Job ID = 10194875 sra ファイルのダウンロード中... Completed: 172481K bytes transferred in 5 seconds (239337K bits/sec), in 1 file. Completed: 193057K bytes transferred in 6 seconds (227270K bits/sec), in 1 file. Completed: 190810K bytes transferred in 6 seconds (225310K bits/sec), in 1 file. Completed: 164353K bytes transferred in 8 seconds (158927K bits/sec), in 1 file. Completed: 166398K bytes transferred in 9 seconds (143973K bits/sec), in 1 file. Completed: 172961K bytes transferred in 8 seconds (166318K 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 3759216 spots for /home/okishinya/chipatlas/results/rn6/SRX2202871/SRR4319772.sra Written 3759216 spots total Written 3721594 spots for /home/okishinya/chipatlas/results/rn6/SRX2202871/SRR4319773.sra Written 3721594 spots total Written 3884065 spots for /home/okishinya/chipatlas/results/rn6/SRX2202871/SRR4319770.sra Written 3884065 spots total Written 3881010 spots for /home/okishinya/chipatlas/results/rn6/SRX2202871/SRR4319771.sra Written 3881010 spots total Written 4230323 spots for /home/okishinya/chipatlas/results/rn6/SRX2202871/SRR4319775.sra Written 4230323 spots total Written 4197194 spots for /home/okishinya/chipatlas/results/rn6/SRX2202871/SRR4319774.sra Written 4197194 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: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:15:56 23673402 reads; of these: 23673402 (100.00%) were unpaired; of these: 1863298 (7.87%) aligned 0 times 16567368 (69.98%) aligned exactly 1 time 5242736 (22.15%) aligned >1 times 92.13% overall alignment rate Time searching: 00:15:58 Overall time: 00:15:58 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] 1896285 / 21810104 = 0.0869 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 17:51:14: # Command line: callpeak -t SRX2202871.bam -f BAM -g 2.15e9 -n SRX2202871.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2202871.05 # format = BAM # ChIP-seq file = ['SRX2202871.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 17:51:14: #1 read tag files... INFO @ Fri, 10 Nov 2017 17:51:14: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 17:51:14: # Command line: callpeak -t SRX2202871.bam -f BAM -g 2.15e9 -n SRX2202871.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2202871.10 # format = BAM # ChIP-seq file = ['SRX2202871.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 17:51:14: #1 read tag files... INFO @ Fri, 10 Nov 2017 17:51:14: # Command line: callpeak -t SRX2202871.bam -f BAM -g 2.15e9 -n SRX2202871.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2202871.20 # format = BAM # ChIP-seq file = ['SRX2202871.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 17:51:14: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 17:51:14: #1 read tag files... INFO @ Fri, 10 Nov 2017 17:51:14: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 17:51:23: 1000000 INFO @ Fri, 10 Nov 2017 17:51:24: 1000000 INFO @ Fri, 10 Nov 2017 17:51:24: 1000000 INFO @ Fri, 10 Nov 2017 17:51:31: 2000000 INFO @ Fri, 10 Nov 2017 17:51:34: 2000000 INFO @ Fri, 10 Nov 2017 17:51:34: 2000000 INFO @ Fri, 10 Nov 2017 17:51:38: 3000000 INFO @ Fri, 10 Nov 2017 17:51:42: 3000000 INFO @ Fri, 10 Nov 2017 17:51:42: 3000000 INFO @ Fri, 10 Nov 2017 17:51:45: 4000000 INFO @ Fri, 10 Nov 2017 17:51:50: 4000000 INFO @ Fri, 10 Nov 2017 17:51:50: 4000000 INFO @ Fri, 10 Nov 2017 17:51:52: 5000000 INFO @ Fri, 10 Nov 2017 17:51:58: 5000000 INFO @ Fri, 10 Nov 2017 17:51:58: 5000000 INFO @ Fri, 10 Nov 2017 17:52:01: 6000000 INFO @ Fri, 10 Nov 2017 17:52:05: 6000000 INFO @ Fri, 10 Nov 2017 17:52:05: 6000000 INFO @ Fri, 10 Nov 2017 17:52:09: 7000000 INFO @ Fri, 10 Nov 2017 17:52:13: 7000000 INFO @ Fri, 10 Nov 2017 17:52:14: 7000000 INFO @ Fri, 10 Nov 2017 17:52:18: 8000000 INFO @ Fri, 10 Nov 2017 17:52:22: 8000000 INFO @ Fri, 10 Nov 2017 17:52:22: 8000000 INFO @ Fri, 10 Nov 2017 17:52:27: 9000000 INFO @ Fri, 10 Nov 2017 17:52:30: 9000000 INFO @ Fri, 10 Nov 2017 17:52:30: 9000000 INFO @ Fri, 10 Nov 2017 17:52:36: 10000000 INFO @ Fri, 10 Nov 2017 17:52:38: 10000000 INFO @ Fri, 10 Nov 2017 17:52:38: 10000000 INFO @ Fri, 10 Nov 2017 17:52:44: 11000000 INFO @ Fri, 10 Nov 2017 17:52:46: 11000000 INFO @ Fri, 10 Nov 2017 17:52:46: 11000000 INFO @ Fri, 10 Nov 2017 17:52:53: 12000000 INFO @ Fri, 10 Nov 2017 17:52:54: 12000000 INFO @ Fri, 10 Nov 2017 17:52:54: 12000000 INFO @ Fri, 10 Nov 2017 17:53:02: 13000000 INFO @ Fri, 10 Nov 2017 17:53:02: 13000000 INFO @ Fri, 10 Nov 2017 17:53:03: 13000000 INFO @ Fri, 10 Nov 2017 17:53:10: 14000000 INFO @ Fri, 10 Nov 2017 17:53:10: 14000000 INFO @ Fri, 10 Nov 2017 17:53:11: 14000000 INFO @ Fri, 10 Nov 2017 17:53:18: 15000000 INFO @ Fri, 10 Nov 2017 17:53:18: 15000000 INFO @ Fri, 10 Nov 2017 17:53:19: 15000000 INFO @ Fri, 10 Nov 2017 17:53:26: 16000000 INFO @ Fri, 10 Nov 2017 17:53:26: 16000000 INFO @ Fri, 10 Nov 2017 17:53:26: 16000000 INFO @ Fri, 10 Nov 2017 17:53:34: 17000000 INFO @ Fri, 10 Nov 2017 17:53:34: 17000000 INFO @ Fri, 10 Nov 2017 17:53:35: 17000000 INFO @ Fri, 10 Nov 2017 17:53:42: 18000000 INFO @ Fri, 10 Nov 2017 17:53:42: 18000000 INFO @ Fri, 10 Nov 2017 17:53:44: 18000000 INFO @ Fri, 10 Nov 2017 17:53:49: 19000000 INFO @ Fri, 10 Nov 2017 17:53:50: 19000000 INFO @ Fri, 10 Nov 2017 17:53:52: 19000000 INFO @ Fri, 10 Nov 2017 17:53:56: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 17:53:56: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 17:53:56: #1 total tags in treatment: 19913819 INFO @ Fri, 10 Nov 2017 17:53:56: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 17:53:56: #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 17:53:57: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 17:53:57: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 17:53:57: #1 total tags in treatment: 19913819 INFO @ Fri, 10 Nov 2017 17:53:57: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 17:53:57: #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 17:53:57: #1 tags after filtering in treatment: 19913664 INFO @ Fri, 10 Nov 2017 17:53:57: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 17:53:57: #1 finished! INFO @ Fri, 10 Nov 2017 17:53:57: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 17:53:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 17:53:57: #1 tags after filtering in treatment: 19913664 INFO @ Fri, 10 Nov 2017 17:53:57: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 17:53:57: #1 finished! INFO @ Fri, 10 Nov 2017 17:53:57: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 17:53:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 17:53:58: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 17:53:58: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 17:53:58: #1 total tags in treatment: 19913819 INFO @ Fri, 10 Nov 2017 17:53:58: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 17:53:58: #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 17:53:59: #1 tags after filtering in treatment: 19913664 INFO @ Fri, 10 Nov 2017 17:53:59: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 17:53:59: #1 finished! INFO @ Fri, 10 Nov 2017 17:53:59: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 17:53:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 17:54:00: #2 number of paired peaks: 32731 INFO @ Fri, 10 Nov 2017 17:54:00: start model_add_line... INFO @ Fri, 10 Nov 2017 17:54:00: start X-correlation... INFO @ Fri, 10 Nov 2017 17:54:00: end of X-cor INFO @ Fri, 10 Nov 2017 17:54:00: #2 finished! INFO @ Fri, 10 Nov 2017 17:54:00: #2 predicted fragment length is 146 bps INFO @ Fri, 10 Nov 2017 17:54:00: #2 alternative fragment length(s) may be 146 bps INFO @ Fri, 10 Nov 2017 17:54:00: #2.2 Generate R script for model : SRX2202871.10_model.r INFO @ Fri, 10 Nov 2017 17:54:00: #3 Call peaks... INFO @ Fri, 10 Nov 2017 17:54:00: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 17:54:00: #2 number of paired peaks: 32731 INFO @ Fri, 10 Nov 2017 17:54:00: start model_add_line... INFO @ Fri, 10 Nov 2017 17:54:01: start X-correlation... INFO @ Fri, 10 Nov 2017 17:54:01: end of X-cor INFO @ Fri, 10 Nov 2017 17:54:01: #2 finished! INFO @ Fri, 10 Nov 2017 17:54:01: #2 predicted fragment length is 146 bps INFO @ Fri, 10 Nov 2017 17:54:01: #2 alternative fragment length(s) may be 146 bps INFO @ Fri, 10 Nov 2017 17:54:01: #2.2 Generate R script for model : SRX2202871.20_model.r INFO @ Fri, 10 Nov 2017 17:54:01: #3 Call peaks... INFO @ Fri, 10 Nov 2017 17:54:01: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 17:54:02: #2 number of paired peaks: 32731 INFO @ Fri, 10 Nov 2017 17:54:02: start model_add_line... INFO @ Fri, 10 Nov 2017 17:54:02: start X-correlation... INFO @ Fri, 10 Nov 2017 17:54:02: end of X-cor INFO @ Fri, 10 Nov 2017 17:54:02: #2 finished! INFO @ Fri, 10 Nov 2017 17:54:02: #2 predicted fragment length is 146 bps INFO @ Fri, 10 Nov 2017 17:54:02: #2 alternative fragment length(s) may be 146 bps INFO @ Fri, 10 Nov 2017 17:54:02: #2.2 Generate R script for model : SRX2202871.05_model.r INFO @ Fri, 10 Nov 2017 17:54:02: #3 Call peaks... INFO @ Fri, 10 Nov 2017 17:54:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 17:54:47: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 17:54:52: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 17:54:52: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 17:55:14: #4 Write output xls file... SRX2202871.10_peaks.xls INFO @ Fri, 10 Nov 2017 17:55:14: #4 Write peak in narrowPeak format file... SRX2202871.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 17:55:14: #4 Write summits bed file... SRX2202871.10_summits.bed INFO @ Fri, 10 Nov 2017 17:55:14: Done! pass1 - making usageList (49 chroms): 1 millis pass2 - checking and writing primary data (3066 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 17:55:19: #4 Write output xls file... SRX2202871.20_peaks.xls INFO @ Fri, 10 Nov 2017 17:55:19: #4 Write peak in narrowPeak format file... SRX2202871.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 17:55:19: #4 Write summits bed file... SRX2202871.20_summits.bed INFO @ Fri, 10 Nov 2017 17:55:19: Done! pass1 - making usageList (34 chroms): 1 millis pass2 - checking and writing primary data (396 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 17:55:21: #4 Write output xls file... SRX2202871.05_peaks.xls INFO @ Fri, 10 Nov 2017 17:55:22: #4 Write peak in narrowPeak format file... SRX2202871.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 17:55:22: #4 Write summits bed file... SRX2202871.05_summits.bed INFO @ Fri, 10 Nov 2017 17:55:22: Done! pass1 - making usageList (73 chroms): 3 millis pass2 - checking and writing primary data (10158 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。