Job ID = 9029245 sra ファイルのダウンロード中... Completed: 766426K bytes transferred in 11 seconds (544836K 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 0 772 0 --:--:-- 0:00:07 --:--:-- 8022 100 38318 0 38318 0 0 4754 0 --:--:-- 0:00:08 --:--:-- 22849 100 70818 0 70818 0 0 8275 0 --:--:-- 0:00:08 --:--:-- 32574 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 33320815 spots for /home/okishinya/chipatlas/results/dm3/SRX1433394/SRR2919810.sra Written 33320815 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: 00:14:02 33320815 reads; of these: 33320815 (100.00%) were unpaired; of these: 1347112 (4.04%) aligned 0 times 22932106 (68.82%) aligned exactly 1 time 9041597 (27.13%) aligned >1 times 95.96% overall alignment rate Time searching: 00:14:02 Overall time: 00:14:02 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] 5212115 / 31973703 = 0.1630 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 13:16:18: # Command line: callpeak -t SRX1433394.bam -f BAM -g dm -n SRX1433394.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1433394.20 # format = BAM # ChIP-seq file = ['SRX1433394.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 13:16:18: # Command line: callpeak -t SRX1433394.bam -f BAM -g dm -n SRX1433394.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1433394.05 # format = BAM # ChIP-seq file = ['SRX1433394.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 13:16:18: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:16:18: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:16:18: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:16:18: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:16:18: # Command line: callpeak -t SRX1433394.bam -f BAM -g dm -n SRX1433394.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1433394.10 # format = BAM # ChIP-seq file = ['SRX1433394.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 13:16:18: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:16:18: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:16:24: 1000000 INFO @ Sat, 03 Jun 2017 13:16:24: 1000000 INFO @ Sat, 03 Jun 2017 13:16:24: 1000000 INFO @ Sat, 03 Jun 2017 13:16:31: 2000000 INFO @ Sat, 03 Jun 2017 13:16:31: 2000000 INFO @ Sat, 03 Jun 2017 13:16:31: 2000000 INFO @ Sat, 03 Jun 2017 13:16:37: 3000000 INFO @ Sat, 03 Jun 2017 13:16:37: 3000000 INFO @ Sat, 03 Jun 2017 13:16:38: 3000000 INFO @ Sat, 03 Jun 2017 13:16:43: 4000000 INFO @ Sat, 03 Jun 2017 13:16:44: 4000000 INFO @ Sat, 03 Jun 2017 13:16:44: 4000000 INFO @ Sat, 03 Jun 2017 13:16:50: 5000000 INFO @ Sat, 03 Jun 2017 13:16:50: 5000000 INFO @ Sat, 03 Jun 2017 13:16:51: 5000000 INFO @ Sat, 03 Jun 2017 13:16:57: 6000000 INFO @ Sat, 03 Jun 2017 13:16:57: 6000000 INFO @ Sat, 03 Jun 2017 13:16:58: 6000000 INFO @ Sat, 03 Jun 2017 13:17:03: 7000000 INFO @ Sat, 03 Jun 2017 13:17:03: 7000000 INFO @ Sat, 03 Jun 2017 13:17:05: 7000000 INFO @ Sat, 03 Jun 2017 13:17:09: 8000000 INFO @ Sat, 03 Jun 2017 13:17:10: 8000000 INFO @ Sat, 03 Jun 2017 13:17:11: 8000000 INFO @ Sat, 03 Jun 2017 13:17:15: 9000000 INFO @ Sat, 03 Jun 2017 13:17:15: 9000000 INFO @ Sat, 03 Jun 2017 13:17:18: 9000000 INFO @ Sat, 03 Jun 2017 13:17:21: 10000000 INFO @ Sat, 03 Jun 2017 13:17:21: 10000000 INFO @ Sat, 03 Jun 2017 13:17:24: 10000000 INFO @ Sat, 03 Jun 2017 13:17:26: 11000000 INFO @ Sat, 03 Jun 2017 13:17:27: 11000000 INFO @ Sat, 03 Jun 2017 13:17:30: 11000000 INFO @ Sat, 03 Jun 2017 13:17:32: 12000000 INFO @ Sat, 03 Jun 2017 13:17:33: 12000000 INFO @ Sat, 03 Jun 2017 13:17:36: 12000000 INFO @ Sat, 03 Jun 2017 13:17:38: 13000000 INFO @ Sat, 03 Jun 2017 13:17:38: 13000000 INFO @ Sat, 03 Jun 2017 13:17:42: 13000000 INFO @ Sat, 03 Jun 2017 13:17:43: 14000000 INFO @ Sat, 03 Jun 2017 13:17:44: 14000000 INFO @ Sat, 03 Jun 2017 13:17:48: 14000000 INFO @ Sat, 03 Jun 2017 13:17:49: 15000000 INFO @ Sat, 03 Jun 2017 13:17:50: 15000000 INFO @ Sat, 03 Jun 2017 13:17:54: 15000000 INFO @ Sat, 03 Jun 2017 13:17:55: 16000000 INFO @ Sat, 03 Jun 2017 13:17:56: 16000000 INFO @ Sat, 03 Jun 2017 13:18:00: 17000000 INFO @ Sat, 03 Jun 2017 13:18:00: 16000000 INFO @ Sat, 03 Jun 2017 13:18:01: 17000000 INFO @ Sat, 03 Jun 2017 13:18:06: 18000000 INFO @ Sat, 03 Jun 2017 13:18:07: 17000000 INFO @ Sat, 03 Jun 2017 13:18:07: 18000000 INFO @ Sat, 03 Jun 2017 13:18:12: 19000000 INFO @ Sat, 03 Jun 2017 13:18:13: 18000000 INFO @ Sat, 03 Jun 2017 13:18:13: 19000000 INFO @ Sat, 03 Jun 2017 13:18:18: 20000000 INFO @ Sat, 03 Jun 2017 13:18:19: 19000000 INFO @ Sat, 03 Jun 2017 13:18:19: 20000000 INFO @ Sat, 03 Jun 2017 13:18:24: 21000000 INFO @ Sat, 03 Jun 2017 13:18:25: 21000000 INFO @ Sat, 03 Jun 2017 13:18:25: 20000000 INFO @ Sat, 03 Jun 2017 13:18:30: 22000000 INFO @ Sat, 03 Jun 2017 13:18:31: 22000000 INFO @ Sat, 03 Jun 2017 13:18:32: 21000000 INFO @ Sat, 03 Jun 2017 13:18:36: 23000000 INFO @ Sat, 03 Jun 2017 13:18:37: 23000000 INFO @ Sat, 03 Jun 2017 13:18:38: 22000000 INFO @ Sat, 03 Jun 2017 13:18:42: 24000000 INFO @ Sat, 03 Jun 2017 13:18:43: 24000000 INFO @ Sat, 03 Jun 2017 13:18:44: 23000000 INFO @ Sat, 03 Jun 2017 13:18:47: 25000000 INFO @ Sat, 03 Jun 2017 13:18:49: 25000000 INFO @ Sat, 03 Jun 2017 13:18:50: 24000000 INFO @ Sat, 03 Jun 2017 13:18:53: 26000000 INFO @ Sat, 03 Jun 2017 13:18:55: 26000000 INFO @ Sat, 03 Jun 2017 13:18:56: 25000000 INFO @ Sat, 03 Jun 2017 13:18:58: #1 tag size is determined as 49 bps INFO @ Sat, 03 Jun 2017 13:18:58: #1 tag size = 49 INFO @ Sat, 03 Jun 2017 13:18:58: #1 total tags in treatment: 26761588 INFO @ Sat, 03 Jun 2017 13:18:58: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:18:58: #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 13:19:00: #1 tag size is determined as 49 bps INFO @ Sat, 03 Jun 2017 13:19:00: #1 tag size = 49 INFO @ Sat, 03 Jun 2017 13:19:00: #1 total tags in treatment: 26761588 INFO @ Sat, 03 Jun 2017 13:19:00: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:19:00: #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 13:19:02: 26000000 INFO @ Sat, 03 Jun 2017 13:19:03: #1 tags after filtering in treatment: 26753411 INFO @ Sat, 03 Jun 2017 13:19:03: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:19:03: #1 finished! INFO @ Sat, 03 Jun 2017 13:19:03: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:19:04: #1 tags after filtering in treatment: 26753411 INFO @ Sat, 03 Jun 2017 13:19:04: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:19:04: #1 finished! INFO @ Sat, 03 Jun 2017 13:19:04: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:19:06: #1 tag size is determined as 49 bps INFO @ Sat, 03 Jun 2017 13:19:06: #1 tag size = 49 INFO @ Sat, 03 Jun 2017 13:19:06: #1 total tags in treatment: 26761588 INFO @ Sat, 03 Jun 2017 13:19:06: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:19:06: #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 13:19:07: #2 number of paired peaks: 217 WARNING @ Sat, 03 Jun 2017 13:19:07: Fewer paired peaks (217) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 217 pairs to build model! INFO @ Sat, 03 Jun 2017 13:19:07: start model_add_line... INFO @ Sat, 03 Jun 2017 13:19:09: #2 number of paired peaks: 217 WARNING @ Sat, 03 Jun 2017 13:19:09: Fewer paired peaks (217) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 217 pairs to build model! INFO @ Sat, 03 Jun 2017 13:19:09: start model_add_line... INFO @ Sat, 03 Jun 2017 13:19:12: start X-correlation... INFO @ Sat, 03 Jun 2017 13:19:12: end of X-cor INFO @ Sat, 03 Jun 2017 13:19:12: #2 finished! INFO @ Sat, 03 Jun 2017 13:19:12: #2 predicted fragment length is 32 bps INFO @ Sat, 03 Jun 2017 13:19:12: #2 alternative fragment length(s) may be 3,32,536 bps INFO @ Sat, 03 Jun 2017 13:19:12: #2.2 Generate R script for model : SRX1433394.05_model.r WARNING @ Sat, 03 Jun 2017 13:19:12: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:19:12: #2 You may need to consider one of the other alternative d(s): 3,32,536 WARNING @ Sat, 03 Jun 2017 13:19:12: #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 13:19:12: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:19:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:19:13: #1 tags after filtering in treatment: 26753411 INFO @ Sat, 03 Jun 2017 13:19:13: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:19:13: #1 finished! INFO @ Sat, 03 Jun 2017 13:19:13: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:19:14: start X-correlation... INFO @ Sat, 03 Jun 2017 13:19:14: end of X-cor INFO @ Sat, 03 Jun 2017 13:19:14: #2 finished! INFO @ Sat, 03 Jun 2017 13:19:14: #2 predicted fragment length is 32 bps INFO @ Sat, 03 Jun 2017 13:19:14: #2 alternative fragment length(s) may be 3,32,536 bps INFO @ Sat, 03 Jun 2017 13:19:14: #2.2 Generate R script for model : SRX1433394.20_model.r WARNING @ Sat, 03 Jun 2017 13:19:14: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:19:14: #2 You may need to consider one of the other alternative d(s): 3,32,536 WARNING @ Sat, 03 Jun 2017 13:19:14: #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 13:19:14: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:19:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:19:17: #2 number of paired peaks: 217 WARNING @ Sat, 03 Jun 2017 13:19:17: Fewer paired peaks (217) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 217 pairs to build model! INFO @ Sat, 03 Jun 2017 13:19:17: start model_add_line... INFO @ Sat, 03 Jun 2017 13:19:22: start X-correlation... INFO @ Sat, 03 Jun 2017 13:19:22: end of X-cor INFO @ Sat, 03 Jun 2017 13:19:22: #2 finished! INFO @ Sat, 03 Jun 2017 13:19:22: #2 predicted fragment length is 32 bps INFO @ Sat, 03 Jun 2017 13:19:22: #2 alternative fragment length(s) may be 3,32,536 bps INFO @ Sat, 03 Jun 2017 13:19:22: #2.2 Generate R script for model : SRX1433394.10_model.r WARNING @ Sat, 03 Jun 2017 13:19:22: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:19:22: #2 You may need to consider one of the other alternative d(s): 3,32,536 WARNING @ Sat, 03 Jun 2017 13:19:22: #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 13:19:22: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:19:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:21:17: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:21:19: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:21:24: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:22:46: #4 Write output xls file... SRX1433394.10_peaks.xls INFO @ Sat, 03 Jun 2017 13:22:46: #4 Write peak in narrowPeak format file... SRX1433394.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:22:46: #4 Write summits bed file... SRX1433394.10_summits.bed INFO @ Sat, 03 Jun 2017 13:22:46: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2235 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:22:53: #4 Write output xls file... SRX1433394.05_peaks.xls INFO @ Sat, 03 Jun 2017 13:22:53: #4 Write peak in narrowPeak format file... SRX1433394.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:22:53: #4 Write summits bed file... SRX1433394.05_summits.bed INFO @ Sat, 03 Jun 2017 13:22:53: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3490 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:22:58: #4 Write output xls file... SRX1433394.20_peaks.xls INFO @ Sat, 03 Jun 2017 13:22:58: #4 Write peak in narrowPeak format file... SRX1433394.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:22:58: #4 Write summits bed file... SRX1433394.20_summits.bed INFO @ Sat, 03 Jun 2017 13:22:58: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1072 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。