Job ID = 9029494 sra ファイルのダウンロード中... Completed: 265384K bytes transferred in 4 seconds (446598K 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 1054 0 --:--:-- 0:00:07 --:--:-- 10526 100 30318 0 30318 0 0 3668 0 --:--:-- 0:00:08 --:--:-- 17585 100 54318 0 54318 0 0 5972 0 --:--:-- 0:00:09 --:--:-- 21276 100 63338 0 63338 0 0 6963 0 --:--:-- 0:00:09 --:--:-- 24799 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 10337172 spots for /home/okishinya/chipatlas/results/dm3/SRX1794248/SRR3575292.sra Written 10337172 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:39 10337172 reads; of these: 10337172 (100.00%) were unpaired; of these: 601056 (5.81%) aligned 0 times 7815659 (75.61%) aligned exactly 1 time 1920457 (18.58%) aligned >1 times 94.19% overall alignment rate Time searching: 00:03:40 Overall time: 00:03:40 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_rmdupse_core] 1203384 / 9736116 = 0.1236 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 14:01:40: # Command line: callpeak -t SRX1794248.bam -f BAM -g dm -n SRX1794248.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1794248.05 # format = BAM # ChIP-seq file = ['SRX1794248.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 14:01:40: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:01:40: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:01:40: # Command line: callpeak -t SRX1794248.bam -f BAM -g dm -n SRX1794248.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1794248.20 # format = BAM # ChIP-seq file = ['SRX1794248.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 14:01:40: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:01:40: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:01:40: # Command line: callpeak -t SRX1794248.bam -f BAM -g dm -n SRX1794248.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1794248.10 # format = BAM # ChIP-seq file = ['SRX1794248.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 14:01:40: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:01:40: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:01:46: 1000000 INFO @ Sat, 03 Jun 2017 14:01:47: 1000000 INFO @ Sat, 03 Jun 2017 14:01:47: 1000000 INFO @ Sat, 03 Jun 2017 14:01:53: 2000000 INFO @ Sat, 03 Jun 2017 14:01:54: 2000000 INFO @ Sat, 03 Jun 2017 14:01:54: 2000000 INFO @ Sat, 03 Jun 2017 14:01:59: 3000000 INFO @ Sat, 03 Jun 2017 14:02:01: 3000000 INFO @ Sat, 03 Jun 2017 14:02:01: 3000000 INFO @ Sat, 03 Jun 2017 14:02:06: 4000000 INFO @ Sat, 03 Jun 2017 14:02:08: 4000000 INFO @ Sat, 03 Jun 2017 14:02:08: 4000000 INFO @ Sat, 03 Jun 2017 14:02:13: 5000000 INFO @ Sat, 03 Jun 2017 14:02:15: 5000000 INFO @ Sat, 03 Jun 2017 14:02:15: 5000000 INFO @ Sat, 03 Jun 2017 14:02:19: 6000000 INFO @ Sat, 03 Jun 2017 14:02:22: 6000000 INFO @ Sat, 03 Jun 2017 14:02:22: 6000000 INFO @ Sat, 03 Jun 2017 14:02:26: 7000000 INFO @ Sat, 03 Jun 2017 14:02:30: 7000000 INFO @ Sat, 03 Jun 2017 14:02:30: 7000000 INFO @ Sat, 03 Jun 2017 14:02:32: 8000000 INFO @ Sat, 03 Jun 2017 14:02:36: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 14:02:36: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 14:02:36: #1 total tags in treatment: 8532732 INFO @ Sat, 03 Jun 2017 14:02:36: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:02:36: #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 14:02:37: 8000000 INFO @ Sat, 03 Jun 2017 14:02:37: 8000000 INFO @ Sat, 03 Jun 2017 14:02:37: #1 tags after filtering in treatment: 8530390 INFO @ Sat, 03 Jun 2017 14:02:37: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:02:37: #1 finished! INFO @ Sat, 03 Jun 2017 14:02:37: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:02:40: #2 number of paired peaks: 5923 INFO @ Sat, 03 Jun 2017 14:02:40: start model_add_line... INFO @ Sat, 03 Jun 2017 14:02:41: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 14:02:41: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 14:02:41: #1 total tags in treatment: 8532732 INFO @ Sat, 03 Jun 2017 14:02:41: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:02:41: #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 14:02:41: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 14:02:41: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 14:02:41: #1 total tags in treatment: 8532732 INFO @ Sat, 03 Jun 2017 14:02:41: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:02:41: #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 14:02:42: #1 tags after filtering in treatment: 8530390 INFO @ Sat, 03 Jun 2017 14:02:42: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:02:42: #1 finished! INFO @ Sat, 03 Jun 2017 14:02:42: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:02:43: #1 tags after filtering in treatment: 8530390 INFO @ Sat, 03 Jun 2017 14:02:43: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:02:43: #1 finished! INFO @ Sat, 03 Jun 2017 14:02:43: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:02:44: #2 number of paired peaks: 5923 INFO @ Sat, 03 Jun 2017 14:02:44: start model_add_line... INFO @ Sat, 03 Jun 2017 14:02:45: #2 number of paired peaks: 5923 INFO @ Sat, 03 Jun 2017 14:02:45: start model_add_line... INFO @ Sat, 03 Jun 2017 14:03:17: start X-correlation... INFO @ Sat, 03 Jun 2017 14:03:17: end of X-cor INFO @ Sat, 03 Jun 2017 14:03:17: #2 finished! INFO @ Sat, 03 Jun 2017 14:03:17: #2 predicted fragment length is 147 bps INFO @ Sat, 03 Jun 2017 14:03:17: #2 alternative fragment length(s) may be 147 bps INFO @ Sat, 03 Jun 2017 14:03:17: #2.2 Generate R script for model : SRX1794248.10_model.r INFO @ Sat, 03 Jun 2017 14:03:17: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:03:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:03:20: start X-correlation... INFO @ Sat, 03 Jun 2017 14:03:20: end of X-cor INFO @ Sat, 03 Jun 2017 14:03:20: #2 finished! INFO @ Sat, 03 Jun 2017 14:03:20: #2 predicted fragment length is 147 bps INFO @ Sat, 03 Jun 2017 14:03:20: #2 alternative fragment length(s) may be 147 bps INFO @ Sat, 03 Jun 2017 14:03:20: #2.2 Generate R script for model : SRX1794248.05_model.r INFO @ Sat, 03 Jun 2017 14:03:20: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:03:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:03:22: start X-correlation... INFO @ Sat, 03 Jun 2017 14:03:22: end of X-cor INFO @ Sat, 03 Jun 2017 14:03:22: #2 finished! INFO @ Sat, 03 Jun 2017 14:03:22: #2 predicted fragment length is 147 bps INFO @ Sat, 03 Jun 2017 14:03:22: #2 alternative fragment length(s) may be 147 bps INFO @ Sat, 03 Jun 2017 14:03:22: #2.2 Generate R script for model : SRX1794248.20_model.r INFO @ Sat, 03 Jun 2017 14:03:22: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:03:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:04:09: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:04:11: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:04:11: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Jun 2017 14:04:50: #4 Write output xls file... SRX1794248.20_peaks.xls INFO @ Sat, 03 Jun 2017 14:04:51: #4 Write peak in narrowPeak format file... SRX1794248.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:04:51: #4 Write summits bed file... SRX1794248.20_summits.bed INFO @ Sat, 03 Jun 2017 14:04:51: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3764 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 14:04:55: #4 Write output xls file... SRX1794248.10_peaks.xls INFO @ Sat, 03 Jun 2017 14:04:55: #4 Write peak in narrowPeak format file... SRX1794248.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:04:55: #4 Write summits bed file... SRX1794248.10_summits.bed INFO @ Sat, 03 Jun 2017 14:04:56: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7299 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 14:04:58: #4 Write output xls file... SRX1794248.05_peaks.xls INFO @ Sat, 03 Jun 2017 14:04:59: #4 Write peak in narrowPeak format file... SRX1794248.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:04:59: #4 Write summits bed file... SRX1794248.05_summits.bed INFO @ Sat, 03 Jun 2017 14:04:59: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (10541 records, 4 fields): 14 millis CompletedMACS2peakCalling BigWig に変換しました。