Job ID = 9157942 sra ファイルのダウンロード中... Completed: 1267523K bytes transferred in 13 seconds (758004K bits/sec), in 1 file, 2 directories. 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 44828488 spots for /home/okishinya/chipatlas/results/dm3/SRX2033490/SRR4042505.sra Written 44828488 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: 00:11:29 44828488 reads; of these: 44828488 (100.00%) were unpaired; of these: 4108369 (9.16%) aligned 0 times 33489441 (74.71%) aligned exactly 1 time 7230678 (16.13%) aligned >1 times 90.84% overall alignment rate Time searching: 00:11:29 Overall time: 00:11:29 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 20 files... [bam_rmdupse_core] 30217760 / 40720119 = 0.7421 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 @ Tue, 27 Jun 2017 14:33:19: # Command line: callpeak -t SRX2033490.bam -f BAM -g dm -n SRX2033490.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2033490.20 # format = BAM # ChIP-seq file = ['SRX2033490.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 @ Tue, 27 Jun 2017 14:33:19: #1 read tag files... INFO @ Tue, 27 Jun 2017 14:33:19: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 14:33:19: # Command line: callpeak -t SRX2033490.bam -f BAM -g dm -n SRX2033490.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2033490.05 # format = BAM # ChIP-seq file = ['SRX2033490.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 @ Tue, 27 Jun 2017 14:33:19: #1 read tag files... INFO @ Tue, 27 Jun 2017 14:33:19: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 14:33:19: # Command line: callpeak -t SRX2033490.bam -f BAM -g dm -n SRX2033490.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2033490.10 # format = BAM # ChIP-seq file = ['SRX2033490.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 @ Tue, 27 Jun 2017 14:33:19: #1 read tag files... INFO @ Tue, 27 Jun 2017 14:33:19: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 14:33:29: 1000000 INFO @ Tue, 27 Jun 2017 14:33:29: 1000000 INFO @ Tue, 27 Jun 2017 14:33:29: 1000000 INFO @ Tue, 27 Jun 2017 14:33:39: 2000000 INFO @ Tue, 27 Jun 2017 14:33:39: 2000000 INFO @ Tue, 27 Jun 2017 14:33:39: 2000000 INFO @ Tue, 27 Jun 2017 14:33:46: 3000000 INFO @ Tue, 27 Jun 2017 14:33:48: 3000000 INFO @ Tue, 27 Jun 2017 14:33:48: 3000000 INFO @ Tue, 27 Jun 2017 14:33:55: 4000000 INFO @ Tue, 27 Jun 2017 14:33:56: 4000000 INFO @ Tue, 27 Jun 2017 14:33:56: 4000000 INFO @ Tue, 27 Jun 2017 14:34:04: 5000000 INFO @ Tue, 27 Jun 2017 14:34:04: 5000000 INFO @ Tue, 27 Jun 2017 14:34:05: 5000000 INFO @ Tue, 27 Jun 2017 14:34:12: 6000000 INFO @ Tue, 27 Jun 2017 14:34:12: 6000000 INFO @ Tue, 27 Jun 2017 14:34:14: 6000000 INFO @ Tue, 27 Jun 2017 14:34:19: 7000000 INFO @ Tue, 27 Jun 2017 14:34:19: 7000000 INFO @ Tue, 27 Jun 2017 14:34:24: 7000000 INFO @ Tue, 27 Jun 2017 14:34:27: 8000000 INFO @ Tue, 27 Jun 2017 14:34:27: 8000000 INFO @ Tue, 27 Jun 2017 14:34:33: 8000000 INFO @ Tue, 27 Jun 2017 14:34:35: 9000000 INFO @ Tue, 27 Jun 2017 14:34:35: 9000000 INFO @ Tue, 27 Jun 2017 14:34:43: 10000000 INFO @ Tue, 27 Jun 2017 14:34:43: 10000000 INFO @ Tue, 27 Jun 2017 14:34:43: 9000000 INFO @ Tue, 27 Jun 2017 14:34:47: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 14:34:47: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 14:34:47: #1 total tags in treatment: 10502359 INFO @ Tue, 27 Jun 2017 14:34:47: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 14:34:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 14:34:47: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 14:34:47: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 14:34:47: #1 total tags in treatment: 10502359 INFO @ Tue, 27 Jun 2017 14:34:47: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 14:34:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 14:34:47: #1 tags after filtering in treatment: 10502359 INFO @ Tue, 27 Jun 2017 14:34:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 14:34:47: #1 finished! INFO @ Tue, 27 Jun 2017 14:34:47: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 14:34:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 14:34:47: #1 tags after filtering in treatment: 10502359 INFO @ Tue, 27 Jun 2017 14:34:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 14:34:47: #1 finished! INFO @ Tue, 27 Jun 2017 14:34:47: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 14:34:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 14:34:48: #2 number of paired peaks: 4349 INFO @ Tue, 27 Jun 2017 14:34:48: start model_add_line... INFO @ Tue, 27 Jun 2017 14:34:48: #2 number of paired peaks: 4349 INFO @ Tue, 27 Jun 2017 14:34:48: start model_add_line... INFO @ Tue, 27 Jun 2017 14:34:48: start X-correlation... INFO @ Tue, 27 Jun 2017 14:34:48: end of X-cor INFO @ Tue, 27 Jun 2017 14:34:48: #2 finished! INFO @ Tue, 27 Jun 2017 14:34:48: #2 predicted fragment length is 145 bps INFO @ Tue, 27 Jun 2017 14:34:48: #2 alternative fragment length(s) may be 145 bps INFO @ Tue, 27 Jun 2017 14:34:48: #2.2 Generate R script for model : SRX2033490.05_model.r INFO @ Tue, 27 Jun 2017 14:34:48: #3 Call peaks... INFO @ Tue, 27 Jun 2017 14:34:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 14:34:49: start X-correlation... INFO @ Tue, 27 Jun 2017 14:34:49: end of X-cor INFO @ Tue, 27 Jun 2017 14:34:49: #2 finished! INFO @ Tue, 27 Jun 2017 14:34:49: #2 predicted fragment length is 145 bps INFO @ Tue, 27 Jun 2017 14:34:49: #2 alternative fragment length(s) may be 145 bps INFO @ Tue, 27 Jun 2017 14:34:49: #2.2 Generate R script for model : SRX2033490.20_model.r INFO @ Tue, 27 Jun 2017 14:34:49: #3 Call peaks... INFO @ Tue, 27 Jun 2017 14:34:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 14:34:53: 10000000 INFO @ Tue, 27 Jun 2017 14:34:58: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 14:34:58: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 14:34:58: #1 total tags in treatment: 10502359 INFO @ Tue, 27 Jun 2017 14:34:58: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 14:34:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 14:34:58: #1 tags after filtering in treatment: 10502359 INFO @ Tue, 27 Jun 2017 14:34:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 14:34:58: #1 finished! INFO @ Tue, 27 Jun 2017 14:34:58: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 14:34:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 14:35:00: #2 number of paired peaks: 4349 INFO @ Tue, 27 Jun 2017 14:35:00: start model_add_line... INFO @ Tue, 27 Jun 2017 14:35:00: start X-correlation... INFO @ Tue, 27 Jun 2017 14:35:00: end of X-cor INFO @ Tue, 27 Jun 2017 14:35:00: #2 finished! INFO @ Tue, 27 Jun 2017 14:35:00: #2 predicted fragment length is 145 bps INFO @ Tue, 27 Jun 2017 14:35:00: #2 alternative fragment length(s) may be 145 bps INFO @ Tue, 27 Jun 2017 14:35:00: #2.2 Generate R script for model : SRX2033490.10_model.r INFO @ Tue, 27 Jun 2017 14:35:00: #3 Call peaks... INFO @ Tue, 27 Jun 2017 14:35:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 14:35:19: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 14:35:19: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 14:35:30: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 14:35:34: #4 Write output xls file... SRX2033490.20_peaks.xls INFO @ Tue, 27 Jun 2017 14:35:34: #4 Write peak in narrowPeak format file... SRX2033490.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 14:35:34: #4 Write summits bed file... SRX2033490.20_summits.bed INFO @ Tue, 27 Jun 2017 14:35:34: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6306 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 14:35:37: #4 Write output xls file... SRX2033490.05_peaks.xls INFO @ Tue, 27 Jun 2017 14:35:37: #4 Write peak in narrowPeak format file... SRX2033490.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 14:35:37: #4 Write summits bed file... SRX2033490.05_summits.bed INFO @ Tue, 27 Jun 2017 14:35:37: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (13290 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 14:35:44: #4 Write output xls file... SRX2033490.10_peaks.xls INFO @ Tue, 27 Jun 2017 14:35:45: #4 Write peak in narrowPeak format file... SRX2033490.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 14:35:45: #4 Write summits bed file... SRX2033490.10_summits.bed INFO @ Tue, 27 Jun 2017 14:35:45: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9911 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。