Job ID = 9029528 sra ファイルのダウンロード中... Completed: 814071K bytes transferred in 9 seconds (721304K 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 --:--:-- 0:00:06 --:--:-- 0 100 24454 0 24454 0 0 3126 0 --:--:-- 0:00:07 --:--:-- 17862 100 73011 0 73011 0 0 8439 0 --:--:-- 0:00:08 --:--:-- 33217 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 23849105 spots for /home/okishinya/chipatlas/results/dm3/SRX1816637/SRR3620838.sra Written 23849105 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: 00:07:40 23849105 reads; of these: 23849105 (100.00%) were unpaired; of these: 3105623 (13.02%) aligned 0 times 17654934 (74.03%) aligned exactly 1 time 3088548 (12.95%) aligned >1 times 86.98% overall alignment rate Time searching: 00:07:40 Overall time: 00:07:40 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] 3577103 / 20743482 = 0.1724 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 14:16:29: # Command line: callpeak -t SRX1816637.bam -f BAM -g dm -n SRX1816637.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1816637.20 # format = BAM # ChIP-seq file = ['SRX1816637.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 14:16:29: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:16:29: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:16:29: # Command line: callpeak -t SRX1816637.bam -f BAM -g dm -n SRX1816637.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1816637.05 # format = BAM # ChIP-seq file = ['SRX1816637.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 14:16:29: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:16:29: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:16:29: # Command line: callpeak -t SRX1816637.bam -f BAM -g dm -n SRX1816637.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1816637.10 # format = BAM # ChIP-seq file = ['SRX1816637.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 14:16:29: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:16:29: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:16:34: 1000000 INFO @ Sat, 03 Jun 2017 14:16:34: 1000000 INFO @ Sat, 03 Jun 2017 14:16:34: 1000000 INFO @ Sat, 03 Jun 2017 14:16:40: 2000000 INFO @ Sat, 03 Jun 2017 14:16:40: 2000000 INFO @ Sat, 03 Jun 2017 14:16:40: 2000000 INFO @ Sat, 03 Jun 2017 14:16:45: 3000000 INFO @ Sat, 03 Jun 2017 14:16:45: 3000000 INFO @ Sat, 03 Jun 2017 14:16:46: 3000000 INFO @ Sat, 03 Jun 2017 14:16:51: 4000000 INFO @ Sat, 03 Jun 2017 14:16:51: 4000000 INFO @ Sat, 03 Jun 2017 14:16:51: 4000000 INFO @ Sat, 03 Jun 2017 14:16:57: 5000000 INFO @ Sat, 03 Jun 2017 14:16:57: 5000000 INFO @ Sat, 03 Jun 2017 14:16:57: 5000000 INFO @ Sat, 03 Jun 2017 14:17:02: 6000000 INFO @ Sat, 03 Jun 2017 14:17:03: 6000000 INFO @ Sat, 03 Jun 2017 14:17:03: 6000000 INFO @ Sat, 03 Jun 2017 14:17:08: 7000000 INFO @ Sat, 03 Jun 2017 14:17:08: 7000000 INFO @ Sat, 03 Jun 2017 14:17:09: 7000000 INFO @ Sat, 03 Jun 2017 14:17:14: 8000000 INFO @ Sat, 03 Jun 2017 14:17:14: 8000000 INFO @ Sat, 03 Jun 2017 14:17:14: 8000000 INFO @ Sat, 03 Jun 2017 14:17:20: 9000000 INFO @ Sat, 03 Jun 2017 14:17:20: 9000000 INFO @ Sat, 03 Jun 2017 14:17:20: 9000000 INFO @ Sat, 03 Jun 2017 14:17:25: 10000000 INFO @ Sat, 03 Jun 2017 14:17:25: 10000000 INFO @ Sat, 03 Jun 2017 14:17:26: 10000000 INFO @ Sat, 03 Jun 2017 14:17:31: 11000000 INFO @ Sat, 03 Jun 2017 14:17:31: 11000000 INFO @ Sat, 03 Jun 2017 14:17:32: 11000000 INFO @ Sat, 03 Jun 2017 14:17:37: 12000000 INFO @ Sat, 03 Jun 2017 14:17:37: 12000000 INFO @ Sat, 03 Jun 2017 14:17:38: 12000000 INFO @ Sat, 03 Jun 2017 14:17:44: 13000000 INFO @ Sat, 03 Jun 2017 14:17:44: 13000000 INFO @ Sat, 03 Jun 2017 14:17:46: 13000000 INFO @ Sat, 03 Jun 2017 14:17:50: 14000000 INFO @ Sat, 03 Jun 2017 14:17:50: 14000000 INFO @ Sat, 03 Jun 2017 14:17:54: 14000000 INFO @ Sat, 03 Jun 2017 14:17:57: 15000000 INFO @ Sat, 03 Jun 2017 14:17:57: 15000000 INFO @ Sat, 03 Jun 2017 14:18:02: 15000000 INFO @ Sat, 03 Jun 2017 14:18:03: 16000000 INFO @ Sat, 03 Jun 2017 14:18:03: 16000000 INFO @ Sat, 03 Jun 2017 14:18:10: 17000000 INFO @ Sat, 03 Jun 2017 14:18:10: 17000000 INFO @ Sat, 03 Jun 2017 14:18:10: 16000000 INFO @ Sat, 03 Jun 2017 14:18:11: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 14:18:11: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 14:18:11: #1 total tags in treatment: 17166379 INFO @ Sat, 03 Jun 2017 14:18:11: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:18:11: #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 14:18:11: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 14:18:11: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 14:18:11: #1 total tags in treatment: 17166379 INFO @ Sat, 03 Jun 2017 14:18:11: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:18:11: #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 14:18:14: #1 tags after filtering in treatment: 17147925 INFO @ Sat, 03 Jun 2017 14:18:14: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:18:14: #1 finished! INFO @ Sat, 03 Jun 2017 14:18:14: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:18:14: #1 tags after filtering in treatment: 17147925 INFO @ Sat, 03 Jun 2017 14:18:14: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:18:14: #1 finished! INFO @ Sat, 03 Jun 2017 14:18:14: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:18:16: 17000000 INFO @ Sat, 03 Jun 2017 14:18:17: #2 number of paired peaks: 162 WARNING @ Sat, 03 Jun 2017 14:18:17: Fewer paired peaks (162) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 162 pairs to build model! INFO @ Sat, 03 Jun 2017 14:18:17: start model_add_line... INFO @ Sat, 03 Jun 2017 14:18:17: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 14:18:17: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 14:18:17: #1 total tags in treatment: 17166379 INFO @ Sat, 03 Jun 2017 14:18:17: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:18:17: #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 14:18:18: #2 number of paired peaks: 162 WARNING @ Sat, 03 Jun 2017 14:18:18: Fewer paired peaks (162) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 162 pairs to build model! INFO @ Sat, 03 Jun 2017 14:18:18: start model_add_line... INFO @ Sat, 03 Jun 2017 14:18:20: start X-correlation... INFO @ Sat, 03 Jun 2017 14:18:20: end of X-cor INFO @ Sat, 03 Jun 2017 14:18:20: #2 finished! INFO @ Sat, 03 Jun 2017 14:18:20: #2 predicted fragment length is 133 bps INFO @ Sat, 03 Jun 2017 14:18:20: #2 alternative fragment length(s) may be 133 bps INFO @ Sat, 03 Jun 2017 14:18:20: #2.2 Generate R script for model : SRX1816637.05_model.r INFO @ Sat, 03 Jun 2017 14:18:20: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:18:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:18:20: #1 tags after filtering in treatment: 17147925 INFO @ Sat, 03 Jun 2017 14:18:20: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:18:20: #1 finished! INFO @ Sat, 03 Jun 2017 14:18:20: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:18:21: start X-correlation... INFO @ Sat, 03 Jun 2017 14:18:21: end of X-cor INFO @ Sat, 03 Jun 2017 14:18:21: #2 finished! INFO @ Sat, 03 Jun 2017 14:18:21: #2 predicted fragment length is 133 bps INFO @ Sat, 03 Jun 2017 14:18:21: #2 alternative fragment length(s) may be 133 bps INFO @ Sat, 03 Jun 2017 14:18:21: #2.2 Generate R script for model : SRX1816637.10_model.r INFO @ Sat, 03 Jun 2017 14:18:21: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:18:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:18:24: #2 number of paired peaks: 162 WARNING @ Sat, 03 Jun 2017 14:18:24: Fewer paired peaks (162) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 162 pairs to build model! INFO @ Sat, 03 Jun 2017 14:18:24: start model_add_line... INFO @ Sat, 03 Jun 2017 14:18:26: start X-correlation... INFO @ Sat, 03 Jun 2017 14:18:26: end of X-cor INFO @ Sat, 03 Jun 2017 14:18:26: #2 finished! INFO @ Sat, 03 Jun 2017 14:18:26: #2 predicted fragment length is 133 bps INFO @ Sat, 03 Jun 2017 14:18:26: #2 alternative fragment length(s) may be 133 bps INFO @ Sat, 03 Jun 2017 14:18:26: #2.2 Generate R script for model : SRX1816637.20_model.r INFO @ Sat, 03 Jun 2017 14:18:26: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:18:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:19:49: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:19:54: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:19:56: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:21:01: #4 Write output xls file... SRX1816637.10_peaks.xls INFO @ Sat, 03 Jun 2017 14:21:01: #4 Write peak in narrowPeak format file... SRX1816637.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:21:01: #4 Write summits bed file... SRX1816637.10_summits.bed INFO @ Sat, 03 Jun 2017 14:21:01: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (4852 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 14:21:04: #4 Write output xls file... SRX1816637.20_peaks.xls INFO @ Sat, 03 Jun 2017 14:21:04: #4 Write peak in narrowPeak format file... SRX1816637.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:21:04: #4 Write summits bed file... SRX1816637.20_summits.bed INFO @ Sat, 03 Jun 2017 14:21:04: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1422 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 14:21:17: #4 Write output xls file... SRX1816637.05_peaks.xls INFO @ Sat, 03 Jun 2017 14:21:17: #4 Write peak in narrowPeak format file... SRX1816637.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:21:17: #4 Write summits bed file... SRX1816637.05_summits.bed INFO @ Sat, 03 Jun 2017 14:21:17: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (11136 records, 4 fields): 15 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。