Job ID = 10194924 sra ファイルのダウンロード中... Completed: 119683K bytes transferred in 8 seconds (113008K bits/sec), in 1 file. Completed: 117134K bytes transferred in 7 seconds (135525K bits/sec), in 1 file. Completed: 196864K bytes transferred in 12 seconds (128612K bits/sec), in 1 file. Completed: 193024K bytes transferred in 11 seconds (142316K bits/sec), in 1 file. Completed: 194827K bytes transferred in 9 seconds (159715K bits/sec), in 1 file. Completed: 191934K bytes transferred in 14 seconds (109272K 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 2733124 spots for /home/okishinya/chipatlas/results/rn6/SRX2202919/SRR4320059.sra Written 2733124 spots total Written 2804150 spots for /home/okishinya/chipatlas/results/rn6/SRX2202919/SRR4320058.sra Written 2804150 spots total Written 4173958 spots for /home/okishinya/chipatlas/results/rn6/SRX2202919/SRR4320063.sra Written 4173958 spots total Written 4273716 spots for /home/okishinya/chipatlas/results/rn6/SRX2202919/SRR4320060.sra Written 4273716 spots total Written 4228922 spots for /home/okishinya/chipatlas/results/rn6/SRX2202919/SRR4320062.sra Written 4228922 spots total Written 4163835 spots for /home/okishinya/chipatlas/results/rn6/SRX2202919/SRR4320061.sra Written 4163835 spots total rm: cannot remove `[DSE]RX*': No such file or directory 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: 00:36:13 22377705 reads; of these: 22377705 (100.00%) were unpaired; of these: 705559 (3.15%) aligned 0 times 15365282 (68.66%) aligned exactly 1 time 6306864 (28.18%) aligned >1 times 96.85% overall alignment rate Time searching: 00:36:17 Overall time: 00:36:17 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] 1780895 / 21672146 = 0.0822 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, 11 Nov 2017 00:00:05: # Command line: callpeak -t SRX2202919.bam -f BAM -g 2.15e9 -n SRX2202919.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2202919.05 # format = BAM # ChIP-seq file = ['SRX2202919.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 @ Sat, 11 Nov 2017 00:00:05: # Command line: callpeak -t SRX2202919.bam -f BAM -g 2.15e9 -n SRX2202919.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2202919.20 # format = BAM # ChIP-seq file = ['SRX2202919.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 @ Sat, 11 Nov 2017 00:00:05: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:00:05: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:00:05: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:00:05: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:00:05: # Command line: callpeak -t SRX2202919.bam -f BAM -g 2.15e9 -n SRX2202919.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2202919.10 # format = BAM # ChIP-seq file = ['SRX2202919.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 @ Sat, 11 Nov 2017 00:00:05: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:00:05: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:00:16: 1000000 INFO @ Sat, 11 Nov 2017 00:00:22: 1000000 INFO @ Sat, 11 Nov 2017 00:00:24: 1000000 INFO @ Sat, 11 Nov 2017 00:00:26: 2000000 INFO @ Sat, 11 Nov 2017 00:00:35: 3000000 INFO @ Sat, 11 Nov 2017 00:00:41: 2000000 INFO @ Sat, 11 Nov 2017 00:00:44: 2000000 INFO @ Sat, 11 Nov 2017 00:00:45: 4000000 INFO @ Sat, 11 Nov 2017 00:00:55: 5000000 INFO @ Sat, 11 Nov 2017 00:01:00: 3000000 INFO @ Sat, 11 Nov 2017 00:01:02: 3000000 INFO @ Sat, 11 Nov 2017 00:01:08: 6000000 INFO @ Sat, 11 Nov 2017 00:01:17: 7000000 INFO @ Sat, 11 Nov 2017 00:01:18: 4000000 INFO @ Sat, 11 Nov 2017 00:01:21: 4000000 INFO @ Sat, 11 Nov 2017 00:01:27: 8000000 INFO @ Sat, 11 Nov 2017 00:01:37: 9000000 INFO @ Sat, 11 Nov 2017 00:01:37: 5000000 INFO @ Sat, 11 Nov 2017 00:01:39: 5000000 INFO @ Sat, 11 Nov 2017 00:01:47: 10000000 INFO @ Sat, 11 Nov 2017 00:01:54: 6000000 INFO @ Sat, 11 Nov 2017 00:01:56: 6000000 INFO @ Sat, 11 Nov 2017 00:01:57: 11000000 INFO @ Sat, 11 Nov 2017 00:02:08: 12000000 INFO @ Sat, 11 Nov 2017 00:02:11: 7000000 INFO @ Sat, 11 Nov 2017 00:02:15: 7000000 INFO @ Sat, 11 Nov 2017 00:02:21: 13000000 INFO @ Sat, 11 Nov 2017 00:02:29: 8000000 INFO @ Sat, 11 Nov 2017 00:02:33: 14000000 INFO @ Sat, 11 Nov 2017 00:02:35: 8000000 INFO @ Sat, 11 Nov 2017 00:02:45: 15000000 INFO @ Sat, 11 Nov 2017 00:02:51: 9000000 INFO @ Sat, 11 Nov 2017 00:02:54: 9000000 INFO @ Sat, 11 Nov 2017 00:02:57: 16000000 INFO @ Sat, 11 Nov 2017 00:03:09: 17000000 INFO @ Sat, 11 Nov 2017 00:03:12: 10000000 INFO @ Sat, 11 Nov 2017 00:03:14: 10000000 INFO @ Sat, 11 Nov 2017 00:03:21: 18000000 INFO @ Sat, 11 Nov 2017 00:03:30: 11000000 INFO @ Sat, 11 Nov 2017 00:03:34: 19000000 INFO @ Sat, 11 Nov 2017 00:03:35: 11000000 INFO @ Sat, 11 Nov 2017 00:03:45: #1 tag size is determined as 50 bps INFO @ Sat, 11 Nov 2017 00:03:45: #1 tag size = 50 INFO @ Sat, 11 Nov 2017 00:03:45: #1 total tags in treatment: 19891251 INFO @ Sat, 11 Nov 2017 00:03:45: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:03:45: #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 00:03:46: #1 tags after filtering in treatment: 19891120 INFO @ Sat, 11 Nov 2017 00:03:46: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:03:46: #1 finished! INFO @ Sat, 11 Nov 2017 00:03:46: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:03:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:03:47: 12000000 INFO @ Sat, 11 Nov 2017 00:03:51: #2 number of paired peaks: 40254 INFO @ Sat, 11 Nov 2017 00:03:51: start model_add_line... INFO @ Sat, 11 Nov 2017 00:03:51: start X-correlation... INFO @ Sat, 11 Nov 2017 00:03:51: end of X-cor INFO @ Sat, 11 Nov 2017 00:03:51: #2 finished! INFO @ Sat, 11 Nov 2017 00:03:51: #2 predicted fragment length is 129 bps INFO @ Sat, 11 Nov 2017 00:03:51: #2 alternative fragment length(s) may be 129 bps INFO @ Sat, 11 Nov 2017 00:03:51: #2.2 Generate R script for model : SRX2202919.05_model.r INFO @ Sat, 11 Nov 2017 00:03:51: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:03:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 00:03:56: 12000000 INFO @ Sat, 11 Nov 2017 00:04:06: 13000000 INFO @ Sat, 11 Nov 2017 00:04:19: 13000000 INFO @ Sat, 11 Nov 2017 00:04:24: 14000000 INFO @ Sat, 11 Nov 2017 00:04:36: 14000000 INFO @ Sat, 11 Nov 2017 00:04:42: 15000000 INFO @ Sat, 11 Nov 2017 00:04:47: 15000000 INFO @ Sat, 11 Nov 2017 00:04:48: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:05:02: 16000000 INFO @ Sat, 11 Nov 2017 00:05:03: 16000000 INFO @ Sat, 11 Nov 2017 00:05:21: 17000000 INFO @ Sat, 11 Nov 2017 00:05:21: 17000000 INFO @ Sat, 11 Nov 2017 00:05:22: #4 Write output xls file... SRX2202919.05_peaks.xls INFO @ Sat, 11 Nov 2017 00:05:22: #4 Write peak in narrowPeak format file... SRX2202919.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:05:22: #4 Write summits bed file... SRX2202919.05_summits.bed INFO @ Sat, 11 Nov 2017 00:05:22: Done! pass1 - making usageList (96 chroms): 6 millis pass2 - checking and writing primary data (21364 records, 4 fields): 38 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 00:05:32: 18000000 INFO @ Sat, 11 Nov 2017 00:05:40: 18000000 INFO @ Sat, 11 Nov 2017 00:05:41: 19000000 INFO @ Sat, 11 Nov 2017 00:05:50: #1 tag size is determined as 50 bps INFO @ Sat, 11 Nov 2017 00:05:50: #1 tag size = 50 INFO @ Sat, 11 Nov 2017 00:05:50: #1 total tags in treatment: 19891251 INFO @ Sat, 11 Nov 2017 00:05:50: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:05:50: #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 00:05:50: #1 tags after filtering in treatment: 19891120 INFO @ Sat, 11 Nov 2017 00:05:50: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:05:50: #1 finished! INFO @ Sat, 11 Nov 2017 00:05:50: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:05:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:05:54: #2 number of paired peaks: 40254 INFO @ Sat, 11 Nov 2017 00:05:54: start model_add_line... INFO @ Sat, 11 Nov 2017 00:05:55: start X-correlation... INFO @ Sat, 11 Nov 2017 00:05:55: end of X-cor INFO @ Sat, 11 Nov 2017 00:05:55: #2 finished! INFO @ Sat, 11 Nov 2017 00:05:55: #2 predicted fragment length is 129 bps INFO @ Sat, 11 Nov 2017 00:05:55: #2 alternative fragment length(s) may be 129 bps INFO @ Sat, 11 Nov 2017 00:05:55: #2.2 Generate R script for model : SRX2202919.20_model.r INFO @ Sat, 11 Nov 2017 00:05:55: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:05:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 00:05:59: 19000000 INFO @ Sat, 11 Nov 2017 00:06:16: #1 tag size is determined as 50 bps INFO @ Sat, 11 Nov 2017 00:06:16: #1 tag size = 50 INFO @ Sat, 11 Nov 2017 00:06:16: #1 total tags in treatment: 19891251 INFO @ Sat, 11 Nov 2017 00:06:16: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:06:16: #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 00:06:17: #1 tags after filtering in treatment: 19891120 INFO @ Sat, 11 Nov 2017 00:06:17: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:06:17: #1 finished! INFO @ Sat, 11 Nov 2017 00:06:17: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:06:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:06:21: #2 number of paired peaks: 40254 INFO @ Sat, 11 Nov 2017 00:06:21: start model_add_line... INFO @ Sat, 11 Nov 2017 00:06:21: start X-correlation... INFO @ Sat, 11 Nov 2017 00:06:21: end of X-cor INFO @ Sat, 11 Nov 2017 00:06:21: #2 finished! INFO @ Sat, 11 Nov 2017 00:06:21: #2 predicted fragment length is 129 bps INFO @ Sat, 11 Nov 2017 00:06:21: #2 alternative fragment length(s) may be 129 bps INFO @ Sat, 11 Nov 2017 00:06:21: #2.2 Generate R script for model : SRX2202919.10_model.r INFO @ Sat, 11 Nov 2017 00:06:21: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:06:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 00:06:58: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:07:19: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:07:44: #4 Write output xls file... SRX2202919.20_peaks.xls INFO @ Sat, 11 Nov 2017 00:07:44: #4 Write peak in narrowPeak format file... SRX2202919.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:07:44: #4 Write summits bed file... SRX2202919.20_summits.bed INFO @ Sat, 11 Nov 2017 00:07:44: Done! pass1 - making usageList (42 chroms): 3 millis pass2 - checking and writing primary data (4422 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 00:07:53: #4 Write output xls file... SRX2202919.10_peaks.xls INFO @ Sat, 11 Nov 2017 00:07:53: #4 Write peak in narrowPeak format file... SRX2202919.10_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:07:53: #4 Write summits bed file... SRX2202919.10_summits.bed INFO @ Sat, 11 Nov 2017 00:07:53: Done! pass1 - making usageList (77 chroms): 4 millis pass2 - checking and writing primary data (13438 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。