Job ID = 9029857 sra ファイルのダウンロード中... Completed: 322902K bytes transferred in 6 seconds (434683K 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 14324 0 14324 0 0 1843 0 --:--:-- 0:00:07 --:--:-- 11966 100 60734 0 60734 0 0 6927 0 --:--:-- 0:00:08 --:--:-- 27694 100 62605 0 62605 0 0 7140 0 --:--:-- 0:00:08 --:--:-- 28534 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 17873738 spots for /home/okishinya/chipatlas/results/dm3/SRX2385057/SRR5064688.sra Written 17873738 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:48 17873738 reads; of these: 17873738 (100.00%) were unpaired; of these: 523813 (2.93%) aligned 0 times 14771930 (82.65%) aligned exactly 1 time 2577995 (14.42%) aligned >1 times 97.07% overall alignment rate Time searching: 00:05:49 Overall time: 00:05:49 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] 1635084 / 17349925 = 0.0942 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 15:42:04: # Command line: callpeak -t SRX2385057.bam -f BAM -g dm -n SRX2385057.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2385057.10 # format = BAM # ChIP-seq file = ['SRX2385057.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 15:42:04: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:42:04: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:42:04: # Command line: callpeak -t SRX2385057.bam -f BAM -g dm -n SRX2385057.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2385057.20 # format = BAM # ChIP-seq file = ['SRX2385057.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 15:42:04: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:42:04: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:42:04: # Command line: callpeak -t SRX2385057.bam -f BAM -g dm -n SRX2385057.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2385057.05 # format = BAM # ChIP-seq file = ['SRX2385057.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 15:42:04: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:42:04: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:42:09: 1000000 INFO @ Sat, 03 Jun 2017 15:42:09: 1000000 INFO @ Sat, 03 Jun 2017 15:42:10: 1000000 INFO @ Sat, 03 Jun 2017 15:42:15: 2000000 INFO @ Sat, 03 Jun 2017 15:42:15: 2000000 INFO @ Sat, 03 Jun 2017 15:42:16: 2000000 INFO @ Sat, 03 Jun 2017 15:42:21: 3000000 INFO @ Sat, 03 Jun 2017 15:42:21: 3000000 INFO @ Sat, 03 Jun 2017 15:42:22: 3000000 INFO @ Sat, 03 Jun 2017 15:42:27: 4000000 INFO @ Sat, 03 Jun 2017 15:42:27: 4000000 INFO @ Sat, 03 Jun 2017 15:42:28: 4000000 INFO @ Sat, 03 Jun 2017 15:42:33: 5000000 INFO @ Sat, 03 Jun 2017 15:42:33: 5000000 INFO @ Sat, 03 Jun 2017 15:42:35: 5000000 INFO @ Sat, 03 Jun 2017 15:42:39: 6000000 INFO @ Sat, 03 Jun 2017 15:42:39: 6000000 INFO @ Sat, 03 Jun 2017 15:42:41: 6000000 INFO @ Sat, 03 Jun 2017 15:42:45: 7000000 INFO @ Sat, 03 Jun 2017 15:42:45: 7000000 INFO @ Sat, 03 Jun 2017 15:42:47: 7000000 INFO @ Sat, 03 Jun 2017 15:42:51: 8000000 INFO @ Sat, 03 Jun 2017 15:42:51: 8000000 INFO @ Sat, 03 Jun 2017 15:42:54: 8000000 INFO @ Sat, 03 Jun 2017 15:42:57: 9000000 INFO @ Sat, 03 Jun 2017 15:42:57: 9000000 INFO @ Sat, 03 Jun 2017 15:43:00: 9000000 INFO @ Sat, 03 Jun 2017 15:43:02: 10000000 INFO @ Sat, 03 Jun 2017 15:43:02: 10000000 INFO @ Sat, 03 Jun 2017 15:43:06: 10000000 INFO @ Sat, 03 Jun 2017 15:43:08: 11000000 INFO @ Sat, 03 Jun 2017 15:43:08: 11000000 INFO @ Sat, 03 Jun 2017 15:43:12: 11000000 INFO @ Sat, 03 Jun 2017 15:43:14: 12000000 INFO @ Sat, 03 Jun 2017 15:43:14: 12000000 INFO @ Sat, 03 Jun 2017 15:43:18: 12000000 INFO @ Sat, 03 Jun 2017 15:43:20: 13000000 INFO @ Sat, 03 Jun 2017 15:43:20: 13000000 INFO @ Sat, 03 Jun 2017 15:43:25: 13000000 INFO @ Sat, 03 Jun 2017 15:43:26: 14000000 INFO @ Sat, 03 Jun 2017 15:43:26: 14000000 INFO @ Sat, 03 Jun 2017 15:43:31: 14000000 INFO @ Sat, 03 Jun 2017 15:43:32: 15000000 INFO @ Sat, 03 Jun 2017 15:43:32: 15000000 INFO @ Sat, 03 Jun 2017 15:43:36: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 15:43:36: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 15:43:36: #1 total tags in treatment: 15714841 INFO @ Sat, 03 Jun 2017 15:43:36: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:43:36: #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 15:43:36: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 15:43:36: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 15:43:36: #1 total tags in treatment: 15714841 INFO @ Sat, 03 Jun 2017 15:43:36: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:43:36: #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 15:43:37: 15000000 INFO @ Sat, 03 Jun 2017 15:43:39: #1 tags after filtering in treatment: 15710480 INFO @ Sat, 03 Jun 2017 15:43:39: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:43:39: #1 finished! INFO @ Sat, 03 Jun 2017 15:43:39: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:43:39: #1 tags after filtering in treatment: 15710480 INFO @ Sat, 03 Jun 2017 15:43:39: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:43:39: #1 finished! INFO @ Sat, 03 Jun 2017 15:43:39: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:43:41: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 15:43:41: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 15:43:41: #1 total tags in treatment: 15714841 INFO @ Sat, 03 Jun 2017 15:43:41: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:43:41: #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 15:43:42: #2 number of paired peaks: 1289 INFO @ Sat, 03 Jun 2017 15:43:42: start model_add_line... INFO @ Sat, 03 Jun 2017 15:43:42: #2 number of paired peaks: 1289 INFO @ Sat, 03 Jun 2017 15:43:42: start model_add_line... INFO @ Sat, 03 Jun 2017 15:43:44: #1 tags after filtering in treatment: 15710480 INFO @ Sat, 03 Jun 2017 15:43:44: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:43:44: #1 finished! INFO @ Sat, 03 Jun 2017 15:43:44: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:43:47: #2 number of paired peaks: 1289 INFO @ Sat, 03 Jun 2017 15:43:47: start model_add_line... INFO @ Sat, 03 Jun 2017 15:43:54: start X-correlation... INFO @ Sat, 03 Jun 2017 15:43:54: end of X-cor INFO @ Sat, 03 Jun 2017 15:43:54: #2 finished! INFO @ Sat, 03 Jun 2017 15:43:54: #2 predicted fragment length is 159 bps INFO @ Sat, 03 Jun 2017 15:43:54: #2 alternative fragment length(s) may be 159 bps INFO @ Sat, 03 Jun 2017 15:43:54: #2.2 Generate R script for model : SRX2385057.05_model.r INFO @ Sat, 03 Jun 2017 15:43:54: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:43:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:43:55: start X-correlation... INFO @ Sat, 03 Jun 2017 15:43:55: end of X-cor INFO @ Sat, 03 Jun 2017 15:43:55: #2 finished! INFO @ Sat, 03 Jun 2017 15:43:55: #2 predicted fragment length is 159 bps INFO @ Sat, 03 Jun 2017 15:43:55: #2 alternative fragment length(s) may be 159 bps INFO @ Sat, 03 Jun 2017 15:43:55: #2.2 Generate R script for model : SRX2385057.20_model.r INFO @ Sat, 03 Jun 2017 15:43:55: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:43:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:44:00: start X-correlation... INFO @ Sat, 03 Jun 2017 15:44:00: end of X-cor INFO @ Sat, 03 Jun 2017 15:44:00: #2 finished! INFO @ Sat, 03 Jun 2017 15:44:00: #2 predicted fragment length is 159 bps INFO @ Sat, 03 Jun 2017 15:44:00: #2 alternative fragment length(s) may be 159 bps INFO @ Sat, 03 Jun 2017 15:44:00: #2.2 Generate R script for model : SRX2385057.10_model.r INFO @ Sat, 03 Jun 2017 15:44:00: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:44:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:45:17: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:45:24: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:45:27: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:46:20: #4 Write output xls file... SRX2385057.20_peaks.xls INFO @ Sat, 03 Jun 2017 15:46:20: #4 Write peak in narrowPeak format file... SRX2385057.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:46:20: #4 Write summits bed file... SRX2385057.20_summits.bed INFO @ Sat, 03 Jun 2017 15:46:20: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2024 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 15:46:35: #4 Write output xls file... SRX2385057.10_peaks.xls INFO @ Sat, 03 Jun 2017 15:46:35: #4 Write peak in narrowPeak format file... SRX2385057.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:46:35: #4 Write summits bed file... SRX2385057.10_summits.bed INFO @ Sat, 03 Jun 2017 15:46:35: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4367 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 15:46:38: #4 Write output xls file... SRX2385057.05_peaks.xls INFO @ Sat, 03 Jun 2017 15:46:38: #4 Write peak in narrowPeak format file... SRX2385057.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:46:38: #4 Write summits bed file... SRX2385057.05_summits.bed INFO @ Sat, 03 Jun 2017 15:46:38: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6892 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。