Job ID = 9029217 sra ファイルのダウンロード中... Completed: 798989K bytes transferred in 12 seconds (530139K 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 21558 0 21558 0 0 2818 0 --:--:-- 0:00:07 --:--:-- 16270 100 50518 0 50518 0 0 5843 0 --:--:-- 0:00:08 --:--:-- 21765 100 63413 0 63413 0 0 7196 0 --:--:-- 0:00:08 --:--:-- 25497 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 33152210 spots for /home/okishinya/chipatlas/results/dm3/SRX1433357/SRR2919822.sra Written 33152210 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: 00:12:53 33152210 reads; of these: 33152210 (100.00%) were unpaired; of these: 886312 (2.67%) aligned 0 times 25285234 (76.27%) aligned exactly 1 time 6980664 (21.06%) aligned >1 times 97.33% overall alignment rate Time searching: 00:12:53 Overall time: 00:12:53 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] 8191496 / 32265898 = 0.2539 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 13:14:16: # Command line: callpeak -t SRX1433357.bam -f BAM -g dm -n SRX1433357.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1433357.10 # format = BAM # ChIP-seq file = ['SRX1433357.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 13:14:16: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:14:16: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:14:16: # Command line: callpeak -t SRX1433357.bam -f BAM -g dm -n SRX1433357.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1433357.05 # format = BAM # ChIP-seq file = ['SRX1433357.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 13:14:16: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:14:16: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:14:16: # Command line: callpeak -t SRX1433357.bam -f BAM -g dm -n SRX1433357.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1433357.20 # format = BAM # ChIP-seq file = ['SRX1433357.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 13:14:16: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:14:16: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:14:22: 1000000 INFO @ Sat, 03 Jun 2017 13:14:22: 1000000 INFO @ Sat, 03 Jun 2017 13:14:22: 1000000 INFO @ Sat, 03 Jun 2017 13:14:28: 2000000 INFO @ Sat, 03 Jun 2017 13:14:29: 2000000 INFO @ Sat, 03 Jun 2017 13:14:29: 2000000 INFO @ Sat, 03 Jun 2017 13:14:34: 3000000 INFO @ Sat, 03 Jun 2017 13:14:36: 3000000 INFO @ Sat, 03 Jun 2017 13:14:36: 3000000 INFO @ Sat, 03 Jun 2017 13:14:40: 4000000 INFO @ Sat, 03 Jun 2017 13:14:42: 4000000 INFO @ Sat, 03 Jun 2017 13:14:42: 4000000 INFO @ Sat, 03 Jun 2017 13:14:46: 5000000 INFO @ Sat, 03 Jun 2017 13:14:49: 5000000 INFO @ Sat, 03 Jun 2017 13:14:49: 5000000 INFO @ Sat, 03 Jun 2017 13:14:51: 6000000 INFO @ Sat, 03 Jun 2017 13:14:56: 6000000 INFO @ Sat, 03 Jun 2017 13:14:56: 6000000 INFO @ Sat, 03 Jun 2017 13:14:57: 7000000 INFO @ Sat, 03 Jun 2017 13:15:02: 7000000 INFO @ Sat, 03 Jun 2017 13:15:02: 7000000 INFO @ Sat, 03 Jun 2017 13:15:04: 8000000 INFO @ Sat, 03 Jun 2017 13:15:09: 8000000 INFO @ Sat, 03 Jun 2017 13:15:09: 8000000 INFO @ Sat, 03 Jun 2017 13:15:10: 9000000 INFO @ Sat, 03 Jun 2017 13:15:16: 10000000 INFO @ Sat, 03 Jun 2017 13:15:16: 9000000 INFO @ Sat, 03 Jun 2017 13:15:16: 9000000 INFO @ Sat, 03 Jun 2017 13:15:22: 11000000 INFO @ Sat, 03 Jun 2017 13:15:23: 10000000 INFO @ Sat, 03 Jun 2017 13:15:23: 10000000 INFO @ Sat, 03 Jun 2017 13:15:28: 12000000 INFO @ Sat, 03 Jun 2017 13:15:29: 11000000 INFO @ Sat, 03 Jun 2017 13:15:29: 11000000 INFO @ Sat, 03 Jun 2017 13:15:34: 13000000 INFO @ Sat, 03 Jun 2017 13:15:36: 12000000 INFO @ Sat, 03 Jun 2017 13:15:36: 12000000 INFO @ Sat, 03 Jun 2017 13:15:40: 14000000 INFO @ Sat, 03 Jun 2017 13:15:43: 13000000 INFO @ Sat, 03 Jun 2017 13:15:43: 13000000 INFO @ Sat, 03 Jun 2017 13:15:46: 15000000 INFO @ Sat, 03 Jun 2017 13:15:50: 14000000 INFO @ Sat, 03 Jun 2017 13:15:50: 14000000 INFO @ Sat, 03 Jun 2017 13:15:52: 16000000 INFO @ Sat, 03 Jun 2017 13:15:56: 15000000 INFO @ Sat, 03 Jun 2017 13:15:56: 15000000 INFO @ Sat, 03 Jun 2017 13:15:58: 17000000 INFO @ Sat, 03 Jun 2017 13:16:03: 16000000 INFO @ Sat, 03 Jun 2017 13:16:03: 16000000 INFO @ Sat, 03 Jun 2017 13:16:04: 18000000 INFO @ Sat, 03 Jun 2017 13:16:10: 19000000 INFO @ Sat, 03 Jun 2017 13:16:10: 17000000 INFO @ Sat, 03 Jun 2017 13:16:10: 17000000 INFO @ Sat, 03 Jun 2017 13:16:16: 20000000 INFO @ Sat, 03 Jun 2017 13:16:17: 18000000 INFO @ Sat, 03 Jun 2017 13:16:17: 18000000 INFO @ Sat, 03 Jun 2017 13:16:22: 21000000 INFO @ Sat, 03 Jun 2017 13:16:23: 19000000 INFO @ Sat, 03 Jun 2017 13:16:23: 19000000 INFO @ Sat, 03 Jun 2017 13:16:28: 22000000 INFO @ Sat, 03 Jun 2017 13:16:30: 20000000 INFO @ Sat, 03 Jun 2017 13:16:30: 20000000 INFO @ Sat, 03 Jun 2017 13:16:34: 23000000 INFO @ Sat, 03 Jun 2017 13:16:37: 21000000 INFO @ Sat, 03 Jun 2017 13:16:37: 21000000 INFO @ Sat, 03 Jun 2017 13:16:40: 24000000 INFO @ Sat, 03 Jun 2017 13:16:41: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 13:16:41: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 13:16:41: #1 total tags in treatment: 24074402 INFO @ Sat, 03 Jun 2017 13:16:41: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:16:41: #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 13:16:44: 22000000 INFO @ Sat, 03 Jun 2017 13:16:44: 22000000 INFO @ Sat, 03 Jun 2017 13:16:45: #1 tags after filtering in treatment: 24067858 INFO @ Sat, 03 Jun 2017 13:16:45: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:16:45: #1 finished! INFO @ Sat, 03 Jun 2017 13:16:45: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:16:49: #2 number of paired peaks: 118 WARNING @ Sat, 03 Jun 2017 13:16:49: Fewer paired peaks (118) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 118 pairs to build model! INFO @ Sat, 03 Jun 2017 13:16:49: start model_add_line... INFO @ Sat, 03 Jun 2017 13:16:51: 23000000 INFO @ Sat, 03 Jun 2017 13:16:51: 23000000 INFO @ Sat, 03 Jun 2017 13:16:53: start X-correlation... INFO @ Sat, 03 Jun 2017 13:16:53: end of X-cor INFO @ Sat, 03 Jun 2017 13:16:53: #2 finished! INFO @ Sat, 03 Jun 2017 13:16:53: #2 predicted fragment length is 60 bps INFO @ Sat, 03 Jun 2017 13:16:53: #2 alternative fragment length(s) may be 2,60,119,133,147 bps INFO @ Sat, 03 Jun 2017 13:16:53: #2.2 Generate R script for model : SRX1433357.10_model.r WARNING @ Sat, 03 Jun 2017 13:16:53: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:16:53: #2 You may need to consider one of the other alternative d(s): 2,60,119,133,147 WARNING @ Sat, 03 Jun 2017 13:16:53: #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 13:16:53: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:16:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:16:58: 24000000 INFO @ Sat, 03 Jun 2017 13:16:58: 24000000 INFO @ Sat, 03 Jun 2017 13:16:59: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 13:16:59: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 13:16:59: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 13:16:59: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 13:16:59: #1 total tags in treatment: 24074402 INFO @ Sat, 03 Jun 2017 13:16:59: #1 total tags in treatment: 24074402 INFO @ Sat, 03 Jun 2017 13:16:59: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:16:59: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:16:59: #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 13:16:59: #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 13:17:03: #1 tags after filtering in treatment: 24067858 INFO @ Sat, 03 Jun 2017 13:17:03: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:17:03: #1 finished! INFO @ Sat, 03 Jun 2017 13:17:03: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:17:03: #1 tags after filtering in treatment: 24067858 INFO @ Sat, 03 Jun 2017 13:17:03: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:17:03: #1 finished! INFO @ Sat, 03 Jun 2017 13:17:03: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:17:07: #2 number of paired peaks: 118 WARNING @ Sat, 03 Jun 2017 13:17:07: Fewer paired peaks (118) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 118 pairs to build model! INFO @ Sat, 03 Jun 2017 13:17:07: start model_add_line... INFO @ Sat, 03 Jun 2017 13:17:07: #2 number of paired peaks: 118 WARNING @ Sat, 03 Jun 2017 13:17:07: Fewer paired peaks (118) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 118 pairs to build model! INFO @ Sat, 03 Jun 2017 13:17:07: start model_add_line... INFO @ Sat, 03 Jun 2017 13:17:10: start X-correlation... INFO @ Sat, 03 Jun 2017 13:17:10: end of X-cor INFO @ Sat, 03 Jun 2017 13:17:10: #2 finished! INFO @ Sat, 03 Jun 2017 13:17:10: #2 predicted fragment length is 60 bps INFO @ Sat, 03 Jun 2017 13:17:10: #2 alternative fragment length(s) may be 2,60,119,133,147 bps INFO @ Sat, 03 Jun 2017 13:17:10: #2.2 Generate R script for model : SRX1433357.05_model.r WARNING @ Sat, 03 Jun 2017 13:17:10: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:17:10: #2 You may need to consider one of the other alternative d(s): 2,60,119,133,147 WARNING @ Sat, 03 Jun 2017 13:17:10: #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 13:17:10: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:17:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:17:11: start X-correlation... INFO @ Sat, 03 Jun 2017 13:17:11: end of X-cor INFO @ Sat, 03 Jun 2017 13:17:11: #2 finished! INFO @ Sat, 03 Jun 2017 13:17:11: #2 predicted fragment length is 60 bps INFO @ Sat, 03 Jun 2017 13:17:11: #2 alternative fragment length(s) may be 2,60,119,133,147 bps INFO @ Sat, 03 Jun 2017 13:17:11: #2.2 Generate R script for model : SRX1433357.20_model.r WARNING @ Sat, 03 Jun 2017 13:17:11: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:17:11: #2 You may need to consider one of the other alternative d(s): 2,60,119,133,147 WARNING @ Sat, 03 Jun 2017 13:17:11: #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 13:17:11: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:17:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:18:43: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:19:08: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:19:12: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:20:05: #4 Write output xls file... SRX1433357.10_peaks.xls INFO @ Sat, 03 Jun 2017 13:20:05: #4 Write peak in narrowPeak format file... SRX1433357.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:20:05: #4 Write summits bed file... SRX1433357.10_summits.bed INFO @ Sat, 03 Jun 2017 13:20:05: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1358 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:20:30: #4 Write output xls file... SRX1433357.20_peaks.xls INFO @ Sat, 03 Jun 2017 13:20:30: #4 Write peak in narrowPeak format file... SRX1433357.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:20:30: #4 Write summits bed file... SRX1433357.20_summits.bed INFO @ Sat, 03 Jun 2017 13:20:30: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (742 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:20:41: #4 Write output xls file... SRX1433357.05_peaks.xls INFO @ Sat, 03 Jun 2017 13:20:41: #4 Write peak in narrowPeak format file... SRX1433357.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:20:41: #4 Write summits bed file... SRX1433357.05_summits.bed INFO @ Sat, 03 Jun 2017 13:20:41: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2171 records, 4 fields): 21 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。