Job ID = 10194910 sra ファイルのダウンロード中... Completed: 199752K bytes transferred in 22 seconds (72563K bits/sec), in 1 file. Completed: 195344K bytes transferred in 13 seconds (120570K bits/sec), in 1 file. Completed: 325900K bytes transferred in 17 seconds (148540K bits/sec), in 1 file. Completed: 319669K bytes transferred in 16 seconds (163446K bits/sec), in 1 file. Completed: 321091K bytes transferred in 21 seconds (121264K bits/sec), in 1 file. Completed: 315968K bytes transferred in 14 seconds (178277K 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... Written 4583571 spots for /home/okishinya/chipatlas/results/rn6/SRX2202905/SRR4319975.sra Written 4583571 spots total Written 4709427 spots for /home/okishinya/chipatlas/results/rn6/SRX2202905/SRR4319974.sra Written 4709427 spots total Written 6961491 spots for /home/okishinya/chipatlas/results/rn6/SRX2202905/SRR4319979.sra Written 6961491 spots total Written 7063434 spots for /home/okishinya/chipatlas/results/rn6/SRX2202905/SRR4319978.sra Written 7063434 spots total Written 6981236 spots for /home/okishinya/chipatlas/results/rn6/SRX2202905/SRR4319977.sra Written 6981236 spots total Written 7168734 spots for /home/okishinya/chipatlas/results/rn6/SRX2202905/SRR4319976.sra Written 7168734 spots total 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: 00:00:01 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 01:15:38 37467893 reads; of these: 37467893 (100.00%) were unpaired; of these: 1392038 (3.72%) aligned 0 times 25588905 (68.30%) aligned exactly 1 time 10486950 (27.99%) aligned >1 times 96.28% overall alignment rate Time searching: 01:15:42 Overall time: 01:15:42 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 3064445 / 36075855 = 0.0849 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 @ Fri, 10 Nov 2017 23:49:07: # Command line: callpeak -t SRX2202905.bam -f BAM -g 2.15e9 -n SRX2202905.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2202905.10 # format = BAM # ChIP-seq file = ['SRX2202905.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Fri, 10 Nov 2017 23:49:07: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:49:07: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:49:07: # Command line: callpeak -t SRX2202905.bam -f BAM -g 2.15e9 -n SRX2202905.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2202905.05 # format = BAM # ChIP-seq file = ['SRX2202905.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Fri, 10 Nov 2017 23:49:07: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:49:07: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:49:07: # Command line: callpeak -t SRX2202905.bam -f BAM -g 2.15e9 -n SRX2202905.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2202905.20 # format = BAM # ChIP-seq file = ['SRX2202905.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Fri, 10 Nov 2017 23:49:07: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:49:07: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:49:19: 1000000 INFO @ Fri, 10 Nov 2017 23:49:23: 1000000 INFO @ Fri, 10 Nov 2017 23:49:24: 1000000 INFO @ Fri, 10 Nov 2017 23:49:33: 2000000 INFO @ Fri, 10 Nov 2017 23:49:38: 2000000 INFO @ Fri, 10 Nov 2017 23:49:41: 2000000 INFO @ Fri, 10 Nov 2017 23:49:46: 3000000 INFO @ Fri, 10 Nov 2017 23:49:54: 3000000 INFO @ Fri, 10 Nov 2017 23:49:58: 3000000 INFO @ Fri, 10 Nov 2017 23:49:59: 4000000 INFO @ Fri, 10 Nov 2017 23:50:11: 4000000 INFO @ Fri, 10 Nov 2017 23:50:12: 5000000 INFO @ Fri, 10 Nov 2017 23:50:16: 4000000 INFO @ Fri, 10 Nov 2017 23:50:25: 6000000 INFO @ Fri, 10 Nov 2017 23:50:28: 5000000 INFO @ Fri, 10 Nov 2017 23:50:35: 5000000 INFO @ Fri, 10 Nov 2017 23:50:39: 7000000 INFO @ Fri, 10 Nov 2017 23:50:46: 6000000 INFO @ Fri, 10 Nov 2017 23:50:52: 8000000 INFO @ Fri, 10 Nov 2017 23:50:53: 6000000 INFO @ Fri, 10 Nov 2017 23:51:03: 7000000 INFO @ Fri, 10 Nov 2017 23:51:07: 9000000 INFO @ Fri, 10 Nov 2017 23:51:12: 7000000 INFO @ Fri, 10 Nov 2017 23:51:18: 8000000 INFO @ Fri, 10 Nov 2017 23:51:20: 10000000 INFO @ Fri, 10 Nov 2017 23:51:29: 8000000 INFO @ Fri, 10 Nov 2017 23:51:32: 9000000 INFO @ Fri, 10 Nov 2017 23:51:33: 11000000 INFO @ Fri, 10 Nov 2017 23:51:41: 9000000 INFO @ Fri, 10 Nov 2017 23:51:46: 12000000 INFO @ Fri, 10 Nov 2017 23:51:46: 10000000 INFO @ Fri, 10 Nov 2017 23:51:54: 10000000 INFO @ Fri, 10 Nov 2017 23:51:58: 13000000 INFO @ Fri, 10 Nov 2017 23:52:04: 11000000 INFO @ Fri, 10 Nov 2017 23:52:10: 11000000 INFO @ Fri, 10 Nov 2017 23:52:10: 14000000 INFO @ Fri, 10 Nov 2017 23:52:23: 12000000 INFO @ Fri, 10 Nov 2017 23:52:24: 15000000 INFO @ Fri, 10 Nov 2017 23:52:27: 12000000 INFO @ Fri, 10 Nov 2017 23:52:37: 16000000 INFO @ Fri, 10 Nov 2017 23:52:43: 13000000 INFO @ Fri, 10 Nov 2017 23:52:43: 13000000 INFO @ Fri, 10 Nov 2017 23:52:50: 17000000 INFO @ Fri, 10 Nov 2017 23:52:59: 14000000 INFO @ Fri, 10 Nov 2017 23:53:03: 14000000 INFO @ Fri, 10 Nov 2017 23:53:03: 18000000 INFO @ Fri, 10 Nov 2017 23:53:16: 15000000 INFO @ Fri, 10 Nov 2017 23:53:17: 19000000 INFO @ Fri, 10 Nov 2017 23:53:23: 15000000 INFO @ Fri, 10 Nov 2017 23:53:30: 20000000 INFO @ Fri, 10 Nov 2017 23:53:33: 16000000 INFO @ Fri, 10 Nov 2017 23:53:43: 21000000 INFO @ Fri, 10 Nov 2017 23:53:43: 16000000 INFO @ Fri, 10 Nov 2017 23:53:51: 17000000 INFO @ Fri, 10 Nov 2017 23:53:57: 22000000 INFO @ Fri, 10 Nov 2017 23:54:04: 17000000 INFO @ Fri, 10 Nov 2017 23:54:08: 18000000 INFO @ Fri, 10 Nov 2017 23:54:10: 23000000 INFO @ Fri, 10 Nov 2017 23:54:24: 24000000 INFO @ Fri, 10 Nov 2017 23:54:25: 18000000 INFO @ Fri, 10 Nov 2017 23:54:29: 19000000 INFO @ Fri, 10 Nov 2017 23:54:38: 25000000 INFO @ Fri, 10 Nov 2017 23:54:45: 19000000 INFO @ Fri, 10 Nov 2017 23:54:50: 20000000 INFO @ Fri, 10 Nov 2017 23:54:51: 26000000 INFO @ Fri, 10 Nov 2017 23:55:03: 27000000 INFO @ Fri, 10 Nov 2017 23:55:06: 20000000 INFO @ Fri, 10 Nov 2017 23:55:11: 21000000 INFO @ Fri, 10 Nov 2017 23:55:15: 28000000 INFO @ Fri, 10 Nov 2017 23:55:27: 21000000 INFO @ Fri, 10 Nov 2017 23:55:28: 29000000 INFO @ Fri, 10 Nov 2017 23:55:32: 22000000 INFO @ Fri, 10 Nov 2017 23:55:41: 30000000 INFO @ Fri, 10 Nov 2017 23:55:46: 22000000 INFO @ Fri, 10 Nov 2017 23:55:51: 23000000 INFO @ Fri, 10 Nov 2017 23:55:53: 31000000 INFO @ Fri, 10 Nov 2017 23:56:06: 23000000 INFO @ Fri, 10 Nov 2017 23:56:07: 32000000 INFO @ Fri, 10 Nov 2017 23:56:11: 24000000 INFO @ Fri, 10 Nov 2017 23:56:22: 33000000 INFO @ Fri, 10 Nov 2017 23:56:22: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 23:56:22: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 23:56:22: #1 total tags in treatment: 33011410 INFO @ Fri, 10 Nov 2017 23:56:22: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 23:56:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 23:56:24: #1 tags after filtering in treatment: 33011315 INFO @ Fri, 10 Nov 2017 23:56:24: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 23:56:24: #1 finished! INFO @ Fri, 10 Nov 2017 23:56:24: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 23:56:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 23:56:26: 24000000 INFO @ Fri, 10 Nov 2017 23:56:30: #2 number of paired peaks: 40757 INFO @ Fri, 10 Nov 2017 23:56:30: start model_add_line... INFO @ Fri, 10 Nov 2017 23:56:31: start X-correlation... INFO @ Fri, 10 Nov 2017 23:56:31: end of X-cor INFO @ Fri, 10 Nov 2017 23:56:31: #2 finished! INFO @ Fri, 10 Nov 2017 23:56:31: #2 predicted fragment length is 131 bps INFO @ Fri, 10 Nov 2017 23:56:31: #2 alternative fragment length(s) may be 131 bps INFO @ Fri, 10 Nov 2017 23:56:31: #2.2 Generate R script for model : SRX2202905.10_model.r INFO @ Fri, 10 Nov 2017 23:56:31: #3 Call peaks... INFO @ Fri, 10 Nov 2017 23:56:31: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 23:56:31: 25000000 INFO @ Fri, 10 Nov 2017 23:56:45: 25000000 INFO @ Fri, 10 Nov 2017 23:56:51: 26000000 INFO @ Fri, 10 Nov 2017 23:57:01: 26000000 INFO @ Fri, 10 Nov 2017 23:57:11: 27000000 INFO @ Fri, 10 Nov 2017 23:57:15: 27000000 INFO @ Fri, 10 Nov 2017 23:57:30: 28000000 INFO @ Fri, 10 Nov 2017 23:57:30: 28000000 INFO @ Fri, 10 Nov 2017 23:57:46: 29000000 INFO @ Fri, 10 Nov 2017 23:57:48: 29000000 INFO @ Fri, 10 Nov 2017 23:58:01: 30000000 INFO @ Fri, 10 Nov 2017 23:58:06: 30000000 INFO @ Fri, 10 Nov 2017 23:58:17: 31000000 INFO @ Fri, 10 Nov 2017 23:58:23: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 23:58:25: 31000000 INFO @ Fri, 10 Nov 2017 23:58:36: 32000000 INFO @ Fri, 10 Nov 2017 23:58:42: 32000000 INFO @ Fri, 10 Nov 2017 23:58:55: 33000000 INFO @ Fri, 10 Nov 2017 23:58:56: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 23:58:56: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 23:58:56: #1 total tags in treatment: 33011410 INFO @ Fri, 10 Nov 2017 23:58:56: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 23:58:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 23:58:56: 33000000 INFO @ Fri, 10 Nov 2017 23:58:57: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 23:58:57: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 23:58:57: #1 total tags in treatment: 33011410 INFO @ Fri, 10 Nov 2017 23:58:57: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 23:58:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 23:58:57: #1 tags after filtering in treatment: 33011315 INFO @ Fri, 10 Nov 2017 23:58:57: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 23:58:57: #1 finished! INFO @ Fri, 10 Nov 2017 23:58:57: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 23:58:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 23:58:58: #1 tags after filtering in treatment: 33011315 INFO @ Fri, 10 Nov 2017 23:58:58: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 23:58:58: #1 finished! INFO @ Fri, 10 Nov 2017 23:58:58: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 23:58:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 23:59:04: #2 number of paired peaks: 40757 INFO @ Fri, 10 Nov 2017 23:59:04: start model_add_line... INFO @ Fri, 10 Nov 2017 23:59:05: #2 number of paired peaks: 40757 INFO @ Fri, 10 Nov 2017 23:59:05: start model_add_line... INFO @ Fri, 10 Nov 2017 23:59:05: start X-correlation... INFO @ Fri, 10 Nov 2017 23:59:05: end of X-cor INFO @ Fri, 10 Nov 2017 23:59:05: #2 finished! INFO @ Fri, 10 Nov 2017 23:59:05: #2 predicted fragment length is 131 bps INFO @ Fri, 10 Nov 2017 23:59:05: #2 alternative fragment length(s) may be 131 bps INFO @ Fri, 10 Nov 2017 23:59:05: #2.2 Generate R script for model : SRX2202905.20_model.r INFO @ Fri, 10 Nov 2017 23:59:05: #3 Call peaks... INFO @ Fri, 10 Nov 2017 23:59:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 23:59:06: start X-correlation... INFO @ Fri, 10 Nov 2017 23:59:06: end of X-cor INFO @ Fri, 10 Nov 2017 23:59:06: #2 finished! INFO @ Fri, 10 Nov 2017 23:59:06: #2 predicted fragment length is 131 bps INFO @ Fri, 10 Nov 2017 23:59:06: #2 alternative fragment length(s) may be 131 bps INFO @ Fri, 10 Nov 2017 23:59:06: #2.2 Generate R script for model : SRX2202905.05_model.r INFO @ Fri, 10 Nov 2017 23:59:06: #3 Call peaks... INFO @ Fri, 10 Nov 2017 23:59:06: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 23:59:36: #4 Write output xls file... SRX2202905.10_peaks.xls INFO @ Fri, 10 Nov 2017 23:59:36: #4 Write peak in narrowPeak format file... SRX2202905.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 23:59:36: #4 Write summits bed file... SRX2202905.10_summits.bed INFO @ Fri, 10 Nov 2017 23:59:36: Done! pass1 - making usageList (91 chroms): 10 millis pass2 - checking and writing primary data (19958 records, 4 fields): 43 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 00:00:56: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:00:58: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:02:08: #4 Write output xls file... SRX2202905.20_peaks.xls INFO @ Sat, 11 Nov 2017 00:02:09: #4 Write peak in narrowPeak format file... SRX2202905.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:02:09: #4 Write summits bed file... SRX2202905.20_summits.bed INFO @ Sat, 11 Nov 2017 00:02:09: Done! pass1 - making usageList (63 chroms): 5 millis pass2 - checking and writing primary data (11470 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 00:02:10: #4 Write output xls file... SRX2202905.05_peaks.xls INFO @ Sat, 11 Nov 2017 00:02:11: #4 Write peak in narrowPeak format file... SRX2202905.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:02:11: #4 Write summits bed file... SRX2202905.05_summits.bed INFO @ Sat, 11 Nov 2017 00:02:11: Done! pass1 - making usageList (114 chroms): 8 millis pass2 - checking and writing primary data (27507 records, 4 fields): 55 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。