Job ID = 10195036 sra ファイルのダウンロード中... Completed: 131860K bytes transferred in 5 seconds (180724K bits/sec), in 1 file. Completed: 1070030K bytes transferred in 20 seconds (434358K 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 5614938 spots for /home/okishinya/chipatlas/results/rn6/SRX913505/SRR1870946.sra Written 5614938 spots total Written 33849248 spots for /home/okishinya/chipatlas/results/rn6/SRX913505/SRR1870947.sra Written 33849248 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: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:25:11 39464186 reads; of these: 39464186 (100.00%) were unpaired; of these: 4812415 (12.19%) aligned 0 times 25640557 (64.97%) aligned exactly 1 time 9011214 (22.83%) aligned >1 times 87.81% overall alignment rate Time searching: 00:25:15 Overall time: 00:25:15 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] 4714730 / 34651771 = 0.1361 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 07:15:29: # Command line: callpeak -t SRX913505.bam -f BAM -g 2.15e9 -n SRX913505.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX913505.20 # format = BAM # ChIP-seq file = ['SRX913505.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 07:15:29: # Command line: callpeak -t SRX913505.bam -f BAM -g 2.15e9 -n SRX913505.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX913505.05 # format = BAM # ChIP-seq file = ['SRX913505.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 07:15:29: # Command line: callpeak -t SRX913505.bam -f BAM -g 2.15e9 -n SRX913505.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX913505.10 # format = BAM # ChIP-seq file = ['SRX913505.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 07:15:29: #1 read tag files... INFO @ Sat, 11 Nov 2017 07:15:29: #1 read tag files... INFO @ Sat, 11 Nov 2017 07:15:29: #1 read tag files... INFO @ Sat, 11 Nov 2017 07:15:29: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 07:15:29: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 07:15:29: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 07:15:35: 1000000 INFO @ Sat, 11 Nov 2017 07:15:35: 1000000 INFO @ Sat, 11 Nov 2017 07:15:35: 1000000 INFO @ Sat, 11 Nov 2017 07:15:41: 2000000 INFO @ Sat, 11 Nov 2017 07:15:42: 2000000 INFO @ Sat, 11 Nov 2017 07:15:42: 2000000 INFO @ Sat, 11 Nov 2017 07:15:48: 3000000 INFO @ Sat, 11 Nov 2017 07:15:48: 3000000 INFO @ Sat, 11 Nov 2017 07:15:49: 3000000 INFO @ Sat, 11 Nov 2017 07:15:54: 4000000 INFO @ Sat, 11 Nov 2017 07:15:54: 4000000 INFO @ Sat, 11 Nov 2017 07:15:56: 4000000 INFO @ Sat, 11 Nov 2017 07:16:00: 5000000 INFO @ Sat, 11 Nov 2017 07:16:01: 5000000 INFO @ Sat, 11 Nov 2017 07:16:02: 5000000 INFO @ Sat, 11 Nov 2017 07:16:07: 6000000 INFO @ Sat, 11 Nov 2017 07:16:07: 6000000 INFO @ Sat, 11 Nov 2017 07:16:09: 6000000 INFO @ Sat, 11 Nov 2017 07:16:13: 7000000 INFO @ Sat, 11 Nov 2017 07:16:14: 7000000 INFO @ Sat, 11 Nov 2017 07:16:16: 7000000 INFO @ Sat, 11 Nov 2017 07:16:19: 8000000 INFO @ Sat, 11 Nov 2017 07:16:21: 8000000 INFO @ Sat, 11 Nov 2017 07:16:23: 8000000 INFO @ Sat, 11 Nov 2017 07:16:25: 9000000 INFO @ Sat, 11 Nov 2017 07:16:27: 9000000 INFO @ Sat, 11 Nov 2017 07:16:30: 9000000 INFO @ Sat, 11 Nov 2017 07:16:32: 10000000 INFO @ Sat, 11 Nov 2017 07:16:34: 10000000 INFO @ Sat, 11 Nov 2017 07:16:38: 10000000 INFO @ Sat, 11 Nov 2017 07:16:38: 11000000 INFO @ Sat, 11 Nov 2017 07:16:41: 11000000 INFO @ Sat, 11 Nov 2017 07:16:44: 12000000 INFO @ Sat, 11 Nov 2017 07:16:45: 11000000 INFO @ Sat, 11 Nov 2017 07:16:47: 12000000 INFO @ Sat, 11 Nov 2017 07:16:51: 13000000 INFO @ Sat, 11 Nov 2017 07:16:52: 12000000 INFO @ Sat, 11 Nov 2017 07:16:54: 13000000 INFO @ Sat, 11 Nov 2017 07:16:57: 14000000 INFO @ Sat, 11 Nov 2017 07:16:59: 13000000 INFO @ Sat, 11 Nov 2017 07:17:01: 14000000 INFO @ Sat, 11 Nov 2017 07:17:03: 15000000 INFO @ Sat, 11 Nov 2017 07:17:06: 14000000 INFO @ Sat, 11 Nov 2017 07:17:07: 15000000 INFO @ Sat, 11 Nov 2017 07:17:10: 16000000 INFO @ Sat, 11 Nov 2017 07:17:13: 15000000 INFO @ Sat, 11 Nov 2017 07:17:14: 16000000 INFO @ Sat, 11 Nov 2017 07:17:16: 17000000 INFO @ Sat, 11 Nov 2017 07:17:20: 16000000 INFO @ Sat, 11 Nov 2017 07:17:21: 17000000 INFO @ Sat, 11 Nov 2017 07:17:22: 18000000 INFO @ Sat, 11 Nov 2017 07:17:27: 17000000 INFO @ Sat, 11 Nov 2017 07:17:27: 18000000 INFO @ Sat, 11 Nov 2017 07:17:29: 19000000 INFO @ Sat, 11 Nov 2017 07:17:34: 18000000 INFO @ Sat, 11 Nov 2017 07:17:34: 19000000 INFO @ Sat, 11 Nov 2017 07:17:35: 20000000 INFO @ Sat, 11 Nov 2017 07:17:40: 20000000 INFO @ Sat, 11 Nov 2017 07:17:41: 19000000 INFO @ Sat, 11 Nov 2017 07:17:41: 21000000 INFO @ Sat, 11 Nov 2017 07:17:47: 21000000 INFO @ Sat, 11 Nov 2017 07:17:47: 22000000 INFO @ Sat, 11 Nov 2017 07:17:48: 20000000 INFO @ Sat, 11 Nov 2017 07:17:54: 23000000 INFO @ Sat, 11 Nov 2017 07:17:54: 22000000 INFO @ Sat, 11 Nov 2017 07:17:55: 21000000 INFO @ Sat, 11 Nov 2017 07:18:00: 24000000 INFO @ Sat, 11 Nov 2017 07:18:00: 23000000 INFO @ Sat, 11 Nov 2017 07:18:01: 22000000 INFO @ Sat, 11 Nov 2017 07:18:06: 25000000 INFO @ Sat, 11 Nov 2017 07:18:07: 24000000 INFO @ Sat, 11 Nov 2017 07:18:08: 23000000 INFO @ Sat, 11 Nov 2017 07:18:12: 26000000 INFO @ Sat, 11 Nov 2017 07:18:14: 25000000 INFO @ Sat, 11 Nov 2017 07:18:15: 24000000 INFO @ Sat, 11 Nov 2017 07:18:19: 27000000 INFO @ Sat, 11 Nov 2017 07:18:21: 26000000 INFO @ Sat, 11 Nov 2017 07:18:22: 25000000 INFO @ Sat, 11 Nov 2017 07:18:25: 28000000 INFO @ Sat, 11 Nov 2017 07:18:27: 27000000 INFO @ Sat, 11 Nov 2017 07:18:29: 26000000 INFO @ Sat, 11 Nov 2017 07:18:32: 29000000 INFO @ Sat, 11 Nov 2017 07:18:33: 28000000 INFO @ Sat, 11 Nov 2017 07:18:36: 27000000 INFO @ Sat, 11 Nov 2017 07:18:38: #1 tag size is determined as 47 bps INFO @ Sat, 11 Nov 2017 07:18:38: #1 tag size = 47 INFO @ Sat, 11 Nov 2017 07:18:38: #1 total tags in treatment: 29937041 INFO @ Sat, 11 Nov 2017 07:18:38: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 07:18:38: #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 07:18:39: #1 tags after filtering in treatment: 29936947 INFO @ Sat, 11 Nov 2017 07:18:39: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 07:18:39: #1 finished! INFO @ Sat, 11 Nov 2017 07:18:39: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 07:18:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 07:18:39: 29000000 INFO @ Sat, 11 Nov 2017 07:18:42: 28000000 INFO @ Sat, 11 Nov 2017 07:18:42: #2 number of paired peaks: 10170 INFO @ Sat, 11 Nov 2017 07:18:42: start model_add_line... INFO @ Sat, 11 Nov 2017 07:18:43: start X-correlation... INFO @ Sat, 11 Nov 2017 07:18:43: end of X-cor INFO @ Sat, 11 Nov 2017 07:18:43: #2 finished! INFO @ Sat, 11 Nov 2017 07:18:43: #2 predicted fragment length is 101 bps INFO @ Sat, 11 Nov 2017 07:18:43: #2 alternative fragment length(s) may be 101 bps INFO @ Sat, 11 Nov 2017 07:18:43: #2.2 Generate R script for model : SRX913505.05_model.r INFO @ Sat, 11 Nov 2017 07:18:43: #3 Call peaks... INFO @ Sat, 11 Nov 2017 07:18:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 07:18:46: #1 tag size is determined as 47 bps INFO @ Sat, 11 Nov 2017 07:18:46: #1 tag size = 47 INFO @ Sat, 11 Nov 2017 07:18:46: #1 total tags in treatment: 29937041 INFO @ Sat, 11 Nov 2017 07:18:46: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 07:18:46: #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 07:18:46: #1 tags after filtering in treatment: 29936947 INFO @ Sat, 11 Nov 2017 07:18:46: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 07:18:46: #1 finished! INFO @ Sat, 11 Nov 2017 07:18:46: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 07:18:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 07:18:49: 29000000 INFO @ Sat, 11 Nov 2017 07:18:50: #2 number of paired peaks: 10170 INFO @ Sat, 11 Nov 2017 07:18:50: start model_add_line... INFO @ Sat, 11 Nov 2017 07:18:50: start X-correlation... INFO @ Sat, 11 Nov 2017 07:18:50: end of X-cor INFO @ Sat, 11 Nov 2017 07:18:50: #2 finished! INFO @ Sat, 11 Nov 2017 07:18:50: #2 predicted fragment length is 101 bps INFO @ Sat, 11 Nov 2017 07:18:50: #2 alternative fragment length(s) may be 101 bps INFO @ Sat, 11 Nov 2017 07:18:50: #2.2 Generate R script for model : SRX913505.10_model.r INFO @ Sat, 11 Nov 2017 07:18:50: #3 Call peaks... INFO @ Sat, 11 Nov 2017 07:18:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 07:18:55: #1 tag size is determined as 47 bps INFO @ Sat, 11 Nov 2017 07:18:55: #1 tag size = 47 INFO @ Sat, 11 Nov 2017 07:18:55: #1 total tags in treatment: 29937041 INFO @ Sat, 11 Nov 2017 07:18:55: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 07:18:55: #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 07:18:56: #1 tags after filtering in treatment: 29936947 INFO @ Sat, 11 Nov 2017 07:18:56: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 07:18:56: #1 finished! INFO @ Sat, 11 Nov 2017 07:18:56: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 07:18:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 07:18:59: #2 number of paired peaks: 10170 INFO @ Sat, 11 Nov 2017 07:18:59: start model_add_line... INFO @ Sat, 11 Nov 2017 07:18:59: start X-correlation... INFO @ Sat, 11 Nov 2017 07:18:59: end of X-cor INFO @ Sat, 11 Nov 2017 07:18:59: #2 finished! INFO @ Sat, 11 Nov 2017 07:18:59: #2 predicted fragment length is 101 bps INFO @ Sat, 11 Nov 2017 07:18:59: #2 alternative fragment length(s) may be 101 bps INFO @ Sat, 11 Nov 2017 07:18:59: #2.2 Generate R script for model : SRX913505.20_model.r INFO @ Sat, 11 Nov 2017 07:18:59: #3 Call peaks... INFO @ Sat, 11 Nov 2017 07:18:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 07:19:55: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 07:20:01: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 07:20:09: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 07:20:34: #4 Write output xls file... SRX913505.05_peaks.xls INFO @ Sat, 11 Nov 2017 07:20:34: #4 Write peak in narrowPeak format file... SRX913505.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 07:20:34: #4 Write summits bed file... SRX913505.05_summits.bed INFO @ Sat, 11 Nov 2017 07:20:34: Done! pass1 - making usageList (66 chroms): 1 millis pass2 - checking and writing primary data (1276 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 07:20:44: #4 Write output xls file... SRX913505.10_peaks.xls INFO @ Sat, 11 Nov 2017 07:20:44: #4 Write peak in narrowPeak format file... SRX913505.10_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 07:20:44: #4 Write summits bed file... SRX913505.10_summits.bed INFO @ Sat, 11 Nov 2017 07:20:44: Done! pass1 - making usageList (47 chroms): 0 millis pass2 - checking and writing primary data (530 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 07:20:50: #4 Write output xls file... SRX913505.20_peaks.xls INFO @ Sat, 11 Nov 2017 07:20:50: #4 Write peak in narrowPeak format file... SRX913505.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 07:20:50: #4 Write summits bed file... SRX913505.20_summits.bed INFO @ Sat, 11 Nov 2017 07:20:50: Done! pass1 - making usageList (32 chroms): 1 millis pass2 - checking and writing primary data (190 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。