Job ID = 11171289 sra ファイルのダウンロード中... Completed: 117331K bytes transferred in 4 seconds (204335K bits/sec), in 1 file. Completed: 117354K bytes transferred in 5 seconds (173082K bits/sec), in 1 file. Completed: 117252K bytes transferred in 6 seconds (147011K bits/sec), in 1 file. Completed: 116678K bytes transferred in 5 seconds (175435K 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 6221978 spots for /home/okishinya/chipatlas/results/dm3/SRX3020534/SRR5850398.sra Written 6221978 spots for /home/okishinya/chipatlas/results/dm3/SRX3020534/SRR5850398.sra Read 6175098 spots for /home/okishinya/chipatlas/results/dm3/SRX3020534/SRR5850399.sra Written 6175098 spots for /home/okishinya/chipatlas/results/dm3/SRX3020534/SRR5850399.sra Read 6231133 spots for /home/okishinya/chipatlas/results/dm3/SRX3020534/SRR5850396.sra Written 6231133 spots for /home/okishinya/chipatlas/results/dm3/SRX3020534/SRR5850396.sra Read 6215521 spots for /home/okishinya/chipatlas/results/dm3/SRX3020534/SRR5850397.sra Written 6215521 spots for /home/okishinya/chipatlas/results/dm3/SRX3020534/SRR5850397.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: 00:08:33 24843730 reads; of these: 24843730 (100.00%) were unpaired; of these: 2561815 (10.31%) aligned 0 times 17141143 (69.00%) aligned exactly 1 time 5140772 (20.69%) aligned >1 times 89.69% overall alignment rate Time searching: 00:08:33 Overall time: 00:08:33 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] 4690772 / 22281915 = 0.2105 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 13:41:50: # Command line: callpeak -t SRX3020534.bam -f BAM -g dm -n SRX3020534.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3020534.05 # format = BAM # ChIP-seq file = ['SRX3020534.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 13:41:50: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:41:50: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:41:50: # Command line: callpeak -t SRX3020534.bam -f BAM -g dm -n SRX3020534.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3020534.10 # format = BAM # ChIP-seq file = ['SRX3020534.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 13:41:50: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:41:50: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:41:50: # Command line: callpeak -t SRX3020534.bam -f BAM -g dm -n SRX3020534.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3020534.20 # format = BAM # ChIP-seq file = ['SRX3020534.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 13:41:50: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:41:50: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:41:55: 1000000 INFO @ Sat, 08 Sep 2018 13:41:56: 1000000 INFO @ Sat, 08 Sep 2018 13:41:56: 1000000 INFO @ Sat, 08 Sep 2018 13:42:01: 2000000 INFO @ Sat, 08 Sep 2018 13:42:02: 2000000 INFO @ Sat, 08 Sep 2018 13:42:02: 2000000 INFO @ Sat, 08 Sep 2018 13:42:07: 3000000 INFO @ Sat, 08 Sep 2018 13:42:08: 3000000 INFO @ Sat, 08 Sep 2018 13:42:09: 3000000 INFO @ Sat, 08 Sep 2018 13:42:12: 4000000 INFO @ Sat, 08 Sep 2018 13:42:14: 4000000 INFO @ Sat, 08 Sep 2018 13:42:15: 4000000 INFO @ Sat, 08 Sep 2018 13:42:18: 5000000 INFO @ Sat, 08 Sep 2018 13:42:21: 5000000 INFO @ Sat, 08 Sep 2018 13:42:22: 5000000 INFO @ Sat, 08 Sep 2018 13:42:24: 6000000 INFO @ Sat, 08 Sep 2018 13:42:27: 6000000 INFO @ Sat, 08 Sep 2018 13:42:28: 6000000 INFO @ Sat, 08 Sep 2018 13:42:30: 7000000 INFO @ Sat, 08 Sep 2018 13:42:34: 7000000 INFO @ Sat, 08 Sep 2018 13:42:35: 7000000 INFO @ Sat, 08 Sep 2018 13:42:35: 8000000 INFO @ Sat, 08 Sep 2018 13:42:41: 8000000 INFO @ Sat, 08 Sep 2018 13:42:41: 9000000 INFO @ Sat, 08 Sep 2018 13:42:42: 8000000 INFO @ Sat, 08 Sep 2018 13:42:47: 10000000 INFO @ Sat, 08 Sep 2018 13:42:47: 9000000 INFO @ Sat, 08 Sep 2018 13:42:48: 9000000 INFO @ Sat, 08 Sep 2018 13:42:52: 11000000 INFO @ Sat, 08 Sep 2018 13:42:54: 10000000 INFO @ Sat, 08 Sep 2018 13:42:55: 10000000 INFO @ Sat, 08 Sep 2018 13:42:58: 12000000 INFO @ Sat, 08 Sep 2018 13:43:00: 11000000 INFO @ Sat, 08 Sep 2018 13:43:02: 11000000 INFO @ Sat, 08 Sep 2018 13:43:04: 13000000 INFO @ Sat, 08 Sep 2018 13:43:07: 12000000 INFO @ Sat, 08 Sep 2018 13:43:09: 12000000 INFO @ Sat, 08 Sep 2018 13:43:10: 14000000 INFO @ Sat, 08 Sep 2018 13:43:14: 13000000 INFO @ Sat, 08 Sep 2018 13:43:15: 13000000 INFO @ Sat, 08 Sep 2018 13:43:15: 15000000 INFO @ Sat, 08 Sep 2018 13:43:20: 14000000 INFO @ Sat, 08 Sep 2018 13:43:21: 16000000 INFO @ Sat, 08 Sep 2018 13:43:22: 14000000 INFO @ Sat, 08 Sep 2018 13:43:27: 15000000 INFO @ Sat, 08 Sep 2018 13:43:27: 17000000 INFO @ Sat, 08 Sep 2018 13:43:29: 15000000 INFO @ Sat, 08 Sep 2018 13:43:30: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 13:43:30: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 13:43:30: #1 total tags in treatment: 17591143 INFO @ Sat, 08 Sep 2018 13:43:30: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:43:30: #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 13:43:31: #1 tags after filtering in treatment: 17591143 INFO @ Sat, 08 Sep 2018 13:43:31: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:43:31: #1 finished! INFO @ Sat, 08 Sep 2018 13:43:31: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:43:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:43:33: #2 number of paired peaks: 4565 INFO @ Sat, 08 Sep 2018 13:43:33: start model_add_line... INFO @ Sat, 08 Sep 2018 13:43:33: start X-correlation... INFO @ Sat, 08 Sep 2018 13:43:33: end of X-cor INFO @ Sat, 08 Sep 2018 13:43:33: #2 finished! INFO @ Sat, 08 Sep 2018 13:43:33: #2 predicted fragment length is 143 bps INFO @ Sat, 08 Sep 2018 13:43:33: #2 alternative fragment length(s) may be 3,143 bps INFO @ Sat, 08 Sep 2018 13:43:33: #2.2 Generate R script for model : SRX3020534.20_model.r INFO @ Sat, 08 Sep 2018 13:43:33: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:43:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:43:34: 16000000 INFO @ Sat, 08 Sep 2018 13:43:36: 16000000 INFO @ Sat, 08 Sep 2018 13:43:40: 17000000 INFO @ Sat, 08 Sep 2018 13:43:43: 17000000 INFO @ Sat, 08 Sep 2018 13:43:44: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 13:43:44: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 13:43:44: #1 total tags in treatment: 17591143 INFO @ Sat, 08 Sep 2018 13:43:44: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:43:44: #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 13:43:45: #1 tags after filtering in treatment: 17591143 INFO @ Sat, 08 Sep 2018 13:43:45: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:43:45: #1 finished! INFO @ Sat, 08 Sep 2018 13:43:45: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:43:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:43:46: #2 number of paired peaks: 4565 INFO @ Sat, 08 Sep 2018 13:43:46: start model_add_line... INFO @ Sat, 08 Sep 2018 13:43:46: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 13:43:46: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 13:43:46: #1 total tags in treatment: 17591143 INFO @ Sat, 08 Sep 2018 13:43:46: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:43:46: #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 13:43:47: start X-correlation... INFO @ Sat, 08 Sep 2018 13:43:47: end of X-cor INFO @ Sat, 08 Sep 2018 13:43:47: #2 finished! INFO @ Sat, 08 Sep 2018 13:43:47: #2 predicted fragment length is 143 bps INFO @ Sat, 08 Sep 2018 13:43:47: #2 alternative fragment length(s) may be 3,143 bps INFO @ Sat, 08 Sep 2018 13:43:47: #2.2 Generate R script for model : SRX3020534.05_model.r INFO @ Sat, 08 Sep 2018 13:43:47: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:43:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:43:47: #1 tags after filtering in treatment: 17591143 INFO @ Sat, 08 Sep 2018 13:43:47: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:43:47: #1 finished! INFO @ Sat, 08 Sep 2018 13:43:47: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:43:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:43:49: #2 number of paired peaks: 4565 INFO @ Sat, 08 Sep 2018 13:43:49: start model_add_line... INFO @ Sat, 08 Sep 2018 13:43:49: start X-correlation... INFO @ Sat, 08 Sep 2018 13:43:49: end of X-cor INFO @ Sat, 08 Sep 2018 13:43:49: #2 finished! INFO @ Sat, 08 Sep 2018 13:43:49: #2 predicted fragment length is 143 bps INFO @ Sat, 08 Sep 2018 13:43:49: #2 alternative fragment length(s) may be 3,143 bps INFO @ Sat, 08 Sep 2018 13:43:49: #2.2 Generate R script for model : SRX3020534.10_model.r INFO @ Sat, 08 Sep 2018 13:43:49: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:43:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:44:24: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:44:36: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:44:38: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:44:45: #4 Write output xls file... SRX3020534.20_peaks.xls INFO @ Sat, 08 Sep 2018 13:44:45: #4 Write peak in narrowPeak format file... SRX3020534.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:44:45: #4 Write summits bed file... SRX3020534.20_summits.bed INFO @ Sat, 08 Sep 2018 13:44:45: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1888 records, 4 fields): 66 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 13:44:59: #4 Write output xls file... SRX3020534.05_peaks.xls INFO @ Sat, 08 Sep 2018 13:44:59: #4 Write peak in narrowPeak format file... SRX3020534.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:44:59: #4 Write summits bed file... SRX3020534.05_summits.bed INFO @ Sat, 08 Sep 2018 13:44:59: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9113 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 13:45:01: #4 Write output xls file... SRX3020534.10_peaks.xls INFO @ Sat, 08 Sep 2018 13:45:01: #4 Write peak in narrowPeak format file... SRX3020534.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:45:01: #4 Write summits bed file... SRX3020534.10_summits.bed INFO @ Sat, 08 Sep 2018 13:45:01: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5295 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。