Job ID = 9029779 sra ファイルのダウンロード中... Completed: 556079K bytes transferred in 8 seconds (569011K 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 --:--:-- 0 100 7663 0 7663 0 0 1065 0 --:--:-- 0:00:07 --:--:-- 11789 100 29046 0 29046 0 0 3620 0 --:--:-- 0:00:08 --:--:-- 19638 100 30917 0 30917 0 0 3852 0 --:--:-- 0:00:08 --:--:-- 20889 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 23814936 spots for /home/okishinya/chipatlas/results/dm3/SRX2055961/SRR4069193.sra Written 23814936 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: 00:09:43 23814936 reads; of these: 23814936 (100.00%) were unpaired; of these: 6869067 (28.84%) aligned 0 times 10770732 (45.23%) aligned exactly 1 time 6175137 (25.93%) aligned >1 times 71.16% overall alignment rate Time searching: 00:09:43 Overall time: 00:09:43 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 8 files... [bam_rmdupse_core] 5612365 / 16945869 = 0.3312 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 15:25:43: # Command line: callpeak -t SRX2055961.bam -f BAM -g dm -n SRX2055961.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2055961.20 # format = BAM # ChIP-seq file = ['SRX2055961.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 15:25:43: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:25:43: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:25:43: # Command line: callpeak -t SRX2055961.bam -f BAM -g dm -n SRX2055961.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2055961.10 # format = BAM # ChIP-seq file = ['SRX2055961.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 15:25:43: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:25:43: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:25:43: # Command line: callpeak -t SRX2055961.bam -f BAM -g dm -n SRX2055961.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2055961.05 # format = BAM # ChIP-seq file = ['SRX2055961.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 15:25:43: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:25:43: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:25:49: 1000000 INFO @ Sat, 03 Jun 2017 15:25:50: 1000000 INFO @ Sat, 03 Jun 2017 15:25:50: 1000000 INFO @ Sat, 03 Jun 2017 15:25:55: 2000000 INFO @ Sat, 03 Jun 2017 15:25:57: 2000000 INFO @ Sat, 03 Jun 2017 15:25:57: 2000000 INFO @ Sat, 03 Jun 2017 15:26:01: 3000000 INFO @ Sat, 03 Jun 2017 15:26:04: 3000000 INFO @ Sat, 03 Jun 2017 15:26:04: 3000000 INFO @ Sat, 03 Jun 2017 15:26:07: 4000000 INFO @ Sat, 03 Jun 2017 15:26:11: 4000000 INFO @ Sat, 03 Jun 2017 15:26:11: 4000000 INFO @ Sat, 03 Jun 2017 15:26:13: 5000000 INFO @ Sat, 03 Jun 2017 15:26:18: 5000000 INFO @ Sat, 03 Jun 2017 15:26:18: 5000000 INFO @ Sat, 03 Jun 2017 15:26:19: 6000000 INFO @ Sat, 03 Jun 2017 15:26:25: 7000000 INFO @ Sat, 03 Jun 2017 15:26:25: 6000000 INFO @ Sat, 03 Jun 2017 15:26:25: 6000000 INFO @ Sat, 03 Jun 2017 15:26:30: 8000000 INFO @ Sat, 03 Jun 2017 15:26:32: 7000000 INFO @ Sat, 03 Jun 2017 15:26:32: 7000000 INFO @ Sat, 03 Jun 2017 15:26:36: 9000000 INFO @ Sat, 03 Jun 2017 15:26:39: 8000000 INFO @ Sat, 03 Jun 2017 15:26:39: 8000000 INFO @ Sat, 03 Jun 2017 15:26:42: 10000000 INFO @ Sat, 03 Jun 2017 15:26:47: 9000000 INFO @ Sat, 03 Jun 2017 15:26:47: 9000000 INFO @ Sat, 03 Jun 2017 15:26:49: 11000000 INFO @ Sat, 03 Jun 2017 15:26:51: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 15:26:51: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 15:26:51: #1 total tags in treatment: 11333504 INFO @ Sat, 03 Jun 2017 15:26:51: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:26:51: #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 15:26:53: #1 tags after filtering in treatment: 11330364 INFO @ Sat, 03 Jun 2017 15:26:53: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:26:53: #1 finished! INFO @ Sat, 03 Jun 2017 15:26:53: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:26:55: 10000000 INFO @ Sat, 03 Jun 2017 15:26:55: 10000000 INFO @ Sat, 03 Jun 2017 15:26:55: #2 number of paired peaks: 1769 INFO @ Sat, 03 Jun 2017 15:26:55: start model_add_line... INFO @ Sat, 03 Jun 2017 15:27:03: 11000000 INFO @ Sat, 03 Jun 2017 15:27:03: 11000000 INFO @ Sat, 03 Jun 2017 15:27:06: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 15:27:06: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 15:27:06: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 15:27:06: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 15:27:06: #1 total tags in treatment: 11333504 INFO @ Sat, 03 Jun 2017 15:27:06: #1 total tags in treatment: 11333504 INFO @ Sat, 03 Jun 2017 15:27:06: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:27:06: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:27:06: #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 15:27:06: #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 15:27:08: #1 tags after filtering in treatment: 11330364 INFO @ Sat, 03 Jun 2017 15:27:08: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:27:08: #1 finished! INFO @ Sat, 03 Jun 2017 15:27:08: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:27:09: #1 tags after filtering in treatment: 11330364 INFO @ Sat, 03 Jun 2017 15:27:09: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:27:09: #1 finished! INFO @ Sat, 03 Jun 2017 15:27:09: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:27:09: start X-correlation... INFO @ Sat, 03 Jun 2017 15:27:09: end of X-cor INFO @ Sat, 03 Jun 2017 15:27:09: #2 finished! INFO @ Sat, 03 Jun 2017 15:27:09: #2 predicted fragment length is 53 bps INFO @ Sat, 03 Jun 2017 15:27:09: #2 alternative fragment length(s) may be 53 bps INFO @ Sat, 03 Jun 2017 15:27:09: #2.2 Generate R script for model : SRX2055961.05_model.r WARNING @ Sat, 03 Jun 2017 15:27:09: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 15:27:09: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Sat, 03 Jun 2017 15:27:09: #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 15:27:09: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:27:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:27:10: #2 number of paired peaks: 1769 INFO @ Sat, 03 Jun 2017 15:27:10: start model_add_line... INFO @ Sat, 03 Jun 2017 15:27:11: #2 number of paired peaks: 1769 INFO @ Sat, 03 Jun 2017 15:27:11: start model_add_line... INFO @ Sat, 03 Jun 2017 15:27:24: start X-correlation... INFO @ Sat, 03 Jun 2017 15:27:24: end of X-cor INFO @ Sat, 03 Jun 2017 15:27:24: #2 finished! INFO @ Sat, 03 Jun 2017 15:27:24: #2 predicted fragment length is 53 bps INFO @ Sat, 03 Jun 2017 15:27:24: #2 alternative fragment length(s) may be 53 bps INFO @ Sat, 03 Jun 2017 15:27:24: #2.2 Generate R script for model : SRX2055961.20_model.r WARNING @ Sat, 03 Jun 2017 15:27:24: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 15:27:24: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Sat, 03 Jun 2017 15:27:24: #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 15:27:24: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:27:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:27:24: start X-correlation... INFO @ Sat, 03 Jun 2017 15:27:24: end of X-cor INFO @ Sat, 03 Jun 2017 15:27:24: #2 finished! INFO @ Sat, 03 Jun 2017 15:27:24: #2 predicted fragment length is 53 bps INFO @ Sat, 03 Jun 2017 15:27:24: #2 alternative fragment length(s) may be 53 bps INFO @ Sat, 03 Jun 2017 15:27:24: #2.2 Generate R script for model : SRX2055961.10_model.r WARNING @ Sat, 03 Jun 2017 15:27:24: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 15:27:24: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Sat, 03 Jun 2017 15:27:24: #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 15:27:24: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:27:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:28:12: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:28:28: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:28:31: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:29:01: #4 Write output xls file... SRX2055961.05_peaks.xls INFO @ Sat, 03 Jun 2017 15:29:01: #4 Write peak in narrowPeak format file... SRX2055961.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:29:01: #4 Write summits bed file... SRX2055961.05_summits.bed INFO @ Sat, 03 Jun 2017 15:29:01: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4196 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 15:29:14: #4 Write output xls file... SRX2055961.20_peaks.xls INFO @ Sat, 03 Jun 2017 15:29:14: #4 Write peak in narrowPeak format file... SRX2055961.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:29:14: #4 Write summits bed file... SRX2055961.20_summits.bed INFO @ Sat, 03 Jun 2017 15:29:14: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1663 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 15:29:17: #4 Write output xls file... SRX2055961.10_peaks.xls INFO @ Sat, 03 Jun 2017 15:29:17: #4 Write peak in narrowPeak format file... SRX2055961.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:29:17: #4 Write summits bed file... SRX2055961.10_summits.bed INFO @ Sat, 03 Jun 2017 15:29:17: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2854 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。