Job ID = 10194825 sra ファイルのダウンロード中... Completed: 635027K bytes transferred in 12 seconds (415736K 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 32819825 spots for /home/okishinya/chipatlas/results/rn6/SRX1977115/SRR3952247.sra Written 32819825 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: 00:51:33 32819825 reads; of these: 32819825 (100.00%) were unpaired; of these: 7471336 (22.76%) aligned 0 times 14068346 (42.87%) aligned exactly 1 time 11280143 (34.37%) aligned >1 times 77.24% overall alignment rate Time searching: 00:51:35 Overall time: 00:51:35 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 12 files... [bam_rmdupse_core] 2458056 / 25348489 = 0.0970 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 @ Sat, 11 Nov 2017 01:59:21: # Command line: callpeak -t SRX1977115.bam -f BAM -g 2.15e9 -n SRX1977115.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1977115.10 # format = BAM # ChIP-seq file = ['SRX1977115.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 @ Sat, 11 Nov 2017 01:59:21: #1 read tag files... INFO @ Sat, 11 Nov 2017 01:59:21: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 01:59:21: # Command line: callpeak -t SRX1977115.bam -f BAM -g 2.15e9 -n SRX1977115.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1977115.20 # format = BAM # ChIP-seq file = ['SRX1977115.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 @ Sat, 11 Nov 2017 01:59:21: #1 read tag files... INFO @ Sat, 11 Nov 2017 01:59:21: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 01:59:21: # Command line: callpeak -t SRX1977115.bam -f BAM -g 2.15e9 -n SRX1977115.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1977115.05 # format = BAM # ChIP-seq file = ['SRX1977115.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 @ Sat, 11 Nov 2017 01:59:21: #1 read tag files... INFO @ Sat, 11 Nov 2017 01:59:21: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 01:59:29: 1000000 INFO @ Sat, 11 Nov 2017 01:59:29: 1000000 INFO @ Sat, 11 Nov 2017 01:59:29: 1000000 INFO @ Sat, 11 Nov 2017 01:59:37: 2000000 INFO @ Sat, 11 Nov 2017 01:59:37: 2000000 INFO @ Sat, 11 Nov 2017 01:59:37: 2000000 INFO @ Sat, 11 Nov 2017 01:59:45: 3000000 INFO @ Sat, 11 Nov 2017 01:59:45: 3000000 INFO @ Sat, 11 Nov 2017 01:59:45: 3000000 INFO @ Sat, 11 Nov 2017 01:59:53: 4000000 INFO @ Sat, 11 Nov 2017 01:59:53: 4000000 INFO @ Sat, 11 Nov 2017 01:59:53: 4000000 INFO @ Sat, 11 Nov 2017 02:00:02: 5000000 INFO @ Sat, 11 Nov 2017 02:00:02: 5000000 INFO @ Sat, 11 Nov 2017 02:00:02: 5000000 INFO @ Sat, 11 Nov 2017 02:00:10: 6000000 INFO @ Sat, 11 Nov 2017 02:00:10: 6000000 INFO @ Sat, 11 Nov 2017 02:00:10: 6000000 INFO @ Sat, 11 Nov 2017 02:00:18: 7000000 INFO @ Sat, 11 Nov 2017 02:00:18: 7000000 INFO @ Sat, 11 Nov 2017 02:00:18: 7000000 INFO @ Sat, 11 Nov 2017 02:00:27: 8000000 INFO @ Sat, 11 Nov 2017 02:00:27: 8000000 INFO @ Sat, 11 Nov 2017 02:00:27: 8000000 INFO @ Sat, 11 Nov 2017 02:00:35: 9000000 INFO @ Sat, 11 Nov 2017 02:00:35: 9000000 INFO @ Sat, 11 Nov 2017 02:00:35: 9000000 INFO @ Sat, 11 Nov 2017 02:00:43: 10000000 INFO @ Sat, 11 Nov 2017 02:00:43: 10000000 INFO @ Sat, 11 Nov 2017 02:00:43: 10000000 INFO @ Sat, 11 Nov 2017 02:00:52: 11000000 INFO @ Sat, 11 Nov 2017 02:00:52: 11000000 INFO @ Sat, 11 Nov 2017 02:00:52: 11000000 INFO @ Sat, 11 Nov 2017 02:01:00: 12000000 INFO @ Sat, 11 Nov 2017 02:01:00: 12000000 INFO @ Sat, 11 Nov 2017 02:01:00: 12000000 INFO @ Sat, 11 Nov 2017 02:01:08: 13000000 INFO @ Sat, 11 Nov 2017 02:01:09: 13000000 INFO @ Sat, 11 Nov 2017 02:01:09: 13000000 INFO @ Sat, 11 Nov 2017 02:01:17: 14000000 INFO @ Sat, 11 Nov 2017 02:01:17: 14000000 INFO @ Sat, 11 Nov 2017 02:01:17: 14000000 INFO @ Sat, 11 Nov 2017 02:01:25: 15000000 INFO @ Sat, 11 Nov 2017 02:01:25: 15000000 INFO @ Sat, 11 Nov 2017 02:01:25: 15000000 INFO @ Sat, 11 Nov 2017 02:01:33: 16000000 INFO @ Sat, 11 Nov 2017 02:01:34: 16000000 INFO @ Sat, 11 Nov 2017 02:01:34: 16000000 INFO @ Sat, 11 Nov 2017 02:01:42: 17000000 INFO @ Sat, 11 Nov 2017 02:01:42: 17000000 INFO @ Sat, 11 Nov 2017 02:01:42: 17000000 INFO @ Sat, 11 Nov 2017 02:01:50: 18000000 INFO @ Sat, 11 Nov 2017 02:01:50: 18000000 INFO @ Sat, 11 Nov 2017 02:01:50: 18000000 INFO @ Sat, 11 Nov 2017 02:01:57: 19000000 INFO @ Sat, 11 Nov 2017 02:01:58: 19000000 INFO @ Sat, 11 Nov 2017 02:01:59: 19000000 INFO @ Sat, 11 Nov 2017 02:02:05: 20000000 INFO @ Sat, 11 Nov 2017 02:02:05: 20000000 INFO @ Sat, 11 Nov 2017 02:02:07: 20000000 INFO @ Sat, 11 Nov 2017 02:02:13: 21000000 INFO @ Sat, 11 Nov 2017 02:02:13: 21000000 INFO @ Sat, 11 Nov 2017 02:02:16: 21000000 INFO @ Sat, 11 Nov 2017 02:02:20: 22000000 INFO @ Sat, 11 Nov 2017 02:02:21: 22000000 INFO @ Sat, 11 Nov 2017 02:02:25: 22000000 INFO @ Sat, 11 Nov 2017 02:02:27: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 02:02:27: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 02:02:27: #1 total tags in treatment: 22890433 INFO @ Sat, 11 Nov 2017 02:02:27: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 02:02:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 02:02:28: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 02:02:28: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 02:02:28: #1 total tags in treatment: 22890433 INFO @ Sat, 11 Nov 2017 02:02:28: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 02:02:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 02:02:28: #1 tags after filtering in treatment: 22890340 INFO @ Sat, 11 Nov 2017 02:02:28: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 02:02:28: #1 finished! INFO @ Sat, 11 Nov 2017 02:02:28: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 02:02:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 02:02:28: #1 tags after filtering in treatment: 22890340 INFO @ Sat, 11 Nov 2017 02:02:28: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 02:02:28: #1 finished! INFO @ Sat, 11 Nov 2017 02:02:28: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 02:02:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 02:02:31: #2 number of paired peaks: 31010 INFO @ Sat, 11 Nov 2017 02:02:31: start model_add_line... INFO @ Sat, 11 Nov 2017 02:02:32: #2 number of paired peaks: 31010 INFO @ Sat, 11 Nov 2017 02:02:32: start model_add_line... INFO @ Sat, 11 Nov 2017 02:02:32: start X-correlation... INFO @ Sat, 11 Nov 2017 02:02:32: end of X-cor INFO @ Sat, 11 Nov 2017 02:02:32: #2 finished! INFO @ Sat, 11 Nov 2017 02:02:32: #2 predicted fragment length is 172 bps INFO @ Sat, 11 Nov 2017 02:02:32: #2 alternative fragment length(s) may be 172 bps INFO @ Sat, 11 Nov 2017 02:02:32: #2.2 Generate R script for model : SRX1977115.05_model.r INFO @ Sat, 11 Nov 2017 02:02:32: #3 Call peaks... INFO @ Sat, 11 Nov 2017 02:02:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 02:02:32: start X-correlation... INFO @ Sat, 11 Nov 2017 02:02:32: end of X-cor INFO @ Sat, 11 Nov 2017 02:02:32: #2 finished! INFO @ Sat, 11 Nov 2017 02:02:32: #2 predicted fragment length is 172 bps INFO @ Sat, 11 Nov 2017 02:02:32: #2 alternative fragment length(s) may be 172 bps INFO @ Sat, 11 Nov 2017 02:02:32: #2.2 Generate R script for model : SRX1977115.10_model.r INFO @ Sat, 11 Nov 2017 02:02:32: #3 Call peaks... INFO @ Sat, 11 Nov 2017 02:02:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 02:02:32: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 02:02:32: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 02:02:32: #1 total tags in treatment: 22890433 INFO @ Sat, 11 Nov 2017 02:02:32: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 02:02:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 02:02:33: #1 tags after filtering in treatment: 22890340 INFO @ Sat, 11 Nov 2017 02:02:33: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 02:02:33: #1 finished! INFO @ Sat, 11 Nov 2017 02:02:33: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 02:02:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 02:02:36: #2 number of paired peaks: 31010 INFO @ Sat, 11 Nov 2017 02:02:36: start model_add_line... INFO @ Sat, 11 Nov 2017 02:02:37: start X-correlation... INFO @ Sat, 11 Nov 2017 02:02:37: end of X-cor INFO @ Sat, 11 Nov 2017 02:02:37: #2 finished! INFO @ Sat, 11 Nov 2017 02:02:37: #2 predicted fragment length is 172 bps INFO @ Sat, 11 Nov 2017 02:02:37: #2 alternative fragment length(s) may be 172 bps INFO @ Sat, 11 Nov 2017 02:02:37: #2.2 Generate R script for model : SRX1977115.20_model.r INFO @ Sat, 11 Nov 2017 02:02:37: #3 Call peaks... INFO @ Sat, 11 Nov 2017 02:02:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 02:03:29: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 02:03:32: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 02:03:40: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 02:04:03: #4 Write output xls file... SRX1977115.05_peaks.xls INFO @ Sat, 11 Nov 2017 02:04:04: #4 Write peak in narrowPeak format file... SRX1977115.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 02:04:04: #4 Write summits bed file... SRX1977115.05_summits.bed INFO @ Sat, 11 Nov 2017 02:04:04: Done! pass1 - making usageList (151 chroms): 6 millis pass2 - checking and writing primary data (28024 records, 4 fields): 37 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 02:04:07: #4 Write output xls file... SRX1977115.10_peaks.xls INFO @ Sat, 11 Nov 2017 02:04:07: #4 Write peak in narrowPeak format file... SRX1977115.10_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 02:04:07: #4 Write summits bed file... SRX1977115.10_summits.bed INFO @ Sat, 11 Nov 2017 02:04:07: Done! pass1 - making usageList (89 chroms): 2 millis pass2 - checking and writing primary data (6863 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 02:04:14: #4 Write output xls file... SRX1977115.20_peaks.xls INFO @ Sat, 11 Nov 2017 02:04:14: #4 Write peak in narrowPeak format file... SRX1977115.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 02:04:14: #4 Write summits bed file... SRX1977115.20_summits.bed INFO @ Sat, 11 Nov 2017 02:04:14: Done! pass1 - making usageList (58 chroms): 1 millis pass2 - checking and writing primary data (1505 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。