Job ID = 9028809 sra ファイルのダウンロード中... Completed: 1111290K bytes transferred in 12 seconds (701187K 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 0 0 0 0 0 0 0 0 --:--:-- 0:00:07 --:--:-- 0 100 28797 0 28797 0 0 3365 0 --:--:-- 0:00:08 --:--:-- 13791 100 82373 0 82373 0 0 8775 0 --:--:-- 0:00:09 --:--:-- 28229 100 97559 0 97559 0 0 10212 0 --:--:-- 0:00:09 --:--:-- 31633 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 34130372 spots for /home/okishinya/chipatlas/results/ce10/SRX958295/SRR1917668.sra Written 34130372 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: 00:11:18 34130372 reads; of these: 34130372 (100.00%) were unpaired; of these: 4880650 (14.30%) aligned 0 times 17279513 (50.63%) aligned exactly 1 time 11970209 (35.07%) aligned >1 times 85.70% overall alignment rate Time searching: 00:11:18 Overall time: 00:11:18 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 20089239 / 29249722 = 0.6868 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 12:09:29: # Command line: callpeak -t SRX958295.bam -f BAM -g ce -n SRX958295.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX958295.20 # format = BAM # ChIP-seq file = ['SRX958295.bam'] # control file = None # effective genome size = 9.00e+07 # 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 12:09:29: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:09:29: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:09:29: # Command line: callpeak -t SRX958295.bam -f BAM -g ce -n SRX958295.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX958295.05 # format = BAM # ChIP-seq file = ['SRX958295.bam'] # control file = None # effective genome size = 9.00e+07 # 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 12:09:29: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:09:29: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:09:29: # Command line: callpeak -t SRX958295.bam -f BAM -g ce -n SRX958295.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX958295.10 # format = BAM # ChIP-seq file = ['SRX958295.bam'] # control file = None # effective genome size = 9.00e+07 # 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 12:09:29: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:09:29: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:09:36: 1000000 INFO @ Sat, 03 Jun 2017 12:09:36: 1000000 INFO @ Sat, 03 Jun 2017 12:09:36: 1000000 INFO @ Sat, 03 Jun 2017 12:09:42: 2000000 INFO @ Sat, 03 Jun 2017 12:09:43: 2000000 INFO @ Sat, 03 Jun 2017 12:09:43: 2000000 INFO @ Sat, 03 Jun 2017 12:09:48: 3000000 INFO @ Sat, 03 Jun 2017 12:09:50: 3000000 INFO @ Sat, 03 Jun 2017 12:09:50: 3000000 INFO @ Sat, 03 Jun 2017 12:09:55: 4000000 INFO @ Sat, 03 Jun 2017 12:09:57: 4000000 INFO @ Sat, 03 Jun 2017 12:09:57: 4000000 INFO @ Sat, 03 Jun 2017 12:10:01: 5000000 INFO @ Sat, 03 Jun 2017 12:10:04: 5000000 INFO @ Sat, 03 Jun 2017 12:10:04: 5000000 INFO @ Sat, 03 Jun 2017 12:10:08: 6000000 INFO @ Sat, 03 Jun 2017 12:10:11: 6000000 INFO @ Sat, 03 Jun 2017 12:10:12: 6000000 INFO @ Sat, 03 Jun 2017 12:10:15: 7000000 INFO @ Sat, 03 Jun 2017 12:10:18: 7000000 INFO @ Sat, 03 Jun 2017 12:10:19: 7000000 INFO @ Sat, 03 Jun 2017 12:10:22: 8000000 INFO @ Sat, 03 Jun 2017 12:10:25: 8000000 INFO @ Sat, 03 Jun 2017 12:10:26: 8000000 INFO @ Sat, 03 Jun 2017 12:10:29: 9000000 INFO @ Sat, 03 Jun 2017 12:10:30: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:10:30: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:10:30: #1 total tags in treatment: 9160483 INFO @ Sat, 03 Jun 2017 12:10:30: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:10:30: #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 12:10:32: #1 tags after filtering in treatment: 9154433 INFO @ Sat, 03 Jun 2017 12:10:32: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:10:32: #1 finished! INFO @ Sat, 03 Jun 2017 12:10:32: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:10:32: 9000000 INFO @ Sat, 03 Jun 2017 12:10:33: 9000000 INFO @ Sat, 03 Jun 2017 12:10:33: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:10:33: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:10:33: #1 total tags in treatment: 9160483 INFO @ Sat, 03 Jun 2017 12:10:33: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:10:33: #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 12:10:34: #2 number of paired peaks: 4774 INFO @ Sat, 03 Jun 2017 12:10:34: start model_add_line... INFO @ Sat, 03 Jun 2017 12:10:34: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:10:34: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:10:34: #1 total tags in treatment: 9160483 INFO @ Sat, 03 Jun 2017 12:10:34: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:10:34: #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 12:10:35: #1 tags after filtering in treatment: 9154433 INFO @ Sat, 03 Jun 2017 12:10:35: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:10:35: #1 finished! INFO @ Sat, 03 Jun 2017 12:10:35: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:10:36: #1 tags after filtering in treatment: 9154433 INFO @ Sat, 03 Jun 2017 12:10:36: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:10:36: #1 finished! INFO @ Sat, 03 Jun 2017 12:10:36: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:10:37: #2 number of paired peaks: 4774 INFO @ Sat, 03 Jun 2017 12:10:37: start model_add_line... INFO @ Sat, 03 Jun 2017 12:10:38: #2 number of paired peaks: 4774 INFO @ Sat, 03 Jun 2017 12:10:38: start model_add_line... INFO @ Sat, 03 Jun 2017 12:11:20: start X-correlation... INFO @ Sat, 03 Jun 2017 12:11:20: end of X-cor INFO @ Sat, 03 Jun 2017 12:11:20: #2 finished! INFO @ Sat, 03 Jun 2017 12:11:20: #2 predicted fragment length is 228 bps INFO @ Sat, 03 Jun 2017 12:11:20: #2 alternative fragment length(s) may be 228 bps INFO @ Sat, 03 Jun 2017 12:11:20: #2.2 Generate R script for model : SRX958295.20_model.r INFO @ Sat, 03 Jun 2017 12:11:20: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:11:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:11:24: start X-correlation... INFO @ Sat, 03 Jun 2017 12:11:24: end of X-cor INFO @ Sat, 03 Jun 2017 12:11:24: #2 finished! INFO @ Sat, 03 Jun 2017 12:11:24: #2 predicted fragment length is 228 bps INFO @ Sat, 03 Jun 2017 12:11:24: #2 alternative fragment length(s) may be 228 bps INFO @ Sat, 03 Jun 2017 12:11:24: #2.2 Generate R script for model : SRX958295.05_model.r INFO @ Sat, 03 Jun 2017 12:11:24: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:11:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:11:24: start X-correlation... INFO @ Sat, 03 Jun 2017 12:11:24: end of X-cor INFO @ Sat, 03 Jun 2017 12:11:24: #2 finished! INFO @ Sat, 03 Jun 2017 12:11:24: #2 predicted fragment length is 228 bps INFO @ Sat, 03 Jun 2017 12:11:24: #2 alternative fragment length(s) may be 228 bps INFO @ Sat, 03 Jun 2017 12:11:24: #2.2 Generate R script for model : SRX958295.10_model.r INFO @ Sat, 03 Jun 2017 12:11:24: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:11:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:12:29: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:12:30: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:12:35: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sat, 03 Jun 2017 12:13:12: #4 Write output xls file... SRX958295.20_peaks.xls INFO @ Sat, 03 Jun 2017 12:13:12: #4 Write peak in narrowPeak format file... SRX958295.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:13:12: #4 Write summits bed file... SRX958295.20_summits.bed INFO @ Sat, 03 Jun 2017 12:13:12: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3775 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 12:13:19: #4 Write output xls file... SRX958295.10_peaks.xls INFO @ Sat, 03 Jun 2017 12:13:19: #4 Write peak in narrowPeak format file... SRX958295.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:13:19: #4 Write summits bed file... SRX958295.10_summits.bed INFO @ Sat, 03 Jun 2017 12:13:19: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5673 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 12:13:29: #4 Write output xls file... SRX958295.05_peaks.xls INFO @ Sat, 03 Jun 2017 12:13:29: #4 Write peak in narrowPeak format file... SRX958295.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:13:29: #4 Write summits bed file... SRX958295.05_summits.bed INFO @ Sat, 03 Jun 2017 12:13:29: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (7472 records, 4 fields): 10 millis CompletedMACS2peakCalling