Job ID = 10714567 sra ファイルのダウンロード中... Completed: 288691K bytes transferred in 18 seconds (125443K 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... Read 15237629 spots for /home/okishinya/chipatlas/results/dm3/SRX4053301/SRR7132412.sra Written 15237629 spots for /home/okishinya/chipatlas/results/dm3/SRX4053301/SRR7132412.sra 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: 00:05:27 15237629 reads; of these: 15237629 (100.00%) were unpaired; of these: 1841275 (12.08%) aligned 0 times 10612192 (69.64%) aligned exactly 1 time 2784162 (18.27%) aligned >1 times 87.92% overall alignment rate Time searching: 00:05:27 Overall time: 00:05:27 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 8 files... [bam_rmdupse_core] 4113276 / 13396354 = 0.3070 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 @ Sun, 03 Jun 2018 13:38:06: # Command line: callpeak -t SRX4053301.bam -f BAM -g dm -n SRX4053301.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4053301.20 # format = BAM # ChIP-seq file = ['SRX4053301.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 @ Sun, 03 Jun 2018 13:38:06: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:38:06: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:38:06: # Command line: callpeak -t SRX4053301.bam -f BAM -g dm -n SRX4053301.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4053301.10 # format = BAM # ChIP-seq file = ['SRX4053301.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 @ Sun, 03 Jun 2018 13:38:06: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:38:06: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:38:06: # Command line: callpeak -t SRX4053301.bam -f BAM -g dm -n SRX4053301.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4053301.05 # format = BAM # ChIP-seq file = ['SRX4053301.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 @ Sun, 03 Jun 2018 13:38:06: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:38:06: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:38:14: 1000000 INFO @ Sun, 03 Jun 2018 13:38:14: 1000000 INFO @ Sun, 03 Jun 2018 13:38:14: 1000000 INFO @ Sun, 03 Jun 2018 13:38:22: 2000000 INFO @ Sun, 03 Jun 2018 13:38:23: 2000000 INFO @ Sun, 03 Jun 2018 13:38:23: 2000000 INFO @ Sun, 03 Jun 2018 13:38:30: 3000000 INFO @ Sun, 03 Jun 2018 13:38:31: 3000000 INFO @ Sun, 03 Jun 2018 13:38:31: 3000000 INFO @ Sun, 03 Jun 2018 13:38:38: 4000000 INFO @ Sun, 03 Jun 2018 13:38:40: 4000000 INFO @ Sun, 03 Jun 2018 13:38:40: 4000000 INFO @ Sun, 03 Jun 2018 13:38:46: 5000000 INFO @ Sun, 03 Jun 2018 13:38:48: 5000000 INFO @ Sun, 03 Jun 2018 13:38:48: 5000000 INFO @ Sun, 03 Jun 2018 13:38:54: 6000000 INFO @ Sun, 03 Jun 2018 13:38:57: 6000000 INFO @ Sun, 03 Jun 2018 13:38:57: 6000000 INFO @ Sun, 03 Jun 2018 13:39:01: 7000000 INFO @ Sun, 03 Jun 2018 13:39:05: 7000000 INFO @ Sun, 03 Jun 2018 13:39:05: 7000000 INFO @ Sun, 03 Jun 2018 13:39:09: 8000000 INFO @ Sun, 03 Jun 2018 13:39:14: 8000000 INFO @ Sun, 03 Jun 2018 13:39:14: 8000000 INFO @ Sun, 03 Jun 2018 13:39:17: 9000000 INFO @ Sun, 03 Jun 2018 13:39:19: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 13:39:19: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 13:39:19: #1 total tags in treatment: 9283078 INFO @ Sun, 03 Jun 2018 13:39:19: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:39:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 13:39:19: #1 tags after filtering in treatment: 9283078 INFO @ Sun, 03 Jun 2018 13:39:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 13:39:19: #1 finished! INFO @ Sun, 03 Jun 2018 13:39:19: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:39:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:39:20: #2 number of paired peaks: 5906 INFO @ Sun, 03 Jun 2018 13:39:20: start model_add_line... INFO @ Sun, 03 Jun 2018 13:39:20: start X-correlation... INFO @ Sun, 03 Jun 2018 13:39:20: end of X-cor INFO @ Sun, 03 Jun 2018 13:39:20: #2 finished! INFO @ Sun, 03 Jun 2018 13:39:20: #2 predicted fragment length is 202 bps INFO @ Sun, 03 Jun 2018 13:39:20: #2 alternative fragment length(s) may be 2,202 bps INFO @ Sun, 03 Jun 2018 13:39:20: #2.2 Generate R script for model : SRX4053301.20_model.r INFO @ Sun, 03 Jun 2018 13:39:20: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:39:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:39:22: 9000000 INFO @ Sun, 03 Jun 2018 13:39:22: 9000000 INFO @ Sun, 03 Jun 2018 13:39:25: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 13:39:25: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 13:39:25: #1 total tags in treatment: 9283078 INFO @ Sun, 03 Jun 2018 13:39:25: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:39:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 13:39:25: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 13:39:25: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 13:39:25: #1 total tags in treatment: 9283078 INFO @ Sun, 03 Jun 2018 13:39:25: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:39:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 13:39:25: #1 tags after filtering in treatment: 9283078 INFO @ Sun, 03 Jun 2018 13:39:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 13:39:25: #1 finished! INFO @ Sun, 03 Jun 2018 13:39:25: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:39:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:39:25: #1 tags after filtering in treatment: 9283078 INFO @ Sun, 03 Jun 2018 13:39:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 13:39:25: #1 finished! INFO @ Sun, 03 Jun 2018 13:39:25: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:39:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:39:26: #2 number of paired peaks: 5906 INFO @ Sun, 03 Jun 2018 13:39:26: start model_add_line... INFO @ Sun, 03 Jun 2018 13:39:26: #2 number of paired peaks: 5906 INFO @ Sun, 03 Jun 2018 13:39:26: start model_add_line... INFO @ Sun, 03 Jun 2018 13:39:26: start X-correlation... INFO @ Sun, 03 Jun 2018 13:39:26: end of X-cor INFO @ Sun, 03 Jun 2018 13:39:26: #2 finished! INFO @ Sun, 03 Jun 2018 13:39:26: #2 predicted fragment length is 202 bps INFO @ Sun, 03 Jun 2018 13:39:26: #2 alternative fragment length(s) may be 2,202 bps INFO @ Sun, 03 Jun 2018 13:39:26: #2.2 Generate R script for model : SRX4053301.05_model.r INFO @ Sun, 03 Jun 2018 13:39:26: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:39:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:39:26: start X-correlation... INFO @ Sun, 03 Jun 2018 13:39:26: end of X-cor INFO @ Sun, 03 Jun 2018 13:39:26: #2 finished! INFO @ Sun, 03 Jun 2018 13:39:26: #2 predicted fragment length is 202 bps INFO @ Sun, 03 Jun 2018 13:39:26: #2 alternative fragment length(s) may be 2,202 bps INFO @ Sun, 03 Jun 2018 13:39:26: #2.2 Generate R script for model : SRX4053301.10_model.r INFO @ Sun, 03 Jun 2018 13:39:26: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:39:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:39:52: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:39:57: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:39:58: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:40:05: #4 Write output xls file... SRX4053301.20_peaks.xls INFO @ Sun, 03 Jun 2018 13:40:05: #4 Write peak in narrowPeak format file... SRX4053301.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:40:05: #4 Write summits bed file... SRX4053301.20_summits.bed INFO @ Sun, 03 Jun 2018 13:40:05: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (667 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:40:10: #4 Write output xls file... SRX4053301.05_peaks.xls INFO @ Sun, 03 Jun 2018 13:40:10: #4 Write peak in narrowPeak format file... SRX4053301.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:40:10: #4 Write summits bed file... SRX4053301.05_summits.bed INFO @ Sun, 03 Jun 2018 13:40:10: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2371 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:40:11: #4 Write output xls file... SRX4053301.10_peaks.xls INFO @ Sun, 03 Jun 2018 13:40:11: #4 Write peak in narrowPeak format file... SRX4053301.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:40:11: #4 Write summits bed file... SRX4053301.10_summits.bed INFO @ Sun, 03 Jun 2018 13:40:11: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1315 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。