Job ID = 10194890 sra ファイルのダウンロード中... Completed: 263063K bytes transferred in 12 seconds (171168K bits/sec), in 1 file. Completed: 263369K bytes transferred in 10 seconds (202015K bits/sec), in 1 file. Completed: 251024K bytes transferred in 8 seconds (231767K bits/sec), in 1 file. Completed: 248021K bytes transferred in 8 seconds (225970K bits/sec), in 1 file. Completed: 301538K bytes transferred in 9 seconds (270521K bits/sec), in 1 file. Completed: 303618K bytes transferred in 9 seconds (272002K 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 5587837 spots for /home/okishinya/chipatlas/results/rn6/SRX2202885/SRR4319857.sra Written 5587837 spots total Written 5641436 spots for /home/okishinya/chipatlas/results/rn6/SRX2202885/SRR4319856.sra Written 5641436 spots total Written 5885757 spots for /home/okishinya/chipatlas/results/rn6/SRX2202885/SRR4319855.sra Written 5885757 spots total Written 5903626 spots for /home/okishinya/chipatlas/results/rn6/SRX2202885/SRR4319854.sra Written 5903626 spots total Written 6629374 spots for /home/okishinya/chipatlas/results/rn6/SRX2202885/SRR4319858.sra Written 6629374 spots total Written 6646400 spots for /home/okishinya/chipatlas/results/rn6/SRX2202885/SRR4319859.sra Written 6646400 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: 00:00:00 Multiseed full-index search: 00:22:05 36294430 reads; of these: 36294430 (100.00%) were unpaired; of these: 6371369 (17.55%) aligned 0 times 24111721 (66.43%) aligned exactly 1 time 5811340 (16.01%) aligned >1 times 82.45% overall alignment rate Time searching: 00:22:08 Overall time: 00:22:08 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] 7531966 / 29923061 = 0.2517 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 18:23:58: # Command line: callpeak -t SRX2202885.bam -f BAM -g 2.15e9 -n SRX2202885.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2202885.20 # format = BAM # ChIP-seq file = ['SRX2202885.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 18:23:58: # Command line: callpeak -t SRX2202885.bam -f BAM -g 2.15e9 -n SRX2202885.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2202885.10 # format = BAM # ChIP-seq file = ['SRX2202885.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 18:23:58: # Command line: callpeak -t SRX2202885.bam -f BAM -g 2.15e9 -n SRX2202885.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2202885.05 # format = BAM # ChIP-seq file = ['SRX2202885.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 18:23:58: #1 read tag files... INFO @ Fri, 10 Nov 2017 18:23:58: #1 read tag files... INFO @ Fri, 10 Nov 2017 18:23:58: #1 read tag files... INFO @ Fri, 10 Nov 2017 18:23:58: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 18:23:58: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 18:23:58: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 18:24:05: 1000000 INFO @ Fri, 10 Nov 2017 18:24:05: 1000000 INFO @ Fri, 10 Nov 2017 18:24:05: 1000000 INFO @ Fri, 10 Nov 2017 18:24:11: 2000000 INFO @ Fri, 10 Nov 2017 18:24:12: 2000000 INFO @ Fri, 10 Nov 2017 18:24:12: 2000000 INFO @ Fri, 10 Nov 2017 18:24:18: 3000000 INFO @ Fri, 10 Nov 2017 18:24:19: 3000000 INFO @ Fri, 10 Nov 2017 18:24:20: 3000000 INFO @ Fri, 10 Nov 2017 18:24:24: 4000000 INFO @ Fri, 10 Nov 2017 18:24:26: 4000000 INFO @ Fri, 10 Nov 2017 18:24:27: 4000000 INFO @ Fri, 10 Nov 2017 18:24:30: 5000000 INFO @ Fri, 10 Nov 2017 18:24:33: 5000000 INFO @ Fri, 10 Nov 2017 18:24:35: 5000000 INFO @ Fri, 10 Nov 2017 18:24:37: 6000000 INFO @ Fri, 10 Nov 2017 18:24:40: 6000000 INFO @ Fri, 10 Nov 2017 18:24:42: 6000000 INFO @ Fri, 10 Nov 2017 18:24:43: 7000000 INFO @ Fri, 10 Nov 2017 18:24:47: 7000000 INFO @ Fri, 10 Nov 2017 18:24:49: 7000000 INFO @ Fri, 10 Nov 2017 18:24:50: 8000000 INFO @ Fri, 10 Nov 2017 18:24:54: 8000000 INFO @ Fri, 10 Nov 2017 18:24:56: 9000000 INFO @ Fri, 10 Nov 2017 18:24:57: 8000000 INFO @ Fri, 10 Nov 2017 18:25:01: 9000000 INFO @ Fri, 10 Nov 2017 18:25:02: 10000000 INFO @ Fri, 10 Nov 2017 18:25:04: 9000000 INFO @ Fri, 10 Nov 2017 18:25:08: 10000000 INFO @ Fri, 10 Nov 2017 18:25:09: 11000000 INFO @ Fri, 10 Nov 2017 18:25:11: 10000000 INFO @ Fri, 10 Nov 2017 18:25:15: 12000000 INFO @ Fri, 10 Nov 2017 18:25:16: 11000000 INFO @ Fri, 10 Nov 2017 18:25:19: 11000000 INFO @ Fri, 10 Nov 2017 18:25:21: 13000000 INFO @ Fri, 10 Nov 2017 18:25:23: 12000000 INFO @ Fri, 10 Nov 2017 18:25:26: 12000000 INFO @ Fri, 10 Nov 2017 18:25:28: 14000000 INFO @ Fri, 10 Nov 2017 18:25:30: 13000000 INFO @ Fri, 10 Nov 2017 18:25:34: 13000000 INFO @ Fri, 10 Nov 2017 18:25:34: 15000000 INFO @ Fri, 10 Nov 2017 18:25:37: 14000000 INFO @ Fri, 10 Nov 2017 18:25:41: 16000000 INFO @ Fri, 10 Nov 2017 18:25:41: 14000000 INFO @ Fri, 10 Nov 2017 18:25:44: 15000000 INFO @ Fri, 10 Nov 2017 18:25:47: 17000000 INFO @ Fri, 10 Nov 2017 18:25:48: 15000000 INFO @ Fri, 10 Nov 2017 18:25:51: 16000000 INFO @ Fri, 10 Nov 2017 18:25:53: 18000000 INFO @ Fri, 10 Nov 2017 18:25:56: 16000000 INFO @ Fri, 10 Nov 2017 18:25:58: 17000000 INFO @ Fri, 10 Nov 2017 18:26:00: 19000000 INFO @ Fri, 10 Nov 2017 18:26:03: 17000000 INFO @ Fri, 10 Nov 2017 18:26:05: 18000000 INFO @ Fri, 10 Nov 2017 18:26:06: 20000000 INFO @ Fri, 10 Nov 2017 18:26:10: 18000000 INFO @ Fri, 10 Nov 2017 18:26:12: 19000000 INFO @ Fri, 10 Nov 2017 18:26:12: 21000000 INFO @ Fri, 10 Nov 2017 18:26:18: 19000000 INFO @ Fri, 10 Nov 2017 18:26:19: 22000000 INFO @ Fri, 10 Nov 2017 18:26:19: 20000000 INFO @ Fri, 10 Nov 2017 18:26:22: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 18:26:22: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 18:26:22: #1 total tags in treatment: 22391095 INFO @ Fri, 10 Nov 2017 18:26:22: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 18:26:22: #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 18:26:22: #1 tags after filtering in treatment: 22390946 INFO @ Fri, 10 Nov 2017 18:26:22: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 18:26:22: #1 finished! INFO @ Fri, 10 Nov 2017 18:26:22: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 18:26:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 18:26:25: 20000000 INFO @ Fri, 10 Nov 2017 18:26:27: 21000000 INFO @ Fri, 10 Nov 2017 18:26:27: #2 number of paired peaks: 65331 INFO @ Fri, 10 Nov 2017 18:26:27: start model_add_line... INFO @ Fri, 10 Nov 2017 18:26:27: start X-correlation... INFO @ Fri, 10 Nov 2017 18:26:27: end of X-cor INFO @ Fri, 10 Nov 2017 18:26:27: #2 finished! INFO @ Fri, 10 Nov 2017 18:26:27: #2 predicted fragment length is 156 bps INFO @ Fri, 10 Nov 2017 18:26:27: #2 alternative fragment length(s) may be 156 bps INFO @ Fri, 10 Nov 2017 18:26:27: #2.2 Generate R script for model : SRX2202885.05_model.r INFO @ Fri, 10 Nov 2017 18:26:27: #3 Call peaks... INFO @ Fri, 10 Nov 2017 18:26:27: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 18:26:33: 21000000 INFO @ Fri, 10 Nov 2017 18:26:34: 22000000 INFO @ Fri, 10 Nov 2017 18:26:37: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 18:26:37: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 18:26:37: #1 total tags in treatment: 22391095 INFO @ Fri, 10 Nov 2017 18:26:37: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 18:26:37: #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 18:26:37: #1 tags after filtering in treatment: 22390946 INFO @ Fri, 10 Nov 2017 18:26:37: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 18:26:37: #1 finished! INFO @ Fri, 10 Nov 2017 18:26:37: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 18:26:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 18:26:40: 22000000 INFO @ Fri, 10 Nov 2017 18:26:42: #2 number of paired peaks: 65331 INFO @ Fri, 10 Nov 2017 18:26:42: start model_add_line... INFO @ Fri, 10 Nov 2017 18:26:42: start X-correlation... INFO @ Fri, 10 Nov 2017 18:26:42: end of X-cor INFO @ Fri, 10 Nov 2017 18:26:42: #2 finished! INFO @ Fri, 10 Nov 2017 18:26:42: #2 predicted fragment length is 156 bps INFO @ Fri, 10 Nov 2017 18:26:42: #2 alternative fragment length(s) may be 156 bps INFO @ Fri, 10 Nov 2017 18:26:42: #2.2 Generate R script for model : SRX2202885.10_model.r INFO @ Fri, 10 Nov 2017 18:26:42: #3 Call peaks... INFO @ Fri, 10 Nov 2017 18:26:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 18:26:42: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 18:26:42: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 18:26:42: #1 total tags in treatment: 22391095 INFO @ Fri, 10 Nov 2017 18:26:42: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 18:26:42: #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 18:26:43: #1 tags after filtering in treatment: 22390946 INFO @ Fri, 10 Nov 2017 18:26:43: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 18:26:43: #1 finished! INFO @ Fri, 10 Nov 2017 18:26:43: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 18:26:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 18:26:48: #2 number of paired peaks: 65331 INFO @ Fri, 10 Nov 2017 18:26:48: start model_add_line... INFO @ Fri, 10 Nov 2017 18:26:48: start X-correlation... INFO @ Fri, 10 Nov 2017 18:26:48: end of X-cor INFO @ Fri, 10 Nov 2017 18:26:48: #2 finished! INFO @ Fri, 10 Nov 2017 18:26:48: #2 predicted fragment length is 156 bps INFO @ Fri, 10 Nov 2017 18:26:48: #2 alternative fragment length(s) may be 156 bps INFO @ Fri, 10 Nov 2017 18:26:48: #2.2 Generate R script for model : SRX2202885.20_model.r INFO @ Fri, 10 Nov 2017 18:26:48: #3 Call peaks... INFO @ Fri, 10 Nov 2017 18:26:48: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 18:27:25: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 18:27:41: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 18:27:43: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 18:27:58: #4 Write output xls file... SRX2202885.05_peaks.xls INFO @ Fri, 10 Nov 2017 18:27:59: #4 Write peak in narrowPeak format file... SRX2202885.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 18:27:59: #4 Write summits bed file... SRX2202885.05_summits.bed INFO @ Fri, 10 Nov 2017 18:27:59: Done! pass1 - making usageList (106 chroms): 5 millis pass2 - checking and writing primary data (25990 records, 4 fields): 34 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 18:28:16: #4 Write output xls file... SRX2202885.20_peaks.xls INFO @ Fri, 10 Nov 2017 18:28:16: #4 Write peak in narrowPeak format file... SRX2202885.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 18:28:16: #4 Write summits bed file... SRX2202885.20_summits.bed INFO @ Fri, 10 Nov 2017 18:28:17: Done! pass1 - making usageList (45 chroms): 2 millis pass2 - checking and writing primary data (5813 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 18:28:18: #4 Write output xls file... SRX2202885.10_peaks.xls INFO @ Fri, 10 Nov 2017 18:28:18: #4 Write peak in narrowPeak format file... SRX2202885.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 18:28:18: #4 Write summits bed file... SRX2202885.10_summits.bed INFO @ Fri, 10 Nov 2017 18:28:18: Done! pass1 - making usageList (77 chroms): 3 millis pass2 - checking and writing primary data (15224 records, 4 fields): 21 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。