Job ID = 11388788 sra ファイルのダウンロード中... Completed: 1006123K bytes transferred in 17 seconds (484227K 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 32980122 spots for /home/okishinya/chipatlas/results/rn6/SRX1453552/SRR2962628.sra Written 32980122 spots for /home/okishinya/chipatlas/results/rn6/SRX1453552/SRR2962628.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: 00:00:01 Time loading forward index: 00:00:03 Time loading mirror index: 00:00:01 Multiseed full-index search: 02:48:30 32980122 reads; of these: 32980122 (100.00%) were unpaired; of these: 2986146 (9.05%) aligned 0 times 16243830 (49.25%) aligned exactly 1 time 13750146 (41.69%) aligned >1 times 90.95% overall alignment rate Time searching: 02:48:35 Overall time: 02:48:35 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] 8775944 / 29993976 = 0.2926 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 @ Thu, 13 Dec 2018 01:27:02: # Command line: callpeak -t SRX1453552.bam -f BAM -g 2.15e9 -n SRX1453552.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1453552.10 # format = BAM # ChIP-seq file = ['SRX1453552.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 @ Thu, 13 Dec 2018 01:27:02: #1 read tag files... INFO @ Thu, 13 Dec 2018 01:27:02: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 01:27:02: # Command line: callpeak -t SRX1453552.bam -f BAM -g 2.15e9 -n SRX1453552.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1453552.05 # format = BAM # ChIP-seq file = ['SRX1453552.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 @ Thu, 13 Dec 2018 01:27:02: #1 read tag files... INFO @ Thu, 13 Dec 2018 01:27:02: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 01:27:02: # Command line: callpeak -t SRX1453552.bam -f BAM -g 2.15e9 -n SRX1453552.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1453552.20 # format = BAM # ChIP-seq file = ['SRX1453552.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 @ Thu, 13 Dec 2018 01:27:02: #1 read tag files... INFO @ Thu, 13 Dec 2018 01:27:02: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 01:27:15: 1000000 INFO @ Thu, 13 Dec 2018 01:27:15: 1000000 INFO @ Thu, 13 Dec 2018 01:27:15: 1000000 INFO @ Thu, 13 Dec 2018 01:27:28: 2000000 INFO @ Thu, 13 Dec 2018 01:27:29: 2000000 INFO @ Thu, 13 Dec 2018 01:27:30: 2000000 INFO @ Thu, 13 Dec 2018 01:27:42: 3000000 INFO @ Thu, 13 Dec 2018 01:27:44: 3000000 INFO @ Thu, 13 Dec 2018 01:27:46: 3000000 INFO @ Thu, 13 Dec 2018 01:27:56: 4000000 INFO @ Thu, 13 Dec 2018 01:27:58: 4000000 INFO @ Thu, 13 Dec 2018 01:28:03: 4000000 INFO @ Thu, 13 Dec 2018 01:28:09: 5000000 INFO @ Thu, 13 Dec 2018 01:28:13: 5000000 INFO @ Thu, 13 Dec 2018 01:28:19: 5000000 INFO @ Thu, 13 Dec 2018 01:28:23: 6000000 INFO @ Thu, 13 Dec 2018 01:28:27: 6000000 INFO @ Thu, 13 Dec 2018 01:28:35: 6000000 INFO @ Thu, 13 Dec 2018 01:28:36: 7000000 INFO @ Thu, 13 Dec 2018 01:28:42: 7000000 INFO @ Thu, 13 Dec 2018 01:28:50: 8000000 INFO @ Thu, 13 Dec 2018 01:28:52: 7000000 INFO @ Thu, 13 Dec 2018 01:28:57: 8000000 INFO @ Thu, 13 Dec 2018 01:29:04: 9000000 INFO @ Thu, 13 Dec 2018 01:29:09: 8000000 INFO @ Thu, 13 Dec 2018 01:29:12: 9000000 INFO @ Thu, 13 Dec 2018 01:29:18: 10000000 INFO @ Thu, 13 Dec 2018 01:29:26: 9000000 INFO @ Thu, 13 Dec 2018 01:29:26: 10000000 INFO @ Thu, 13 Dec 2018 01:29:32: 11000000 INFO @ Thu, 13 Dec 2018 01:29:36: 11000000 INFO @ Thu, 13 Dec 2018 01:29:40: 10000000 INFO @ Thu, 13 Dec 2018 01:29:45: 12000000 INFO @ Thu, 13 Dec 2018 01:29:47: 12000000 INFO @ Thu, 13 Dec 2018 01:29:56: 11000000 INFO @ Thu, 13 Dec 2018 01:29:58: 13000000 INFO @ Thu, 13 Dec 2018 01:29:59: 13000000 INFO @ Thu, 13 Dec 2018 01:30:09: 14000000 INFO @ Thu, 13 Dec 2018 01:30:10: 12000000 INFO @ Thu, 13 Dec 2018 01:30:12: 14000000 INFO @ Thu, 13 Dec 2018 01:30:19: 15000000 INFO @ Thu, 13 Dec 2018 01:30:24: 13000000 INFO @ Thu, 13 Dec 2018 01:30:24: 15000000 INFO @ Thu, 13 Dec 2018 01:30:30: 16000000 INFO @ Thu, 13 Dec 2018 01:30:37: 16000000 INFO @ Thu, 13 Dec 2018 01:30:38: 14000000 INFO @ Thu, 13 Dec 2018 01:30:40: 17000000 INFO @ Thu, 13 Dec 2018 01:30:50: 17000000 INFO @ Thu, 13 Dec 2018 01:30:50: 18000000 INFO @ Thu, 13 Dec 2018 01:30:52: 15000000 INFO @ Thu, 13 Dec 2018 01:31:02: 19000000 INFO @ Thu, 13 Dec 2018 01:31:03: 18000000 INFO @ Thu, 13 Dec 2018 01:31:05: 16000000 INFO @ Thu, 13 Dec 2018 01:31:15: 19000000 INFO @ Thu, 13 Dec 2018 01:31:16: 20000000 INFO @ Thu, 13 Dec 2018 01:31:20: 17000000 INFO @ Thu, 13 Dec 2018 01:31:25: 20000000 INFO @ Thu, 13 Dec 2018 01:31:29: 21000000 INFO @ Thu, 13 Dec 2018 01:31:33: #1 tag size is determined as 51 bps INFO @ Thu, 13 Dec 2018 01:31:33: #1 tag size = 51 INFO @ Thu, 13 Dec 2018 01:31:33: #1 total tags in treatment: 21218032 INFO @ Thu, 13 Dec 2018 01:31:33: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 01:31:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 13 Dec 2018 01:31:34: #1 tags after filtering in treatment: 21217931 INFO @ Thu, 13 Dec 2018 01:31:34: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 13 Dec 2018 01:31:34: #1 finished! INFO @ Thu, 13 Dec 2018 01:31:34: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 01:31:34: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 01:31:34: 21000000 INFO @ Thu, 13 Dec 2018 01:31:35: 18000000 INFO @ Thu, 13 Dec 2018 01:31:37: #1 tag size is determined as 51 bps INFO @ Thu, 13 Dec 2018 01:31:37: #1 tag size = 51 INFO @ Thu, 13 Dec 2018 01:31:37: #1 total tags in treatment: 21218032 INFO @ Thu, 13 Dec 2018 01:31:37: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 01:31:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 13 Dec 2018 01:31:38: #1 tags after filtering in treatment: 21217931 INFO @ Thu, 13 Dec 2018 01:31:38: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 13 Dec 2018 01:31:38: #1 finished! INFO @ Thu, 13 Dec 2018 01:31:38: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 01:31:38: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 01:31:39: #2 number of paired peaks: 48935 INFO @ Thu, 13 Dec 2018 01:31:39: start model_add_line... INFO @ Thu, 13 Dec 2018 01:31:39: start X-correlation... INFO @ Thu, 13 Dec 2018 01:31:39: end of X-cor INFO @ Thu, 13 Dec 2018 01:31:39: #2 finished! INFO @ Thu, 13 Dec 2018 01:31:39: #2 predicted fragment length is 110 bps INFO @ Thu, 13 Dec 2018 01:31:39: #2 alternative fragment length(s) may be 110 bps INFO @ Thu, 13 Dec 2018 01:31:39: #2.2 Generate R script for model : SRX1453552.05_model.r INFO @ Thu, 13 Dec 2018 01:31:39: #3 Call peaks... INFO @ Thu, 13 Dec 2018 01:31:39: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 13 Dec 2018 01:31:43: #2 number of paired peaks: 48935 INFO @ Thu, 13 Dec 2018 01:31:43: start model_add_line... INFO @ Thu, 13 Dec 2018 01:31:43: start X-correlation... INFO @ Thu, 13 Dec 2018 01:31:43: end of X-cor INFO @ Thu, 13 Dec 2018 01:31:43: #2 finished! INFO @ Thu, 13 Dec 2018 01:31:43: #2 predicted fragment length is 110 bps INFO @ Thu, 13 Dec 2018 01:31:43: #2 alternative fragment length(s) may be 110 bps INFO @ Thu, 13 Dec 2018 01:31:43: #2.2 Generate R script for model : SRX1453552.10_model.r INFO @ Thu, 13 Dec 2018 01:31:43: #3 Call peaks... INFO @ Thu, 13 Dec 2018 01:31:43: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 13 Dec 2018 01:31:48: 19000000 INFO @ Thu, 13 Dec 2018 01:32:01: 20000000 INFO @ Thu, 13 Dec 2018 01:32:14: 21000000 INFO @ Thu, 13 Dec 2018 01:32:17: #1 tag size is determined as 51 bps INFO @ Thu, 13 Dec 2018 01:32:17: #1 tag size = 51 INFO @ Thu, 13 Dec 2018 01:32:17: #1 total tags in treatment: 21218032 INFO @ Thu, 13 Dec 2018 01:32:17: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 01:32:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 13 Dec 2018 01:32:18: #1 tags after filtering in treatment: 21217931 INFO @ Thu, 13 Dec 2018 01:32:18: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 13 Dec 2018 01:32:18: #1 finished! INFO @ Thu, 13 Dec 2018 01:32:18: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 01:32:18: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 01:32:24: #2 number of paired peaks: 48935 INFO @ Thu, 13 Dec 2018 01:32:24: start model_add_line... INFO @ Thu, 13 Dec 2018 01:32:24: start X-correlation... INFO @ Thu, 13 Dec 2018 01:32:24: end of X-cor INFO @ Thu, 13 Dec 2018 01:32:24: #2 finished! INFO @ Thu, 13 Dec 2018 01:32:24: #2 predicted fragment length is 110 bps INFO @ Thu, 13 Dec 2018 01:32:24: #2 alternative fragment length(s) may be 110 bps INFO @ Thu, 13 Dec 2018 01:32:24: #2.2 Generate R script for model : SRX1453552.20_model.r INFO @ Thu, 13 Dec 2018 01:32:24: #3 Call peaks... INFO @ Thu, 13 Dec 2018 01:32:24: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 13 Dec 2018 01:32:52: #3 Call peaks for each chromosome... INFO @ Thu, 13 Dec 2018 01:32:55: #3 Call peaks for each chromosome... INFO @ Thu, 13 Dec 2018 01:33:32: #4 Write output xls file... SRX1453552.10_peaks.xls INFO @ Thu, 13 Dec 2018 01:33:33: #4 Write peak in narrowPeak format file... SRX1453552.10_peaks.narrowPeak INFO @ Thu, 13 Dec 2018 01:33:33: #4 Write summits bed file... SRX1453552.10_summits.bed INFO @ Thu, 13 Dec 2018 01:33:33: Done! pass1 - making usageList (86 chroms): 5 millis pass2 - checking and writing primary data (4935 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Thu, 13 Dec 2018 01:33:33: #3 Call peaks for each chromosome... INFO @ Thu, 13 Dec 2018 01:33:47: #4 Write output xls file... SRX1453552.05_peaks.xls INFO @ Thu, 13 Dec 2018 01:33:48: #4 Write peak in narrowPeak format file... SRX1453552.05_peaks.narrowPeak INFO @ Thu, 13 Dec 2018 01:33:48: #4 Write summits bed file... SRX1453552.05_summits.bed INFO @ Thu, 13 Dec 2018 01:33:48: Done! pass1 - making usageList (170 chroms): 11 millis pass2 - checking and writing primary data (25387 records, 4 fields): 54 millis CompletedMACS2peakCalling INFO @ Thu, 13 Dec 2018 01:34:15: #4 Write output xls file... SRX1453552.20_peaks.xls INFO @ Thu, 13 Dec 2018 01:34:15: #4 Write peak in narrowPeak format file... SRX1453552.20_peaks.narrowPeak INFO @ Thu, 13 Dec 2018 01:34:15: #4 Write summits bed file... SRX1453552.20_summits.bed INFO @ Thu, 13 Dec 2018 01:34:15: Done! pass1 - making usageList (47 chroms): 6 millis pass2 - checking and writing primary data (997 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。