Job ID = 9028926 sra ファイルのダウンロード中... Completed: 807260K bytes transferred in 17 seconds (370840K 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 1073 0 --:--:-- 0:00:07 --:--:-- 10717 100 38245 0 38245 0 0 4609 0 --:--:-- 0:00:08 --:--:-- 20386 100 86101 0 86101 0 0 9433 0 --:--:-- 0:00:09 --:--:-- 31818 100 107k 0 107k 0 0 11670 0 --:--:-- 0:00:09 --:--:-- 36350 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 37754539 spots for /home/okishinya/chipatlas/results/ce10/SRX997747/SRR1977494.sra Written 37754539 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: 00:06:22 37754539 reads; of these: 37754539 (100.00%) were unpaired; of these: 17761749 (47.05%) aligned 0 times 16186952 (42.87%) aligned exactly 1 time 3805838 (10.08%) aligned >1 times 52.95% overall alignment rate Time searching: 00:06:22 Overall time: 00:06:22 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 8 files... [bam_rmdupse_core] 12552392 / 19992790 = 0.6278 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 12:35:57: # Command line: callpeak -t SRX997747.bam -f BAM -g ce -n SRX997747.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX997747.05 # format = BAM # ChIP-seq file = ['SRX997747.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 12:35:57: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:35:57: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:35:57: # Command line: callpeak -t SRX997747.bam -f BAM -g ce -n SRX997747.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX997747.20 # format = BAM # ChIP-seq file = ['SRX997747.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 12:35:57: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:35:57: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:35:57: # Command line: callpeak -t SRX997747.bam -f BAM -g ce -n SRX997747.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX997747.10 # format = BAM # ChIP-seq file = ['SRX997747.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 12:35:57: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:35:57: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:36:03: 1000000 INFO @ Sat, 03 Jun 2017 12:36:03: 1000000 INFO @ Sat, 03 Jun 2017 12:36:03: 1000000 INFO @ Sat, 03 Jun 2017 12:36:08: 2000000 INFO @ Sat, 03 Jun 2017 12:36:08: 2000000 INFO @ Sat, 03 Jun 2017 12:36:09: 2000000 INFO @ Sat, 03 Jun 2017 12:36:13: 3000000 INFO @ Sat, 03 Jun 2017 12:36:13: 3000000 INFO @ Sat, 03 Jun 2017 12:36:14: 3000000 INFO @ Sat, 03 Jun 2017 12:36:18: 4000000 INFO @ Sat, 03 Jun 2017 12:36:18: 4000000 INFO @ Sat, 03 Jun 2017 12:36:20: 4000000 INFO @ Sat, 03 Jun 2017 12:36:23: 5000000 INFO @ Sat, 03 Jun 2017 12:36:23: 5000000 INFO @ Sat, 03 Jun 2017 12:36:25: 5000000 INFO @ Sat, 03 Jun 2017 12:36:28: 6000000 INFO @ Sat, 03 Jun 2017 12:36:28: 6000000 INFO @ Sat, 03 Jun 2017 12:36:31: 6000000 INFO @ Sat, 03 Jun 2017 12:36:33: 7000000 INFO @ Sat, 03 Jun 2017 12:36:33: 7000000 INFO @ Sat, 03 Jun 2017 12:36:36: #1 tag size is determined as 36 bps INFO @ Sat, 03 Jun 2017 12:36:36: #1 tag size = 36 INFO @ Sat, 03 Jun 2017 12:36:36: #1 total tags in treatment: 7440398 INFO @ Sat, 03 Jun 2017 12:36:36: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:36:36: #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 12:36:36: #1 tag size is determined as 36 bps INFO @ Sat, 03 Jun 2017 12:36:36: #1 tag size = 36 INFO @ Sat, 03 Jun 2017 12:36:36: #1 total tags in treatment: 7440398 INFO @ Sat, 03 Jun 2017 12:36:36: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:36:36: #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 12:36:37: 7000000 INFO @ Sat, 03 Jun 2017 12:36:37: #1 tags after filtering in treatment: 7437930 INFO @ Sat, 03 Jun 2017 12:36:37: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:36:37: #1 finished! INFO @ Sat, 03 Jun 2017 12:36:37: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:36:37: #1 tags after filtering in treatment: 7437930 INFO @ Sat, 03 Jun 2017 12:36:37: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:36:37: #1 finished! INFO @ Sat, 03 Jun 2017 12:36:37: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:36:39: #2 number of paired peaks: 1196 INFO @ Sat, 03 Jun 2017 12:36:39: start model_add_line... INFO @ Sat, 03 Jun 2017 12:36:39: #2 number of paired peaks: 1196 INFO @ Sat, 03 Jun 2017 12:36:39: start model_add_line... INFO @ Sat, 03 Jun 2017 12:36:39: #1 tag size is determined as 36 bps INFO @ Sat, 03 Jun 2017 12:36:39: #1 tag size = 36 INFO @ Sat, 03 Jun 2017 12:36:39: #1 total tags in treatment: 7440398 INFO @ Sat, 03 Jun 2017 12:36:39: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:36:39: #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 12:36:40: #1 tags after filtering in treatment: 7437930 INFO @ Sat, 03 Jun 2017 12:36:40: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:36:40: #1 finished! INFO @ Sat, 03 Jun 2017 12:36:40: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:36:42: #2 number of paired peaks: 1196 INFO @ Sat, 03 Jun 2017 12:36:42: start model_add_line... INFO @ Sat, 03 Jun 2017 12:36:47: start X-correlation... INFO @ Sat, 03 Jun 2017 12:36:47: end of X-cor INFO @ Sat, 03 Jun 2017 12:36:47: #2 finished! INFO @ Sat, 03 Jun 2017 12:36:47: #2 predicted fragment length is 157 bps INFO @ Sat, 03 Jun 2017 12:36:47: #2 alternative fragment length(s) may be 157 bps INFO @ Sat, 03 Jun 2017 12:36:47: #2.2 Generate R script for model : SRX997747.20_model.r INFO @ Sat, 03 Jun 2017 12:36:47: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:36:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:36:48: start X-correlation... INFO @ Sat, 03 Jun 2017 12:36:48: end of X-cor INFO @ Sat, 03 Jun 2017 12:36:48: #2 finished! INFO @ Sat, 03 Jun 2017 12:36:48: #2 predicted fragment length is 157 bps INFO @ Sat, 03 Jun 2017 12:36:48: #2 alternative fragment length(s) may be 157 bps INFO @ Sat, 03 Jun 2017 12:36:48: #2.2 Generate R script for model : SRX997747.05_model.r INFO @ Sat, 03 Jun 2017 12:36:48: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:36:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:36:50: start X-correlation... INFO @ Sat, 03 Jun 2017 12:36:50: end of X-cor INFO @ Sat, 03 Jun 2017 12:36:50: #2 finished! INFO @ Sat, 03 Jun 2017 12:36:50: #2 predicted fragment length is 157 bps INFO @ Sat, 03 Jun 2017 12:36:50: #2 alternative fragment length(s) may be 157 bps INFO @ Sat, 03 Jun 2017 12:36:50: #2.2 Generate R script for model : SRX997747.10_model.r INFO @ Sat, 03 Jun 2017 12:36:51: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:36:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:37:34: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:37:35: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:37:36: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:38:10: #4 Write output xls file... SRX997747.10_peaks.xls INFO @ Sat, 03 Jun 2017 12:38:10: #4 Write peak in narrowPeak format file... SRX997747.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:38:10: #4 Write summits bed file... SRX997747.10_summits.bed INFO @ Sat, 03 Jun 2017 12:38:10: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (5284 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 12:38:11: #4 Write output xls file... SRX997747.20_peaks.xls INFO @ Sat, 03 Jun 2017 12:38:11: #4 Write peak in narrowPeak format file... SRX997747.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:38:11: #4 Write summits bed file... SRX997747.20_summits.bed INFO @ Sat, 03 Jun 2017 12:38:11: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2953 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 12:38:15: #4 Write output xls file... SRX997747.05_peaks.xls INFO @ Sat, 03 Jun 2017 12:38:15: #4 Write peak in narrowPeak format file... SRX997747.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:38:15: #4 Write summits bed file... SRX997747.05_summits.bed INFO @ Sat, 03 Jun 2017 12:38:15: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (8288 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。