Job ID = 10194873 sra ファイルのダウンロード中... Completed: 195897K bytes transferred in 7 seconds (216174K bits/sec), in 1 file. Completed: 196803K bytes transferred in 6 seconds (248240K bits/sec), in 1 file. Completed: 185832K bytes transferred in 9 seconds (157117K bits/sec), in 1 file. Completed: 183465K bytes transferred in 7 seconds (201262K bits/sec), in 1 file. Completed: 212865K bytes transferred in 7 seconds (226066K bits/sec), in 1 file. Completed: 215871K bytes transferred in 10 seconds (161229K 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 4157775 spots for /home/okishinya/chipatlas/results/rn6/SRX2202869/SRR4319761.sra Written 4157775 spots total Written 4200713 spots for /home/okishinya/chipatlas/results/rn6/SRX2202869/SRR4319760.sra Written 4200713 spots total Written 4411226 spots for /home/okishinya/chipatlas/results/rn6/SRX2202869/SRR4319758.sra Written 4411226 spots total Written 4417065 spots for /home/okishinya/chipatlas/results/rn6/SRX2202869/SRR4319759.sra Written 4417065 spots total Written 4685654 spots for /home/okishinya/chipatlas/results/rn6/SRX2202869/SRR4319762.sra Written 4685654 spots total Written 4733154 spots for /home/okishinya/chipatlas/results/rn6/SRX2202869/SRR4319763.sra Written 4733154 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: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:20:06 26605587 reads; of these: 26605587 (100.00%) were unpaired; of these: 964544 (3.63%) aligned 0 times 19097690 (71.78%) aligned exactly 1 time 6543353 (24.59%) aligned >1 times 96.37% overall alignment rate Time searching: 00:20:10 Overall time: 00:20:10 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] 1949856 / 25641043 = 0.0760 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 17:54:54: # Command line: callpeak -t SRX2202869.bam -f BAM -g 2.15e9 -n SRX2202869.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2202869.20 # format = BAM # ChIP-seq file = ['SRX2202869.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 17:54:54: # Command line: callpeak -t SRX2202869.bam -f BAM -g 2.15e9 -n SRX2202869.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2202869.10 # format = BAM # ChIP-seq file = ['SRX2202869.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 17:54:54: # Command line: callpeak -t SRX2202869.bam -f BAM -g 2.15e9 -n SRX2202869.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2202869.05 # format = BAM # ChIP-seq file = ['SRX2202869.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 17:54:54: #1 read tag files... INFO @ Fri, 10 Nov 2017 17:54:54: #1 read tag files... INFO @ Fri, 10 Nov 2017 17:54:54: #1 read tag files... INFO @ Fri, 10 Nov 2017 17:54:54: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 17:54:54: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 17:54:54: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 17:55:01: 1000000 INFO @ Fri, 10 Nov 2017 17:55:01: 1000000 INFO @ Fri, 10 Nov 2017 17:55:01: 1000000 INFO @ Fri, 10 Nov 2017 17:55:08: 2000000 INFO @ Fri, 10 Nov 2017 17:55:08: 2000000 INFO @ Fri, 10 Nov 2017 17:55:08: 2000000 INFO @ Fri, 10 Nov 2017 17:55:15: 3000000 INFO @ Fri, 10 Nov 2017 17:55:15: 3000000 INFO @ Fri, 10 Nov 2017 17:55:16: 3000000 INFO @ Fri, 10 Nov 2017 17:55:22: 4000000 INFO @ Fri, 10 Nov 2017 17:55:23: 4000000 INFO @ Fri, 10 Nov 2017 17:55:23: 4000000 INFO @ Fri, 10 Nov 2017 17:55:29: 5000000 INFO @ Fri, 10 Nov 2017 17:55:30: 5000000 INFO @ Fri, 10 Nov 2017 17:55:30: 5000000 INFO @ Fri, 10 Nov 2017 17:55:36: 6000000 INFO @ Fri, 10 Nov 2017 17:55:37: 6000000 INFO @ Fri, 10 Nov 2017 17:55:37: 6000000 INFO @ Fri, 10 Nov 2017 17:55:43: 7000000 INFO @ Fri, 10 Nov 2017 17:55:44: 7000000 INFO @ Fri, 10 Nov 2017 17:55:44: 7000000 INFO @ Fri, 10 Nov 2017 17:55:50: 8000000 INFO @ Fri, 10 Nov 2017 17:55:51: 8000000 INFO @ Fri, 10 Nov 2017 17:55:51: 8000000 INFO @ Fri, 10 Nov 2017 17:55:58: 9000000 INFO @ Fri, 10 Nov 2017 17:55:58: 9000000 INFO @ Fri, 10 Nov 2017 17:55:58: 9000000 INFO @ Fri, 10 Nov 2017 17:56:05: 10000000 INFO @ Fri, 10 Nov 2017 17:56:05: 10000000 INFO @ Fri, 10 Nov 2017 17:56:05: 10000000 INFO @ Fri, 10 Nov 2017 17:56:12: 11000000 INFO @ Fri, 10 Nov 2017 17:56:12: 11000000 INFO @ Fri, 10 Nov 2017 17:56:12: 11000000 INFO @ Fri, 10 Nov 2017 17:56:19: 12000000 INFO @ Fri, 10 Nov 2017 17:56:19: 12000000 INFO @ Fri, 10 Nov 2017 17:56:19: 12000000 INFO @ Fri, 10 Nov 2017 17:56:26: 13000000 INFO @ Fri, 10 Nov 2017 17:56:26: 13000000 INFO @ Fri, 10 Nov 2017 17:56:26: 13000000 INFO @ Fri, 10 Nov 2017 17:56:33: 14000000 INFO @ Fri, 10 Nov 2017 17:56:33: 14000000 INFO @ Fri, 10 Nov 2017 17:56:33: 14000000 INFO @ Fri, 10 Nov 2017 17:56:40: 15000000 INFO @ Fri, 10 Nov 2017 17:56:40: 15000000 INFO @ Fri, 10 Nov 2017 17:56:40: 15000000 INFO @ Fri, 10 Nov 2017 17:56:47: 16000000 INFO @ Fri, 10 Nov 2017 17:56:48: 16000000 INFO @ Fri, 10 Nov 2017 17:56:48: 16000000 INFO @ Fri, 10 Nov 2017 17:56:54: 17000000 INFO @ Fri, 10 Nov 2017 17:56:55: 17000000 INFO @ Fri, 10 Nov 2017 17:56:55: 17000000 INFO @ Fri, 10 Nov 2017 17:57:01: 18000000 INFO @ Fri, 10 Nov 2017 17:57:02: 18000000 INFO @ Fri, 10 Nov 2017 17:57:02: 18000000 INFO @ Fri, 10 Nov 2017 17:57:08: 19000000 INFO @ Fri, 10 Nov 2017 17:57:10: 19000000 INFO @ Fri, 10 Nov 2017 17:57:10: 19000000 INFO @ Fri, 10 Nov 2017 17:57:15: 20000000 INFO @ Fri, 10 Nov 2017 17:57:17: 20000000 INFO @ Fri, 10 Nov 2017 17:57:17: 20000000 INFO @ Fri, 10 Nov 2017 17:57:22: 21000000 INFO @ Fri, 10 Nov 2017 17:57:24: 21000000 INFO @ Fri, 10 Nov 2017 17:57:24: 21000000 INFO @ Fri, 10 Nov 2017 17:57:29: 22000000 INFO @ Fri, 10 Nov 2017 17:57:31: 22000000 INFO @ Fri, 10 Nov 2017 17:57:31: 22000000 INFO @ Fri, 10 Nov 2017 17:57:36: 23000000 INFO @ Fri, 10 Nov 2017 17:57:39: 23000000 INFO @ Fri, 10 Nov 2017 17:57:39: 23000000 INFO @ Fri, 10 Nov 2017 17:57:41: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 17:57:41: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 17:57:41: #1 total tags in treatment: 23691187 INFO @ Fri, 10 Nov 2017 17:57:41: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 17:57:41: #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 17:57:42: #1 tags after filtering in treatment: 23691064 INFO @ Fri, 10 Nov 2017 17:57:42: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 17:57:42: #1 finished! INFO @ Fri, 10 Nov 2017 17:57:42: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 17:57:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 17:57:44: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 17:57:44: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 17:57:44: #1 total tags in treatment: 23691187 INFO @ Fri, 10 Nov 2017 17:57:44: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 17:57:44: #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 17:57:44: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 17:57:44: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 17:57:44: #1 total tags in treatment: 23691187 INFO @ Fri, 10 Nov 2017 17:57:44: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 17:57:44: #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 17:57:45: #2 number of paired peaks: 26294 INFO @ Fri, 10 Nov 2017 17:57:45: start model_add_line... INFO @ Fri, 10 Nov 2017 17:57:45: #1 tags after filtering in treatment: 23691064 INFO @ Fri, 10 Nov 2017 17:57:45: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 17:57:45: #1 finished! INFO @ Fri, 10 Nov 2017 17:57:45: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 17:57:45: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 17:57:45: #1 tags after filtering in treatment: 23691064 INFO @ Fri, 10 Nov 2017 17:57:45: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 17:57:45: #1 finished! INFO @ Fri, 10 Nov 2017 17:57:45: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 17:57:45: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 17:57:45: start X-correlation... INFO @ Fri, 10 Nov 2017 17:57:45: end of X-cor INFO @ Fri, 10 Nov 2017 17:57:45: #2 finished! INFO @ Fri, 10 Nov 2017 17:57:45: #2 predicted fragment length is 128 bps INFO @ Fri, 10 Nov 2017 17:57:45: #2 alternative fragment length(s) may be 128 bps INFO @ Fri, 10 Nov 2017 17:57:45: #2.2 Generate R script for model : SRX2202869.10_model.r INFO @ Fri, 10 Nov 2017 17:57:45: #3 Call peaks... INFO @ Fri, 10 Nov 2017 17:57:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 17:57:48: #2 number of paired peaks: 26294 INFO @ Fri, 10 Nov 2017 17:57:48: start model_add_line... INFO @ Fri, 10 Nov 2017 17:57:48: #2 number of paired peaks: 26294 INFO @ Fri, 10 Nov 2017 17:57:48: start model_add_line... INFO @ Fri, 10 Nov 2017 17:57:48: start X-correlation... INFO @ Fri, 10 Nov 2017 17:57:48: end of X-cor INFO @ Fri, 10 Nov 2017 17:57:48: #2 finished! INFO @ Fri, 10 Nov 2017 17:57:48: #2 predicted fragment length is 128 bps INFO @ Fri, 10 Nov 2017 17:57:48: #2 alternative fragment length(s) may be 128 bps INFO @ Fri, 10 Nov 2017 17:57:48: #2.2 Generate R script for model : SRX2202869.20_model.r INFO @ Fri, 10 Nov 2017 17:57:48: #3 Call peaks... INFO @ Fri, 10 Nov 2017 17:57:48: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 17:57:48: start X-correlation... INFO @ Fri, 10 Nov 2017 17:57:48: end of X-cor INFO @ Fri, 10 Nov 2017 17:57:48: #2 finished! INFO @ Fri, 10 Nov 2017 17:57:48: #2 predicted fragment length is 128 bps INFO @ Fri, 10 Nov 2017 17:57:48: #2 alternative fragment length(s) may be 128 bps INFO @ Fri, 10 Nov 2017 17:57:48: #2.2 Generate R script for model : SRX2202869.05_model.r INFO @ Fri, 10 Nov 2017 17:57:48: #3 Call peaks... INFO @ Fri, 10 Nov 2017 17:57:48: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 17:58:42: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 17:58:46: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 17:58:53: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 17:59:15: #4 Write output xls file... SRX2202869.10_peaks.xls INFO @ Fri, 10 Nov 2017 17:59:15: #4 Write peak in narrowPeak format file... SRX2202869.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 17:59:15: #4 Write summits bed file... SRX2202869.10_summits.bed INFO @ Fri, 10 Nov 2017 17:59:15: Done! pass1 - making usageList (48 chroms): 1 millis pass2 - checking and writing primary data (4445 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 17:59:20: #4 Write output xls file... SRX2202869.20_peaks.xls INFO @ Fri, 10 Nov 2017 17:59:20: #4 Write peak in narrowPeak format file... SRX2202869.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 17:59:21: #4 Write summits bed file... SRX2202869.20_summits.bed INFO @ Fri, 10 Nov 2017 17:59:21: Done! pass1 - making usageList (37 chroms): 2 millis pass2 - checking and writing primary data (651 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 17:59:30: #4 Write output xls file... SRX2202869.05_peaks.xls INFO @ Fri, 10 Nov 2017 17:59:30: #4 Write peak in narrowPeak format file... SRX2202869.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 17:59:30: #4 Write summits bed file... SRX2202869.05_summits.bed INFO @ Fri, 10 Nov 2017 17:59:31: Done! pass1 - making usageList (73 chroms): 3 millis pass2 - checking and writing primary data (11846 records, 4 fields): 16 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。