Job ID = 9029248 sra ファイルのダウンロード中... Completed: 865632K bytes transferred in 12 seconds (545726K 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 14324 0 14324 0 0 1893 0 --:--:-- 0:00:07 --:--:-- 10379 100 38317 0 38317 0 0 4475 0 --:--:-- 0:00:08 --:--:-- 16119 100 91821 0 91821 0 0 9605 0 --:--:-- 0:00:09 --:--:-- 27214 100 100k 0 100k 0 0 10534 0 --:--:-- 0:00:09 --:--:-- 28941 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 37027407 spots for /home/okishinya/chipatlas/results/dm3/SRX1433397/SRR2919813.sra Written 37027407 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: 00:14:45 37027407 reads; of these: 37027407 (100.00%) were unpaired; of these: 2577935 (6.96%) aligned 0 times 25019297 (67.57%) aligned exactly 1 time 9430175 (25.47%) aligned >1 times 93.04% overall alignment rate Time searching: 00:14:45 Overall time: 00:14:45 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 16 files... [bam_rmdupse_core] 7089530 / 34449472 = 0.2058 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 13:17:39: # Command line: callpeak -t SRX1433397.bam -f BAM -g dm -n SRX1433397.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1433397.20 # format = BAM # ChIP-seq file = ['SRX1433397.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 13:17:39: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:17:39: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:17:39: # Command line: callpeak -t SRX1433397.bam -f BAM -g dm -n SRX1433397.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1433397.10 # format = BAM # ChIP-seq file = ['SRX1433397.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 13:17:39: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:17:39: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:17:39: # Command line: callpeak -t SRX1433397.bam -f BAM -g dm -n SRX1433397.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1433397.05 # format = BAM # ChIP-seq file = ['SRX1433397.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 13:17:39: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:17:39: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:17:45: 1000000 INFO @ Sat, 03 Jun 2017 13:17:45: 1000000 INFO @ Sat, 03 Jun 2017 13:17:45: 1000000 INFO @ Sat, 03 Jun 2017 13:17:52: 2000000 INFO @ Sat, 03 Jun 2017 13:17:52: 2000000 INFO @ Sat, 03 Jun 2017 13:17:52: 2000000 INFO @ Sat, 03 Jun 2017 13:17:58: 3000000 INFO @ Sat, 03 Jun 2017 13:17:58: 3000000 INFO @ Sat, 03 Jun 2017 13:17:58: 3000000 INFO @ Sat, 03 Jun 2017 13:18:05: 4000000 INFO @ Sat, 03 Jun 2017 13:18:05: 4000000 INFO @ Sat, 03 Jun 2017 13:18:05: 4000000 INFO @ Sat, 03 Jun 2017 13:18:11: 5000000 INFO @ Sat, 03 Jun 2017 13:18:11: 5000000 INFO @ Sat, 03 Jun 2017 13:18:11: 5000000 INFO @ Sat, 03 Jun 2017 13:18:18: 6000000 INFO @ Sat, 03 Jun 2017 13:18:18: 6000000 INFO @ Sat, 03 Jun 2017 13:18:18: 6000000 INFO @ Sat, 03 Jun 2017 13:18:24: 7000000 INFO @ Sat, 03 Jun 2017 13:18:24: 7000000 INFO @ Sat, 03 Jun 2017 13:18:24: 7000000 INFO @ Sat, 03 Jun 2017 13:18:31: 8000000 INFO @ Sat, 03 Jun 2017 13:18:31: 8000000 INFO @ Sat, 03 Jun 2017 13:18:31: 8000000 INFO @ Sat, 03 Jun 2017 13:18:37: 9000000 INFO @ Sat, 03 Jun 2017 13:18:37: 9000000 INFO @ Sat, 03 Jun 2017 13:18:37: 9000000 INFO @ Sat, 03 Jun 2017 13:18:44: 10000000 INFO @ Sat, 03 Jun 2017 13:18:44: 10000000 INFO @ Sat, 03 Jun 2017 13:18:44: 10000000 INFO @ Sat, 03 Jun 2017 13:18:50: 11000000 INFO @ Sat, 03 Jun 2017 13:18:50: 11000000 INFO @ Sat, 03 Jun 2017 13:18:50: 11000000 INFO @ Sat, 03 Jun 2017 13:18:57: 12000000 INFO @ Sat, 03 Jun 2017 13:18:57: 12000000 INFO @ Sat, 03 Jun 2017 13:18:57: 12000000 INFO @ Sat, 03 Jun 2017 13:19:04: 13000000 INFO @ Sat, 03 Jun 2017 13:19:04: 13000000 INFO @ Sat, 03 Jun 2017 13:19:04: 13000000 INFO @ Sat, 03 Jun 2017 13:19:10: 14000000 INFO @ Sat, 03 Jun 2017 13:19:10: 14000000 INFO @ Sat, 03 Jun 2017 13:19:10: 14000000 INFO @ Sat, 03 Jun 2017 13:19:17: 15000000 INFO @ Sat, 03 Jun 2017 13:19:17: 15000000 INFO @ Sat, 03 Jun 2017 13:19:17: 15000000 INFO @ Sat, 03 Jun 2017 13:19:23: 16000000 INFO @ Sat, 03 Jun 2017 13:19:23: 16000000 INFO @ Sat, 03 Jun 2017 13:19:23: 16000000 INFO @ Sat, 03 Jun 2017 13:19:29: 17000000 INFO @ Sat, 03 Jun 2017 13:19:29: 17000000 INFO @ Sat, 03 Jun 2017 13:19:29: 17000000 INFO @ Sat, 03 Jun 2017 13:19:34: 18000000 INFO @ Sat, 03 Jun 2017 13:19:35: 18000000 INFO @ Sat, 03 Jun 2017 13:19:35: 18000000 INFO @ Sat, 03 Jun 2017 13:19:40: 19000000 INFO @ Sat, 03 Jun 2017 13:19:41: 19000000 INFO @ Sat, 03 Jun 2017 13:19:41: 19000000 INFO @ Sat, 03 Jun 2017 13:19:46: 20000000 INFO @ Sat, 03 Jun 2017 13:19:47: 20000000 INFO @ Sat, 03 Jun 2017 13:19:47: 20000000 INFO @ Sat, 03 Jun 2017 13:19:52: 21000000 INFO @ Sat, 03 Jun 2017 13:19:53: 21000000 INFO @ Sat, 03 Jun 2017 13:19:53: 21000000 INFO @ Sat, 03 Jun 2017 13:19:57: 22000000 INFO @ Sat, 03 Jun 2017 13:19:59: 22000000 INFO @ Sat, 03 Jun 2017 13:19:59: 22000000 INFO @ Sat, 03 Jun 2017 13:20:03: 23000000 INFO @ Sat, 03 Jun 2017 13:20:05: 23000000 INFO @ Sat, 03 Jun 2017 13:20:05: 23000000 INFO @ Sat, 03 Jun 2017 13:20:08: 24000000 INFO @ Sat, 03 Jun 2017 13:20:12: 24000000 INFO @ Sat, 03 Jun 2017 13:20:12: 24000000 INFO @ Sat, 03 Jun 2017 13:20:14: 25000000 INFO @ Sat, 03 Jun 2017 13:20:18: 25000000 INFO @ Sat, 03 Jun 2017 13:20:18: 25000000 INFO @ Sat, 03 Jun 2017 13:20:20: 26000000 INFO @ Sat, 03 Jun 2017 13:20:23: 26000000 INFO @ Sat, 03 Jun 2017 13:20:23: 26000000 INFO @ Sat, 03 Jun 2017 13:20:25: 27000000 INFO @ Sat, 03 Jun 2017 13:20:28: #1 tag size is determined as 49 bps INFO @ Sat, 03 Jun 2017 13:20:28: #1 tag size = 49 INFO @ Sat, 03 Jun 2017 13:20:28: #1 total tags in treatment: 27359942 INFO @ Sat, 03 Jun 2017 13:20:28: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:20:28: #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 13:20:29: 27000000 INFO @ Sat, 03 Jun 2017 13:20:29: 27000000 INFO @ Sat, 03 Jun 2017 13:20:32: #1 tag size is determined as 49 bps INFO @ Sat, 03 Jun 2017 13:20:32: #1 tag size = 49 INFO @ Sat, 03 Jun 2017 13:20:32: #1 total tags in treatment: 27359942 INFO @ Sat, 03 Jun 2017 13:20:32: #1 tag size is determined as 49 bps INFO @ Sat, 03 Jun 2017 13:20:32: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:20:32: #1 tag size = 49 INFO @ Sat, 03 Jun 2017 13:20:32: #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 13:20:32: #1 total tags in treatment: 27359942 INFO @ Sat, 03 Jun 2017 13:20:32: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:20:32: #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 13:20:34: #1 tags after filtering in treatment: 27349383 INFO @ Sat, 03 Jun 2017 13:20:34: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:20:34: #1 finished! INFO @ Sat, 03 Jun 2017 13:20:34: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:20:37: #1 tags after filtering in treatment: 27349383 INFO @ Sat, 03 Jun 2017 13:20:37: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:20:37: #1 finished! INFO @ Sat, 03 Jun 2017 13:20:37: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:20:38: #1 tags after filtering in treatment: 27349383 INFO @ Sat, 03 Jun 2017 13:20:38: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:20:38: #1 finished! INFO @ Sat, 03 Jun 2017 13:20:38: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:20:39: #2 number of paired peaks: 220 WARNING @ Sat, 03 Jun 2017 13:20:39: Fewer paired peaks (220) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 220 pairs to build model! INFO @ Sat, 03 Jun 2017 13:20:39: start model_add_line... INFO @ Sat, 03 Jun 2017 13:20:42: #2 number of paired peaks: 220 WARNING @ Sat, 03 Jun 2017 13:20:42: Fewer paired peaks (220) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 220 pairs to build model! INFO @ Sat, 03 Jun 2017 13:20:42: start model_add_line... INFO @ Sat, 03 Jun 2017 13:20:43: #2 number of paired peaks: 220 WARNING @ Sat, 03 Jun 2017 13:20:43: Fewer paired peaks (220) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 220 pairs to build model! INFO @ Sat, 03 Jun 2017 13:20:43: start model_add_line... INFO @ Sat, 03 Jun 2017 13:20:44: start X-correlation... INFO @ Sat, 03 Jun 2017 13:20:44: end of X-cor INFO @ Sat, 03 Jun 2017 13:20:44: #2 finished! INFO @ Sat, 03 Jun 2017 13:20:44: #2 predicted fragment length is 59 bps INFO @ Sat, 03 Jun 2017 13:20:44: #2 alternative fragment length(s) may be 3,59,579,584 bps INFO @ Sat, 03 Jun 2017 13:20:44: #2.2 Generate R script for model : SRX1433397.20_model.r WARNING @ Sat, 03 Jun 2017 13:20:44: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:20:44: #2 You may need to consider one of the other alternative d(s): 3,59,579,584 WARNING @ Sat, 03 Jun 2017 13:20:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 13:20:44: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:20:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:20:47: start X-correlation... INFO @ Sat, 03 Jun 2017 13:20:47: end of X-cor INFO @ Sat, 03 Jun 2017 13:20:47: #2 finished! INFO @ Sat, 03 Jun 2017 13:20:47: #2 predicted fragment length is 59 bps INFO @ Sat, 03 Jun 2017 13:20:47: #2 alternative fragment length(s) may be 3,59,579,584 bps INFO @ Sat, 03 Jun 2017 13:20:47: #2.2 Generate R script for model : SRX1433397.10_model.r WARNING @ Sat, 03 Jun 2017 13:20:47: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:20:47: #2 You may need to consider one of the other alternative d(s): 3,59,579,584 WARNING @ Sat, 03 Jun 2017 13:20:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 13:20:47: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:20:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:20:48: start X-correlation... INFO @ Sat, 03 Jun 2017 13:20:48: end of X-cor INFO @ Sat, 03 Jun 2017 13:20:48: #2 finished! INFO @ Sat, 03 Jun 2017 13:20:48: #2 predicted fragment length is 59 bps INFO @ Sat, 03 Jun 2017 13:20:48: #2 alternative fragment length(s) may be 3,59,579,584 bps INFO @ Sat, 03 Jun 2017 13:20:48: #2.2 Generate R script for model : SRX1433397.05_model.r WARNING @ Sat, 03 Jun 2017 13:20:48: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:20:48: #2 You may need to consider one of the other alternative d(s): 3,59,579,584 WARNING @ Sat, 03 Jun 2017 13:20:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 13:20:48: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:20:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:22:49: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:22:54: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:22:54: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:24:21: #4 Write output xls file... SRX1433397.10_peaks.xls INFO @ Sat, 03 Jun 2017 13:24:21: #4 Write peak in narrowPeak format file... SRX1433397.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:24:21: #4 Write summits bed file... SRX1433397.10_summits.bed INFO @ Sat, 03 Jun 2017 13:24:21: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2957 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:24:25: #4 Write output xls file... SRX1433397.20_peaks.xls INFO @ Sat, 03 Jun 2017 13:24:25: #4 Write peak in narrowPeak format file... SRX1433397.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:24:25: #4 Write summits bed file... SRX1433397.20_summits.bed INFO @ Sat, 03 Jun 2017 13:24:25: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1653 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:24:35: #4 Write output xls file... SRX1433397.05_peaks.xls INFO @ Sat, 03 Jun 2017 13:24:35: #4 Write peak in narrowPeak format file... SRX1433397.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:24:35: #4 Write summits bed file... SRX1433397.05_summits.bed INFO @ Sat, 03 Jun 2017 13:24:35: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4612 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。