Job ID = 8696831 sra ファイルのダウンロード中... Completed: 497465K bytes transferred in 9 seconds (428636K 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 7663 0 7663 0 0 927 0 --:--:-- 0:00:08 --:--:-- 4245 100 22575 0 22575 0 0 2520 0 --:--:-- 0:00:08 --:--:-- 9015 100 31490 0 31490 0 0 3384 0 --:--:-- 0:00:09 --:--:-- 11037 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 37717682 spots for /home/okishinya/chipatlas/results/dm3/SRX110769/SRR388351.sra Written 37717682 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: 00:33:37 37717682 reads; of these: 37717682 (100.00%) were unpaired; of these: 2222421 (5.89%) aligned 0 times 21776275 (57.73%) aligned exactly 1 time 13718986 (36.37%) aligned >1 times 94.11% overall alignment rate Time searching: 00:33:38 Overall time: 00:33:38 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 12 files... [bam_rmdupse_core] 11578729 / 35495261 = 0.3262 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 @ Fri, 10 Mar 2017 12:41:50: # Command line: callpeak -t SRX110769.bam -f BAM -g dm -n SRX110769.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX110769.20 # format = BAM # ChIP-seq file = ['SRX110769.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 @ Fri, 10 Mar 2017 12:41:50: #1 read tag files... INFO @ Fri, 10 Mar 2017 12:41:50: #1 read treatment tags... INFO @ Fri, 10 Mar 2017 12:41:50: # Command line: callpeak -t SRX110769.bam -f BAM -g dm -n SRX110769.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX110769.10 # format = BAM # ChIP-seq file = ['SRX110769.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 @ Fri, 10 Mar 2017 12:41:50: #1 read tag files... INFO @ Fri, 10 Mar 2017 12:41:50: #1 read treatment tags... INFO @ Fri, 10 Mar 2017 12:41:50: # Command line: callpeak -t SRX110769.bam -f BAM -g dm -n SRX110769.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX110769.05 # format = BAM # ChIP-seq file = ['SRX110769.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 @ Fri, 10 Mar 2017 12:41:50: #1 read tag files... INFO @ Fri, 10 Mar 2017 12:41:50: #1 read treatment tags... INFO @ Fri, 10 Mar 2017 12:41:58: 1000000 INFO @ Fri, 10 Mar 2017 12:41:59: 1000000 INFO @ Fri, 10 Mar 2017 12:42:00: 1000000 INFO @ Fri, 10 Mar 2017 12:42:07: 2000000 INFO @ Fri, 10 Mar 2017 12:42:08: 2000000 INFO @ Fri, 10 Mar 2017 12:42:12: 2000000 INFO @ Fri, 10 Mar 2017 12:42:17: 3000000 INFO @ Fri, 10 Mar 2017 12:42:18: 3000000 INFO @ Fri, 10 Mar 2017 12:42:24: 3000000 INFO @ Fri, 10 Mar 2017 12:42:26: 4000000 INFO @ Fri, 10 Mar 2017 12:42:27: 4000000 INFO @ Fri, 10 Mar 2017 12:42:35: 5000000 INFO @ Fri, 10 Mar 2017 12:42:36: 4000000 INFO @ Fri, 10 Mar 2017 12:42:37: 5000000 INFO @ Fri, 10 Mar 2017 12:42:43: 6000000 INFO @ Fri, 10 Mar 2017 12:42:46: 6000000 INFO @ Fri, 10 Mar 2017 12:42:47: 5000000 INFO @ Fri, 10 Mar 2017 12:42:52: 7000000 INFO @ Fri, 10 Mar 2017 12:42:56: 7000000 INFO @ Fri, 10 Mar 2017 12:42:58: 6000000 INFO @ Fri, 10 Mar 2017 12:43:01: 8000000 INFO @ Fri, 10 Mar 2017 12:43:05: 8000000 INFO @ Fri, 10 Mar 2017 12:43:10: 9000000 INFO @ Fri, 10 Mar 2017 12:43:12: 7000000 INFO @ Fri, 10 Mar 2017 12:43:14: 9000000 INFO @ Fri, 10 Mar 2017 12:43:19: 10000000 INFO @ Fri, 10 Mar 2017 12:43:24: 10000000 INFO @ Fri, 10 Mar 2017 12:43:27: 8000000 INFO @ Fri, 10 Mar 2017 12:43:28: 11000000 INFO @ Fri, 10 Mar 2017 12:43:33: 11000000 INFO @ Fri, 10 Mar 2017 12:43:38: 12000000 INFO @ Fri, 10 Mar 2017 12:43:41: 9000000 INFO @ Fri, 10 Mar 2017 12:43:43: 12000000 INFO @ Fri, 10 Mar 2017 12:43:47: 13000000 INFO @ Fri, 10 Mar 2017 12:43:51: 13000000 INFO @ Fri, 10 Mar 2017 12:43:56: 10000000 INFO @ Fri, 10 Mar 2017 12:43:57: 14000000 INFO @ Fri, 10 Mar 2017 12:44:01: 14000000 INFO @ Fri, 10 Mar 2017 12:44:08: 15000000 INFO @ Fri, 10 Mar 2017 12:44:10: 15000000 INFO @ Fri, 10 Mar 2017 12:44:11: 11000000 INFO @ Fri, 10 Mar 2017 12:44:19: 16000000 INFO @ Fri, 10 Mar 2017 12:44:20: 16000000 INFO @ Fri, 10 Mar 2017 12:44:26: 12000000 INFO @ Fri, 10 Mar 2017 12:44:29: 17000000 INFO @ Fri, 10 Mar 2017 12:44:29: 17000000 INFO @ Fri, 10 Mar 2017 12:44:38: 18000000 INFO @ Fri, 10 Mar 2017 12:44:39: 18000000 INFO @ Fri, 10 Mar 2017 12:44:40: 13000000 INFO @ Fri, 10 Mar 2017 12:44:47: 19000000 INFO @ Fri, 10 Mar 2017 12:44:50: 19000000 INFO @ Fri, 10 Mar 2017 12:44:54: 14000000 INFO @ Fri, 10 Mar 2017 12:44:57: 20000000 INFO @ Fri, 10 Mar 2017 12:45:02: 20000000 INFO @ Fri, 10 Mar 2017 12:45:11: 15000000 INFO @ Fri, 10 Mar 2017 12:45:12: 21000000 INFO @ Fri, 10 Mar 2017 12:45:16: 21000000 INFO @ Fri, 10 Mar 2017 12:45:26: 22000000 INFO @ Fri, 10 Mar 2017 12:45:28: 16000000 INFO @ Fri, 10 Mar 2017 12:45:29: 22000000 INFO @ Fri, 10 Mar 2017 12:45:39: 23000000 INFO @ Fri, 10 Mar 2017 12:45:40: 23000000 INFO @ Fri, 10 Mar 2017 12:45:42: 17000000 INFO @ Fri, 10 Mar 2017 12:45:49: #1 tag size is determined as 18 bps INFO @ Fri, 10 Mar 2017 12:45:49: #1 tag size = 18 INFO @ Fri, 10 Mar 2017 12:45:49: #1 total tags in treatment: 23916532 INFO @ Fri, 10 Mar 2017 12:45:49: #1 user defined the maximum tags... INFO @ Fri, 10 Mar 2017 12:45:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Mar 2017 12:45:53: #1 tag size is determined as 18 bps INFO @ Fri, 10 Mar 2017 12:45:53: #1 tag size = 18 INFO @ Fri, 10 Mar 2017 12:45:53: #1 total tags in treatment: 23916532 INFO @ Fri, 10 Mar 2017 12:45:53: #1 user defined the maximum tags... INFO @ Fri, 10 Mar 2017 12:45:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Mar 2017 12:45:54: #1 tags after filtering in treatment: 23916532 INFO @ Fri, 10 Mar 2017 12:45:54: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Mar 2017 12:45:54: #1 finished! INFO @ Fri, 10 Mar 2017 12:45:54: #2 Build Peak Model... INFO @ Fri, 10 Mar 2017 12:45:57: 18000000 INFO @ Fri, 10 Mar 2017 12:45:58: #1 tags after filtering in treatment: 23916532 INFO @ Fri, 10 Mar 2017 12:45:58: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Mar 2017 12:45:58: #1 finished! INFO @ Fri, 10 Mar 2017 12:45:58: #2 Build Peak Model... INFO @ Fri, 10 Mar 2017 12:46:00: #2 number of paired peaks: 2022 INFO @ Fri, 10 Mar 2017 12:46:00: start model_add_line... INFO @ Fri, 10 Mar 2017 12:46:04: #2 number of paired peaks: 2022 INFO @ Fri, 10 Mar 2017 12:46:04: start model_add_line... INFO @ Fri, 10 Mar 2017 12:46:14: 19000000 INFO @ Fri, 10 Mar 2017 12:46:35: 20000000 INFO @ Fri, 10 Mar 2017 12:46:35: start X-correlation... INFO @ Fri, 10 Mar 2017 12:46:35: end of X-cor INFO @ Fri, 10 Mar 2017 12:46:35: #2 finished! INFO @ Fri, 10 Mar 2017 12:46:35: #2 predicted fragment length is 76 bps INFO @ Fri, 10 Mar 2017 12:46:35: #2 alternative fragment length(s) may be 76 bps INFO @ Fri, 10 Mar 2017 12:46:35: #2.2 Generate R script for model : SRX110769.10_model.r INFO @ Fri, 10 Mar 2017 12:46:35: #3 Call peaks... INFO @ Fri, 10 Mar 2017 12:46:35: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Mar 2017 12:46:38: start X-correlation... INFO @ Fri, 10 Mar 2017 12:46:38: end of X-cor INFO @ Fri, 10 Mar 2017 12:46:38: #2 finished! INFO @ Fri, 10 Mar 2017 12:46:38: #2 predicted fragment length is 76 bps INFO @ Fri, 10 Mar 2017 12:46:38: #2 alternative fragment length(s) may be 76 bps INFO @ Fri, 10 Mar 2017 12:46:38: #2.2 Generate R script for model : SRX110769.05_model.r INFO @ Fri, 10 Mar 2017 12:46:38: #3 Call peaks... INFO @ Fri, 10 Mar 2017 12:46:38: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Mar 2017 12:46:55: 21000000 INFO @ Fri, 10 Mar 2017 12:47:12: 22000000 INFO @ Fri, 10 Mar 2017 12:47:32: 23000000 INFO @ Fri, 10 Mar 2017 12:47:49: #1 tag size is determined as 18 bps INFO @ Fri, 10 Mar 2017 12:47:49: #1 tag size = 18 INFO @ Fri, 10 Mar 2017 12:47:49: #1 total tags in treatment: 23916532 INFO @ Fri, 10 Mar 2017 12:47:49: #1 user defined the maximum tags... INFO @ Fri, 10 Mar 2017 12:47:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Mar 2017 12:47:54: #1 tags after filtering in treatment: 23916532 INFO @ Fri, 10 Mar 2017 12:47:54: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Mar 2017 12:47:54: #1 finished! INFO @ Fri, 10 Mar 2017 12:47:54: #2 Build Peak Model... INFO @ Fri, 10 Mar 2017 12:47:59: #2 number of paired peaks: 2022 INFO @ Fri, 10 Mar 2017 12:47:59: start model_add_line... INFO @ Fri, 10 Mar 2017 12:48:33: start X-correlation... INFO @ Fri, 10 Mar 2017 12:48:33: end of X-cor INFO @ Fri, 10 Mar 2017 12:48:33: #2 finished! INFO @ Fri, 10 Mar 2017 12:48:33: #2 predicted fragment length is 76 bps INFO @ Fri, 10 Mar 2017 12:48:33: #2 alternative fragment length(s) may be 76 bps INFO @ Fri, 10 Mar 2017 12:48:33: #2.2 Generate R script for model : SRX110769.20_model.r INFO @ Fri, 10 Mar 2017 12:48:33: #3 Call peaks... INFO @ Fri, 10 Mar 2017 12:48:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Mar 2017 12:48:56: #3 Call peaks for each chromosome... INFO @ Fri, 10 Mar 2017 12:49:15: #3 Call peaks for each chromosome... INFO @ Fri, 10 Mar 2017 12:50:53: #4 Write output xls file... SRX110769.10_peaks.xls INFO @ Fri, 10 Mar 2017 12:50:53: #4 Write peak in narrowPeak format file... SRX110769.10_peaks.narrowPeak INFO @ Fri, 10 Mar 2017 12:50:54: #4 Write summits bed file... SRX110769.10_summits.bed INFO @ Fri, 10 Mar 2017 12:50:54: Done! pass1 - making usageList (13 chroms): 5 millis pass2 - checking and writing primary data (15212 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Fri, 10 Mar 2017 12:50:58: #3 Call peaks for each chromosome... INFO @ Fri, 10 Mar 2017 12:51:33: #4 Write output xls file... SRX110769.05_peaks.xls INFO @ Fri, 10 Mar 2017 12:51:33: #4 Write peak in narrowPeak format file... SRX110769.05_peaks.narrowPeak INFO @ Fri, 10 Mar 2017 12:51:34: #4 Write summits bed file... SRX110769.05_summits.bed INFO @ Fri, 10 Mar 2017 12:51:34: Done! pass1 - making usageList (14 chroms): 7 millis pass2 - checking and writing primary data (22872 records, 4 fields): 39 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Mar 2017 12:53:14: #4 Write output xls file... SRX110769.20_peaks.xls INFO @ Fri, 10 Mar 2017 12:53:15: #4 Write peak in narrowPeak format file... SRX110769.20_peaks.narrowPeak INFO @ Fri, 10 Mar 2017 12:53:15: #4 Write summits bed file... SRX110769.20_summits.bed INFO @ Fri, 10 Mar 2017 12:53:15: Done! pass1 - making usageList (13 chroms): 6 millis pass2 - checking and writing primary data (8480 records, 4 fields): 31 millis CompletedMACS2peakCalling BigWig に変換しました。