Job ID = 11171292 sra ファイルのダウンロード中... Completed: 140260K bytes transferred in 22 seconds (51435K bits/sec), in 1 file. Completed: 140437K bytes transferred in 7 seconds (151827K bits/sec), in 1 file. Completed: 140200K bytes transferred in 7 seconds (153414K bits/sec), in 1 file. Completed: 139738K bytes transferred in 5 seconds (208162K 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 7416886 spots for /home/okishinya/chipatlas/results/dm3/SRX3020536/SRR5850407.sra Written 7416886 spots for /home/okishinya/chipatlas/results/dm3/SRX3020536/SRR5850407.sra Read 7468333 spots for /home/okishinya/chipatlas/results/dm3/SRX3020536/SRR5850404.sra Written 7468333 spots for /home/okishinya/chipatlas/results/dm3/SRX3020536/SRR5850404.sra Read 7458215 spots for /home/okishinya/chipatlas/results/dm3/SRX3020536/SRR5850405.sra Written 7458215 spots for /home/okishinya/chipatlas/results/dm3/SRX3020536/SRR5850405.sra Read 7462041 spots for /home/okishinya/chipatlas/results/dm3/SRX3020536/SRR5850406.sra Written 7462041 spots for /home/okishinya/chipatlas/results/dm3/SRX3020536/SRR5850406.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:09:59 29805475 reads; of these: 29805475 (100.00%) were unpaired; of these: 4808081 (16.13%) aligned 0 times 19030179 (63.85%) aligned exactly 1 time 5967215 (20.02%) aligned >1 times 83.87% overall alignment rate Time searching: 00:10:00 Overall time: 00:10:00 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] 5216056 / 24997394 = 0.2087 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 13:45:26: # Command line: callpeak -t SRX3020536.bam -f BAM -g dm -n SRX3020536.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3020536.20 # format = BAM # ChIP-seq file = ['SRX3020536.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 13:45:26: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:45:26: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:45:26: # Command line: callpeak -t SRX3020536.bam -f BAM -g dm -n SRX3020536.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3020536.05 # format = BAM # ChIP-seq file = ['SRX3020536.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 13:45:26: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:45:26: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:45:26: # Command line: callpeak -t SRX3020536.bam -f BAM -g dm -n SRX3020536.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3020536.10 # format = BAM # ChIP-seq file = ['SRX3020536.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 13:45:26: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:45:26: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:45:33: 1000000 INFO @ Sat, 08 Sep 2018 13:45:33: 1000000 INFO @ Sat, 08 Sep 2018 13:45:33: 1000000 INFO @ Sat, 08 Sep 2018 13:45:39: 2000000 INFO @ Sat, 08 Sep 2018 13:45:39: 2000000 INFO @ Sat, 08 Sep 2018 13:45:40: 2000000 INFO @ Sat, 08 Sep 2018 13:45:46: 3000000 INFO @ Sat, 08 Sep 2018 13:45:46: 3000000 INFO @ Sat, 08 Sep 2018 13:45:46: 3000000 INFO @ Sat, 08 Sep 2018 13:45:52: 4000000 INFO @ Sat, 08 Sep 2018 13:45:52: 4000000 INFO @ Sat, 08 Sep 2018 13:45:54: 4000000 INFO @ Sat, 08 Sep 2018 13:45:59: 5000000 INFO @ Sat, 08 Sep 2018 13:45:59: 5000000 INFO @ Sat, 08 Sep 2018 13:46:01: 5000000 INFO @ Sat, 08 Sep 2018 13:46:06: 6000000 INFO @ Sat, 08 Sep 2018 13:46:06: 6000000 INFO @ Sat, 08 Sep 2018 13:46:08: 6000000 INFO @ Sat, 08 Sep 2018 13:46:12: 7000000 INFO @ Sat, 08 Sep 2018 13:46:13: 7000000 INFO @ Sat, 08 Sep 2018 13:46:15: 7000000 INFO @ Sat, 08 Sep 2018 13:46:19: 8000000 INFO @ Sat, 08 Sep 2018 13:46:19: 8000000 INFO @ Sat, 08 Sep 2018 13:46:22: 8000000 INFO @ Sat, 08 Sep 2018 13:46:26: 9000000 INFO @ Sat, 08 Sep 2018 13:46:26: 9000000 INFO @ Sat, 08 Sep 2018 13:46:29: 9000000 INFO @ Sat, 08 Sep 2018 13:46:32: 10000000 INFO @ Sat, 08 Sep 2018 13:46:33: 10000000 INFO @ Sat, 08 Sep 2018 13:46:36: 10000000 INFO @ Sat, 08 Sep 2018 13:46:39: 11000000 INFO @ Sat, 08 Sep 2018 13:46:40: 11000000 INFO @ Sat, 08 Sep 2018 13:46:44: 11000000 INFO @ Sat, 08 Sep 2018 13:46:46: 12000000 INFO @ Sat, 08 Sep 2018 13:46:47: 12000000 INFO @ Sat, 08 Sep 2018 13:46:51: 12000000 INFO @ Sat, 08 Sep 2018 13:46:53: 13000000 INFO @ Sat, 08 Sep 2018 13:46:54: 13000000 INFO @ Sat, 08 Sep 2018 13:46:58: 13000000 INFO @ Sat, 08 Sep 2018 13:47:00: 14000000 INFO @ Sat, 08 Sep 2018 13:47:01: 14000000 INFO @ Sat, 08 Sep 2018 13:47:05: 14000000 INFO @ Sat, 08 Sep 2018 13:47:07: 15000000 INFO @ Sat, 08 Sep 2018 13:47:08: 15000000 INFO @ Sat, 08 Sep 2018 13:47:12: 15000000 INFO @ Sat, 08 Sep 2018 13:47:14: 16000000 INFO @ Sat, 08 Sep 2018 13:47:15: 16000000 INFO @ Sat, 08 Sep 2018 13:47:19: 16000000 INFO @ Sat, 08 Sep 2018 13:47:21: 17000000 INFO @ Sat, 08 Sep 2018 13:47:22: 17000000 INFO @ Sat, 08 Sep 2018 13:47:27: 17000000 INFO @ Sat, 08 Sep 2018 13:47:28: 18000000 INFO @ Sat, 08 Sep 2018 13:47:29: 18000000 INFO @ Sat, 08 Sep 2018 13:47:34: 18000000 INFO @ Sat, 08 Sep 2018 13:47:35: 19000000 INFO @ Sat, 08 Sep 2018 13:47:37: 19000000 INFO @ Sat, 08 Sep 2018 13:47:40: #1 tag size is determined as 51 bps INFO @ Sat, 08 Sep 2018 13:47:40: #1 tag size = 51 INFO @ Sat, 08 Sep 2018 13:47:40: #1 total tags in treatment: 19781338 INFO @ Sat, 08 Sep 2018 13:47:40: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:47:40: #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 13:47:41: #1 tags after filtering in treatment: 19781338 INFO @ Sat, 08 Sep 2018 13:47:41: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:47:41: #1 finished! INFO @ Sat, 08 Sep 2018 13:47:41: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:47:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:47:41: 19000000 INFO @ Sat, 08 Sep 2018 13:47:42: #1 tag size is determined as 51 bps INFO @ Sat, 08 Sep 2018 13:47:42: #1 tag size = 51 INFO @ Sat, 08 Sep 2018 13:47:42: #1 total tags in treatment: 19781338 INFO @ Sat, 08 Sep 2018 13:47:42: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:47:42: #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 13:47:42: #1 tags after filtering in treatment: 19781338 INFO @ Sat, 08 Sep 2018 13:47:42: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:47:42: #1 finished! INFO @ Sat, 08 Sep 2018 13:47:42: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:47:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:47:43: #2 number of paired peaks: 3444 INFO @ Sat, 08 Sep 2018 13:47:43: start model_add_line... INFO @ Sat, 08 Sep 2018 13:47:43: start X-correlation... INFO @ Sat, 08 Sep 2018 13:47:43: end of X-cor INFO @ Sat, 08 Sep 2018 13:47:43: #2 finished! INFO @ Sat, 08 Sep 2018 13:47:43: #2 predicted fragment length is 132 bps INFO @ Sat, 08 Sep 2018 13:47:43: #2 alternative fragment length(s) may be 3,132 bps INFO @ Sat, 08 Sep 2018 13:47:43: #2.2 Generate R script for model : SRX3020536.10_model.r INFO @ Sat, 08 Sep 2018 13:47:43: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:47:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:47:45: #2 number of paired peaks: 3444 INFO @ Sat, 08 Sep 2018 13:47:45: start model_add_line... INFO @ Sat, 08 Sep 2018 13:47:45: start X-correlation... INFO @ Sat, 08 Sep 2018 13:47:45: end of X-cor INFO @ Sat, 08 Sep 2018 13:47:45: #2 finished! INFO @ Sat, 08 Sep 2018 13:47:45: #2 predicted fragment length is 132 bps INFO @ Sat, 08 Sep 2018 13:47:45: #2 alternative fragment length(s) may be 3,132 bps INFO @ Sat, 08 Sep 2018 13:47:45: #2.2 Generate R script for model : SRX3020536.05_model.r INFO @ Sat, 08 Sep 2018 13:47:45: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:47:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:47:46: #1 tag size is determined as 51 bps INFO @ Sat, 08 Sep 2018 13:47:46: #1 tag size = 51 INFO @ Sat, 08 Sep 2018 13:47:46: #1 total tags in treatment: 19781338 INFO @ Sat, 08 Sep 2018 13:47:46: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:47:46: #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 13:47:47: #1 tags after filtering in treatment: 19781338 INFO @ Sat, 08 Sep 2018 13:47:47: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:47:47: #1 finished! INFO @ Sat, 08 Sep 2018 13:47:47: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:47:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:47:48: #2 number of paired peaks: 3444 INFO @ Sat, 08 Sep 2018 13:47:48: start model_add_line... INFO @ Sat, 08 Sep 2018 13:47:49: start X-correlation... INFO @ Sat, 08 Sep 2018 13:47:49: end of X-cor INFO @ Sat, 08 Sep 2018 13:47:49: #2 finished! INFO @ Sat, 08 Sep 2018 13:47:49: #2 predicted fragment length is 132 bps INFO @ Sat, 08 Sep 2018 13:47:49: #2 alternative fragment length(s) may be 3,132 bps INFO @ Sat, 08 Sep 2018 13:47:49: #2.2 Generate R script for model : SRX3020536.20_model.r INFO @ Sat, 08 Sep 2018 13:47:49: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:47:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:48:36: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:48:38: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:48:39: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:49:01: #4 Write output xls file... SRX3020536.10_peaks.xls INFO @ Sat, 08 Sep 2018 13:49:01: #4 Write peak in narrowPeak format file... SRX3020536.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:49:01: #4 Write summits bed file... SRX3020536.10_summits.bed INFO @ Sat, 08 Sep 2018 13:49:01: Done! INFO @ Sat, 08 Sep 2018 13:49:02: #4 Write output xls file... SRX3020536.20_peaks.xls INFO @ Sat, 08 Sep 2018 13:49:02: #4 Write peak in narrowPeak format file... SRX3020536.20_peaks.narrowPeak pass1 - making usageList (15 chroms): 66 millis pass2 - checking and writing primary data (5440 records, 4 fields): 8 millis INFO @ Sat, 08 Sep 2018 13:49:02: #4 Write summits bed file... SRX3020536.20_summits.bed INFO @ Sat, 08 Sep 2018 13:49:02: Done! CompletedMACS2peakCalling pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (1943 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 13:49:02: #4 Write output xls file... SRX3020536.05_peaks.xls INFO @ Sat, 08 Sep 2018 13:49:02: #4 Write peak in narrowPeak format file... SRX3020536.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:49:02: #4 Write summits bed file... SRX3020536.05_summits.bed INFO @ Sat, 08 Sep 2018 13:49:02: Done! pass1 - making usageList (15 chroms): 10 millis pass2 - checking and writing primary data (9824 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。