Job ID = 11171272 sra ファイルのダウンロード中... Completed: 97427K bytes transferred in 4 seconds (169265K bits/sec), in 1 file. Completed: 95960K bytes transferred in 5 seconds (137706K bits/sec), in 1 file. Completed: 96340K bytes transferred in 14 seconds (53150K bits/sec), in 1 file. Completed: 95629K bytes transferred in 6 seconds (125380K 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 5064659 spots for /home/okishinya/chipatlas/results/dm3/SRX3020539/SRR5850417.sra Written 5064659 spots for /home/okishinya/chipatlas/results/dm3/SRX3020539/SRR5850417.sra Read 5032197 spots for /home/okishinya/chipatlas/results/dm3/SRX3020539/SRR5850419.sra Written 5032197 spots for /home/okishinya/chipatlas/results/dm3/SRX3020539/SRR5850419.sra Read 5077820 spots for /home/okishinya/chipatlas/results/dm3/SRX3020539/SRR5850418.sra Written 5077820 spots for /home/okishinya/chipatlas/results/dm3/SRX3020539/SRR5850418.sra Read 5135703 spots for /home/okishinya/chipatlas/results/dm3/SRX3020539/SRR5850416.sra Written 5135703 spots for /home/okishinya/chipatlas/results/dm3/SRX3020539/SRR5850416.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 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: 00:07:41 20310379 reads; of these: 20310379 (100.00%) were unpaired; of these: 542431 (2.67%) aligned 0 times 14969611 (73.70%) aligned exactly 1 time 4798337 (23.63%) aligned >1 times 97.33% overall alignment rate Time searching: 00:07:41 Overall time: 00:07:41 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] 2936510 / 19767948 = 0.1485 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, 08 Sep 2018 13:34:44: # Command line: callpeak -t SRX3020539.bam -f BAM -g dm -n SRX3020539.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3020539.10 # format = BAM # ChIP-seq file = ['SRX3020539.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 @ Sat, 08 Sep 2018 13:34:44: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:34:44: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:34:44: # Command line: callpeak -t SRX3020539.bam -f BAM -g dm -n SRX3020539.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3020539.20 # format = BAM # ChIP-seq file = ['SRX3020539.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 @ Sat, 08 Sep 2018 13:34:44: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:34:44: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:34:44: # Command line: callpeak -t SRX3020539.bam -f BAM -g dm -n SRX3020539.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3020539.05 # format = BAM # ChIP-seq file = ['SRX3020539.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 @ Sat, 08 Sep 2018 13:34:44: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:34:44: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:34:51: 1000000 INFO @ Sat, 08 Sep 2018 13:34:51: 1000000 INFO @ Sat, 08 Sep 2018 13:34:51: 1000000 INFO @ Sat, 08 Sep 2018 13:34:57: 2000000 INFO @ Sat, 08 Sep 2018 13:34:58: 2000000 INFO @ Sat, 08 Sep 2018 13:34:58: 2000000 INFO @ Sat, 08 Sep 2018 13:35:04: 3000000 INFO @ Sat, 08 Sep 2018 13:35:05: 3000000 INFO @ Sat, 08 Sep 2018 13:35:05: 3000000 INFO @ Sat, 08 Sep 2018 13:35:10: 4000000 INFO @ Sat, 08 Sep 2018 13:35:11: 4000000 INFO @ Sat, 08 Sep 2018 13:35:12: 4000000 INFO @ Sat, 08 Sep 2018 13:35:17: 5000000 INFO @ Sat, 08 Sep 2018 13:35:18: 5000000 INFO @ Sat, 08 Sep 2018 13:35:19: 5000000 INFO @ Sat, 08 Sep 2018 13:35:23: 6000000 INFO @ Sat, 08 Sep 2018 13:35:25: 6000000 INFO @ Sat, 08 Sep 2018 13:35:26: 6000000 INFO @ Sat, 08 Sep 2018 13:35:30: 7000000 INFO @ Sat, 08 Sep 2018 13:35:32: 7000000 INFO @ Sat, 08 Sep 2018 13:35:34: 7000000 INFO @ Sat, 08 Sep 2018 13:35:36: 8000000 INFO @ Sat, 08 Sep 2018 13:35:40: 8000000 INFO @ Sat, 08 Sep 2018 13:35:41: 8000000 INFO @ Sat, 08 Sep 2018 13:35:43: 9000000 INFO @ Sat, 08 Sep 2018 13:35:47: 9000000 INFO @ Sat, 08 Sep 2018 13:35:48: 9000000 INFO @ Sat, 08 Sep 2018 13:35:50: 10000000 INFO @ Sat, 08 Sep 2018 13:35:54: 10000000 INFO @ Sat, 08 Sep 2018 13:35:56: 10000000 INFO @ Sat, 08 Sep 2018 13:35:56: 11000000 INFO @ Sat, 08 Sep 2018 13:36:01: 11000000 INFO @ Sat, 08 Sep 2018 13:36:03: 12000000 INFO @ Sat, 08 Sep 2018 13:36:03: 11000000 INFO @ Sat, 08 Sep 2018 13:36:08: 12000000 INFO @ Sat, 08 Sep 2018 13:36:09: 13000000 INFO @ Sat, 08 Sep 2018 13:36:10: 12000000 INFO @ Sat, 08 Sep 2018 13:36:15: 13000000 INFO @ Sat, 08 Sep 2018 13:36:16: 14000000 INFO @ Sat, 08 Sep 2018 13:36:18: 13000000 INFO @ Sat, 08 Sep 2018 13:36:22: 14000000 INFO @ Sat, 08 Sep 2018 13:36:22: 15000000 INFO @ Sat, 08 Sep 2018 13:36:25: 14000000 INFO @ Sat, 08 Sep 2018 13:36:29: 16000000 INFO @ Sat, 08 Sep 2018 13:36:29: 15000000 INFO @ Sat, 08 Sep 2018 13:36:32: 15000000 INFO @ Sat, 08 Sep 2018 13:36:34: #1 tag size is determined as 49 bps INFO @ Sat, 08 Sep 2018 13:36:34: #1 tag size = 49 INFO @ Sat, 08 Sep 2018 13:36:34: #1 total tags in treatment: 16831438 INFO @ Sat, 08 Sep 2018 13:36:34: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:36:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 13:36:35: #1 tags after filtering in treatment: 16831438 INFO @ Sat, 08 Sep 2018 13:36:35: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:36:35: #1 finished! INFO @ Sat, 08 Sep 2018 13:36:35: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:36:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:36:36: #2 number of paired peaks: 1025 INFO @ Sat, 08 Sep 2018 13:36:36: start model_add_line... INFO @ Sat, 08 Sep 2018 13:36:36: start X-correlation... INFO @ Sat, 08 Sep 2018 13:36:36: end of X-cor INFO @ Sat, 08 Sep 2018 13:36:36: #2 finished! INFO @ Sat, 08 Sep 2018 13:36:36: #2 predicted fragment length is 109 bps INFO @ Sat, 08 Sep 2018 13:36:36: #2 alternative fragment length(s) may be 3,87,101,109 bps INFO @ Sat, 08 Sep 2018 13:36:36: #2.2 Generate R script for model : SRX3020539.10_model.r INFO @ Sat, 08 Sep 2018 13:36:36: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:36:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:36:36: 16000000 INFO @ Sat, 08 Sep 2018 13:36:40: 16000000 INFO @ Sat, 08 Sep 2018 13:36:42: #1 tag size is determined as 49 bps INFO @ Sat, 08 Sep 2018 13:36:42: #1 tag size = 49 INFO @ Sat, 08 Sep 2018 13:36:42: #1 total tags in treatment: 16831438 INFO @ Sat, 08 Sep 2018 13:36:42: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:36:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 13:36:43: #1 tags after filtering in treatment: 16831438 INFO @ Sat, 08 Sep 2018 13:36:43: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:36:43: #1 finished! INFO @ Sat, 08 Sep 2018 13:36:43: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:36:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:36:44: #2 number of paired peaks: 1025 INFO @ Sat, 08 Sep 2018 13:36:44: start model_add_line... INFO @ Sat, 08 Sep 2018 13:36:44: start X-correlation... INFO @ Sat, 08 Sep 2018 13:36:44: end of X-cor INFO @ Sat, 08 Sep 2018 13:36:44: #2 finished! INFO @ Sat, 08 Sep 2018 13:36:44: #2 predicted fragment length is 109 bps INFO @ Sat, 08 Sep 2018 13:36:44: #2 alternative fragment length(s) may be 3,87,101,109 bps INFO @ Sat, 08 Sep 2018 13:36:44: #2.2 Generate R script for model : SRX3020539.20_model.r INFO @ Sat, 08 Sep 2018 13:36:44: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:36:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:36:46: #1 tag size is determined as 49 bps INFO @ Sat, 08 Sep 2018 13:36:46: #1 tag size = 49 INFO @ Sat, 08 Sep 2018 13:36:46: #1 total tags in treatment: 16831438 INFO @ Sat, 08 Sep 2018 13:36:46: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:36:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 13:36:46: #1 tags after filtering in treatment: 16831438 INFO @ Sat, 08 Sep 2018 13:36:46: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:36:46: #1 finished! INFO @ Sat, 08 Sep 2018 13:36:46: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:36:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:36:47: #2 number of paired peaks: 1025 INFO @ Sat, 08 Sep 2018 13:36:47: start model_add_line... INFO @ Sat, 08 Sep 2018 13:36:47: start X-correlation... INFO @ Sat, 08 Sep 2018 13:36:47: end of X-cor INFO @ Sat, 08 Sep 2018 13:36:47: #2 finished! INFO @ Sat, 08 Sep 2018 13:36:47: #2 predicted fragment length is 109 bps INFO @ Sat, 08 Sep 2018 13:36:47: #2 alternative fragment length(s) may be 3,87,101,109 bps INFO @ Sat, 08 Sep 2018 13:36:47: #2.2 Generate R script for model : SRX3020539.05_model.r INFO @ Sat, 08 Sep 2018 13:36:47: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:36:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:37:17: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:37:25: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:37:27: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:37:37: #4 Write output xls file... SRX3020539.10_peaks.xls INFO @ Sat, 08 Sep 2018 13:37:37: #4 Write peak in narrowPeak format file... SRX3020539.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:37:37: #4 Write summits bed file... SRX3020539.10_summits.bed INFO @ Sat, 08 Sep 2018 13:37:37: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1945 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 13:37:48: #4 Write output xls file... SRX3020539.20_peaks.xls INFO @ Sat, 08 Sep 2018 13:37:48: #4 Write peak in narrowPeak format file... SRX3020539.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:37:48: #4 Write summits bed file... SRX3020539.20_summits.bed INFO @ Sat, 08 Sep 2018 13:37:48: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (707 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 13:37:48: #4 Write output xls file... SRX3020539.05_peaks.xls INFO @ Sat, 08 Sep 2018 13:37:48: #4 Write peak in narrowPeak format file... SRX3020539.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:37:48: #4 Write summits bed file... SRX3020539.05_summits.bed INFO @ Sat, 08 Sep 2018 13:37:48: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5295 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。