Job ID = 11632726 sra ファイルのダウンロード中... Completed: 563570K bytes transferred in 7 seconds (578571K 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... Read 30111520 spots for /home/okishinya/chipatlas/results/rn6/SRX4497196/SRR7633466.sra Written 30111520 spots for /home/okishinya/chipatlas/results/rn6/SRX4497196/SRR7633466.sra 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: 00:24:03 30111520 reads; of these: 30111520 (100.00%) were unpaired; of these: 1180648 (3.92%) aligned 0 times 21087940 (70.03%) aligned exactly 1 time 7842932 (26.05%) aligned >1 times 96.08% overall alignment rate Time searching: 00:24:05 Overall time: 00:24:05 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] 3883414 / 28930872 = 0.1342 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, 15 Feb 2019 07:20:17: # Command line: callpeak -t SRX4497196.bam -f BAM -g 2.15e9 -n SRX4497196.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4497196.05 # format = BAM # ChIP-seq file = ['SRX4497196.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, 15 Feb 2019 07:20:17: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:20:17: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:20:17: # Command line: callpeak -t SRX4497196.bam -f BAM -g 2.15e9 -n SRX4497196.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4497196.10 # format = BAM # ChIP-seq file = ['SRX4497196.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, 15 Feb 2019 07:20:17: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:20:17: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:20:17: # Command line: callpeak -t SRX4497196.bam -f BAM -g 2.15e9 -n SRX4497196.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4497196.20 # format = BAM # ChIP-seq file = ['SRX4497196.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, 15 Feb 2019 07:20:17: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:20:17: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:20:23: 1000000 INFO @ Fri, 15 Feb 2019 07:20:23: 1000000 INFO @ Fri, 15 Feb 2019 07:20:24: 1000000 INFO @ Fri, 15 Feb 2019 07:20:30: 2000000 INFO @ Fri, 15 Feb 2019 07:20:30: 2000000 INFO @ Fri, 15 Feb 2019 07:20:30: 2000000 INFO @ Fri, 15 Feb 2019 07:20:36: 3000000 INFO @ Fri, 15 Feb 2019 07:20:36: 3000000 INFO @ Fri, 15 Feb 2019 07:20:36: 3000000 INFO @ Fri, 15 Feb 2019 07:20:42: 4000000 INFO @ Fri, 15 Feb 2019 07:20:43: 4000000 INFO @ Fri, 15 Feb 2019 07:20:43: 4000000 INFO @ Fri, 15 Feb 2019 07:20:49: 5000000 INFO @ Fri, 15 Feb 2019 07:20:49: 5000000 INFO @ Fri, 15 Feb 2019 07:20:49: 5000000 INFO @ Fri, 15 Feb 2019 07:20:55: 6000000 INFO @ Fri, 15 Feb 2019 07:20:55: 6000000 INFO @ Fri, 15 Feb 2019 07:20:56: 6000000 INFO @ Fri, 15 Feb 2019 07:21:02: 7000000 INFO @ Fri, 15 Feb 2019 07:21:02: 7000000 INFO @ Fri, 15 Feb 2019 07:21:02: 7000000 INFO @ Fri, 15 Feb 2019 07:21:08: 8000000 INFO @ Fri, 15 Feb 2019 07:21:08: 8000000 INFO @ Fri, 15 Feb 2019 07:21:08: 8000000 INFO @ Fri, 15 Feb 2019 07:21:15: 9000000 INFO @ Fri, 15 Feb 2019 07:21:15: 9000000 INFO @ Fri, 15 Feb 2019 07:21:15: 9000000 INFO @ Fri, 15 Feb 2019 07:21:21: 10000000 INFO @ Fri, 15 Feb 2019 07:21:21: 10000000 INFO @ Fri, 15 Feb 2019 07:21:22: 10000000 INFO @ Fri, 15 Feb 2019 07:21:28: 11000000 INFO @ Fri, 15 Feb 2019 07:21:28: 11000000 INFO @ Fri, 15 Feb 2019 07:21:28: 11000000 INFO @ Fri, 15 Feb 2019 07:21:34: 12000000 INFO @ Fri, 15 Feb 2019 07:21:34: 12000000 INFO @ Fri, 15 Feb 2019 07:21:35: 12000000 INFO @ Fri, 15 Feb 2019 07:21:40: 13000000 INFO @ Fri, 15 Feb 2019 07:21:41: 13000000 INFO @ Fri, 15 Feb 2019 07:21:42: 13000000 INFO @ Fri, 15 Feb 2019 07:21:47: 14000000 INFO @ Fri, 15 Feb 2019 07:21:47: 14000000 INFO @ Fri, 15 Feb 2019 07:21:49: 14000000 INFO @ Fri, 15 Feb 2019 07:21:53: 15000000 INFO @ Fri, 15 Feb 2019 07:21:54: 15000000 INFO @ Fri, 15 Feb 2019 07:21:55: 15000000 INFO @ Fri, 15 Feb 2019 07:21:59: 16000000 INFO @ Fri, 15 Feb 2019 07:22:00: 16000000 INFO @ Fri, 15 Feb 2019 07:22:01: 16000000 INFO @ Fri, 15 Feb 2019 07:22:06: 17000000 INFO @ Fri, 15 Feb 2019 07:22:07: 17000000 INFO @ Fri, 15 Feb 2019 07:22:08: 17000000 INFO @ Fri, 15 Feb 2019 07:22:12: 18000000 INFO @ Fri, 15 Feb 2019 07:22:13: 18000000 INFO @ Fri, 15 Feb 2019 07:22:14: 18000000 INFO @ Fri, 15 Feb 2019 07:22:19: 19000000 INFO @ Fri, 15 Feb 2019 07:22:20: 19000000 INFO @ Fri, 15 Feb 2019 07:22:21: 19000000 INFO @ Fri, 15 Feb 2019 07:22:25: 20000000 INFO @ Fri, 15 Feb 2019 07:22:26: 20000000 INFO @ Fri, 15 Feb 2019 07:22:27: 20000000 INFO @ Fri, 15 Feb 2019 07:22:31: 21000000 INFO @ Fri, 15 Feb 2019 07:22:33: 21000000 INFO @ Fri, 15 Feb 2019 07:22:33: 21000000 INFO @ Fri, 15 Feb 2019 07:22:38: 22000000 INFO @ Fri, 15 Feb 2019 07:22:39: 22000000 INFO @ Fri, 15 Feb 2019 07:22:40: 22000000 INFO @ Fri, 15 Feb 2019 07:22:44: 23000000 INFO @ Fri, 15 Feb 2019 07:22:45: 23000000 INFO @ Fri, 15 Feb 2019 07:22:46: 23000000 INFO @ Fri, 15 Feb 2019 07:22:51: 24000000 INFO @ Fri, 15 Feb 2019 07:22:53: 24000000 INFO @ Fri, 15 Feb 2019 07:22:54: 24000000 INFO @ Fri, 15 Feb 2019 07:22:59: 25000000 INFO @ Fri, 15 Feb 2019 07:23:00: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 07:23:00: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 07:23:00: #1 total tags in treatment: 25047458 INFO @ Fri, 15 Feb 2019 07:23:00: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:23:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 07:23:01: #1 tags after filtering in treatment: 25047317 INFO @ Fri, 15 Feb 2019 07:23:01: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:23:01: #1 finished! INFO @ Fri, 15 Feb 2019 07:23:01: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:23:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:23:01: 25000000 INFO @ Fri, 15 Feb 2019 07:23:01: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 07:23:01: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 07:23:01: #1 total tags in treatment: 25047458 INFO @ Fri, 15 Feb 2019 07:23:01: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:23:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 07:23:02: #1 tags after filtering in treatment: 25047317 INFO @ Fri, 15 Feb 2019 07:23:02: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:23:02: #1 finished! INFO @ Fri, 15 Feb 2019 07:23:02: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:23:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:23:03: 25000000 INFO @ Fri, 15 Feb 2019 07:23:04: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 07:23:04: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 07:23:04: #1 total tags in treatment: 25047458 INFO @ Fri, 15 Feb 2019 07:23:04: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:23:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 07:23:04: #1 tags after filtering in treatment: 25047317 INFO @ Fri, 15 Feb 2019 07:23:04: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:23:04: #1 finished! INFO @ Fri, 15 Feb 2019 07:23:04: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:23:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:23:04: #2 number of paired peaks: 31467 INFO @ Fri, 15 Feb 2019 07:23:04: start model_add_line... INFO @ Fri, 15 Feb 2019 07:23:05: start X-correlation... INFO @ Fri, 15 Feb 2019 07:23:05: end of X-cor INFO @ Fri, 15 Feb 2019 07:23:05: #2 finished! INFO @ Fri, 15 Feb 2019 07:23:05: #2 predicted fragment length is 236 bps INFO @ Fri, 15 Feb 2019 07:23:05: #2 alternative fragment length(s) may be 236 bps INFO @ Fri, 15 Feb 2019 07:23:05: #2.2 Generate R script for model : SRX4497196.10_model.r INFO @ Fri, 15 Feb 2019 07:23:05: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:23:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:23:06: #2 number of paired peaks: 31467 INFO @ Fri, 15 Feb 2019 07:23:06: start model_add_line... INFO @ Fri, 15 Feb 2019 07:23:06: start X-correlation... INFO @ Fri, 15 Feb 2019 07:23:06: end of X-cor INFO @ Fri, 15 Feb 2019 07:23:06: #2 finished! INFO @ Fri, 15 Feb 2019 07:23:06: #2 predicted fragment length is 236 bps INFO @ Fri, 15 Feb 2019 07:23:06: #2 alternative fragment length(s) may be 236 bps INFO @ Fri, 15 Feb 2019 07:23:06: #2.2 Generate R script for model : SRX4497196.05_model.r INFO @ Fri, 15 Feb 2019 07:23:06: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:23:06: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:23:08: #2 number of paired peaks: 31467 INFO @ Fri, 15 Feb 2019 07:23:08: start model_add_line... INFO @ Fri, 15 Feb 2019 07:23:09: start X-correlation... INFO @ Fri, 15 Feb 2019 07:23:09: end of X-cor INFO @ Fri, 15 Feb 2019 07:23:09: #2 finished! INFO @ Fri, 15 Feb 2019 07:23:09: #2 predicted fragment length is 236 bps INFO @ Fri, 15 Feb 2019 07:23:09: #2 alternative fragment length(s) may be 236 bps INFO @ Fri, 15 Feb 2019 07:23:09: #2.2 Generate R script for model : SRX4497196.20_model.r INFO @ Fri, 15 Feb 2019 07:23:09: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:23:09: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:24:10: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:24:10: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:24:14: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:24:46: #4 Write output xls file... SRX4497196.10_peaks.xls INFO @ Fri, 15 Feb 2019 07:24:46: #4 Write peak in narrowPeak format file... SRX4497196.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:24:46: #4 Write summits bed file... SRX4497196.10_summits.bed INFO @ Fri, 15 Feb 2019 07:24:46: Done! pass1 - making usageList (41 chroms): 6 millis pass2 - checking and writing primary data (579 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 07:24:47: #4 Write output xls file... SRX4497196.05_peaks.xls INFO @ Fri, 15 Feb 2019 07:24:47: #4 Write peak in narrowPeak format file... SRX4497196.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:24:47: #4 Write summits bed file... SRX4497196.05_summits.bed INFO @ Fri, 15 Feb 2019 07:24:47: Done! pass1 - making usageList (60 chroms): 7 millis pass2 - checking and writing primary data (1130 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 07:24:50: #4 Write output xls file... SRX4497196.20_peaks.xls INFO @ Fri, 15 Feb 2019 07:24:50: #4 Write peak in narrowPeak format file... SRX4497196.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:24:50: #4 Write summits bed file... SRX4497196.20_summits.bed INFO @ Fri, 15 Feb 2019 07:24:50: Done! pass1 - making usageList (31 chroms): 7 millis pass2 - checking and writing primary data (276 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。