrowPeak format file... SRX475420.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 20:54:41: #4 Write summits bed file... SRX475420.05_summits.bed INFO @ Sat, 03 Jun 2017 20:54:41: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (16604 records, 4 fields): 20 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。