Job ID = 10194782 sra ファイルのダウンロード中... Completed: 465152K bytes transferred in 6 seconds (563719K 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 19747110 spots for /home/okishinya/chipatlas/results/rn6/SRX1774914/SRR3544946.sra Written 19747110 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: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:14:06 19747110 reads; of these: 19747110 (100.00%) were unpaired; of these: 653845 (3.31%) aligned 0 times 15482528 (78.40%) aligned exactly 1 time 3610737 (18.28%) aligned >1 times 96.69% overall alignment rate Time searching: 00:14:08 Overall time: 00:14:08 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] 3073211 / 19093265 = 0.1610 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 17:14:32: # Command line: callpeak -t SRX1774914.bam -f BAM -g 2.15e9 -n SRX1774914.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1774914.05 # format = BAM # ChIP-seq file = ['SRX1774914.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 17:14:32: #1 read tag files... INFO @ Fri, 10 Nov 2017 17:14:32: # Command line: callpeak -t SRX1774914.bam -f BAM -g 2.15e9 -n SRX1774914.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1774914.10 # format = BAM # ChIP-seq file = ['SRX1774914.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 17:14:32: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 17:14:32: #1 read tag files... INFO @ Fri, 10 Nov 2017 17:14:32: # Command line: callpeak -t SRX1774914.bam -f BAM -g 2.15e9 -n SRX1774914.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1774914.20 # format = BAM # ChIP-seq file = ['SRX1774914.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 17:14:32: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 17:14:32: #1 read tag files... INFO @ Fri, 10 Nov 2017 17:14:32: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 17:14:39: 1000000 INFO @ Fri, 10 Nov 2017 17:14:40: 1000000 INFO @ Fri, 10 Nov 2017 17:14:40: 1000000 INFO @ Fri, 10 Nov 2017 17:14:46: 2000000 INFO @ Fri, 10 Nov 2017 17:14:48: 2000000 INFO @ Fri, 10 Nov 2017 17:14:48: 2000000 INFO @ Fri, 10 Nov 2017 17:14:53: 3000000 INFO @ Fri, 10 Nov 2017 17:14:56: 3000000 INFO @ Fri, 10 Nov 2017 17:14:57: 3000000 INFO @ Fri, 10 Nov 2017 17:15:01: 4000000 INFO @ Fri, 10 Nov 2017 17:15:04: 4000000 INFO @ Fri, 10 Nov 2017 17:15:06: 4000000 INFO @ Fri, 10 Nov 2017 17:15:09: 5000000 INFO @ Fri, 10 Nov 2017 17:15:12: 5000000 INFO @ Fri, 10 Nov 2017 17:15:15: 5000000 INFO @ Fri, 10 Nov 2017 17:15:16: 6000000 INFO @ Fri, 10 Nov 2017 17:15:20: 6000000 INFO @ Fri, 10 Nov 2017 17:15:23: 7000000 INFO @ Fri, 10 Nov 2017 17:15:24: 6000000 INFO @ Fri, 10 Nov 2017 17:15:28: 7000000 INFO @ Fri, 10 Nov 2017 17:15:31: 8000000 INFO @ Fri, 10 Nov 2017 17:15:32: 7000000 INFO @ Fri, 10 Nov 2017 17:15:37: 8000000 INFO @ Fri, 10 Nov 2017 17:15:38: 9000000 INFO @ Fri, 10 Nov 2017 17:15:41: 8000000 INFO @ Fri, 10 Nov 2017 17:15:45: 9000000 INFO @ Fri, 10 Nov 2017 17:15:46: 10000000 INFO @ Fri, 10 Nov 2017 17:15:49: 9000000 INFO @ Fri, 10 Nov 2017 17:15:53: 11000000 INFO @ Fri, 10 Nov 2017 17:15:54: 10000000 INFO @ Fri, 10 Nov 2017 17:15:58: 10000000 INFO @ Fri, 10 Nov 2017 17:16:00: 12000000 INFO @ Fri, 10 Nov 2017 17:16:02: 11000000 INFO @ Fri, 10 Nov 2017 17:16:06: 11000000 INFO @ Fri, 10 Nov 2017 17:16:08: 13000000 INFO @ Fri, 10 Nov 2017 17:16:10: 12000000 INFO @ Fri, 10 Nov 2017 17:16:15: 14000000 INFO @ Fri, 10 Nov 2017 17:16:15: 12000000 INFO @ Fri, 10 Nov 2017 17:16:19: 13000000 INFO @ Fri, 10 Nov 2017 17:16:22: 15000000 INFO @ Fri, 10 Nov 2017 17:16:23: 13000000 INFO @ Fri, 10 Nov 2017 17:16:27: 14000000 INFO @ Fri, 10 Nov 2017 17:16:29: 16000000 INFO @ Fri, 10 Nov 2017 17:16:29: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 17:16:29: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 17:16:29: #1 total tags in treatment: 16020054 INFO @ Fri, 10 Nov 2017 17:16:29: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 17:16:29: #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 17:16:30: #1 tags after filtering in treatment: 16019831 INFO @ Fri, 10 Nov 2017 17:16:30: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 17:16:30: #1 finished! INFO @ Fri, 10 Nov 2017 17:16:30: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 17:16:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 17:16:32: 14000000 INFO @ Fri, 10 Nov 2017 17:16:33: #2 number of paired peaks: 57129 INFO @ Fri, 10 Nov 2017 17:16:33: start model_add_line... INFO @ Fri, 10 Nov 2017 17:16:33: start X-correlation... INFO @ Fri, 10 Nov 2017 17:16:33: end of X-cor INFO @ Fri, 10 Nov 2017 17:16:33: #2 finished! INFO @ Fri, 10 Nov 2017 17:16:33: #2 predicted fragment length is 180 bps INFO @ Fri, 10 Nov 2017 17:16:33: #2 alternative fragment length(s) may be 180 bps INFO @ Fri, 10 Nov 2017 17:16:33: #2.2 Generate R script for model : SRX1774914.05_model.r INFO @ Fri, 10 Nov 2017 17:16:33: #3 Call peaks... INFO @ Fri, 10 Nov 2017 17:16:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 17:16:36: 15000000 INFO @ Fri, 10 Nov 2017 17:16:41: 15000000 INFO @ Fri, 10 Nov 2017 17:16:44: 16000000 INFO @ Fri, 10 Nov 2017 17:16:45: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 17:16:45: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 17:16:45: #1 total tags in treatment: 16020054 INFO @ Fri, 10 Nov 2017 17:16:45: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 17:16:45: #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 17:16:45: #1 tags after filtering in treatment: 16019831 INFO @ Fri, 10 Nov 2017 17:16:45: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 17:16:45: #1 finished! INFO @ Fri, 10 Nov 2017 17:16:45: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 17:16:45: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 17:16:49: #2 number of paired peaks: 57129 INFO @ Fri, 10 Nov 2017 17:16:49: start model_add_line... INFO @ Fri, 10 Nov 2017 17:16:49: 16000000 INFO @ Fri, 10 Nov 2017 17:16:49: start X-correlation... INFO @ Fri, 10 Nov 2017 17:16:49: end of X-cor INFO @ Fri, 10 Nov 2017 17:16:49: #2 finished! INFO @ Fri, 10 Nov 2017 17:16:49: #2 predicted fragment length is 180 bps INFO @ Fri, 10 Nov 2017 17:16:49: #2 alternative fragment length(s) may be 180 bps INFO @ Fri, 10 Nov 2017 17:16:49: #2.2 Generate R script for model : SRX1774914.20_model.r INFO @ Fri, 10 Nov 2017 17:16:49: #3 Call peaks... INFO @ Fri, 10 Nov 2017 17:16:49: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 17:16:49: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 17:16:49: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 17:16:49: #1 total tags in treatment: 16020054 INFO @ Fri, 10 Nov 2017 17:16:49: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 17:16:49: #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 17:16:50: #1 tags after filtering in treatment: 16019831 INFO @ Fri, 10 Nov 2017 17:16:50: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 17:16:50: #1 finished! INFO @ Fri, 10 Nov 2017 17:16:50: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 17:16:50: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 17:16:54: #2 number of paired peaks: 57129 INFO @ Fri, 10 Nov 2017 17:16:54: start model_add_line... INFO @ Fri, 10 Nov 2017 17:16:54: start X-correlation... INFO @ Fri, 10 Nov 2017 17:16:54: end of X-cor INFO @ Fri, 10 Nov 2017 17:16:54: #2 finished! INFO @ Fri, 10 Nov 2017 17:16:54: #2 predicted fragment length is 180 bps INFO @ Fri, 10 Nov 2017 17:16:54: #2 alternative fragment length(s) may be 180 bps INFO @ Fri, 10 Nov 2017 17:16:54: #2.2 Generate R script for model : SRX1774914.10_model.r INFO @ Fri, 10 Nov 2017 17:16:54: #3 Call peaks... INFO @ Fri, 10 Nov 2017 17:16:54: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 17:17:17: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 17:17:31: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 17:17:36: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 17:17:44: #4 Write output xls file... SRX1774914.05_peaks.xls INFO @ Fri, 10 Nov 2017 17:17:45: #4 Write peak in narrowPeak format file... SRX1774914.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 17:17:45: #4 Write summits bed file... SRX1774914.05_summits.bed INFO @ Fri, 10 Nov 2017 17:17:45: Done! pass1 - making usageList (114 chroms): 7 millis pass2 - checking and writing primary data (37361 records, 4 fields): 49 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 17:17:57: #4 Write output xls file... SRX1774914.20_peaks.xls INFO @ Fri, 10 Nov 2017 17:17:57: #4 Write peak in narrowPeak format file... SRX1774914.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 17:17:57: #4 Write summits bed file... SRX1774914.20_summits.bed INFO @ Fri, 10 Nov 2017 17:17:57: Done! pass1 - making usageList (62 chroms): 3 millis pass2 - checking and writing primary data (13931 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 17:18:02: #4 Write output xls file... SRX1774914.10_peaks.xls INFO @ Fri, 10 Nov 2017 17:18:02: #4 Write peak in narrowPeak format file... SRX1774914.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 17:18:02: #4 Write summits bed file... SRX1774914.10_summits.bed INFO @ Fri, 10 Nov 2017 17:18:03: Done! pass1 - making usageList (91 chroms): 5 millis pass2 - checking and writing primary data (24159 records, 4 fields): 32 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。