Job ID = 9031597 sra ファイルのダウンロード中... Completed: 1742861K bytes transferred in 27 seconds (513689K bits/sec), in 14 files, 15 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 7663 0 7663 0 0 1046 0 --:--:-- 0:00:07 --:--:-- 10732 100 30318 0 30318 0 0 3643 0 --:--:-- 0:00:08 --:--:-- 17729 100 54318 0 54318 0 0 5935 0 --:--:-- 0:00:09 --:--:-- 21385 100 62302 0 62302 0 0 6807 0 --:--:-- 0:00:09 --:--:-- 24518 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 762900 spots for /home/okishinya/chipatlas/results/dm3/SRX475423/SRR1175630.sra Written 762900 spots total Written 4000000 spots for /home/okishinya/chipatlas/results/dm3/SRX475423/SRR1175637.sra Written 4000000 spots total Written 4000000 spots for /home/okishinya/chipatlas/results/dm3/SRX475423/SRR1175631.sra Written 4000000 spots total Written 4000000 spots for /home/okishinya/chipatlas/results/dm3/SRX475423/SRR1175635.sra Written 4000000 spots total Written 4000000 spots for /home/okishinya/chipatlas/results/dm3/SRX475423/SRR1175628.sra Written 4000000 spots total Written 4000000 spots for /home/okishinya/chipatlas/results/dm3/SRX475423/SRR1175632.sra Written 4000000 spots total Written 4000000 spots for /home/okishinya/chipatlas/results/dm3/SRX475423/SRR1175626.sra Written 4000000 spots total Written 4000000 spots for /home/okishinya/chipatlas/results/dm3/SRX475423/SRR1175634.sra Written 4000000 spots total Written 4000000 spots for /home/okishinya/chipatlas/results/dm3/SRX475423/SRR1175638.sra Written 4000000 spots total Written 4000000 spots for /home/okishinya/chipatlas/results/dm3/SRX475423/SRR1175627.sra Written 4000000 spots total Written 4000000 spots for /home/okishinya/chipatlas/results/dm3/SRX475423/SRR1175625.sra Written 4000000 spots total Written 4000000 spots for /home/okishinya/chipatlas/results/dm3/SRX475423/SRR1175629.sra Written 4000000 spots total Written 4000000 spots for /home/okishinya/chipatlas/results/dm3/SRX475423/SRR1175636.sra Written 4000000 spots total Written 4000000 spots for /home/okishinya/chipatlas/results/dm3/SRX475423/SRR1175633.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: 00:21:37 52762900 reads; of these: 52762900 (100.00%) were unpaired; of these: 14113207 (26.75%) aligned 0 times 23570118 (44.67%) aligned exactly 1 time 15079575 (28.58%) aligned >1 times 73.25% overall alignment rate Time searching: 00:21:37 Overall time: 00:21:37 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] 23337054 / 38649693 = 0.6038 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 20:51:13: # Command line: callpeak -t SRX475423.bam -f BAM -g dm -n SRX475423.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX475423.05 # format = BAM # ChIP-seq file = ['SRX475423.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 20:51:13: #1 read tag files... INFO @ Sat, 03 Jun 2017 20:51:13: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 20:51:13: # Command line: callpeak -t SRX475423.bam -f BAM -g dm -n SRX475423.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX475423.20 # format = BAM # ChIP-seq file = ['SRX475423.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 20:51:13: #1 read tag files... INFO @ Sat, 03 Jun 2017 20:51:13: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 20:51:13: # Command line: callpeak -t SRX475423.bam -f BAM -g dm -n SRX475423.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX475423.10 # format = BAM # ChIP-seq file = ['SRX475423.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 20:51:13: #1 read tag files... INFO @ Sat, 03 Jun 2017 20:51:13: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 20:51:19: 1000000 INFO @ Sat, 03 Jun 2017 20:51:19: 1000000 INFO @ Sat, 03 Jun 2017 20:51:19: 1000000 INFO @ Sat, 03 Jun 2017 20:51:24: 2000000 INFO @ Sat, 03 Jun 2017 20:51:25: 2000000 INFO @ Sat, 03 Jun 2017 20:51:25: 2000000 INFO @ Sat, 03 Jun 2017 20:51:29: 3000000 INFO @ Sat, 03 Jun 2017 20:51:31: 3000000 INFO @ Sat, 03 Jun 2017 20:51:31: 3000000 INFO @ Sat, 03 Jun 2017 20:51:35: 4000000 INFO @ Sat, 03 Jun 2017 20:51:37: 4000000 INFO @ Sat, 03 Jun 2017 20:51:37: 4000000 INFO @ Sat, 03 Jun 2017 20:51:40: 5000000 INFO @ Sat, 03 Jun 2017 20:51:43: 5000000 INFO @ Sat, 03 Jun 2017 20:51:43: 5000000 INFO @ Sat, 03 Jun 2017 20:51:45: 6000000 INFO @ Sat, 03 Jun 2017 20:51:49: 6000000 INFO @ Sat, 03 Jun 2017 20:51:49: 6000000 INFO @ Sat, 03 Jun 2017 20:51:51: 7000000 INFO @ Sat, 03 Jun 2017 20:51:55: 7000000 INFO @ Sat, 03 Jun 2017 20:51:56: 7000000 INFO @ Sat, 03 Jun 2017 20:51:56: 8000000 INFO @ Sat, 03 Jun 2017 20:52:01: 8000000 INFO @ Sat, 03 Jun 2017 20:52:02: 9000000 INFO @ Sat, 03 Jun 2017 20:52:02: 8000000 INFO @ Sat, 03 Jun 2017 20:52:07: 10000000 INFO @ Sat, 03 Jun 2017 20:52:08: 9000000 INFO @ Sat, 03 Jun 2017 20:52:08: 9000000 INFO @ Sat, 03 Jun 2017 20:52:12: 11000000 INFO @ Sat, 03 Jun 2017 20:52:14: 10000000 INFO @ Sat, 03 Jun 2017 20:52:15: 10000000 INFO @ Sat, 03 Jun 2017 20:52:18: 12000000 INFO @ Sat, 03 Jun 2017 20:52:21: 11000000 INFO @ Sat, 03 Jun 2017 20:52:22: 11000000 INFO @ Sat, 03 Jun 2017 20:52:23: 13000000 INFO @ Sat, 03 Jun 2017 20:52:27: 12000000 INFO @ Sat, 03 Jun 2017 20:52:28: 12000000 INFO @ Sat, 03 Jun 2017 20:52:29: 14000000 INFO @ Sat, 03 Jun 2017 20:52:34: 13000000 INFO @ Sat, 03 Jun 2017 20:52:34: 15000000 INFO @ Sat, 03 Jun 2017 20:52:35: 13000000 INFO @ Sat, 03 Jun 2017 20:52:36: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 20:52:36: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 20:52:36: #1 total tags in treatment: 15312639 INFO @ Sat, 03 Jun 2017 20:52:36: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 20:52:36: #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 20:52:39: #1 tags after filtering in treatment: 15307770 INFO @ Sat, 03 Jun 2017 20:52:39: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 20:52:39: #1 finished! INFO @ Sat, 03 Jun 2017 20:52:39: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 20:52:40: 14000000 INFO @ Sat, 03 Jun 2017 20:52:42: 14000000 INFO @ Sat, 03 Jun 2017 20:52:42: #2 number of paired peaks: 2410 INFO @ Sat, 03 Jun 2017 20:52:42: start model_add_line... INFO @ Sat, 03 Jun 2017 20:52:47: 15000000 INFO @ Sat, 03 Jun 2017 20:52:48: 15000000 INFO @ Sat, 03 Jun 2017 20:52:49: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 20:52:49: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 20:52:49: #1 total tags in treatment: 15312639 INFO @ Sat, 03 Jun 2017 20:52:49: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 20:52:49: #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 20:52:50: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 20:52:50: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 20:52:50: #1 total tags in treatment: 15312639 INFO @ Sat, 03 Jun 2017 20:52:50: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 20:52:50: #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 20:52:52: #1 tags after filtering in treatment: 15307770 INFO @ Sat, 03 Jun 2017 20:52:52: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 20:52:52: #1 finished! INFO @ Sat, 03 Jun 2017 20:52:52: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 20:52:53: #1 tags after filtering in treatment: 15307770 INFO @ Sat, 03 Jun 2017 20:52:53: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 20:52:53: #1 finished! INFO @ Sat, 03 Jun 2017 20:52:53: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 20:52:55: #2 number of paired peaks: 2410 INFO @ Sat, 03 Jun 2017 20:52:55: start model_add_line... INFO @ Sat, 03 Jun 2017 20:52:56: #2 number of paired peaks: 2410 INFO @ Sat, 03 Jun 2017 20:52:56: start model_add_line... INFO @ Sat, 03 Jun 2017 20:53:08: start X-correlation... INFO @ Sat, 03 Jun 2017 20:53:08: end of X-cor INFO @ Sat, 03 Jun 2017 20:53:08: #2 finished! INFO @ Sat, 03 Jun 2017 20:53:08: #2 predicted fragment length is 63 bps INFO @ Sat, 03 Jun 2017 20:53:08: #2 alternative fragment length(s) may be 3,63 bps INFO @ Sat, 03 Jun 2017 20:53:08: #2.2 Generate R script for model : SRX475423.20_model.r WARNING @ Sat, 03 Jun 2017 20:53:08: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 20:53:08: #2 You may need to consider one of the other alternative d(s): 3,63 WARNING @ Sat, 03 Jun 2017 20:53:08: #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 20:53:08: #3 Call peaks... INFO @ Sat, 03 Jun 2017 20:53:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 20:53:22: start X-correlation... INFO @ Sat, 03 Jun 2017 20:53:22: end of X-cor INFO @ Sat, 03 Jun 2017 20:53:22: #2 finished! INFO @ Sat, 03 Jun 2017 20:53:22: #2 predicted fragment length is 63 bps INFO @ Sat, 03 Jun 2017 20:53:22: #2 alternative fragment length(s) may be 3,63 bps INFO @ Sat, 03 Jun 2017 20:53:22: #2.2 Generate R script for model : SRX475423.05_model.r WARNING @ Sat, 03 Jun 2017 20:53:22: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 20:53:22: #2 You may need to consider one of the other alternative d(s): 3,63 WARNING @ Sat, 03 Jun 2017 20:53:22: #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 20:53:22: #3 Call peaks... INFO @ Sat, 03 Jun 2017 20:53:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 20:53:22: start X-correlation... INFO @ Sat, 03 Jun 2017 20:53:22: end of X-cor INFO @ Sat, 03 Jun 2017 20:53:22: #2 finished! INFO @ Sat, 03 Jun 2017 20:53:22: #2 predicted fragment length is 63 bps INFO @ Sat, 03 Jun 2017 20:53:22: #2 alternative fragment length(s) may be 3,63 bps INFO @ Sat, 03 Jun 2017 20:53:22: #2.2 Generate R script for model : SRX475423.10_model.r WARNING @ Sat, 03 Jun 2017 20:53:22: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 20:53:22: #2 You may need to consider one of the other alternative d(s): 3,63 WARNING @ Sat, 03 Jun 2017 20:53:22: #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 20:53:22: #3 Call peaks... INFO @ Sat, 03 Jun 2017 20:53:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 20:54:31: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 20:54:41: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 20:54:51: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 20:55:31: #4 Write output xls file... SRX475423.20_peaks.xls INFO @ Sat, 03 Jun 2017 20:55:31: #4 Write peak in narrowPeak format file... SRX475423.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 20:55:31: #4 Write summits bed file... SRX475423.20_summits.bed INFO @ Sat, 03 Jun 2017 20:55:31: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2516 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 20:55:47: #4 Write output xls file... SRX475423.05_peaks.xls INFO @ Sat, 03 Jun 2017 20:55:47: #4 Write peak in narrowPeak format file... SRX475423.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 20:55:47: #4 Write summits bed file... SRX475423.05_summits.bed INFO @ Sat, 03 Jun 2017 20:55:47: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6586 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 20:55:57: #4 Write output xls file... SRX475423.10_peaks.xls INFO @ Sat, 03 Jun 2017 20:55:57: #4 Write peak in narrowPeak format file... SRX475423.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 20:55:57: #4 Write summits bed file... SRX475423.10_summits.bed INFO @ Sat, 03 Jun 2017 20:55:57: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3904 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。