Job ID = 10194871 sra ファイルのダウンロード中... Completed: 196231K bytes transferred in 8 seconds (189431K bits/sec), in 1 file. Completed: 196460K bytes transferred in 6 seconds (231557K bits/sec), in 1 file. Completed: 187529K bytes transferred in 7 seconds (205710K bits/sec), in 1 file. Completed: 185095K bytes transferred in 4 seconds (304465K bits/sec), in 1 file. Completed: 210858K bytes transferred in 7 seconds (225749K bits/sec), in 1 file. Completed: 212756K bytes transferred in 7 seconds (243669K 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 4185660 spots for /home/okishinya/chipatlas/results/rn6/SRX2202867/SRR4319749.sra Written 4185660 spots total Written 4230540 spots for /home/okishinya/chipatlas/results/rn6/SRX2202867/SRR4319748.sra Written 4230540 spots total Written 4413739 spots for /home/okishinya/chipatlas/results/rn6/SRX2202867/SRR4319746.sra Written 4413739 spots total Written 4404800 spots for /home/okishinya/chipatlas/results/rn6/SRX2202867/SRR4319747.sra Written 4404800 spots total Written 4636903 spots for /home/okishinya/chipatlas/results/rn6/SRX2202867/SRR4319750.sra Written 4636903 spots total Written 4661235 spots for /home/okishinya/chipatlas/results/rn6/SRX2202867/SRR4319751.sra Written 4661235 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: 00:00:00 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:19:23 26532877 reads; of these: 26532877 (100.00%) were unpaired; of these: 1491067 (5.62%) aligned 0 times 19010101 (71.65%) aligned exactly 1 time 6031709 (22.73%) aligned >1 times 94.38% overall alignment rate Time searching: 00:19:26 Overall time: 00:19:26 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] 4943558 / 25041810 = 0.1974 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 17:49:00: # Command line: callpeak -t SRX2202867.bam -f BAM -g 2.15e9 -n SRX2202867.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2202867.05 # format = BAM # ChIP-seq file = ['SRX2202867.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 17:49:00: # Command line: callpeak -t SRX2202867.bam -f BAM -g 2.15e9 -n SRX2202867.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2202867.10 # format = BAM # ChIP-seq file = ['SRX2202867.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 17:49:00: # Command line: callpeak -t SRX2202867.bam -f BAM -g 2.15e9 -n SRX2202867.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2202867.20 # format = BAM # ChIP-seq file = ['SRX2202867.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 17:49:00: #1 read tag files... INFO @ Fri, 10 Nov 2017 17:49:00: #1 read tag files... INFO @ Fri, 10 Nov 2017 17:49:00: #1 read tag files... INFO @ Fri, 10 Nov 2017 17:49:00: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 17:49:00: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 17:49:00: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 17:49:08: 1000000 INFO @ Fri, 10 Nov 2017 17:49:08: 1000000 INFO @ Fri, 10 Nov 2017 17:49:08: 1000000 INFO @ Fri, 10 Nov 2017 17:49:15: 2000000 INFO @ Fri, 10 Nov 2017 17:49:16: 2000000 INFO @ Fri, 10 Nov 2017 17:49:16: 2000000 INFO @ Fri, 10 Nov 2017 17:49:23: 3000000 INFO @ Fri, 10 Nov 2017 17:49:23: 3000000 INFO @ Fri, 10 Nov 2017 17:49:23: 3000000 INFO @ Fri, 10 Nov 2017 17:49:30: 4000000 INFO @ Fri, 10 Nov 2017 17:49:31: 4000000 INFO @ Fri, 10 Nov 2017 17:49:31: 4000000 INFO @ Fri, 10 Nov 2017 17:49:37: 5000000 INFO @ Fri, 10 Nov 2017 17:49:39: 5000000 INFO @ Fri, 10 Nov 2017 17:49:39: 5000000 INFO @ Fri, 10 Nov 2017 17:49:45: 6000000 INFO @ Fri, 10 Nov 2017 17:49:46: 6000000 INFO @ Fri, 10 Nov 2017 17:49:47: 6000000 INFO @ Fri, 10 Nov 2017 17:49:52: 7000000 INFO @ Fri, 10 Nov 2017 17:49:54: 7000000 INFO @ Fri, 10 Nov 2017 17:49:54: 7000000 INFO @ Fri, 10 Nov 2017 17:49:59: 8000000 INFO @ Fri, 10 Nov 2017 17:50:02: 8000000 INFO @ Fri, 10 Nov 2017 17:50:02: 8000000 INFO @ Fri, 10 Nov 2017 17:50:07: 9000000 INFO @ Fri, 10 Nov 2017 17:50:09: 9000000 INFO @ Fri, 10 Nov 2017 17:50:09: 9000000 INFO @ Fri, 10 Nov 2017 17:50:14: 10000000 INFO @ Fri, 10 Nov 2017 17:50:17: 10000000 INFO @ Fri, 10 Nov 2017 17:50:17: 10000000 INFO @ Fri, 10 Nov 2017 17:50:21: 11000000 INFO @ Fri, 10 Nov 2017 17:50:25: 11000000 INFO @ Fri, 10 Nov 2017 17:50:25: 11000000 INFO @ Fri, 10 Nov 2017 17:50:28: 12000000 INFO @ Fri, 10 Nov 2017 17:50:32: 12000000 INFO @ Fri, 10 Nov 2017 17:50:32: 12000000 INFO @ Fri, 10 Nov 2017 17:50:36: 13000000 INFO @ Fri, 10 Nov 2017 17:50:40: 13000000 INFO @ Fri, 10 Nov 2017 17:50:40: 13000000 INFO @ Fri, 10 Nov 2017 17:50:43: 14000000 INFO @ Fri, 10 Nov 2017 17:50:48: 14000000 INFO @ Fri, 10 Nov 2017 17:50:48: 14000000 INFO @ Fri, 10 Nov 2017 17:50:50: 15000000 INFO @ Fri, 10 Nov 2017 17:50:55: 15000000 INFO @ Fri, 10 Nov 2017 17:50:56: 15000000 INFO @ Fri, 10 Nov 2017 17:50:57: 16000000 INFO @ Fri, 10 Nov 2017 17:51:03: 16000000 INFO @ Fri, 10 Nov 2017 17:51:03: 16000000 INFO @ Fri, 10 Nov 2017 17:51:05: 17000000 INFO @ Fri, 10 Nov 2017 17:51:11: 17000000 INFO @ Fri, 10 Nov 2017 17:51:11: 17000000 INFO @ Fri, 10 Nov 2017 17:51:12: 18000000 INFO @ Fri, 10 Nov 2017 17:51:19: 18000000 INFO @ Fri, 10 Nov 2017 17:51:20: 18000000 INFO @ Fri, 10 Nov 2017 17:51:21: 19000000 INFO @ Fri, 10 Nov 2017 17:51:29: 19000000 INFO @ Fri, 10 Nov 2017 17:51:29: 19000000 INFO @ Fri, 10 Nov 2017 17:51:31: 20000000 INFO @ Fri, 10 Nov 2017 17:51:32: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 17:51:32: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 17:51:32: #1 total tags in treatment: 20098252 INFO @ Fri, 10 Nov 2017 17:51:32: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 17:51:32: #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 17:51:33: #1 tags after filtering in treatment: 20098115 INFO @ Fri, 10 Nov 2017 17:51:33: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 17:51:33: #1 finished! INFO @ Fri, 10 Nov 2017 17:51:33: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 17:51:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 17:51:36: #2 number of paired peaks: 36534 INFO @ Fri, 10 Nov 2017 17:51:36: start model_add_line... INFO @ Fri, 10 Nov 2017 17:51:36: start X-correlation... INFO @ Fri, 10 Nov 2017 17:51:36: end of X-cor INFO @ Fri, 10 Nov 2017 17:51:36: #2 finished! INFO @ Fri, 10 Nov 2017 17:51:36: #2 predicted fragment length is 144 bps INFO @ Fri, 10 Nov 2017 17:51:36: #2 alternative fragment length(s) may be 144 bps INFO @ Fri, 10 Nov 2017 17:51:36: #2.2 Generate R script for model : SRX2202867.10_model.r INFO @ Fri, 10 Nov 2017 17:51:36: #3 Call peaks... INFO @ Fri, 10 Nov 2017 17:51:36: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 17:51:39: 20000000 INFO @ Fri, 10 Nov 2017 17:51:39: 20000000 INFO @ Fri, 10 Nov 2017 17:51:40: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 17:51:40: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 17:51:40: #1 total tags in treatment: 20098252 INFO @ Fri, 10 Nov 2017 17:51:40: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 17:51:40: #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 17:51:40: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 17:51:40: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 17:51:40: #1 total tags in treatment: 20098252 INFO @ Fri, 10 Nov 2017 17:51:40: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 17:51:40: #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 17:51:40: #1 tags after filtering in treatment: 20098115 INFO @ Fri, 10 Nov 2017 17:51:40: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 17:51:40: #1 finished! INFO @ Fri, 10 Nov 2017 17:51:40: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 17:51:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 17:51:41: #1 tags after filtering in treatment: 20098115 INFO @ Fri, 10 Nov 2017 17:51:41: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 17:51:41: #1 finished! INFO @ Fri, 10 Nov 2017 17:51:41: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 17:51:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 17:51:43: #2 number of paired peaks: 36534 INFO @ Fri, 10 Nov 2017 17:51:43: start model_add_line... INFO @ Fri, 10 Nov 2017 17:51:44: start X-correlation... INFO @ Fri, 10 Nov 2017 17:51:44: end of X-cor INFO @ Fri, 10 Nov 2017 17:51:44: #2 finished! INFO @ Fri, 10 Nov 2017 17:51:44: #2 predicted fragment length is 144 bps INFO @ Fri, 10 Nov 2017 17:51:44: #2 alternative fragment length(s) may be 144 bps INFO @ Fri, 10 Nov 2017 17:51:44: #2.2 Generate R script for model : SRX2202867.05_model.r INFO @ Fri, 10 Nov 2017 17:51:44: #3 Call peaks... INFO @ Fri, 10 Nov 2017 17:51:44: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 17:51:44: #2 number of paired peaks: 36534 INFO @ Fri, 10 Nov 2017 17:51:44: start model_add_line... INFO @ Fri, 10 Nov 2017 17:51:44: start X-correlation... INFO @ Fri, 10 Nov 2017 17:51:44: end of X-cor INFO @ Fri, 10 Nov 2017 17:51:44: #2 finished! INFO @ Fri, 10 Nov 2017 17:51:44: #2 predicted fragment length is 144 bps INFO @ Fri, 10 Nov 2017 17:51:44: #2 alternative fragment length(s) may be 144 bps INFO @ Fri, 10 Nov 2017 17:51:44: #2.2 Generate R script for model : SRX2202867.20_model.r INFO @ Fri, 10 Nov 2017 17:51:44: #3 Call peaks... INFO @ Fri, 10 Nov 2017 17:51:44: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 17:52:23: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 17:52:34: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 17:52:37: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 17:52:53: #4 Write output xls file... SRX2202867.10_peaks.xls INFO @ Fri, 10 Nov 2017 17:52:53: #4 Write peak in narrowPeak format file... SRX2202867.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 17:52:53: #4 Write summits bed file... SRX2202867.10_summits.bed INFO @ Fri, 10 Nov 2017 17:52:53: Done! pass1 - making usageList (54 chroms): 2 millis pass2 - checking and writing primary data (5376 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 17:53:03: #4 Write output xls file... SRX2202867.05_peaks.xls INFO @ Fri, 10 Nov 2017 17:53:04: #4 Write peak in narrowPeak format file... SRX2202867.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 17:53:04: #4 Write summits bed file... SRX2202867.05_summits.bed INFO @ Fri, 10 Nov 2017 17:53:04: Done! pass1 - making usageList (77 chroms): 3 millis pass2 - checking and writing primary data (13220 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 17:53:06: #4 Write output xls file... SRX2202867.20_peaks.xls INFO @ Fri, 10 Nov 2017 17:53:06: #4 Write peak in narrowPeak format file... SRX2202867.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 17:53:06: #4 Write summits bed file... SRX2202867.20_summits.bed INFO @ Fri, 10 Nov 2017 17:53:06: Done! pass1 - making usageList (34 chroms): 1 millis pass2 - checking and writing primary data (788 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。