Job ID = 10194719 sra ファイルのダウンロード中... Completed: 685520K bytes transferred in 14 seconds (392485K 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 30702529 spots for /home/okishinya/chipatlas/results/rn6/SRX058448/SRR189592.sra Written 30702529 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 rm: cannot remove `[DSE]RR*.fastq': 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: 00:00:01 Multiseed full-index search: 00:36:29 30702529 reads; of these: 30702529 (100.00%) were unpaired; of these: 1372584 (4.47%) aligned 0 times 20987701 (68.36%) aligned exactly 1 time 8342244 (27.17%) aligned >1 times 95.53% overall alignment rate Time searching: 00:36:32 Overall time: 00:36:32 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 8 files... [bam_rmdupse_core] 6517328 / 29329945 = 0.2222 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 19:40:00: # Command line: callpeak -t SRX058448.bam -f BAM -g 2.15e9 -n SRX058448.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX058448.20 # format = BAM # ChIP-seq file = ['SRX058448.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 19:40:00: #1 read tag files... INFO @ Fri, 10 Nov 2017 19:40:00: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 19:40:00: # Command line: callpeak -t SRX058448.bam -f BAM -g 2.15e9 -n SRX058448.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX058448.10 # format = BAM # ChIP-seq file = ['SRX058448.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 19:40:00: #1 read tag files... INFO @ Fri, 10 Nov 2017 19:40:00: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 19:40:00: # Command line: callpeak -t SRX058448.bam -f BAM -g 2.15e9 -n SRX058448.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX058448.05 # format = BAM # ChIP-seq file = ['SRX058448.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 19:40:00: #1 read tag files... INFO @ Fri, 10 Nov 2017 19:40:00: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 19:40:08: 1000000 INFO @ Fri, 10 Nov 2017 19:40:11: 1000000 INFO @ Fri, 10 Nov 2017 19:40:13: 1000000 INFO @ Fri, 10 Nov 2017 19:40:15: 2000000 INFO @ Fri, 10 Nov 2017 19:40:22: 2000000 INFO @ Fri, 10 Nov 2017 19:40:23: 3000000 INFO @ Fri, 10 Nov 2017 19:40:27: 2000000 INFO @ Fri, 10 Nov 2017 19:40:30: 4000000 INFO @ Fri, 10 Nov 2017 19:40:33: 3000000 INFO @ Fri, 10 Nov 2017 19:40:38: 5000000 INFO @ Fri, 10 Nov 2017 19:40:40: 3000000 INFO @ Fri, 10 Nov 2017 19:40:45: 4000000 INFO @ Fri, 10 Nov 2017 19:40:45: 6000000 INFO @ Fri, 10 Nov 2017 19:40:52: 7000000 INFO @ Fri, 10 Nov 2017 19:40:53: 4000000 INFO @ Fri, 10 Nov 2017 19:40:57: 5000000 INFO @ Fri, 10 Nov 2017 19:41:00: 8000000 INFO @ Fri, 10 Nov 2017 19:41:05: 5000000 INFO @ Fri, 10 Nov 2017 19:41:07: 9000000 INFO @ Fri, 10 Nov 2017 19:41:09: 6000000 INFO @ Fri, 10 Nov 2017 19:41:15: 10000000 INFO @ Fri, 10 Nov 2017 19:41:18: 6000000 INFO @ Fri, 10 Nov 2017 19:41:21: 7000000 INFO @ Fri, 10 Nov 2017 19:41:22: 11000000 INFO @ Fri, 10 Nov 2017 19:41:30: 12000000 INFO @ Fri, 10 Nov 2017 19:41:31: 7000000 INFO @ Fri, 10 Nov 2017 19:41:32: 8000000 INFO @ Fri, 10 Nov 2017 19:41:37: 13000000 INFO @ Fri, 10 Nov 2017 19:41:43: 9000000 INFO @ Fri, 10 Nov 2017 19:41:43: 8000000 INFO @ Fri, 10 Nov 2017 19:41:45: 14000000 INFO @ Fri, 10 Nov 2017 19:41:52: 15000000 INFO @ Fri, 10 Nov 2017 19:41:54: 10000000 INFO @ Fri, 10 Nov 2017 19:41:56: 9000000 INFO @ Fri, 10 Nov 2017 19:41:59: 16000000 INFO @ Fri, 10 Nov 2017 19:42:05: 11000000 INFO @ Fri, 10 Nov 2017 19:42:07: 17000000 INFO @ Fri, 10 Nov 2017 19:42:08: 10000000 INFO @ Fri, 10 Nov 2017 19:42:14: 18000000 INFO @ Fri, 10 Nov 2017 19:42:15: 12000000 INFO @ Fri, 10 Nov 2017 19:42:20: 11000000 INFO @ Fri, 10 Nov 2017 19:42:22: 19000000 INFO @ Fri, 10 Nov 2017 19:42:26: 13000000 INFO @ Fri, 10 Nov 2017 19:42:29: 20000000 INFO @ Fri, 10 Nov 2017 19:42:33: 12000000 INFO @ Fri, 10 Nov 2017 19:42:37: 14000000 INFO @ Fri, 10 Nov 2017 19:42:37: 21000000 INFO @ Fri, 10 Nov 2017 19:42:45: 22000000 INFO @ Fri, 10 Nov 2017 19:42:45: 13000000 INFO @ Fri, 10 Nov 2017 19:42:48: 15000000 INFO @ Fri, 10 Nov 2017 19:42:51: #1 tag size is determined as 40 bps INFO @ Fri, 10 Nov 2017 19:42:51: #1 tag size = 40 INFO @ Fri, 10 Nov 2017 19:42:51: #1 total tags in treatment: 22812617 INFO @ Fri, 10 Nov 2017 19:42:51: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 19:42:51: #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 19:42:52: #1 tags after filtering in treatment: 22812498 INFO @ Fri, 10 Nov 2017 19:42:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 19:42:52: #1 finished! INFO @ Fri, 10 Nov 2017 19:42:52: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 19:42:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 19:42:55: #2 number of paired peaks: 10018 INFO @ Fri, 10 Nov 2017 19:42:55: start model_add_line... INFO @ Fri, 10 Nov 2017 19:42:56: start X-correlation... INFO @ Fri, 10 Nov 2017 19:42:56: end of X-cor INFO @ Fri, 10 Nov 2017 19:42:56: #2 finished! INFO @ Fri, 10 Nov 2017 19:42:56: #2 predicted fragment length is 81 bps INFO @ Fri, 10 Nov 2017 19:42:56: #2 alternative fragment length(s) may be 81 bps INFO @ Fri, 10 Nov 2017 19:42:56: #2.2 Generate R script for model : SRX058448.20_model.r INFO @ Fri, 10 Nov 2017 19:42:56: #3 Call peaks... INFO @ Fri, 10 Nov 2017 19:42:56: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 19:42:56: 14000000 INFO @ Fri, 10 Nov 2017 19:42:59: 16000000 INFO @ Fri, 10 Nov 2017 19:43:08: 15000000 INFO @ Fri, 10 Nov 2017 19:43:09: 17000000 INFO @ Fri, 10 Nov 2017 19:43:20: 16000000 INFO @ Fri, 10 Nov 2017 19:43:20: 18000000 INFO @ Fri, 10 Nov 2017 19:43:31: 19000000 INFO @ Fri, 10 Nov 2017 19:43:32: 17000000 INFO @ Fri, 10 Nov 2017 19:43:42: 20000000 INFO @ Fri, 10 Nov 2017 19:43:45: 18000000 INFO @ Fri, 10 Nov 2017 19:43:53: 21000000 INFO @ Fri, 10 Nov 2017 19:43:57: 19000000 INFO @ Fri, 10 Nov 2017 19:44:02: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 19:44:04: 22000000 INFO @ Fri, 10 Nov 2017 19:44:10: 20000000 INFO @ Fri, 10 Nov 2017 19:44:13: #1 tag size is determined as 40 bps INFO @ Fri, 10 Nov 2017 19:44:13: #1 tag size = 40 INFO @ Fri, 10 Nov 2017 19:44:13: #1 total tags in treatment: 22812617 INFO @ Fri, 10 Nov 2017 19:44:13: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 19:44:13: #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 19:44:13: #1 tags after filtering in treatment: 22812498 INFO @ Fri, 10 Nov 2017 19:44:13: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 19:44:13: #1 finished! INFO @ Fri, 10 Nov 2017 19:44:13: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 19:44:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 19:44:17: #2 number of paired peaks: 10018 INFO @ Fri, 10 Nov 2017 19:44:17: start model_add_line... INFO @ Fri, 10 Nov 2017 19:44:17: start X-correlation... INFO @ Fri, 10 Nov 2017 19:44:17: end of X-cor INFO @ Fri, 10 Nov 2017 19:44:17: #2 finished! INFO @ Fri, 10 Nov 2017 19:44:17: #2 predicted fragment length is 81 bps INFO @ Fri, 10 Nov 2017 19:44:17: #2 alternative fragment length(s) may be 81 bps INFO @ Fri, 10 Nov 2017 19:44:17: #2.2 Generate R script for model : SRX058448.05_model.r INFO @ Fri, 10 Nov 2017 19:44:17: #3 Call peaks... INFO @ Fri, 10 Nov 2017 19:44:17: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 19:44:22: 21000000 INFO @ Fri, 10 Nov 2017 19:44:35: 22000000 INFO @ Fri, 10 Nov 2017 19:44:43: #4 Write output xls file... SRX058448.20_peaks.xls INFO @ Fri, 10 Nov 2017 19:44:43: #4 Write peak in narrowPeak format file... SRX058448.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 19:44:43: #4 Write summits bed file... SRX058448.20_summits.bed INFO @ Fri, 10 Nov 2017 19:44:43: Done! pass1 - making usageList (29 chroms): 10 millis pass2 - checking and writing primary data (404 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 19:44:45: #1 tag size is determined as 40 bps INFO @ Fri, 10 Nov 2017 19:44:45: #1 tag size = 40 INFO @ Fri, 10 Nov 2017 19:44:45: #1 total tags in treatment: 22812617 INFO @ Fri, 10 Nov 2017 19:44:45: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 19:44:45: #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 19:44:46: #1 tags after filtering in treatment: 22812498 INFO @ Fri, 10 Nov 2017 19:44:46: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 19:44:46: #1 finished! INFO @ Fri, 10 Nov 2017 19:44:46: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 19:44:46: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 19:44:49: #2 number of paired peaks: 10018 INFO @ Fri, 10 Nov 2017 19:44:49: start model_add_line... INFO @ Fri, 10 Nov 2017 19:44:50: start X-correlation... INFO @ Fri, 10 Nov 2017 19:44:50: end of X-cor INFO @ Fri, 10 Nov 2017 19:44:50: #2 finished! INFO @ Fri, 10 Nov 2017 19:44:50: #2 predicted fragment length is 81 bps INFO @ Fri, 10 Nov 2017 19:44:50: #2 alternative fragment length(s) may be 81 bps INFO @ Fri, 10 Nov 2017 19:44:50: #2.2 Generate R script for model : SRX058448.10_model.r INFO @ Fri, 10 Nov 2017 19:44:50: #3 Call peaks... INFO @ Fri, 10 Nov 2017 19:44:50: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 19:45:23: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 19:45:55: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 19:46:04: #4 Write output xls file... SRX058448.05_peaks.xls INFO @ Fri, 10 Nov 2017 19:46:05: #4 Write peak in narrowPeak format file... SRX058448.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 19:46:05: #4 Write summits bed file... SRX058448.05_summits.bed INFO @ Fri, 10 Nov 2017 19:46:05: Done! pass1 - making usageList (72 chroms): 3 millis pass2 - checking and writing primary data (6884 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 19:46:35: #4 Write output xls file... SRX058448.10_peaks.xls INFO @ Fri, 10 Nov 2017 19:46:35: #4 Write peak in narrowPeak format file... SRX058448.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 19:46:35: #4 Write summits bed file... SRX058448.10_summits.bed INFO @ Fri, 10 Nov 2017 19:46:35: Done! pass1 - making usageList (48 chroms): 2 millis pass2 - checking and writing primary data (1985 records, 4 fields): 213 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。