Job ID = 9033116 sra ファイルのダウンロード中... Completed: 790136K bytes transferred in 9 seconds (657541K 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 --:--:-- 0 101 5455 0 5455 0 0 770 0 --:--:-- 0:00:07 --:--:-- 9811 100 24454 0 24454 0 0 3029 0 --:--:-- 0:00:08 --:--:-- 15766 100 54398 0 54398 0 0 6111 0 --:--:-- 0:00:08 --:--:-- 22865 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 28633023 spots for /home/okishinya/chipatlas/results/dm3/SRX914955/SRR1873265.sra Written 28633023 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: 00:06:04 28633023 reads; of these: 28633023 (100.00%) were unpaired; of these: 2029369 (7.09%) aligned 0 times 23781819 (83.06%) aligned exactly 1 time 2821835 (9.86%) aligned >1 times 92.91% overall alignment rate Time searching: 00:06:04 Overall time: 00:06:04 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] 5655266 / 26603654 = 0.2126 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 @ Sun, 04 Jun 2017 00:15:55: # Command line: callpeak -t SRX914955.bam -f BAM -g dm -n SRX914955.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX914955.05 # format = BAM # ChIP-seq file = ['SRX914955.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 @ Sun, 04 Jun 2017 00:15:55: #1 read tag files... INFO @ Sun, 04 Jun 2017 00:15:55: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 00:15:55: # Command line: callpeak -t SRX914955.bam -f BAM -g dm -n SRX914955.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX914955.10 # format = BAM # ChIP-seq file = ['SRX914955.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 @ Sun, 04 Jun 2017 00:15:55: #1 read tag files... INFO @ Sun, 04 Jun 2017 00:15:55: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 00:15:55: # Command line: callpeak -t SRX914955.bam -f BAM -g dm -n SRX914955.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX914955.20 # format = BAM # ChIP-seq file = ['SRX914955.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 @ Sun, 04 Jun 2017 00:15:55: #1 read tag files... INFO @ Sun, 04 Jun 2017 00:15:55: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 00:16:01: 1000000 INFO @ Sun, 04 Jun 2017 00:16:02: 1000000 INFO @ Sun, 04 Jun 2017 00:16:02: 1000000 INFO @ Sun, 04 Jun 2017 00:16:08: 2000000 INFO @ Sun, 04 Jun 2017 00:16:08: 2000000 INFO @ Sun, 04 Jun 2017 00:16:08: 2000000 INFO @ Sun, 04 Jun 2017 00:16:14: 3000000 INFO @ Sun, 04 Jun 2017 00:16:14: 3000000 INFO @ Sun, 04 Jun 2017 00:16:14: 3000000 INFO @ Sun, 04 Jun 2017 00:16:20: 4000000 INFO @ Sun, 04 Jun 2017 00:16:21: 4000000 INFO @ Sun, 04 Jun 2017 00:16:21: 4000000 INFO @ Sun, 04 Jun 2017 00:16:26: 5000000 INFO @ Sun, 04 Jun 2017 00:16:27: 5000000 INFO @ Sun, 04 Jun 2017 00:16:27: 5000000 INFO @ Sun, 04 Jun 2017 00:16:32: 6000000 INFO @ Sun, 04 Jun 2017 00:16:33: 6000000 INFO @ Sun, 04 Jun 2017 00:16:33: 6000000 INFO @ Sun, 04 Jun 2017 00:16:38: 7000000 INFO @ Sun, 04 Jun 2017 00:16:39: 7000000 INFO @ Sun, 04 Jun 2017 00:16:40: 7000000 INFO @ Sun, 04 Jun 2017 00:16:44: 8000000 INFO @ Sun, 04 Jun 2017 00:16:46: 8000000 INFO @ Sun, 04 Jun 2017 00:16:46: 8000000 INFO @ Sun, 04 Jun 2017 00:16:50: 9000000 INFO @ Sun, 04 Jun 2017 00:16:52: 9000000 INFO @ Sun, 04 Jun 2017 00:16:52: 9000000 INFO @ Sun, 04 Jun 2017 00:16:56: 10000000 INFO @ Sun, 04 Jun 2017 00:16:58: 10000000 INFO @ Sun, 04 Jun 2017 00:16:59: 10000000 INFO @ Sun, 04 Jun 2017 00:17:03: 11000000 INFO @ Sun, 04 Jun 2017 00:17:05: 11000000 INFO @ Sun, 04 Jun 2017 00:17:05: 11000000 INFO @ Sun, 04 Jun 2017 00:17:09: 12000000 INFO @ Sun, 04 Jun 2017 00:17:11: 12000000 INFO @ Sun, 04 Jun 2017 00:17:11: 12000000 INFO @ Sun, 04 Jun 2017 00:17:15: 13000000 INFO @ Sun, 04 Jun 2017 00:17:17: 13000000 INFO @ Sun, 04 Jun 2017 00:17:17: 13000000 INFO @ Sun, 04 Jun 2017 00:17:21: 14000000 INFO @ Sun, 04 Jun 2017 00:17:23: 14000000 INFO @ Sun, 04 Jun 2017 00:17:24: 14000000 INFO @ Sun, 04 Jun 2017 00:17:27: 15000000 INFO @ Sun, 04 Jun 2017 00:17:30: 15000000 INFO @ Sun, 04 Jun 2017 00:17:30: 15000000 INFO @ Sun, 04 Jun 2017 00:17:33: 16000000 INFO @ Sun, 04 Jun 2017 00:17:36: 16000000 INFO @ Sun, 04 Jun 2017 00:17:36: 16000000 INFO @ Sun, 04 Jun 2017 00:17:39: 17000000 INFO @ Sun, 04 Jun 2017 00:17:42: 17000000 INFO @ Sun, 04 Jun 2017 00:17:43: 17000000 INFO @ Sun, 04 Jun 2017 00:17:45: 18000000 INFO @ Sun, 04 Jun 2017 00:17:49: 18000000 INFO @ Sun, 04 Jun 2017 00:17:49: 18000000 INFO @ Sun, 04 Jun 2017 00:17:51: 19000000 INFO @ Sun, 04 Jun 2017 00:17:55: 19000000 INFO @ Sun, 04 Jun 2017 00:17:55: 19000000 INFO @ Sun, 04 Jun 2017 00:17:57: 20000000 INFO @ Sun, 04 Jun 2017 00:18:01: 20000000 INFO @ Sun, 04 Jun 2017 00:18:02: 20000000 INFO @ Sun, 04 Jun 2017 00:18:03: #1 tag size is determined as 40 bps INFO @ Sun, 04 Jun 2017 00:18:03: #1 tag size = 40 INFO @ Sun, 04 Jun 2017 00:18:03: #1 total tags in treatment: 20948388 INFO @ Sun, 04 Jun 2017 00:18:03: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 00:18:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 00:18:07: #1 tags after filtering in treatment: 20942199 INFO @ Sun, 04 Jun 2017 00:18:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 00:18:07: #1 finished! INFO @ Sun, 04 Jun 2017 00:18:07: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 00:18:07: #1 tag size is determined as 40 bps INFO @ Sun, 04 Jun 2017 00:18:07: #1 tag size = 40 INFO @ Sun, 04 Jun 2017 00:18:07: #1 total tags in treatment: 20948388 INFO @ Sun, 04 Jun 2017 00:18:07: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 00:18:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 00:18:08: #1 tag size is determined as 40 bps INFO @ Sun, 04 Jun 2017 00:18:08: #1 tag size = 40 INFO @ Sun, 04 Jun 2017 00:18:08: #1 total tags in treatment: 20948388 INFO @ Sun, 04 Jun 2017 00:18:08: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 00:18:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 00:18:10: #2 number of paired peaks: 239 WARNING @ Sun, 04 Jun 2017 00:18:10: Fewer paired peaks (239) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 239 pairs to build model! INFO @ Sun, 04 Jun 2017 00:18:10: start model_add_line... INFO @ Sun, 04 Jun 2017 00:18:11: #1 tags after filtering in treatment: 20942199 INFO @ Sun, 04 Jun 2017 00:18:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 00:18:11: #1 finished! INFO @ Sun, 04 Jun 2017 00:18:11: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 00:18:12: #1 tags after filtering in treatment: 20942199 INFO @ Sun, 04 Jun 2017 00:18:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 00:18:12: #1 finished! INFO @ Sun, 04 Jun 2017 00:18:12: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 00:18:15: #2 number of paired peaks: 239 WARNING @ Sun, 04 Jun 2017 00:18:15: Fewer paired peaks (239) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 239 pairs to build model! INFO @ Sun, 04 Jun 2017 00:18:15: start model_add_line... INFO @ Sun, 04 Jun 2017 00:18:15: #2 number of paired peaks: 239 WARNING @ Sun, 04 Jun 2017 00:18:15: Fewer paired peaks (239) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 239 pairs to build model! INFO @ Sun, 04 Jun 2017 00:18:15: start model_add_line... INFO @ Sun, 04 Jun 2017 00:18:16: start X-correlation... INFO @ Sun, 04 Jun 2017 00:18:16: end of X-cor INFO @ Sun, 04 Jun 2017 00:18:16: #2 finished! INFO @ Sun, 04 Jun 2017 00:18:16: #2 predicted fragment length is 142 bps INFO @ Sun, 04 Jun 2017 00:18:16: #2 alternative fragment length(s) may be 3,142 bps INFO @ Sun, 04 Jun 2017 00:18:16: #2.2 Generate R script for model : SRX914955.20_model.r INFO @ Sun, 04 Jun 2017 00:18:16: #3 Call peaks... INFO @ Sun, 04 Jun 2017 00:18:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 00:18:20: start X-correlation... INFO @ Sun, 04 Jun 2017 00:18:20: end of X-cor INFO @ Sun, 04 Jun 2017 00:18:20: #2 finished! INFO @ Sun, 04 Jun 2017 00:18:20: #2 predicted fragment length is 142 bps INFO @ Sun, 04 Jun 2017 00:18:20: #2 alternative fragment length(s) may be 3,142 bps INFO @ Sun, 04 Jun 2017 00:18:20: #2.2 Generate R script for model : SRX914955.10_model.r INFO @ Sun, 04 Jun 2017 00:18:20: #3 Call peaks... INFO @ Sun, 04 Jun 2017 00:18:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 00:18:20: start X-correlation... INFO @ Sun, 04 Jun 2017 00:18:20: end of X-cor INFO @ Sun, 04 Jun 2017 00:18:20: #2 finished! INFO @ Sun, 04 Jun 2017 00:18:20: #2 predicted fragment length is 142 bps INFO @ Sun, 04 Jun 2017 00:18:20: #2 alternative fragment length(s) may be 3,142 bps INFO @ Sun, 04 Jun 2017 00:18:20: #2.2 Generate R script for model : SRX914955.05_model.r INFO @ Sun, 04 Jun 2017 00:18:20: #3 Call peaks... INFO @ Sun, 04 Jun 2017 00:18:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 00:20:09: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 00:20:10: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 00:20:12: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 00:21:29: #4 Write output xls file... SRX914955.20_peaks.xls INFO @ Sun, 04 Jun 2017 00:21:29: #4 Write peak in narrowPeak format file... SRX914955.20_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 00:21:29: #4 Write summits bed file... SRX914955.20_summits.bed INFO @ Sun, 04 Jun 2017 00:21:29: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1494 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 00:21:35: #4 Write output xls file... SRX914955.10_peaks.xls INFO @ Sun, 04 Jun 2017 00:21:35: #4 Write peak in narrowPeak format file... SRX914955.10_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 00:21:35: #4 Write summits bed file... SRX914955.10_summits.bed INFO @ Sun, 04 Jun 2017 00:21:35: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5526 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 00:21:39: #4 Write output xls file... SRX914955.05_peaks.xls INFO @ Sun, 04 Jun 2017 00:21:40: #4 Write peak in narrowPeak format file... SRX914955.05_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 00:21:40: #4 Write summits bed file... SRX914955.05_summits.bed INFO @ Sun, 04 Jun 2017 00:21:40: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (9289 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。