Job ID = 10194918 sra ファイルのダウンロード中... Completed: 155658K bytes transferred in 10 seconds (117196K bits/sec), in 1 file. Completed: 151902K bytes transferred in 10 seconds (113202K bits/sec), in 1 file. Completed: 254792K bytes transferred in 13 seconds (149200K bits/sec), in 1 file. Completed: 250302K bytes transferred in 17 seconds (118406K bits/sec), in 1 file. Completed: 251139K bytes transferred in 12 seconds (165770K bits/sec), in 1 file. Completed: 247412K bytes transferred in 16 seconds (121581K 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 3532741 spots for /home/okishinya/chipatlas/results/rn6/SRX2202913/SRR4320023.sra Written 3532741 spots total Written 3635399 spots for /home/okishinya/chipatlas/results/rn6/SRX2202913/SRR4320022.sra Written 3635399 spots total Written 5384376 spots for /home/okishinya/chipatlas/results/rn6/SRX2202913/SRR4320027.sra Written 5384376 spots total Written 5398369 spots for /home/okishinya/chipatlas/results/rn6/SRX2202913/SRR4320025.sra Written 5398369 spots total Written 5457341 spots for /home/okishinya/chipatlas/results/rn6/SRX2202913/SRR4320026.sra Written 5457341 spots total Written 5534669 spots for /home/okishinya/chipatlas/results/rn6/SRX2202913/SRR4320024.sra Written 5534669 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: 00:53:51 28942895 reads; of these: 28942895 (100.00%) were unpaired; of these: 895977 (3.10%) aligned 0 times 19722939 (68.14%) aligned exactly 1 time 8323979 (28.76%) aligned >1 times 96.90% overall alignment rate Time searching: 00:53:55 Overall time: 00:53:55 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 12 files... [bam_rmdupse_core] 4355586 / 28046918 = 0.1553 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 23:59:15: # Command line: callpeak -t SRX2202913.bam -f BAM -g 2.15e9 -n SRX2202913.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2202913.20 # format = BAM # ChIP-seq file = ['SRX2202913.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 23:59:15: # Command line: callpeak -t SRX2202913.bam -f BAM -g 2.15e9 -n SRX2202913.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2202913.10 # format = BAM # ChIP-seq file = ['SRX2202913.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 23:59:15: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:59:15: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:59:15: # Command line: callpeak -t SRX2202913.bam -f BAM -g 2.15e9 -n SRX2202913.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2202913.05 # format = BAM # ChIP-seq file = ['SRX2202913.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 23:59:15: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:59:15: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:59:15: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:59:15: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:59:24: 1000000 INFO @ Fri, 10 Nov 2017 23:59:28: 1000000 INFO @ Fri, 10 Nov 2017 23:59:30: 1000000 INFO @ Fri, 10 Nov 2017 23:59:34: 2000000 INFO @ Fri, 10 Nov 2017 23:59:42: 2000000 INFO @ Fri, 10 Nov 2017 23:59:42: 2000000 INFO @ Fri, 10 Nov 2017 23:59:43: 3000000 INFO @ Fri, 10 Nov 2017 23:59:53: 4000000 INFO @ Fri, 10 Nov 2017 23:59:53: 3000000 INFO @ Fri, 10 Nov 2017 23:59:54: 3000000 INFO @ Sat, 11 Nov 2017 00:00:03: 5000000 INFO @ Sat, 11 Nov 2017 00:00:05: 4000000 INFO @ Sat, 11 Nov 2017 00:00:05: 4000000 INFO @ Sat, 11 Nov 2017 00:00:17: 6000000 INFO @ Sat, 11 Nov 2017 00:00:17: 5000000 INFO @ Sat, 11 Nov 2017 00:00:19: 5000000 INFO @ Sat, 11 Nov 2017 00:00:28: 6000000 INFO @ Sat, 11 Nov 2017 00:00:30: 7000000 INFO @ Sat, 11 Nov 2017 00:00:34: 6000000 INFO @ Sat, 11 Nov 2017 00:00:39: 7000000 INFO @ Sat, 11 Nov 2017 00:00:43: 8000000 INFO @ Sat, 11 Nov 2017 00:00:49: 7000000 INFO @ Sat, 11 Nov 2017 00:00:49: 8000000 INFO @ Sat, 11 Nov 2017 00:00:57: 9000000 INFO @ Sat, 11 Nov 2017 00:00:59: 9000000 INFO @ Sat, 11 Nov 2017 00:01:03: 8000000 INFO @ Sat, 11 Nov 2017 00:01:10: 10000000 INFO @ Sat, 11 Nov 2017 00:01:11: 10000000 INFO @ Sat, 11 Nov 2017 00:01:17: 9000000 INFO @ Sat, 11 Nov 2017 00:01:20: 11000000 INFO @ Sat, 11 Nov 2017 00:01:24: 11000000 INFO @ Sat, 11 Nov 2017 00:01:31: 12000000 INFO @ Sat, 11 Nov 2017 00:01:31: 10000000 INFO @ Sat, 11 Nov 2017 00:01:36: 12000000 INFO @ Sat, 11 Nov 2017 00:01:41: 13000000 INFO @ Sat, 11 Nov 2017 00:01:45: 11000000 INFO @ Sat, 11 Nov 2017 00:01:49: 13000000 INFO @ Sat, 11 Nov 2017 00:01:52: 14000000 INFO @ Sat, 11 Nov 2017 00:01:59: 12000000 INFO @ Sat, 11 Nov 2017 00:02:01: 14000000 INFO @ Sat, 11 Nov 2017 00:02:02: 15000000 INFO @ Sat, 11 Nov 2017 00:02:12: 16000000 INFO @ Sat, 11 Nov 2017 00:02:13: 13000000 INFO @ Sat, 11 Nov 2017 00:02:14: 15000000 INFO @ Sat, 11 Nov 2017 00:02:22: 17000000 INFO @ Sat, 11 Nov 2017 00:02:27: 16000000 INFO @ Sat, 11 Nov 2017 00:02:27: 14000000 INFO @ Sat, 11 Nov 2017 00:02:32: 18000000 INFO @ Sat, 11 Nov 2017 00:02:39: 17000000 INFO @ Sat, 11 Nov 2017 00:02:41: 15000000 INFO @ Sat, 11 Nov 2017 00:02:43: 19000000 INFO @ Sat, 11 Nov 2017 00:02:52: 18000000 INFO @ Sat, 11 Nov 2017 00:02:55: 20000000 INFO @ Sat, 11 Nov 2017 00:02:56: 16000000 INFO @ Sat, 11 Nov 2017 00:03:07: 19000000 INFO @ Sat, 11 Nov 2017 00:03:09: 21000000 INFO @ Sat, 11 Nov 2017 00:03:12: 17000000 INFO @ Sat, 11 Nov 2017 00:03:20: 20000000 INFO @ Sat, 11 Nov 2017 00:03:22: 22000000 INFO @ Sat, 11 Nov 2017 00:03:29: 18000000 INFO @ Sat, 11 Nov 2017 00:03:31: 21000000 INFO @ Sat, 11 Nov 2017 00:03:36: 23000000 INFO @ Sat, 11 Nov 2017 00:03:42: 22000000 INFO @ Sat, 11 Nov 2017 00:03:45: 19000000 INFO @ Sat, 11 Nov 2017 00:03:46: #1 tag size is determined as 50 bps INFO @ Sat, 11 Nov 2017 00:03:46: #1 tag size = 50 INFO @ Sat, 11 Nov 2017 00:03:46: #1 total tags in treatment: 23691332 INFO @ Sat, 11 Nov 2017 00:03:46: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:03:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 00:03:47: #1 tags after filtering in treatment: 23691212 INFO @ Sat, 11 Nov 2017 00:03:47: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:03:47: #1 finished! INFO @ Sat, 11 Nov 2017 00:03:47: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:03:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:03:52: #2 number of paired peaks: 42195 INFO @ Sat, 11 Nov 2017 00:03:52: start model_add_line... INFO @ Sat, 11 Nov 2017 00:03:53: start X-correlation... INFO @ Sat, 11 Nov 2017 00:03:53: end of X-cor INFO @ Sat, 11 Nov 2017 00:03:53: #2 finished! INFO @ Sat, 11 Nov 2017 00:03:53: #2 predicted fragment length is 127 bps INFO @ Sat, 11 Nov 2017 00:03:53: #2 alternative fragment length(s) may be 127 bps INFO @ Sat, 11 Nov 2017 00:03:53: #2.2 Generate R script for model : SRX2202913.10_model.r INFO @ Sat, 11 Nov 2017 00:03:53: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:03:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 00:03:53: 23000000 INFO @ Sat, 11 Nov 2017 00:04:00: 20000000 INFO @ Sat, 11 Nov 2017 00:04:02: #1 tag size is determined as 50 bps INFO @ Sat, 11 Nov 2017 00:04:02: #1 tag size = 50 INFO @ Sat, 11 Nov 2017 00:04:02: #1 total tags in treatment: 23691332 INFO @ Sat, 11 Nov 2017 00:04:02: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:04:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 00:04:03: #1 tags after filtering in treatment: 23691212 INFO @ Sat, 11 Nov 2017 00:04:03: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:04:03: #1 finished! INFO @ Sat, 11 Nov 2017 00:04:03: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:04:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:04:08: #2 number of paired peaks: 42195 INFO @ Sat, 11 Nov 2017 00:04:08: start model_add_line... INFO @ Sat, 11 Nov 2017 00:04:09: start X-correlation... INFO @ Sat, 11 Nov 2017 00:04:09: end of X-cor INFO @ Sat, 11 Nov 2017 00:04:09: #2 finished! INFO @ Sat, 11 Nov 2017 00:04:09: #2 predicted fragment length is 127 bps INFO @ Sat, 11 Nov 2017 00:04:09: #2 alternative fragment length(s) may be 127 bps INFO @ Sat, 11 Nov 2017 00:04:09: #2.2 Generate R script for model : SRX2202913.05_model.r INFO @ Sat, 11 Nov 2017 00:04:09: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:04:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 00:04:10: 21000000 INFO @ Sat, 11 Nov 2017 00:04:21: 22000000 INFO @ Sat, 11 Nov 2017 00:04:33: 23000000 INFO @ Sat, 11 Nov 2017 00:04:41: #1 tag size is determined as 50 bps INFO @ Sat, 11 Nov 2017 00:04:41: #1 tag size = 50 INFO @ Sat, 11 Nov 2017 00:04:41: #1 total tags in treatment: 23691332 INFO @ Sat, 11 Nov 2017 00:04:41: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:04:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 00:04:42: #1 tags after filtering in treatment: 23691212 INFO @ Sat, 11 Nov 2017 00:04:42: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:04:42: #1 finished! INFO @ Sat, 11 Nov 2017 00:04:42: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:04:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:04:47: #2 number of paired peaks: 42195 INFO @ Sat, 11 Nov 2017 00:04:47: start model_add_line... INFO @ Sat, 11 Nov 2017 00:04:48: start X-correlation... INFO @ Sat, 11 Nov 2017 00:04:48: end of X-cor INFO @ Sat, 11 Nov 2017 00:04:48: #2 finished! INFO @ Sat, 11 Nov 2017 00:04:48: #2 predicted fragment length is 127 bps INFO @ Sat, 11 Nov 2017 00:04:48: #2 alternative fragment length(s) may be 127 bps INFO @ Sat, 11 Nov 2017 00:04:48: #2.2 Generate R script for model : SRX2202913.20_model.r INFO @ Sat, 11 Nov 2017 00:04:48: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:04:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 00:05:11: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:05:25: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:06:09: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:06:15: #4 Write output xls file... SRX2202913.05_peaks.xls INFO @ Sat, 11 Nov 2017 00:06:15: #4 Write peak in narrowPeak format file... SRX2202913.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:06:15: #4 Write summits bed file... SRX2202913.05_summits.bed INFO @ Sat, 11 Nov 2017 00:06:15: Done! pass1 - making usageList (119 chroms): 8 millis pass2 - checking and writing primary data (26022 records, 4 fields): 50 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 00:06:16: #4 Write output xls file... SRX2202913.10_peaks.xls INFO @ Sat, 11 Nov 2017 00:06:16: #4 Write peak in narrowPeak format file... SRX2202913.10_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:06:17: #4 Write summits bed file... SRX2202913.10_summits.bed INFO @ Sat, 11 Nov 2017 00:06:17: Done! pass1 - making usageList (102 chroms): 6 millis pass2 - checking and writing primary data (19640 records, 4 fields): 39 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 00:07:00: #4 Write output xls file... SRX2202913.20_peaks.xls INFO @ Sat, 11 Nov 2017 00:07:00: #4 Write peak in narrowPeak format file... SRX2202913.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:07:00: #4 Write summits bed file... SRX2202913.20_summits.bed INFO @ Sat, 11 Nov 2017 00:07:00: Done! pass1 - making usageList (77 chroms): 5 millis pass2 - checking and writing primary data (12752 records, 4 fields): 28 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。