Job ID = 9029286 sra ファイルのダウンロード中... Completed: 394672K bytes transferred in 6 seconds (480761K 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 14324 0 14324 0 0 1940 0 --:--:-- 0:00:07 --:--:-- 14015 100 34589 0 34589 0 0 4212 0 --:--:-- 0:00:08 --:--:-- 18676 100 75893 0 75893 0 0 8244 0 --:--:-- 0:00:09 --:--:-- 26647 100 85457 0 85457 0 0 9118 0 --:--:-- 0:00:09 --:--:-- 28362 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 13264499 spots for /home/okishinya/chipatlas/results/dm3/SRX1531762/SRR3102820.sra Written 13264499 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: 00:04:30 13264499 reads; of these: 13264499 (100.00%) were unpaired; of these: 1280896 (9.66%) aligned 0 times 10418118 (78.54%) aligned exactly 1 time 1565485 (11.80%) aligned >1 times 90.34% overall alignment rate Time searching: 00:04:30 Overall time: 00:04:30 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] 2821133 / 11983603 = 0.2354 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 13:07:56: # Command line: callpeak -t SRX1531762.bam -f BAM -g dm -n SRX1531762.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1531762.10 # format = BAM # ChIP-seq file = ['SRX1531762.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 13:07:56: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:07:56: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:07:57: # Command line: callpeak -t SRX1531762.bam -f BAM -g dm -n SRX1531762.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1531762.05 # format = BAM # ChIP-seq file = ['SRX1531762.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 13:07:57: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:07:57: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:07:57: # Command line: callpeak -t SRX1531762.bam -f BAM -g dm -n SRX1531762.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1531762.20 # format = BAM # ChIP-seq file = ['SRX1531762.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 13:07:57: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:07:57: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:08:04: 1000000 INFO @ Sat, 03 Jun 2017 13:08:04: 1000000 INFO @ Sat, 03 Jun 2017 13:08:04: 1000000 INFO @ Sat, 03 Jun 2017 13:08:11: 2000000 INFO @ Sat, 03 Jun 2017 13:08:11: 2000000 INFO @ Sat, 03 Jun 2017 13:08:11: 2000000 INFO @ Sat, 03 Jun 2017 13:08:18: 3000000 INFO @ Sat, 03 Jun 2017 13:08:18: 3000000 INFO @ Sat, 03 Jun 2017 13:08:19: 3000000 INFO @ Sat, 03 Jun 2017 13:08:25: 4000000 INFO @ Sat, 03 Jun 2017 13:08:25: 4000000 INFO @ Sat, 03 Jun 2017 13:08:28: 4000000 INFO @ Sat, 03 Jun 2017 13:08:32: 5000000 INFO @ Sat, 03 Jun 2017 13:08:32: 5000000 INFO @ Sat, 03 Jun 2017 13:08:36: 5000000 INFO @ Sat, 03 Jun 2017 13:08:38: 6000000 INFO @ Sat, 03 Jun 2017 13:08:40: 6000000 INFO @ Sat, 03 Jun 2017 13:08:44: 6000000 INFO @ Sat, 03 Jun 2017 13:08:45: 7000000 INFO @ Sat, 03 Jun 2017 13:08:47: 7000000 INFO @ Sat, 03 Jun 2017 13:08:51: 8000000 INFO @ Sat, 03 Jun 2017 13:08:52: 7000000 INFO @ Sat, 03 Jun 2017 13:08:55: 8000000 INFO @ Sat, 03 Jun 2017 13:08:58: 9000000 INFO @ Sat, 03 Jun 2017 13:08:59: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:08:59: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:08:59: #1 total tags in treatment: 9162470 INFO @ Sat, 03 Jun 2017 13:08:59: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:08:59: #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 13:09:00: 8000000 INFO @ Sat, 03 Jun 2017 13:09:01: #1 tags after filtering in treatment: 9157972 INFO @ Sat, 03 Jun 2017 13:09:01: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:09:01: #1 finished! INFO @ Sat, 03 Jun 2017 13:09:01: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:09:02: 9000000 INFO @ Sat, 03 Jun 2017 13:09:03: #2 number of paired peaks: 4244 INFO @ Sat, 03 Jun 2017 13:09:03: start model_add_line... INFO @ Sat, 03 Jun 2017 13:09:04: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:09:04: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:09:04: #1 total tags in treatment: 9162470 INFO @ Sat, 03 Jun 2017 13:09:04: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:09:04: #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 13:09:05: #1 tags after filtering in treatment: 9157972 INFO @ Sat, 03 Jun 2017 13:09:05: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:09:05: #1 finished! INFO @ Sat, 03 Jun 2017 13:09:05: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:09:07: #2 number of paired peaks: 4244 INFO @ Sat, 03 Jun 2017 13:09:07: start model_add_line... INFO @ Sat, 03 Jun 2017 13:09:08: 9000000 INFO @ Sat, 03 Jun 2017 13:09:09: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:09:09: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:09:09: #1 total tags in treatment: 9162470 INFO @ Sat, 03 Jun 2017 13:09:09: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:09:09: #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 13:09:11: #1 tags after filtering in treatment: 9157972 INFO @ Sat, 03 Jun 2017 13:09:11: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:09:11: #1 finished! INFO @ Sat, 03 Jun 2017 13:09:11: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:09:13: #2 number of paired peaks: 4244 INFO @ Sat, 03 Jun 2017 13:09:13: start model_add_line... INFO @ Sat, 03 Jun 2017 13:09:31: start X-correlation... INFO @ Sat, 03 Jun 2017 13:09:31: end of X-cor INFO @ Sat, 03 Jun 2017 13:09:31: #2 finished! INFO @ Sat, 03 Jun 2017 13:09:31: #2 predicted fragment length is 151 bps INFO @ Sat, 03 Jun 2017 13:09:31: #2 alternative fragment length(s) may be 151 bps INFO @ Sat, 03 Jun 2017 13:09:31: #2.2 Generate R script for model : SRX1531762.10_model.r INFO @ Sat, 03 Jun 2017 13:09:31: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:09:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:09:34: start X-correlation... INFO @ Sat, 03 Jun 2017 13:09:34: end of X-cor INFO @ Sat, 03 Jun 2017 13:09:34: #2 finished! INFO @ Sat, 03 Jun 2017 13:09:34: #2 predicted fragment length is 151 bps INFO @ Sat, 03 Jun 2017 13:09:34: #2 alternative fragment length(s) may be 151 bps INFO @ Sat, 03 Jun 2017 13:09:34: #2.2 Generate R script for model : SRX1531762.20_model.r INFO @ Sat, 03 Jun 2017 13:09:34: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:09:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:09:41: start X-correlation... INFO @ Sat, 03 Jun 2017 13:09:41: end of X-cor INFO @ Sat, 03 Jun 2017 13:09:41: #2 finished! INFO @ Sat, 03 Jun 2017 13:09:41: #2 predicted fragment length is 151 bps INFO @ Sat, 03 Jun 2017 13:09:41: #2 alternative fragment length(s) may be 151 bps INFO @ Sat, 03 Jun 2017 13:09:41: #2.2 Generate R script for model : SRX1531762.05_model.r INFO @ Sat, 03 Jun 2017 13:09:41: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:09:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:10:29: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:10:30: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:10:35: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:11:14: #4 Write output xls file... SRX1531762.20_peaks.xls INFO @ Sat, 03 Jun 2017 13:11:14: #4 Write peak in narrowPeak format file... SRX1531762.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:11:14: #4 Write summits bed file... SRX1531762.20_summits.bed INFO @ Sat, 03 Jun 2017 13:11:14: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (4996 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:11:17: #4 Write output xls file... SRX1531762.10_peaks.xls INFO @ Sat, 03 Jun 2017 13:11:17: #4 Write peak in narrowPeak format file... SRX1531762.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:11:17: #4 Write summits bed file... SRX1531762.10_summits.bed INFO @ Sat, 03 Jun 2017 13:11:17: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7690 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Jun 2017 13:11:25: #4 Write output xls file... SRX1531762.05_peaks.xls INFO @ Sat, 03 Jun 2017 13:11:25: #4 Write peak in narrowPeak format file... SRX1531762.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:11:25: #4 Write summits bed file... SRX1531762.05_summits.bed INFO @ Sat, 03 Jun 2017 13:11:25: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (10629 records, 4 fields): 14 millis CompletedMACS2peakCalling BigWig に変換しました。