Job ID = 9028811 sra ファイルのダウンロード中... Completed: 2178579K bytes transferred in 23 seconds (770593K 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 1057 0 --:--:-- 0:00:07 --:--:-- 11319 100 28797 0 28797 0 0 3493 0 --:--:-- 0:00:08 --:--:-- 17212 100 63549 0 63549 0 0 6879 0 --:--:-- 0:00:09 --:--:-- 23810 100 135k 0 135k 0 0 13757 0 --:--:-- 0:00:10 --:--:-- 39293 100 154k 0 154k 0 0 15242 0 --:--:-- 0:00:10 --:--:-- 41377 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 62865092 spots for /home/okishinya/chipatlas/results/ce10/SRX958296/SRR1917669.sra Written 62865092 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: 00:17:44 62865092 reads; of these: 62865092 (100.00%) were unpaired; of these: 23300436 (37.06%) aligned 0 times 23484037 (37.36%) aligned exactly 1 time 16080619 (25.58%) aligned >1 times 62.94% overall alignment rate Time searching: 00:17:44 Overall time: 00:17:44 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 20 files... [bam_rmdupse_core] 26002543 / 39564656 = 0.6572 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 12:20:31: # Command line: callpeak -t SRX958296.bam -f BAM -g ce -n SRX958296.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX958296.05 # format = BAM # ChIP-seq file = ['SRX958296.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 12:20:31: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:20:31: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:20:31: # Command line: callpeak -t SRX958296.bam -f BAM -g ce -n SRX958296.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX958296.20 # format = BAM # ChIP-seq file = ['SRX958296.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 12:20:31: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:20:31: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:20:31: # Command line: callpeak -t SRX958296.bam -f BAM -g ce -n SRX958296.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX958296.10 # format = BAM # ChIP-seq file = ['SRX958296.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 12:20:31: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:20:31: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:20:37: 1000000 INFO @ Sat, 03 Jun 2017 12:20:37: 1000000 INFO @ Sat, 03 Jun 2017 12:20:37: 1000000 INFO @ Sat, 03 Jun 2017 12:20:43: 2000000 INFO @ Sat, 03 Jun 2017 12:20:43: 2000000 INFO @ Sat, 03 Jun 2017 12:20:43: 2000000 INFO @ Sat, 03 Jun 2017 12:20:49: 3000000 INFO @ Sat, 03 Jun 2017 12:20:49: 3000000 INFO @ Sat, 03 Jun 2017 12:20:49: 3000000 INFO @ Sat, 03 Jun 2017 12:20:55: 4000000 INFO @ Sat, 03 Jun 2017 12:20:55: 4000000 INFO @ Sat, 03 Jun 2017 12:20:55: 4000000 INFO @ Sat, 03 Jun 2017 12:21:01: 5000000 INFO @ Sat, 03 Jun 2017 12:21:01: 5000000 INFO @ Sat, 03 Jun 2017 12:21:01: 5000000 INFO @ Sat, 03 Jun 2017 12:21:07: 6000000 INFO @ Sat, 03 Jun 2017 12:21:07: 6000000 INFO @ Sat, 03 Jun 2017 12:21:07: 6000000 INFO @ Sat, 03 Jun 2017 12:21:13: 7000000 INFO @ Sat, 03 Jun 2017 12:21:13: 7000000 INFO @ Sat, 03 Jun 2017 12:21:13: 7000000 INFO @ Sat, 03 Jun 2017 12:21:18: 8000000 INFO @ Sat, 03 Jun 2017 12:21:19: 8000000 INFO @ Sat, 03 Jun 2017 12:21:19: 8000000 INFO @ Sat, 03 Jun 2017 12:21:24: 9000000 INFO @ Sat, 03 Jun 2017 12:21:25: 9000000 INFO @ Sat, 03 Jun 2017 12:21:25: 9000000 INFO @ Sat, 03 Jun 2017 12:21:30: 10000000 INFO @ Sat, 03 Jun 2017 12:21:31: 10000000 INFO @ Sat, 03 Jun 2017 12:21:31: 10000000 INFO @ Sat, 03 Jun 2017 12:21:36: 11000000 INFO @ Sat, 03 Jun 2017 12:21:37: 11000000 INFO @ Sat, 03 Jun 2017 12:21:37: 11000000 INFO @ Sat, 03 Jun 2017 12:21:42: 12000000 INFO @ Sat, 03 Jun 2017 12:21:43: 12000000 INFO @ Sat, 03 Jun 2017 12:21:43: 12000000 INFO @ Sat, 03 Jun 2017 12:21:48: 13000000 INFO @ Sat, 03 Jun 2017 12:21:49: 13000000 INFO @ Sat, 03 Jun 2017 12:21:49: 13000000 INFO @ Sat, 03 Jun 2017 12:21:51: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:21:51: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:21:51: #1 total tags in treatment: 13562113 INFO @ Sat, 03 Jun 2017 12:21:51: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:21:51: #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 12:21:53: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:21:53: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:21:53: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:21:53: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:21:53: #1 total tags in treatment: 13562113 INFO @ Sat, 03 Jun 2017 12:21:53: #1 total tags in treatment: 13562113 INFO @ Sat, 03 Jun 2017 12:21:53: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:21:53: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:21:53: #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 12:21:53: #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 12:21:54: #1 tags after filtering in treatment: 13556154 INFO @ Sat, 03 Jun 2017 12:21:54: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:21:54: #1 finished! INFO @ Sat, 03 Jun 2017 12:21:54: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:21:55: #1 tags after filtering in treatment: 13556154 INFO @ Sat, 03 Jun 2017 12:21:55: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:21:55: #1 finished! INFO @ Sat, 03 Jun 2017 12:21:55: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:21:56: #1 tags after filtering in treatment: 13556154 INFO @ Sat, 03 Jun 2017 12:21:56: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:21:56: #1 finished! INFO @ Sat, 03 Jun 2017 12:21:56: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:21:57: #2 number of paired peaks: 2180 INFO @ Sat, 03 Jun 2017 12:21:57: start model_add_line... INFO @ Sat, 03 Jun 2017 12:21:58: #2 number of paired peaks: 2180 INFO @ Sat, 03 Jun 2017 12:21:58: start model_add_line... INFO @ Sat, 03 Jun 2017 12:21:59: #2 number of paired peaks: 2180 INFO @ Sat, 03 Jun 2017 12:21:59: start model_add_line... INFO @ Sat, 03 Jun 2017 12:22:26: start X-correlation... INFO @ Sat, 03 Jun 2017 12:22:26: end of X-cor INFO @ Sat, 03 Jun 2017 12:22:26: #2 finished! INFO @ Sat, 03 Jun 2017 12:22:26: #2 predicted fragment length is 135 bps INFO @ Sat, 03 Jun 2017 12:22:26: #2 alternative fragment length(s) may be 4,135 bps INFO @ Sat, 03 Jun 2017 12:22:26: #2.2 Generate R script for model : SRX958296.05_model.r INFO @ Sat, 03 Jun 2017 12:22:26: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:22:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:22:27: start X-correlation... INFO @ Sat, 03 Jun 2017 12:22:27: end of X-cor INFO @ Sat, 03 Jun 2017 12:22:27: #2 finished! INFO @ Sat, 03 Jun 2017 12:22:27: #2 predicted fragment length is 135 bps INFO @ Sat, 03 Jun 2017 12:22:27: #2 alternative fragment length(s) may be 4,135 bps INFO @ Sat, 03 Jun 2017 12:22:27: #2.2 Generate R script for model : SRX958296.10_model.r INFO @ Sat, 03 Jun 2017 12:22:27: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:22:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:22:28: start X-correlation... INFO @ Sat, 03 Jun 2017 12:22:28: end of X-cor INFO @ Sat, 03 Jun 2017 12:22:28: #2 finished! INFO @ Sat, 03 Jun 2017 12:22:28: #2 predicted fragment length is 135 bps INFO @ Sat, 03 Jun 2017 12:22:28: #2 alternative fragment length(s) may be 4,135 bps INFO @ Sat, 03 Jun 2017 12:22:28: #2.2 Generate R script for model : SRX958296.20_model.r INFO @ Sat, 03 Jun 2017 12:22:28: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:22:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:23:45: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:23:48: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:23:50: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:24:39: #4 Write output xls file... SRX958296.20_peaks.xls INFO @ Sat, 03 Jun 2017 12:24:39: #4 Write peak in narrowPeak format file... SRX958296.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:24:39: #4 Write summits bed file... SRX958296.20_summits.bed INFO @ Sat, 03 Jun 2017 12:24:39: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (2725 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 12:24:44: #4 Write output xls file... SRX958296.10_peaks.xls INFO @ Sat, 03 Jun 2017 12:24:44: #4 Write peak in narrowPeak format file... SRX958296.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:24:44: #4 Write summits bed file... SRX958296.10_summits.bed INFO @ Sat, 03 Jun 2017 12:24:44: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (5303 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 12:24:55: #4 Write output xls file... SRX958296.05_peaks.xls INFO @ Sat, 03 Jun 2017 12:24:55: #4 Write peak in narrowPeak format file... SRX958296.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:24:55: #4 Write summits bed file... SRX958296.05_summits.bed INFO @ Sat, 03 Jun 2017 12:24:55: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (7987 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。