Job ID = 10194841 sra ファイルのダウンロード中... Completed: 992498K bytes transferred in 17 seconds (461662K 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 47336230 spots for /home/okishinya/chipatlas/results/rn6/SRX1977130/SRR3952262.sra Written 47336230 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: 00:00:01 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 01:22:37 47336230 reads; of these: 47336230 (100.00%) were unpaired; of these: 18336864 (38.74%) aligned 0 times 14855411 (31.38%) aligned exactly 1 time 14143955 (29.88%) aligned >1 times 61.26% overall alignment rate Time searching: 01:22:40 Overall time: 01:22:40 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] 5208727 / 28999366 = 0.1796 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 03:19:50: # Command line: callpeak -t SRX1977130.bam -f BAM -g 2.15e9 -n SRX1977130.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1977130.05 # format = BAM # ChIP-seq file = ['SRX1977130.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 03:19:50: # Command line: callpeak -t SRX1977130.bam -f BAM -g 2.15e9 -n SRX1977130.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1977130.10 # format = BAM # ChIP-seq file = ['SRX1977130.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 03:19:50: # Command line: callpeak -t SRX1977130.bam -f BAM -g 2.15e9 -n SRX1977130.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1977130.20 # format = BAM # ChIP-seq file = ['SRX1977130.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 03:19:50: #1 read tag files... INFO @ Sat, 11 Nov 2017 03:19:50: #1 read tag files... INFO @ Sat, 11 Nov 2017 03:19:50: #1 read tag files... INFO @ Sat, 11 Nov 2017 03:19:50: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 03:19:50: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 03:19:50: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 03:19:57: 1000000 INFO @ Sat, 11 Nov 2017 03:19:57: 1000000 INFO @ Sat, 11 Nov 2017 03:19:57: 1000000 INFO @ Sat, 11 Nov 2017 03:20:03: 2000000 INFO @ Sat, 11 Nov 2017 03:20:03: 2000000 INFO @ Sat, 11 Nov 2017 03:20:03: 2000000 INFO @ Sat, 11 Nov 2017 03:20:10: 3000000 INFO @ Sat, 11 Nov 2017 03:20:10: 3000000 INFO @ Sat, 11 Nov 2017 03:20:10: 3000000 INFO @ Sat, 11 Nov 2017 03:20:16: 4000000 INFO @ Sat, 11 Nov 2017 03:20:16: 4000000 INFO @ Sat, 11 Nov 2017 03:20:16: 4000000 INFO @ Sat, 11 Nov 2017 03:20:22: 5000000 INFO @ Sat, 11 Nov 2017 03:20:22: 5000000 INFO @ Sat, 11 Nov 2017 03:20:23: 5000000 INFO @ Sat, 11 Nov 2017 03:20:29: 6000000 INFO @ Sat, 11 Nov 2017 03:20:29: 6000000 INFO @ Sat, 11 Nov 2017 03:20:29: 6000000 INFO @ Sat, 11 Nov 2017 03:20:35: 7000000 INFO @ Sat, 11 Nov 2017 03:20:35: 7000000 INFO @ Sat, 11 Nov 2017 03:20:36: 7000000 INFO @ Sat, 11 Nov 2017 03:20:42: 8000000 INFO @ Sat, 11 Nov 2017 03:20:42: 8000000 INFO @ Sat, 11 Nov 2017 03:20:42: 8000000 INFO @ Sat, 11 Nov 2017 03:20:48: 9000000 INFO @ Sat, 11 Nov 2017 03:20:48: 9000000 INFO @ Sat, 11 Nov 2017 03:20:49: 9000000 INFO @ Sat, 11 Nov 2017 03:20:54: 10000000 INFO @ Sat, 11 Nov 2017 03:20:55: 10000000 INFO @ Sat, 11 Nov 2017 03:20:55: 10000000 INFO @ Sat, 11 Nov 2017 03:21:01: 11000000 INFO @ Sat, 11 Nov 2017 03:21:02: 11000000 INFO @ Sat, 11 Nov 2017 03:21:02: 11000000 INFO @ Sat, 11 Nov 2017 03:21:07: 12000000 INFO @ Sat, 11 Nov 2017 03:21:08: 12000000 INFO @ Sat, 11 Nov 2017 03:21:09: 12000000 INFO @ Sat, 11 Nov 2017 03:21:13: 13000000 INFO @ Sat, 11 Nov 2017 03:21:15: 13000000 INFO @ Sat, 11 Nov 2017 03:21:16: 13000000 INFO @ Sat, 11 Nov 2017 03:21:19: 14000000 INFO @ Sat, 11 Nov 2017 03:21:22: 14000000 INFO @ Sat, 11 Nov 2017 03:21:22: 14000000 INFO @ Sat, 11 Nov 2017 03:21:26: 15000000 INFO @ Sat, 11 Nov 2017 03:21:28: 15000000 INFO @ Sat, 11 Nov 2017 03:21:29: 15000000 INFO @ Sat, 11 Nov 2017 03:21:32: 16000000 INFO @ Sat, 11 Nov 2017 03:21:35: 16000000 INFO @ Sat, 11 Nov 2017 03:21:35: 16000000 INFO @ Sat, 11 Nov 2017 03:21:38: 17000000 INFO @ Sat, 11 Nov 2017 03:21:42: 17000000 INFO @ Sat, 11 Nov 2017 03:21:42: 17000000 INFO @ Sat, 11 Nov 2017 03:21:44: 18000000 INFO @ Sat, 11 Nov 2017 03:21:48: 18000000 INFO @ Sat, 11 Nov 2017 03:21:49: 18000000 INFO @ Sat, 11 Nov 2017 03:21:50: 19000000 INFO @ Sat, 11 Nov 2017 03:21:55: 19000000 INFO @ Sat, 11 Nov 2017 03:21:55: 19000000 INFO @ Sat, 11 Nov 2017 03:21:57: 20000000 INFO @ Sat, 11 Nov 2017 03:22:02: 20000000 INFO @ Sat, 11 Nov 2017 03:22:02: 20000000 INFO @ Sat, 11 Nov 2017 03:22:03: 21000000 INFO @ Sat, 11 Nov 2017 03:22:08: 21000000 INFO @ Sat, 11 Nov 2017 03:22:08: 21000000 INFO @ Sat, 11 Nov 2017 03:22:09: 22000000 INFO @ Sat, 11 Nov 2017 03:22:15: 22000000 INFO @ Sat, 11 Nov 2017 03:22:15: 22000000 INFO @ Sat, 11 Nov 2017 03:22:16: 23000000 INFO @ Sat, 11 Nov 2017 03:22:21: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 03:22:21: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 03:22:21: #1 total tags in treatment: 23790639 INFO @ Sat, 11 Nov 2017 03:22:21: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 03:22:21: #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 03:22:21: 23000000 INFO @ Sat, 11 Nov 2017 03:22:21: 23000000 INFO @ Sat, 11 Nov 2017 03:22:22: #1 tags after filtering in treatment: 23790546 INFO @ Sat, 11 Nov 2017 03:22:22: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 03:22:22: #1 finished! INFO @ Sat, 11 Nov 2017 03:22:22: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 03:22:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 03:22:26: #2 number of paired peaks: 37792 INFO @ Sat, 11 Nov 2017 03:22:26: start model_add_line... INFO @ Sat, 11 Nov 2017 03:22:26: start X-correlation... INFO @ Sat, 11 Nov 2017 03:22:26: end of X-cor INFO @ Sat, 11 Nov 2017 03:22:26: #2 finished! INFO @ Sat, 11 Nov 2017 03:22:26: #2 predicted fragment length is 125 bps INFO @ Sat, 11 Nov 2017 03:22:26: #2 alternative fragment length(s) may be 59,125 bps INFO @ Sat, 11 Nov 2017 03:22:26: #2.2 Generate R script for model : SRX1977130.10_model.r INFO @ Sat, 11 Nov 2017 03:22:26: #3 Call peaks... INFO @ Sat, 11 Nov 2017 03:22:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 03:22:27: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 03:22:27: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 03:22:27: #1 total tags in treatment: 23790639 INFO @ Sat, 11 Nov 2017 03:22:27: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 03:22:27: #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 03:22:27: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 03:22:27: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 03:22:27: #1 total tags in treatment: 23790639 INFO @ Sat, 11 Nov 2017 03:22:27: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 03:22:27: #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 03:22:27: #1 tags after filtering in treatment: 23790546 INFO @ Sat, 11 Nov 2017 03:22:27: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 03:22:27: #1 finished! INFO @ Sat, 11 Nov 2017 03:22:27: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 03:22:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 03:22:27: #1 tags after filtering in treatment: 23790546 INFO @ Sat, 11 Nov 2017 03:22:27: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 03:22:27: #1 finished! INFO @ Sat, 11 Nov 2017 03:22:27: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 03:22:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 03:22:31: #2 number of paired peaks: 37792 INFO @ Sat, 11 Nov 2017 03:22:31: start model_add_line... INFO @ Sat, 11 Nov 2017 03:22:31: #2 number of paired peaks: 37792 INFO @ Sat, 11 Nov 2017 03:22:31: start model_add_line... INFO @ Sat, 11 Nov 2017 03:22:32: start X-correlation... INFO @ Sat, 11 Nov 2017 03:22:32: end of X-cor INFO @ Sat, 11 Nov 2017 03:22:32: #2 finished! INFO @ Sat, 11 Nov 2017 03:22:32: #2 predicted fragment length is 125 bps INFO @ Sat, 11 Nov 2017 03:22:32: #2 alternative fragment length(s) may be 59,125 bps INFO @ Sat, 11 Nov 2017 03:22:32: #2.2 Generate R script for model : SRX1977130.20_model.r INFO @ Sat, 11 Nov 2017 03:22:32: #3 Call peaks... INFO @ Sat, 11 Nov 2017 03:22:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 03:22:32: start X-correlation... INFO @ Sat, 11 Nov 2017 03:22:32: end of X-cor INFO @ Sat, 11 Nov 2017 03:22:32: #2 finished! INFO @ Sat, 11 Nov 2017 03:22:32: #2 predicted fragment length is 125 bps INFO @ Sat, 11 Nov 2017 03:22:32: #2 alternative fragment length(s) may be 59,125 bps INFO @ Sat, 11 Nov 2017 03:22:32: #2.2 Generate R script for model : SRX1977130.05_model.r INFO @ Sat, 11 Nov 2017 03:22:32: #3 Call peaks... INFO @ Sat, 11 Nov 2017 03:22:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 03:23:26: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 03:23:33: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 03:23:33: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 03:23:59: #4 Write output xls file... SRX1977130.10_peaks.xls INFO @ Sat, 11 Nov 2017 03:23:59: #4 Write peak in narrowPeak format file... SRX1977130.10_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 03:23:59: #4 Write summits bed file... SRX1977130.10_summits.bed INFO @ Sat, 11 Nov 2017 03:23:59: Done! pass1 - making usageList (144 chroms): 37 millis pass2 - checking and writing primary data (17478 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 03:24:06: #4 Write output xls file... SRX1977130.20_peaks.xls INFO @ Sat, 11 Nov 2017 03:24:07: #4 Write peak in narrowPeak format file... SRX1977130.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 03:24:07: #4 Write summits bed file... SRX1977130.20_summits.bed INFO @ Sat, 11 Nov 2017 03:24:07: Done! pass1 - making usageList (89 chroms): 2 millis pass2 - checking and writing primary data (4199 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 03:24:09: #4 Write output xls file... SRX1977130.05_peaks.xls INFO @ Sat, 11 Nov 2017 03:24:09: #4 Write peak in narrowPeak format file... SRX1977130.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 03:24:09: #4 Write summits bed file... SRX1977130.05_summits.bed INFO @ Sat, 11 Nov 2017 03:24:10: Done! pass1 - making usageList (219 chroms): 10 millis pass2 - checking and writing primary data (53160 records, 4 fields): 68 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。