Job ID = 9029774 sra ファイルのダウンロード中... Completed: 482362K bytes transferred in 8 seconds (460614K 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 12695 0 12695 0 0 1708 0 --:--:-- 0:00:07 --:--:-- 12733 100 38318 0 38318 0 0 4548 0 --:--:-- 0:00:08 --:--:-- 19226 100 53127 0 53127 0 0 6066 0 --:--:-- 0:00:08 --:--:-- 22860 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 21646028 spots for /home/okishinya/chipatlas/results/dm3/SRX2055956/SRR4069188.sra Written 21646028 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: 00:11:01 21646028 reads; of these: 21646028 (100.00%) were unpaired; of these: 859353 (3.97%) aligned 0 times 13430892 (62.05%) aligned exactly 1 time 7355783 (33.98%) aligned >1 times 96.03% overall alignment rate Time searching: 00:11:01 Overall time: 00:11:01 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] 2751808 / 20786675 = 0.1324 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 15:25:27: # Command line: callpeak -t SRX2055956.bam -f BAM -g dm -n SRX2055956.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2055956.20 # format = BAM # ChIP-seq file = ['SRX2055956.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 15:25:27: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:25:27: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:25:27: # Command line: callpeak -t SRX2055956.bam -f BAM -g dm -n SRX2055956.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2055956.05 # format = BAM # ChIP-seq file = ['SRX2055956.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 15:25:27: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:25:27: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:25:27: # Command line: callpeak -t SRX2055956.bam -f BAM -g dm -n SRX2055956.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2055956.10 # format = BAM # ChIP-seq file = ['SRX2055956.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 15:25:27: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:25:27: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:25:32: 1000000 INFO @ Sat, 03 Jun 2017 15:25:32: 1000000 INFO @ Sat, 03 Jun 2017 15:25:32: 1000000 INFO @ Sat, 03 Jun 2017 15:25:38: 2000000 INFO @ Sat, 03 Jun 2017 15:25:38: 2000000 INFO @ Sat, 03 Jun 2017 15:25:38: 2000000 INFO @ Sat, 03 Jun 2017 15:25:43: 3000000 INFO @ Sat, 03 Jun 2017 15:25:43: 3000000 INFO @ Sat, 03 Jun 2017 15:25:44: 3000000 INFO @ Sat, 03 Jun 2017 15:25:49: 4000000 INFO @ Sat, 03 Jun 2017 15:25:49: 4000000 INFO @ Sat, 03 Jun 2017 15:25:50: 4000000 INFO @ Sat, 03 Jun 2017 15:25:55: 5000000 INFO @ Sat, 03 Jun 2017 15:25:55: 5000000 INFO @ Sat, 03 Jun 2017 15:25:56: 5000000 INFO @ Sat, 03 Jun 2017 15:26:00: 6000000 INFO @ Sat, 03 Jun 2017 15:26:00: 6000000 INFO @ Sat, 03 Jun 2017 15:26:02: 6000000 INFO @ Sat, 03 Jun 2017 15:26:06: 7000000 INFO @ Sat, 03 Jun 2017 15:26:06: 7000000 INFO @ Sat, 03 Jun 2017 15:26:08: 7000000 INFO @ Sat, 03 Jun 2017 15:26:12: 8000000 INFO @ Sat, 03 Jun 2017 15:26:12: 8000000 INFO @ Sat, 03 Jun 2017 15:26:14: 8000000 INFO @ Sat, 03 Jun 2017 15:26:17: 9000000 INFO @ Sat, 03 Jun 2017 15:26:17: 9000000 INFO @ Sat, 03 Jun 2017 15:26:20: 9000000 INFO @ Sat, 03 Jun 2017 15:26:23: 10000000 INFO @ Sat, 03 Jun 2017 15:26:23: 10000000 INFO @ Sat, 03 Jun 2017 15:26:26: 10000000 INFO @ Sat, 03 Jun 2017 15:26:29: 11000000 INFO @ Sat, 03 Jun 2017 15:26:29: 11000000 INFO @ Sat, 03 Jun 2017 15:26:32: 11000000 INFO @ Sat, 03 Jun 2017 15:26:35: 12000000 INFO @ Sat, 03 Jun 2017 15:26:35: 12000000 INFO @ Sat, 03 Jun 2017 15:26:38: 12000000 INFO @ Sat, 03 Jun 2017 15:26:41: 13000000 INFO @ Sat, 03 Jun 2017 15:26:41: 13000000 INFO @ Sat, 03 Jun 2017 15:26:45: 13000000 INFO @ Sat, 03 Jun 2017 15:26:46: 14000000 INFO @ Sat, 03 Jun 2017 15:26:46: 14000000 INFO @ Sat, 03 Jun 2017 15:26:51: 14000000 INFO @ Sat, 03 Jun 2017 15:26:52: 15000000 INFO @ Sat, 03 Jun 2017 15:26:52: 15000000 INFO @ Sat, 03 Jun 2017 15:26:57: 15000000 INFO @ Sat, 03 Jun 2017 15:26:58: 16000000 INFO @ Sat, 03 Jun 2017 15:26:58: 16000000 INFO @ Sat, 03 Jun 2017 15:27:04: 16000000 INFO @ Sat, 03 Jun 2017 15:27:04: 17000000 INFO @ Sat, 03 Jun 2017 15:27:04: 17000000 INFO @ Sat, 03 Jun 2017 15:27:10: 18000000 INFO @ Sat, 03 Jun 2017 15:27:10: 18000000 INFO @ Sat, 03 Jun 2017 15:27:10: 17000000 INFO @ Sat, 03 Jun 2017 15:27:10: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 15:27:10: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 15:27:10: #1 total tags in treatment: 18034867 INFO @ Sat, 03 Jun 2017 15:27:10: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:27:10: #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 15:27:10: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 15:27:10: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 15:27:10: #1 total tags in treatment: 18034867 INFO @ Sat, 03 Jun 2017 15:27:10: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:27:10: #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 15:27:14: #1 tags after filtering in treatment: 18031931 INFO @ Sat, 03 Jun 2017 15:27:14: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:27:14: #1 finished! INFO @ Sat, 03 Jun 2017 15:27:14: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:27:14: #1 tags after filtering in treatment: 18031931 INFO @ Sat, 03 Jun 2017 15:27:14: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:27:14: #1 finished! INFO @ Sat, 03 Jun 2017 15:27:14: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:27:15: 18000000 INFO @ Sat, 03 Jun 2017 15:27:16: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 15:27:16: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 15:27:16: #1 total tags in treatment: 18034867 INFO @ Sat, 03 Jun 2017 15:27:16: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:27:16: #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 15:27:17: #2 number of paired peaks: 881 WARNING @ Sat, 03 Jun 2017 15:27:17: Fewer paired peaks (881) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 881 pairs to build model! INFO @ Sat, 03 Jun 2017 15:27:17: start model_add_line... INFO @ Sat, 03 Jun 2017 15:27:17: #2 number of paired peaks: 881 WARNING @ Sat, 03 Jun 2017 15:27:17: Fewer paired peaks (881) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 881 pairs to build model! INFO @ Sat, 03 Jun 2017 15:27:17: start model_add_line... INFO @ Sat, 03 Jun 2017 15:27:19: #1 tags after filtering in treatment: 18031931 INFO @ Sat, 03 Jun 2017 15:27:19: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:27:19: #1 finished! INFO @ Sat, 03 Jun 2017 15:27:19: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:27:22: #2 number of paired peaks: 881 WARNING @ Sat, 03 Jun 2017 15:27:22: Fewer paired peaks (881) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 881 pairs to build model! INFO @ Sat, 03 Jun 2017 15:27:22: start model_add_line... INFO @ Sat, 03 Jun 2017 15:27:27: start X-correlation... INFO @ Sat, 03 Jun 2017 15:27:27: end of X-cor INFO @ Sat, 03 Jun 2017 15:27:27: #2 finished! INFO @ Sat, 03 Jun 2017 15:27:27: #2 predicted fragment length is 52 bps INFO @ Sat, 03 Jun 2017 15:27:27: #2 alternative fragment length(s) may be 4,52 bps INFO @ Sat, 03 Jun 2017 15:27:27: #2.2 Generate R script for model : SRX2055956.05_model.r WARNING @ Sat, 03 Jun 2017 15:27:27: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 15:27:27: #2 You may need to consider one of the other alternative d(s): 4,52 WARNING @ Sat, 03 Jun 2017 15:27:27: #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 15:27:27: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:27:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:27:28: start X-correlation... INFO @ Sat, 03 Jun 2017 15:27:28: end of X-cor INFO @ Sat, 03 Jun 2017 15:27:28: #2 finished! INFO @ Sat, 03 Jun 2017 15:27:28: #2 predicted fragment length is 52 bps INFO @ Sat, 03 Jun 2017 15:27:28: #2 alternative fragment length(s) may be 4,52 bps INFO @ Sat, 03 Jun 2017 15:27:28: #2.2 Generate R script for model : SRX2055956.10_model.r WARNING @ Sat, 03 Jun 2017 15:27:28: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 15:27:28: #2 You may need to consider one of the other alternative d(s): 4,52 WARNING @ Sat, 03 Jun 2017 15:27:28: #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 15:27:28: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:27:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:27:32: start X-correlation... INFO @ Sat, 03 Jun 2017 15:27:32: end of X-cor INFO @ Sat, 03 Jun 2017 15:27:32: #2 finished! INFO @ Sat, 03 Jun 2017 15:27:32: #2 predicted fragment length is 52 bps INFO @ Sat, 03 Jun 2017 15:27:32: #2 alternative fragment length(s) may be 4,52 bps INFO @ Sat, 03 Jun 2017 15:27:32: #2.2 Generate R script for model : SRX2055956.20_model.r WARNING @ Sat, 03 Jun 2017 15:27:32: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 15:27:32: #2 You may need to consider one of the other alternative d(s): 4,52 WARNING @ Sat, 03 Jun 2017 15:27:32: #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 15:27:32: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:27:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:28:56: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:29:00: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:29:08: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:30:01: #4 Write output xls file... SRX2055956.10_peaks.xls INFO @ Sat, 03 Jun 2017 15:30:01: #4 Write peak in narrowPeak format file... SRX2055956.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:30:01: #4 Write summits bed file... SRX2055956.10_summits.bed INFO @ Sat, 03 Jun 2017 15:30:01: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2655 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 15:30:10: #4 Write output xls file... SRX2055956.05_peaks.xls INFO @ Sat, 03 Jun 2017 15:30:10: #4 Write peak in narrowPeak format file... SRX2055956.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:30:10: #4 Write summits bed file... SRX2055956.05_summits.bed INFO @ Sat, 03 Jun 2017 15:30:10: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3736 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 15:30:15: #4 Write output xls file... SRX2055956.20_peaks.xls INFO @ Sat, 03 Jun 2017 15:30:15: #4 Write peak in narrowPeak format file... SRX2055956.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:30:15: #4 Write summits bed file... SRX2055956.20_summits.bed INFO @ Sat, 03 Jun 2017 15:30:15: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1504 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。