Job ID = 11632698 sra ファイルのダウンロード中... Completed: 1208030K bytes transferred in 12 seconds (820587K 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 46189357 spots for /home/okishinya/chipatlas/results/rn6/SRX3782457/SRR6826275.sra Written 46189357 spots for /home/okishinya/chipatlas/results/rn6/SRX3782457/SRR6826275.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: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:25:20 46189357 reads; of these: 46189357 (100.00%) were unpaired; of these: 6750826 (14.62%) aligned 0 times 31357248 (67.89%) aligned exactly 1 time 8081283 (17.50%) aligned >1 times 85.38% overall alignment rate Time searching: 00:25:22 Overall time: 00:25:22 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] 27405474 / 39438531 = 0.6949 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 07:48:15: # Command line: callpeak -t SRX3782457.bam -f BAM -g 2.15e9 -n SRX3782457.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3782457.10 # format = BAM # ChIP-seq file = ['SRX3782457.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 07:48:15: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:48:15: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:48:15: # Command line: callpeak -t SRX3782457.bam -f BAM -g 2.15e9 -n SRX3782457.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3782457.05 # format = BAM # ChIP-seq file = ['SRX3782457.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 07:48:15: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:48:15: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:48:15: # Command line: callpeak -t SRX3782457.bam -f BAM -g 2.15e9 -n SRX3782457.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3782457.20 # format = BAM # ChIP-seq file = ['SRX3782457.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 07:48:15: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:48:15: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:48:24: 1000000 INFO @ Fri, 15 Feb 2019 07:48:24: 1000000 INFO @ Fri, 15 Feb 2019 07:48:26: 1000000 INFO @ Fri, 15 Feb 2019 07:48:33: 2000000 INFO @ Fri, 15 Feb 2019 07:48:33: 2000000 INFO @ Fri, 15 Feb 2019 07:48:36: 2000000 INFO @ Fri, 15 Feb 2019 07:48:41: 3000000 INFO @ Fri, 15 Feb 2019 07:48:41: 3000000 INFO @ Fri, 15 Feb 2019 07:48:47: 3000000 INFO @ Fri, 15 Feb 2019 07:48:50: 4000000 INFO @ Fri, 15 Feb 2019 07:48:50: 4000000 INFO @ Fri, 15 Feb 2019 07:48:57: 4000000 INFO @ Fri, 15 Feb 2019 07:48:59: 5000000 INFO @ Fri, 15 Feb 2019 07:48:59: 5000000 INFO @ Fri, 15 Feb 2019 07:49:07: 5000000 INFO @ Fri, 15 Feb 2019 07:49:07: 6000000 INFO @ Fri, 15 Feb 2019 07:49:07: 6000000 INFO @ Fri, 15 Feb 2019 07:49:16: 7000000 INFO @ Fri, 15 Feb 2019 07:49:16: 7000000 INFO @ Fri, 15 Feb 2019 07:49:18: 6000000 INFO @ Fri, 15 Feb 2019 07:49:24: 8000000 INFO @ Fri, 15 Feb 2019 07:49:24: 8000000 INFO @ Fri, 15 Feb 2019 07:49:28: 7000000 INFO @ Fri, 15 Feb 2019 07:49:32: 9000000 INFO @ Fri, 15 Feb 2019 07:49:32: 9000000 INFO @ Fri, 15 Feb 2019 07:49:39: 8000000 INFO @ Fri, 15 Feb 2019 07:49:40: 10000000 INFO @ Fri, 15 Feb 2019 07:49:40: 10000000 INFO @ Fri, 15 Feb 2019 07:49:48: 11000000 INFO @ Fri, 15 Feb 2019 07:49:48: 11000000 INFO @ Fri, 15 Feb 2019 07:49:49: 9000000 INFO @ Fri, 15 Feb 2019 07:49:57: 12000000 INFO @ Fri, 15 Feb 2019 07:49:57: 12000000 INFO @ Fri, 15 Feb 2019 07:49:57: #1 tag size is determined as 43 bps INFO @ Fri, 15 Feb 2019 07:49:57: #1 tag size = 43 INFO @ Fri, 15 Feb 2019 07:49:57: #1 total tags in treatment: 12033057 INFO @ Fri, 15 Feb 2019 07:49:57: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:49:57: #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 07:49:57: #1 tag size is determined as 43 bps INFO @ Fri, 15 Feb 2019 07:49:57: #1 tag size = 43 INFO @ Fri, 15 Feb 2019 07:49:57: #1 total tags in treatment: 12033057 INFO @ Fri, 15 Feb 2019 07:49:57: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:49:57: #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 07:49:58: #1 tags after filtering in treatment: 12032887 INFO @ Fri, 15 Feb 2019 07:49:58: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:49:58: #1 finished! INFO @ Fri, 15 Feb 2019 07:49:58: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:49:58: #1 tags after filtering in treatment: 12032887 INFO @ Fri, 15 Feb 2019 07:49:58: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:49:58: #1 finished! INFO @ Fri, 15 Feb 2019 07:49:58: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:49:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:49:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:49:59: 10000000 INFO @ Fri, 15 Feb 2019 07:50:01: #2 number of paired peaks: 49543 INFO @ Fri, 15 Feb 2019 07:50:01: start model_add_line... INFO @ Fri, 15 Feb 2019 07:50:01: #2 number of paired peaks: 49543 INFO @ Fri, 15 Feb 2019 07:50:01: start model_add_line... INFO @ Fri, 15 Feb 2019 07:50:01: start X-correlation... INFO @ Fri, 15 Feb 2019 07:50:01: end of X-cor INFO @ Fri, 15 Feb 2019 07:50:01: #2 finished! INFO @ Fri, 15 Feb 2019 07:50:01: #2 predicted fragment length is 121 bps INFO @ Fri, 15 Feb 2019 07:50:01: #2 alternative fragment length(s) may be 121 bps INFO @ Fri, 15 Feb 2019 07:50:01: #2.2 Generate R script for model : SRX3782457.05_model.r INFO @ Fri, 15 Feb 2019 07:50:01: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:50:01: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:50:01: start X-correlation... INFO @ Fri, 15 Feb 2019 07:50:01: end of X-cor INFO @ Fri, 15 Feb 2019 07:50:01: #2 finished! INFO @ Fri, 15 Feb 2019 07:50:01: #2 predicted fragment length is 121 bps INFO @ Fri, 15 Feb 2019 07:50:01: #2 alternative fragment length(s) may be 121 bps INFO @ Fri, 15 Feb 2019 07:50:01: #2.2 Generate R script for model : SRX3782457.10_model.r INFO @ Fri, 15 Feb 2019 07:50:01: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:50:01: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:50:09: 11000000 INFO @ Fri, 15 Feb 2019 07:50:19: 12000000 INFO @ Fri, 15 Feb 2019 07:50:20: #1 tag size is determined as 43 bps INFO @ Fri, 15 Feb 2019 07:50:20: #1 tag size = 43 INFO @ Fri, 15 Feb 2019 07:50:20: #1 total tags in treatment: 12033057 INFO @ Fri, 15 Feb 2019 07:50:20: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:50:20: #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 07:50:20: #1 tags after filtering in treatment: 12032887 INFO @ Fri, 15 Feb 2019 07:50:20: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:50:20: #1 finished! INFO @ Fri, 15 Feb 2019 07:50:20: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:50:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:50:23: #2 number of paired peaks: 49543 INFO @ Fri, 15 Feb 2019 07:50:23: start model_add_line... INFO @ Fri, 15 Feb 2019 07:50:23: start X-correlation... INFO @ Fri, 15 Feb 2019 07:50:23: end of X-cor INFO @ Fri, 15 Feb 2019 07:50:23: #2 finished! INFO @ Fri, 15 Feb 2019 07:50:23: #2 predicted fragment length is 121 bps INFO @ Fri, 15 Feb 2019 07:50:23: #2 alternative fragment length(s) may be 121 bps INFO @ Fri, 15 Feb 2019 07:50:23: #2.2 Generate R script for model : SRX3782457.20_model.r INFO @ Fri, 15 Feb 2019 07:50:23: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:50:23: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:50:31: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:50:31: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:50:49: #4 Write output xls file... SRX3782457.10_peaks.xls INFO @ Fri, 15 Feb 2019 07:50:49: #4 Write peak in narrowPeak format file... SRX3782457.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:50:49: #4 Write summits bed file... SRX3782457.10_summits.bed INFO @ Fri, 15 Feb 2019 07:50:50: Done! pass1 - making usageList (36 chroms): 3 millis pass2 - checking and writing primary data (667 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 07:50:50: #4 Write output xls file... SRX3782457.05_peaks.xls INFO @ Fri, 15 Feb 2019 07:50:50: #4 Write peak in narrowPeak format file... SRX3782457.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:50:50: #4 Write summits bed file... SRX3782457.05_summits.bed INFO @ Fri, 15 Feb 2019 07:50:50: Done! pass1 - making usageList (49 chroms): 3 millis pass2 - checking and writing primary data (1511 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 07:50:55: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:51:13: #4 Write output xls file... SRX3782457.20_peaks.xls INFO @ Fri, 15 Feb 2019 07:51:13: #4 Write peak in narrowPeak format file... SRX3782457.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:51:13: #4 Write summits bed file... SRX3782457.20_summits.bed INFO @ Fri, 15 Feb 2019 07:51:13: Done! pass1 - making usageList (32 chroms): 6 millis pass2 - checking and writing primary data (319 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。