Job ID = 9029767 sra ファイルのダウンロード中... Completed: 1140433K bytes transferred in 14 seconds (662148K 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 20110 0 20110 0 0 2586 0 --:--:-- 0:00:07 --:--:-- 17056 100 31051 0 31051 0 0 3830 0 --:--:-- 0:00:08 --:--:-- 20549 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 23443408 spots for /home/okishinya/chipatlas/results/dm3/SRX2055950/SRR4069182.sra Written 23443408 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: 00:10:41 23443408 reads; of these: 23443408 (100.00%) were unpaired; of these: 1883181 (8.03%) aligned 0 times 14611290 (62.33%) aligned exactly 1 time 6948937 (29.64%) aligned >1 times 91.97% overall alignment rate Time searching: 00:10:41 Overall time: 00:10:41 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] 1846663 / 21560227 = 0.0857 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 15:23:40: # Command line: callpeak -t SRX2055950.bam -f BAM -g dm -n SRX2055950.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2055950.05 # format = BAM # ChIP-seq file = ['SRX2055950.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 15:23:40: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:23:40: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:23:40: # Command line: callpeak -t SRX2055950.bam -f BAM -g dm -n SRX2055950.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2055950.10 # format = BAM # ChIP-seq file = ['SRX2055950.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 15:23:40: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:23:40: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:23:40: # Command line: callpeak -t SRX2055950.bam -f BAM -g dm -n SRX2055950.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2055950.20 # format = BAM # ChIP-seq file = ['SRX2055950.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 15:23:40: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:23:40: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:23:46: 1000000 INFO @ Sat, 03 Jun 2017 15:23:47: 1000000 INFO @ Sat, 03 Jun 2017 15:23:47: 1000000 INFO @ Sat, 03 Jun 2017 15:23:52: 2000000 INFO @ Sat, 03 Jun 2017 15:23:53: 2000000 INFO @ Sat, 03 Jun 2017 15:23:53: 2000000 INFO @ Sat, 03 Jun 2017 15:23:58: 3000000 INFO @ Sat, 03 Jun 2017 15:24:00: 3000000 INFO @ Sat, 03 Jun 2017 15:24:00: 3000000 INFO @ Sat, 03 Jun 2017 15:24:04: 4000000 INFO @ Sat, 03 Jun 2017 15:24:07: 4000000 INFO @ Sat, 03 Jun 2017 15:24:07: 4000000 INFO @ Sat, 03 Jun 2017 15:24:10: 5000000 INFO @ Sat, 03 Jun 2017 15:24:14: 5000000 INFO @ Sat, 03 Jun 2017 15:24:14: 5000000 INFO @ Sat, 03 Jun 2017 15:24:16: 6000000 INFO @ Sat, 03 Jun 2017 15:24:20: 6000000 INFO @ Sat, 03 Jun 2017 15:24:20: 6000000 INFO @ Sat, 03 Jun 2017 15:24:22: 7000000 INFO @ Sat, 03 Jun 2017 15:24:27: 7000000 INFO @ Sat, 03 Jun 2017 15:24:27: 7000000 INFO @ Sat, 03 Jun 2017 15:24:28: 8000000 INFO @ Sat, 03 Jun 2017 15:24:34: 8000000 INFO @ Sat, 03 Jun 2017 15:24:34: 8000000 INFO @ Sat, 03 Jun 2017 15:24:35: 9000000 INFO @ Sat, 03 Jun 2017 15:24:41: 10000000 INFO @ Sat, 03 Jun 2017 15:24:41: 9000000 INFO @ Sat, 03 Jun 2017 15:24:41: 9000000 INFO @ Sat, 03 Jun 2017 15:24:47: 11000000 INFO @ Sat, 03 Jun 2017 15:24:48: 10000000 INFO @ Sat, 03 Jun 2017 15:24:48: 10000000 INFO @ Sat, 03 Jun 2017 15:24:53: 12000000 INFO @ Sat, 03 Jun 2017 15:24:55: 11000000 INFO @ Sat, 03 Jun 2017 15:24:55: 11000000 INFO @ Sat, 03 Jun 2017 15:24:59: 13000000 INFO @ Sat, 03 Jun 2017 15:25:01: 12000000 INFO @ Sat, 03 Jun 2017 15:25:02: 12000000 INFO @ Sat, 03 Jun 2017 15:25:05: 14000000 INFO @ Sat, 03 Jun 2017 15:25:08: 13000000 INFO @ Sat, 03 Jun 2017 15:25:08: 13000000 INFO @ Sat, 03 Jun 2017 15:25:11: 15000000 INFO @ Sat, 03 Jun 2017 15:25:15: 14000000 INFO @ Sat, 03 Jun 2017 15:25:15: 14000000 INFO @ Sat, 03 Jun 2017 15:25:17: 16000000 INFO @ Sat, 03 Jun 2017 15:25:22: 15000000 INFO @ Sat, 03 Jun 2017 15:25:22: 15000000 INFO @ Sat, 03 Jun 2017 15:25:23: 17000000 INFO @ Sat, 03 Jun 2017 15:25:29: 16000000 INFO @ Sat, 03 Jun 2017 15:25:29: 16000000 INFO @ Sat, 03 Jun 2017 15:25:29: 18000000 INFO @ Sat, 03 Jun 2017 15:25:35: 19000000 INFO @ Sat, 03 Jun 2017 15:25:36: 17000000 INFO @ Sat, 03 Jun 2017 15:25:36: 17000000 INFO @ Sat, 03 Jun 2017 15:25:40: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 15:25:40: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 15:25:40: #1 total tags in treatment: 19713564 INFO @ Sat, 03 Jun 2017 15:25:40: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:25:40: #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 15:25:44: 18000000 INFO @ Sat, 03 Jun 2017 15:25:44: 18000000 INFO @ Sat, 03 Jun 2017 15:25:44: #1 tags after filtering in treatment: 19710197 INFO @ Sat, 03 Jun 2017 15:25:44: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:25:44: #1 finished! INFO @ Sat, 03 Jun 2017 15:25:44: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:25:47: #2 number of paired peaks: 611 WARNING @ Sat, 03 Jun 2017 15:25:47: Fewer paired peaks (611) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 611 pairs to build model! INFO @ Sat, 03 Jun 2017 15:25:47: start model_add_line... INFO @ Sat, 03 Jun 2017 15:25:51: 19000000 INFO @ Sat, 03 Jun 2017 15:25:51: 19000000 INFO @ Sat, 03 Jun 2017 15:25:56: start X-correlation... INFO @ Sat, 03 Jun 2017 15:25:56: end of X-cor INFO @ Sat, 03 Jun 2017 15:25:56: #2 finished! INFO @ Sat, 03 Jun 2017 15:25:56: #2 predicted fragment length is 56 bps INFO @ Sat, 03 Jun 2017 15:25:56: #2 alternative fragment length(s) may be 3,53,56 bps INFO @ Sat, 03 Jun 2017 15:25:56: #2.2 Generate R script for model : SRX2055950.20_model.r WARNING @ Sat, 03 Jun 2017 15:25:56: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 15:25:56: #2 You may need to consider one of the other alternative d(s): 3,53,56 WARNING @ Sat, 03 Jun 2017 15:25:56: #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 15:25:56: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:25:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:25:56: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 15:25:56: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 15:25:56: #1 total tags in treatment: 19713564 INFO @ Sat, 03 Jun 2017 15:25:56: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:25:56: #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 15:25:56: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 15:25:56: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 15:25:56: #1 total tags in treatment: 19713564 INFO @ Sat, 03 Jun 2017 15:25:56: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:25:56: #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 15:26:00: #1 tags after filtering in treatment: 19710197 INFO @ Sat, 03 Jun 2017 15:26:00: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:26:00: #1 finished! INFO @ Sat, 03 Jun 2017 15:26:00: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:26:00: #1 tags after filtering in treatment: 19710197 INFO @ Sat, 03 Jun 2017 15:26:00: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:26:00: #1 finished! INFO @ Sat, 03 Jun 2017 15:26:00: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:26:03: #2 number of paired peaks: 611 WARNING @ Sat, 03 Jun 2017 15:26:03: Fewer paired peaks (611) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 611 pairs to build model! INFO @ Sat, 03 Jun 2017 15:26:03: start model_add_line... INFO @ Sat, 03 Jun 2017 15:26:04: #2 number of paired peaks: 611 WARNING @ Sat, 03 Jun 2017 15:26:04: Fewer paired peaks (611) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 611 pairs to build model! INFO @ Sat, 03 Jun 2017 15:26:04: start model_add_line... INFO @ Sat, 03 Jun 2017 15:26:11: start X-correlation... INFO @ Sat, 03 Jun 2017 15:26:11: end of X-cor INFO @ Sat, 03 Jun 2017 15:26:11: #2 finished! INFO @ Sat, 03 Jun 2017 15:26:11: #2 predicted fragment length is 56 bps INFO @ Sat, 03 Jun 2017 15:26:11: #2 alternative fragment length(s) may be 3,53,56 bps INFO @ Sat, 03 Jun 2017 15:26:11: #2.2 Generate R script for model : SRX2055950.10_model.r WARNING @ Sat, 03 Jun 2017 15:26:11: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 15:26:11: #2 You may need to consider one of the other alternative d(s): 3,53,56 WARNING @ Sat, 03 Jun 2017 15:26:11: #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 15:26:11: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:26:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:26:12: start X-correlation... INFO @ Sat, 03 Jun 2017 15:26:12: end of X-cor INFO @ Sat, 03 Jun 2017 15:26:12: #2 finished! INFO @ Sat, 03 Jun 2017 15:26:12: #2 predicted fragment length is 56 bps INFO @ Sat, 03 Jun 2017 15:26:12: #2 alternative fragment length(s) may be 3,53,56 bps INFO @ Sat, 03 Jun 2017 15:26:12: #2.2 Generate R script for model : SRX2055950.05_model.r WARNING @ Sat, 03 Jun 2017 15:26:12: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 15:26:12: #2 You may need to consider one of the other alternative d(s): 3,53,56 WARNING @ Sat, 03 Jun 2017 15:26:12: #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 15:26:12: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:26:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:27:33: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:27:54: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:27:58: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:28:47: #4 Write output xls file... SRX2055950.20_peaks.xls INFO @ Sat, 03 Jun 2017 15:28:47: #4 Write peak in narrowPeak format file... SRX2055950.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:28:47: #4 Write summits bed file... SRX2055950.20_summits.bed INFO @ Sat, 03 Jun 2017 15:28:47: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (1282 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 15:29:07: #4 Write output xls file... SRX2055950.10_peaks.xls INFO @ Sat, 03 Jun 2017 15:29:07: #4 Write peak in narrowPeak format file... SRX2055950.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:29:07: #4 Write summits bed file... SRX2055950.10_summits.bed INFO @ Sat, 03 Jun 2017 15:29:07: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2362 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 15:29:19: #4 Write output xls file... SRX2055950.05_peaks.xls INFO @ Sat, 03 Jun 2017 15:29:19: #4 Write peak in narrowPeak format file... SRX2055950.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:29:19: #4 Write summits bed file... SRX2055950.05_summits.bed INFO @ Sat, 03 Jun 2017 15:29:19: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3422 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。