Job ID = 9033144 sra ファイルのダウンロード中... Completed: 455746K bytes transferred in 7 seconds (494485K 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 1030 0 --:--:-- 0:00:07 --:--:-- 8767 100 30317 0 30317 0 0 3667 0 --:--:-- 0:00:08 --:--:-- 17791 100 83733 0 83733 0 0 9204 0 --:--:-- 0:00:09 --:--:-- 33056 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 14056010 spots for /home/okishinya/chipatlas/results/dm3/SRX914959/SRR1873269.sra Written 14056010 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: 00:04:19 14056010 reads; of these: 14056010 (100.00%) were unpaired; of these: 3124000 (22.23%) aligned 0 times 9494818 (67.55%) aligned exactly 1 time 1437192 (10.22%) aligned >1 times 77.77% overall alignment rate Time searching: 00:04:19 Overall time: 00:04:19 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] 5800528 / 10932010 = 0.5306 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 00:11:18: # Command line: callpeak -t SRX914959.bam -f BAM -g dm -n SRX914959.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX914959.20 # format = BAM # ChIP-seq file = ['SRX914959.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 00:11:18: #1 read tag files... INFO @ Sun, 04 Jun 2017 00:11:18: # Command line: callpeak -t SRX914959.bam -f BAM -g dm -n SRX914959.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX914959.10 # format = BAM # ChIP-seq file = ['SRX914959.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 00:11:18: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 00:11:18: #1 read tag files... INFO @ Sun, 04 Jun 2017 00:11:18: # Command line: callpeak -t SRX914959.bam -f BAM -g dm -n SRX914959.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX914959.05 # format = BAM # ChIP-seq file = ['SRX914959.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 00:11:18: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 00:11:18: #1 read tag files... INFO @ Sun, 04 Jun 2017 00:11:18: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 00:11:23: 1000000 INFO @ Sun, 04 Jun 2017 00:11:23: 1000000 INFO @ Sun, 04 Jun 2017 00:11:23: 1000000 INFO @ Sun, 04 Jun 2017 00:11:29: 2000000 INFO @ Sun, 04 Jun 2017 00:11:29: 2000000 INFO @ Sun, 04 Jun 2017 00:11:29: 2000000 INFO @ Sun, 04 Jun 2017 00:11:34: 3000000 INFO @ Sun, 04 Jun 2017 00:11:35: 3000000 INFO @ Sun, 04 Jun 2017 00:11:35: 3000000 INFO @ Sun, 04 Jun 2017 00:11:39: 4000000 INFO @ Sun, 04 Jun 2017 00:11:40: 4000000 INFO @ Sun, 04 Jun 2017 00:11:40: 4000000 INFO @ Sun, 04 Jun 2017 00:11:45: 5000000 INFO @ Sun, 04 Jun 2017 00:11:46: #1 tag size is determined as 50 bps INFO @ Sun, 04 Jun 2017 00:11:46: #1 tag size = 50 INFO @ Sun, 04 Jun 2017 00:11:46: #1 total tags in treatment: 5131482 INFO @ Sun, 04 Jun 2017 00:11:46: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 00:11:46: #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 00:11:46: 5000000 INFO @ Sun, 04 Jun 2017 00:11:46: 5000000 INFO @ Sun, 04 Jun 2017 00:11:47: #1 tag size is determined as 50 bps INFO @ Sun, 04 Jun 2017 00:11:47: #1 tag size = 50 INFO @ Sun, 04 Jun 2017 00:11:47: #1 total tags in treatment: 5131482 INFO @ Sun, 04 Jun 2017 00:11:47: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 00:11:47: #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 00:11:47: #1 tags after filtering in treatment: 5130387 INFO @ Sun, 04 Jun 2017 00:11:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 00:11:47: #1 finished! INFO @ Sun, 04 Jun 2017 00:11:47: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 00:11:47: #1 tag size is determined as 50 bps INFO @ Sun, 04 Jun 2017 00:11:47: #1 tag size = 50 INFO @ Sun, 04 Jun 2017 00:11:47: #1 total tags in treatment: 5131482 INFO @ Sun, 04 Jun 2017 00:11:47: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 00:11:47: #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 00:11:48: #2 number of paired peaks: 412 WARNING @ Sun, 04 Jun 2017 00:11:48: Fewer paired peaks (412) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 412 pairs to build model! INFO @ Sun, 04 Jun 2017 00:11:48: start model_add_line... INFO @ Sun, 04 Jun 2017 00:11:48: #1 tags after filtering in treatment: 5130387 INFO @ Sun, 04 Jun 2017 00:11:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 00:11:48: #1 finished! INFO @ Sun, 04 Jun 2017 00:11:48: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 00:11:48: #1 tags after filtering in treatment: 5130387 INFO @ Sun, 04 Jun 2017 00:11:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 00:11:48: #1 finished! INFO @ Sun, 04 Jun 2017 00:11:48: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 00:11:49: #2 number of paired peaks: 412 WARNING @ Sun, 04 Jun 2017 00:11:49: Fewer paired peaks (412) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 412 pairs to build model! INFO @ Sun, 04 Jun 2017 00:11:49: start model_add_line... INFO @ Sun, 04 Jun 2017 00:11:49: #2 number of paired peaks: 412 WARNING @ Sun, 04 Jun 2017 00:11:49: Fewer paired peaks (412) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 412 pairs to build model! INFO @ Sun, 04 Jun 2017 00:11:49: start model_add_line... INFO @ Sun, 04 Jun 2017 00:11:50: start X-correlation... INFO @ Sun, 04 Jun 2017 00:11:50: end of X-cor INFO @ Sun, 04 Jun 2017 00:11:50: #2 finished! INFO @ Sun, 04 Jun 2017 00:11:50: #2 predicted fragment length is 191 bps INFO @ Sun, 04 Jun 2017 00:11:50: #2 alternative fragment length(s) may be 191 bps INFO @ Sun, 04 Jun 2017 00:11:50: #2.2 Generate R script for model : SRX914959.10_model.r INFO @ Sun, 04 Jun 2017 00:11:50: #3 Call peaks... INFO @ Sun, 04 Jun 2017 00:11:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 00:11:51: start X-correlation... INFO @ Sun, 04 Jun 2017 00:11:51: end of X-cor INFO @ Sun, 04 Jun 2017 00:11:51: #2 finished! INFO @ Sun, 04 Jun 2017 00:11:51: #2 predicted fragment length is 191 bps INFO @ Sun, 04 Jun 2017 00:11:51: #2 alternative fragment length(s) may be 191 bps INFO @ Sun, 04 Jun 2017 00:11:51: #2.2 Generate R script for model : SRX914959.20_model.r INFO @ Sun, 04 Jun 2017 00:11:51: #3 Call peaks... INFO @ Sun, 04 Jun 2017 00:11:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 00:11:51: start X-correlation... INFO @ Sun, 04 Jun 2017 00:11:51: end of X-cor INFO @ Sun, 04 Jun 2017 00:11:51: #2 finished! INFO @ Sun, 04 Jun 2017 00:11:51: #2 predicted fragment length is 191 bps INFO @ Sun, 04 Jun 2017 00:11:51: #2 alternative fragment length(s) may be 191 bps INFO @ Sun, 04 Jun 2017 00:11:51: #2.2 Generate R script for model : SRX914959.05_model.r INFO @ Sun, 04 Jun 2017 00:11:51: #3 Call peaks... INFO @ Sun, 04 Jun 2017 00:11:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 00:12:20: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 00:12:21: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 00:12:22: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 00:12:43: #4 Write output xls file... SRX914959.10_peaks.xls INFO @ Sun, 04 Jun 2017 00:12:43: #4 Write peak in narrowPeak format file... SRX914959.10_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 00:12:43: #4 Write summits bed file... SRX914959.10_summits.bed INFO @ Sun, 04 Jun 2017 00:12:43: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (585 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 00:12:44: #4 Write output xls file... SRX914959.05_peaks.xls INFO @ Sun, 04 Jun 2017 00:12:44: #4 Write peak in narrowPeak format file... SRX914959.05_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 00:12:44: #4 Write summits bed file... SRX914959.05_summits.bed INFO @ Sun, 04 Jun 2017 00:12:44: #4 Write output xls file... SRX914959.20_peaks.xls INFO @ Sun, 04 Jun 2017 00:12:44: #4 Write peak in narrowPeak format file... SRX914959.20_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 00:12:44: #4 Write summits bed file... SRX914959.20_summits.bed INFO @ Sun, 04 Jun 2017 00:12:44: Done! INFO @ Sun, 04 Jun 2017 00:12:44: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (85 records, 4 fields): 2 millis CompletedMACS2peakCalling pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2976 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。