Job ID = 11388786 sra ファイルのダウンロード中... Completed: 908583K bytes transferred in 15 seconds (489713K 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 29844425 spots for /home/okishinya/chipatlas/results/rn6/SRX1453550/SRR2962626.sra Written 29844425 spots for /home/okishinya/chipatlas/results/rn6/SRX1453550/SRR2962626.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: 00:00:02 Time loading forward index: 00:00:03 Time loading mirror index: 00:00:02 Multiseed full-index search: 03:02:38 29844425 reads; of these: 29844425 (100.00%) were unpaired; of these: 2475162 (8.29%) aligned 0 times 10178666 (34.11%) aligned exactly 1 time 17190597 (57.60%) aligned >1 times 91.71% overall alignment rate Time searching: 03:02:46 Overall time: 03:02:46 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] 8172742 / 27369263 = 0.2986 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 01:33:48: # Command line: callpeak -t SRX1453550.bam -f BAM -g 2.15e9 -n SRX1453550.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1453550.10 # format = BAM # ChIP-seq file = ['SRX1453550.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 01:33:48: #1 read tag files... INFO @ Thu, 13 Dec 2018 01:33:48: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 01:33:48: # Command line: callpeak -t SRX1453550.bam -f BAM -g 2.15e9 -n SRX1453550.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1453550.05 # format = BAM # ChIP-seq file = ['SRX1453550.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 01:33:48: #1 read tag files... INFO @ Thu, 13 Dec 2018 01:33:48: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 01:33:48: # Command line: callpeak -t SRX1453550.bam -f BAM -g 2.15e9 -n SRX1453550.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1453550.20 # format = BAM # ChIP-seq file = ['SRX1453550.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 01:33:48: #1 read tag files... INFO @ Thu, 13 Dec 2018 01:33:48: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 01:33:57: 1000000 INFO @ Thu, 13 Dec 2018 01:33:57: 1000000 INFO @ Thu, 13 Dec 2018 01:33:58: 1000000 INFO @ Thu, 13 Dec 2018 01:34:07: 2000000 INFO @ Thu, 13 Dec 2018 01:34:08: 2000000 INFO @ Thu, 13 Dec 2018 01:34:08: 2000000 INFO @ Thu, 13 Dec 2018 01:34:21: 3000000 INFO @ Thu, 13 Dec 2018 01:34:23: 3000000 INFO @ Thu, 13 Dec 2018 01:34:23: 3000000 INFO @ Thu, 13 Dec 2018 01:34:33: 4000000 INFO @ Thu, 13 Dec 2018 01:34:36: 4000000 INFO @ Thu, 13 Dec 2018 01:34:38: 4000000 INFO @ Thu, 13 Dec 2018 01:34:44: 5000000 INFO @ Thu, 13 Dec 2018 01:34:45: 5000000 INFO @ Thu, 13 Dec 2018 01:34:51: 5000000 INFO @ Thu, 13 Dec 2018 01:34:54: 6000000 INFO @ Thu, 13 Dec 2018 01:34:55: 6000000 INFO @ Thu, 13 Dec 2018 01:35:00: 6000000 INFO @ Thu, 13 Dec 2018 01:35:03: 7000000 INFO @ Thu, 13 Dec 2018 01:35:04: 7000000 INFO @ Thu, 13 Dec 2018 01:35:11: 7000000 INFO @ Thu, 13 Dec 2018 01:35:12: 8000000 INFO @ Thu, 13 Dec 2018 01:35:14: 8000000 INFO @ Thu, 13 Dec 2018 01:35:21: 8000000 INFO @ Thu, 13 Dec 2018 01:35:23: 9000000 INFO @ Thu, 13 Dec 2018 01:35:24: 9000000 INFO @ Thu, 13 Dec 2018 01:35:32: 10000000 INFO @ Thu, 13 Dec 2018 01:35:34: 9000000 INFO @ Thu, 13 Dec 2018 01:35:38: 10000000 INFO @ Thu, 13 Dec 2018 01:35:42: 11000000 INFO @ Thu, 13 Dec 2018 01:35:47: 10000000 INFO @ Thu, 13 Dec 2018 01:35:51: 11000000 INFO @ Thu, 13 Dec 2018 01:35:52: 12000000 INFO @ Thu, 13 Dec 2018 01:35:58: 11000000 INFO @ Thu, 13 Dec 2018 01:36:01: 12000000 INFO @ Thu, 13 Dec 2018 01:36:02: 13000000 INFO @ Thu, 13 Dec 2018 01:36:09: 13000000 INFO @ Thu, 13 Dec 2018 01:36:12: 12000000 INFO @ Thu, 13 Dec 2018 01:36:14: 14000000 INFO @ Thu, 13 Dec 2018 01:36:18: 14000000 INFO @ Thu, 13 Dec 2018 01:36:25: 15000000 INFO @ Thu, 13 Dec 2018 01:36:26: 13000000 INFO @ Thu, 13 Dec 2018 01:36:26: 15000000 INFO @ Thu, 13 Dec 2018 01:36:35: 16000000 INFO @ Thu, 13 Dec 2018 01:36:37: 14000000 INFO @ Thu, 13 Dec 2018 01:36:37: 16000000 INFO @ Thu, 13 Dec 2018 01:36:43: 17000000 INFO @ Thu, 13 Dec 2018 01:36:48: 15000000 INFO @ Thu, 13 Dec 2018 01:36:50: 17000000 INFO @ Thu, 13 Dec 2018 01:36:52: 18000000 INFO @ Thu, 13 Dec 2018 01:36:59: 16000000 INFO @ Thu, 13 Dec 2018 01:37:00: 19000000 INFO @ Thu, 13 Dec 2018 01:37:02: 18000000 INFO @ Thu, 13 Dec 2018 01:37:02: #1 tag size is determined as 51 bps INFO @ Thu, 13 Dec 2018 01:37:02: #1 tag size = 51 INFO @ Thu, 13 Dec 2018 01:37:02: #1 total tags in treatment: 19196521 INFO @ Thu, 13 Dec 2018 01:37:02: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 01:37:02: #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 01:37:03: #1 tags after filtering in treatment: 19196404 INFO @ Thu, 13 Dec 2018 01:37:03: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 13 Dec 2018 01:37:03: #1 finished! INFO @ Thu, 13 Dec 2018 01:37:03: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 01:37:03: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 01:37:10: 17000000 INFO @ Thu, 13 Dec 2018 01:37:11: #2 number of paired peaks: 124404 INFO @ Thu, 13 Dec 2018 01:37:11: start model_add_line... INFO @ Thu, 13 Dec 2018 01:37:12: 19000000 INFO @ Thu, 13 Dec 2018 01:37:12: start X-correlation... INFO @ Thu, 13 Dec 2018 01:37:12: end of X-cor INFO @ Thu, 13 Dec 2018 01:37:12: #2 finished! INFO @ Thu, 13 Dec 2018 01:37:12: #2 predicted fragment length is 118 bps INFO @ Thu, 13 Dec 2018 01:37:12: #2 alternative fragment length(s) may be 118 bps INFO @ Thu, 13 Dec 2018 01:37:12: #2.2 Generate R script for model : SRX1453550.05_model.r INFO @ Thu, 13 Dec 2018 01:37:12: #3 Call peaks... INFO @ Thu, 13 Dec 2018 01:37:12: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 13 Dec 2018 01:37:14: #1 tag size is determined as 51 bps INFO @ Thu, 13 Dec 2018 01:37:14: #1 tag size = 51 INFO @ Thu, 13 Dec 2018 01:37:14: #1 total tags in treatment: 19196521 INFO @ Thu, 13 Dec 2018 01:37:14: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 01:37:14: #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 01:37:15: #1 tags after filtering in treatment: 19196404 INFO @ Thu, 13 Dec 2018 01:37:15: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 13 Dec 2018 01:37:15: #1 finished! INFO @ Thu, 13 Dec 2018 01:37:15: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 01:37:15: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 01:37:23: 18000000 INFO @ Thu, 13 Dec 2018 01:37:23: #2 number of paired peaks: 124404 INFO @ Thu, 13 Dec 2018 01:37:23: start model_add_line... INFO @ Thu, 13 Dec 2018 01:37:23: start X-correlation... INFO @ Thu, 13 Dec 2018 01:37:23: end of X-cor INFO @ Thu, 13 Dec 2018 01:37:23: #2 finished! INFO @ Thu, 13 Dec 2018 01:37:23: #2 predicted fragment length is 118 bps INFO @ Thu, 13 Dec 2018 01:37:23: #2 alternative fragment length(s) may be 118 bps INFO @ Thu, 13 Dec 2018 01:37:23: #2.2 Generate R script for model : SRX1453550.20_model.r INFO @ Thu, 13 Dec 2018 01:37:23: #3 Call peaks... INFO @ Thu, 13 Dec 2018 01:37:23: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 13 Dec 2018 01:37:34: 19000000 INFO @ Thu, 13 Dec 2018 01:37:37: #1 tag size is determined as 51 bps INFO @ Thu, 13 Dec 2018 01:37:37: #1 tag size = 51 INFO @ Thu, 13 Dec 2018 01:37:37: #1 total tags in treatment: 19196521 INFO @ Thu, 13 Dec 2018 01:37:37: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 01:37:37: #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 01:37:38: #1 tags after filtering in treatment: 19196404 INFO @ Thu, 13 Dec 2018 01:37:38: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 13 Dec 2018 01:37:38: #1 finished! INFO @ Thu, 13 Dec 2018 01:37:38: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 01:37:38: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 01:37:46: #2 number of paired peaks: 124404 INFO @ Thu, 13 Dec 2018 01:37:46: start model_add_line... INFO @ Thu, 13 Dec 2018 01:37:47: start X-correlation... INFO @ Thu, 13 Dec 2018 01:37:47: end of X-cor INFO @ Thu, 13 Dec 2018 01:37:47: #2 finished! INFO @ Thu, 13 Dec 2018 01:37:47: #2 predicted fragment length is 118 bps INFO @ Thu, 13 Dec 2018 01:37:47: #2 alternative fragment length(s) may be 118 bps INFO @ Thu, 13 Dec 2018 01:37:47: #2.2 Generate R script for model : SRX1453550.10_model.r INFO @ Thu, 13 Dec 2018 01:37:47: #3 Call peaks... INFO @ Thu, 13 Dec 2018 01:37:47: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 13 Dec 2018 01:38:15: #3 Call peaks for each chromosome... INFO @ Thu, 13 Dec 2018 01:38:37: #3 Call peaks for each chromosome... INFO @ Thu, 13 Dec 2018 01:38:59: #3 Call peaks for each chromosome... INFO @ Thu, 13 Dec 2018 01:39:05: #4 Write output xls file... SRX1453550.05_peaks.xls INFO @ Thu, 13 Dec 2018 01:39:05: #4 Write peak in narrowPeak format file... SRX1453550.05_peaks.narrowPeak INFO @ Thu, 13 Dec 2018 01:39:06: #4 Write summits bed file... SRX1453550.05_summits.bed INFO @ Thu, 13 Dec 2018 01:39:06: Done! pass1 - making usageList (195 chroms): 22 millis pass2 - checking and writing primary data (57591 records, 4 fields): 108 millis CompletedMACS2peakCalling INFO @ Thu, 13 Dec 2018 01:39:27: #4 Write output xls file... SRX1453550.20_peaks.xls INFO @ Thu, 13 Dec 2018 01:39:28: #4 Write peak in narrowPeak format file... SRX1453550.20_peaks.narrowPeak INFO @ Thu, 13 Dec 2018 01:39:28: #4 Write summits bed file... SRX1453550.20_summits.bed INFO @ Thu, 13 Dec 2018 01:39:28: Done! pass1 - making usageList (67 chroms): 6 millis pass2 - checking and writing primary data (2992 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Thu, 13 Dec 2018 01:39:41: #4 Write output xls file... SRX1453550.10_peaks.xls INFO @ Thu, 13 Dec 2018 01:39:41: #4 Write peak in narrowPeak format file... SRX1453550.10_peaks.narrowPeak INFO @ Thu, 13 Dec 2018 01:39:41: #4 Write summits bed file... SRX1453550.10_summits.bed INFO @ Thu, 13 Dec 2018 01:39:42: Done! pass1 - making usageList (126 chroms): 7 millis pass2 - checking and writing primary data (18727 records, 4 fields): 41 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。