Job ID = 10175240 sra ファイルのダウンロード中... Completed: 558214K bytes transferred in 27 seconds (164833K bits/sec), in 1 file. 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 31725441 spots for /home/okishinya/chipatlas/results/dm3/SRX2804218/SRR5534646.sra Written 31725441 spots total rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません 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: 00:10:06 31725441 reads; of these: 31725441 (100.00%) were unpaired; of these: 9146292 (28.83%) aligned 0 times 16389436 (51.66%) aligned exactly 1 time 6189713 (19.51%) aligned >1 times 71.17% overall alignment rate Time searching: 00:10:06 Overall time: 00:10:06 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] 5377955 / 22579149 = 0.2382 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 @ Mon, 06 Nov 2017 11:59:18: # Command line: callpeak -t SRX2804218.bam -f BAM -g dm -n SRX2804218.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2804218.05 # format = BAM # ChIP-seq file = ['SRX2804218.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 # Paired-End mode is off INFO @ Mon, 06 Nov 2017 11:59:18: #1 read tag files... INFO @ Mon, 06 Nov 2017 11:59:18: #1 read treatment tags... INFO @ Mon, 06 Nov 2017 11:59:18: # Command line: callpeak -t SRX2804218.bam -f BAM -g dm -n SRX2804218.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2804218.10 # format = BAM # ChIP-seq file = ['SRX2804218.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 # Paired-End mode is off INFO @ Mon, 06 Nov 2017 11:59:18: #1 read tag files... INFO @ Mon, 06 Nov 2017 11:59:18: #1 read treatment tags... INFO @ Mon, 06 Nov 2017 11:59:18: # Command line: callpeak -t SRX2804218.bam -f BAM -g dm -n SRX2804218.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2804218.20 # format = BAM # ChIP-seq file = ['SRX2804218.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 # Paired-End mode is off INFO @ Mon, 06 Nov 2017 11:59:18: #1 read tag files... INFO @ Mon, 06 Nov 2017 11:59:18: #1 read treatment tags... INFO @ Mon, 06 Nov 2017 11:59:24: 1000000 INFO @ Mon, 06 Nov 2017 11:59:24: 1000000 INFO @ Mon, 06 Nov 2017 11:59:24: 1000000 INFO @ Mon, 06 Nov 2017 11:59:30: 2000000 INFO @ Mon, 06 Nov 2017 11:59:30: 2000000 INFO @ Mon, 06 Nov 2017 11:59:30: 2000000 INFO @ Mon, 06 Nov 2017 11:59:36: 3000000 INFO @ Mon, 06 Nov 2017 11:59:36: 3000000 INFO @ Mon, 06 Nov 2017 11:59:37: 3000000 INFO @ Mon, 06 Nov 2017 11:59:42: 4000000 INFO @ Mon, 06 Nov 2017 11:59:42: 4000000 INFO @ Mon, 06 Nov 2017 11:59:43: 4000000 INFO @ Mon, 06 Nov 2017 11:59:48: 5000000 INFO @ Mon, 06 Nov 2017 11:59:48: 5000000 INFO @ Mon, 06 Nov 2017 11:59:49: 5000000 INFO @ Mon, 06 Nov 2017 11:59:54: 6000000 INFO @ Mon, 06 Nov 2017 11:59:54: 6000000 INFO @ Mon, 06 Nov 2017 11:59:55: 6000000 INFO @ Mon, 06 Nov 2017 12:00:00: 7000000 INFO @ Mon, 06 Nov 2017 12:00:00: 7000000 INFO @ Mon, 06 Nov 2017 12:00:02: 7000000 INFO @ Mon, 06 Nov 2017 12:00:06: 8000000 INFO @ Mon, 06 Nov 2017 12:00:06: 8000000 INFO @ Mon, 06 Nov 2017 12:00:08: 8000000 INFO @ Mon, 06 Nov 2017 12:00:12: 9000000 INFO @ Mon, 06 Nov 2017 12:00:12: 9000000 INFO @ Mon, 06 Nov 2017 12:00:14: 9000000 INFO @ Mon, 06 Nov 2017 12:00:18: 10000000 INFO @ Mon, 06 Nov 2017 12:00:18: 10000000 INFO @ Mon, 06 Nov 2017 12:00:21: 10000000 INFO @ Mon, 06 Nov 2017 12:00:24: 11000000 INFO @ Mon, 06 Nov 2017 12:00:24: 11000000 INFO @ Mon, 06 Nov 2017 12:00:27: 11000000 INFO @ Mon, 06 Nov 2017 12:00:29: 12000000 INFO @ Mon, 06 Nov 2017 12:00:30: 12000000 INFO @ Mon, 06 Nov 2017 12:00:33: 12000000 INFO @ Mon, 06 Nov 2017 12:00:35: 13000000 INFO @ Mon, 06 Nov 2017 12:00:36: 13000000 INFO @ Mon, 06 Nov 2017 12:00:40: 13000000 INFO @ Mon, 06 Nov 2017 12:00:41: 14000000 INFO @ Mon, 06 Nov 2017 12:00:42: 14000000 INFO @ Mon, 06 Nov 2017 12:00:46: 14000000 INFO @ Mon, 06 Nov 2017 12:00:47: 15000000 INFO @ Mon, 06 Nov 2017 12:00:48: 15000000 INFO @ Mon, 06 Nov 2017 12:00:52: 15000000 INFO @ Mon, 06 Nov 2017 12:00:53: 16000000 INFO @ Mon, 06 Nov 2017 12:00:54: 16000000 INFO @ Mon, 06 Nov 2017 12:00:59: 16000000 INFO @ Mon, 06 Nov 2017 12:00:59: 17000000 INFO @ Mon, 06 Nov 2017 12:01:00: #1 tag size is determined as 51 bps INFO @ Mon, 06 Nov 2017 12:01:00: #1 tag size = 51 INFO @ Mon, 06 Nov 2017 12:01:00: #1 total tags in treatment: 17201194 INFO @ Mon, 06 Nov 2017 12:01:00: #1 user defined the maximum tags... INFO @ Mon, 06 Nov 2017 12:01:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Nov 2017 12:01:00: #1 tags after filtering in treatment: 17201194 INFO @ Mon, 06 Nov 2017 12:01:00: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Nov 2017 12:01:00: #1 finished! INFO @ Mon, 06 Nov 2017 12:01:00: #2 Build Peak Model... INFO @ Mon, 06 Nov 2017 12:01:00: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Nov 2017 12:01:01: 17000000 INFO @ Mon, 06 Nov 2017 12:01:02: #2 number of paired peaks: 564 WARNING @ Mon, 06 Nov 2017 12:01:02: Fewer paired peaks (564) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 564 pairs to build model! INFO @ Mon, 06 Nov 2017 12:01:02: start model_add_line... INFO @ Mon, 06 Nov 2017 12:01:02: #1 tag size is determined as 51 bps INFO @ Mon, 06 Nov 2017 12:01:02: #1 tag size = 51 INFO @ Mon, 06 Nov 2017 12:01:02: #1 total tags in treatment: 17201194 INFO @ Mon, 06 Nov 2017 12:01:02: #1 user defined the maximum tags... INFO @ Mon, 06 Nov 2017 12:01:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Nov 2017 12:01:02: start X-correlation... INFO @ Mon, 06 Nov 2017 12:01:02: end of X-cor INFO @ Mon, 06 Nov 2017 12:01:02: #2 finished! INFO @ Mon, 06 Nov 2017 12:01:02: #2 predicted fragment length is 125 bps INFO @ Mon, 06 Nov 2017 12:01:02: #2 alternative fragment length(s) may be 125 bps INFO @ Mon, 06 Nov 2017 12:01:02: #2.2 Generate R script for model : SRX2804218.20_model.r INFO @ Mon, 06 Nov 2017 12:01:02: #3 Call peaks... INFO @ Mon, 06 Nov 2017 12:01:02: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Nov 2017 12:01:02: #1 tags after filtering in treatment: 17201194 INFO @ Mon, 06 Nov 2017 12:01:02: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Nov 2017 12:01:02: #1 finished! INFO @ Mon, 06 Nov 2017 12:01:02: #2 Build Peak Model... INFO @ Mon, 06 Nov 2017 12:01:02: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Nov 2017 12:01:03: #2 number of paired peaks: 564 WARNING @ Mon, 06 Nov 2017 12:01:03: Fewer paired peaks (564) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 564 pairs to build model! INFO @ Mon, 06 Nov 2017 12:01:03: start model_add_line... INFO @ Mon, 06 Nov 2017 12:01:04: start X-correlation... INFO @ Mon, 06 Nov 2017 12:01:04: end of X-cor INFO @ Mon, 06 Nov 2017 12:01:04: #2 finished! INFO @ Mon, 06 Nov 2017 12:01:04: #2 predicted fragment length is 125 bps INFO @ Mon, 06 Nov 2017 12:01:04: #2 alternative fragment length(s) may be 125 bps INFO @ Mon, 06 Nov 2017 12:01:04: #2.2 Generate R script for model : SRX2804218.05_model.r INFO @ Mon, 06 Nov 2017 12:01:04: #3 Call peaks... INFO @ Mon, 06 Nov 2017 12:01:04: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Nov 2017 12:01:05: 17000000 INFO @ Mon, 06 Nov 2017 12:01:06: #1 tag size is determined as 51 bps INFO @ Mon, 06 Nov 2017 12:01:06: #1 tag size = 51 INFO @ Mon, 06 Nov 2017 12:01:06: #1 total tags in treatment: 17201194 INFO @ Mon, 06 Nov 2017 12:01:06: #1 user defined the maximum tags... INFO @ Mon, 06 Nov 2017 12:01:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Nov 2017 12:01:06: #1 tags after filtering in treatment: 17201194 INFO @ Mon, 06 Nov 2017 12:01:06: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Nov 2017 12:01:06: #1 finished! INFO @ Mon, 06 Nov 2017 12:01:06: #2 Build Peak Model... INFO @ Mon, 06 Nov 2017 12:01:06: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Nov 2017 12:01:08: #2 number of paired peaks: 564 WARNING @ Mon, 06 Nov 2017 12:01:08: Fewer paired peaks (564) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 564 pairs to build model! INFO @ Mon, 06 Nov 2017 12:01:08: start model_add_line... INFO @ Mon, 06 Nov 2017 12:01:08: start X-correlation... INFO @ Mon, 06 Nov 2017 12:01:08: end of X-cor INFO @ Mon, 06 Nov 2017 12:01:08: #2 finished! INFO @ Mon, 06 Nov 2017 12:01:08: #2 predicted fragment length is 125 bps INFO @ Mon, 06 Nov 2017 12:01:08: #2 alternative fragment length(s) may be 125 bps INFO @ Mon, 06 Nov 2017 12:01:08: #2.2 Generate R script for model : SRX2804218.10_model.r INFO @ Mon, 06 Nov 2017 12:01:08: #3 Call peaks... INFO @ Mon, 06 Nov 2017 12:01:08: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Nov 2017 12:01:39: #3 Call peaks for each chromosome... INFO @ Mon, 06 Nov 2017 12:01:45: #3 Call peaks for each chromosome... INFO @ Mon, 06 Nov 2017 12:01:49: #3 Call peaks for each chromosome... INFO @ Mon, 06 Nov 2017 12:02:02: #4 Write output xls file... SRX2804218.20_peaks.xls INFO @ Mon, 06 Nov 2017 12:02:02: #4 Write peak in narrowPeak format file... SRX2804218.20_peaks.narrowPeak INFO @ Mon, 06 Nov 2017 12:02:02: #4 Write summits bed file... SRX2804218.20_summits.bed INFO @ Mon, 06 Nov 2017 12:02:02: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3024 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 06 Nov 2017 12:02:10: #4 Write output xls file... SRX2804218.05_peaks.xls INFO @ Mon, 06 Nov 2017 12:02:10: #4 Write peak in narrowPeak format file... SRX2804218.05_peaks.narrowPeak INFO @ Mon, 06 Nov 2017 12:02:10: #4 Write summits bed file... SRX2804218.05_summits.bed INFO @ Mon, 06 Nov 2017 12:02:10: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8652 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Mon, 06 Nov 2017 12:02:12: #4 Write output xls file... SRX2804218.10_peaks.xls INFO @ Mon, 06 Nov 2017 12:02:12: #4 Write peak in narrowPeak format file... SRX2804218.10_peaks.narrowPeak INFO @ Mon, 06 Nov 2017 12:02:12: #4 Write summits bed file... SRX2804218.10_summits.bed INFO @ Mon, 06 Nov 2017 12:02:12: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5386 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。