Job ID = 11632700 sra ファイルのダウンロード中... Completed: 1385318K bytes transferred in 13 seconds (837095K 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 54036538 spots for /home/okishinya/chipatlas/results/rn6/SRX3782459/SRR6826277.sra Written 54036538 spots for /home/okishinya/chipatlas/results/rn6/SRX3782459/SRR6826277.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: 00:00:04 Time loading mirror index: 00:00:02 Multiseed full-index search: 00:25:54 54036538 reads; of these: 54036538 (100.00%) were unpaired; of these: 13184820 (24.40%) aligned 0 times 32267962 (59.72%) aligned exactly 1 time 8583756 (15.89%) aligned >1 times 75.60% overall alignment rate Time searching: 00:26:01 Overall time: 00:26:01 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] 25400459 / 40851718 = 0.6218 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 06:36:38: # Command line: callpeak -t SRX3782459.bam -f BAM -g 2.15e9 -n SRX3782459.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3782459.10 # format = BAM # ChIP-seq file = ['SRX3782459.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 06:36:38: # Command line: callpeak -t SRX3782459.bam -f BAM -g 2.15e9 -n SRX3782459.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3782459.20 # format = BAM # ChIP-seq file = ['SRX3782459.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 06:36:38: # Command line: callpeak -t SRX3782459.bam -f BAM -g 2.15e9 -n SRX3782459.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3782459.05 # format = BAM # ChIP-seq file = ['SRX3782459.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 06:36:38: #1 read tag files... INFO @ Fri, 15 Feb 2019 06:36:38: #1 read tag files... INFO @ Fri, 15 Feb 2019 06:36:38: #1 read tag files... INFO @ Fri, 15 Feb 2019 06:36:38: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 06:36:38: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 06:36:38: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 06:36:44: 1000000 INFO @ Fri, 15 Feb 2019 06:36:44: 1000000 INFO @ Fri, 15 Feb 2019 06:36:44: 1000000 INFO @ Fri, 15 Feb 2019 06:36:51: 2000000 INFO @ Fri, 15 Feb 2019 06:36:51: 2000000 INFO @ Fri, 15 Feb 2019 06:36:51: 2000000 INFO @ Fri, 15 Feb 2019 06:36:57: 3000000 INFO @ Fri, 15 Feb 2019 06:36:57: 3000000 INFO @ Fri, 15 Feb 2019 06:36:59: 3000000 INFO @ Fri, 15 Feb 2019 06:37:03: 4000000 INFO @ Fri, 15 Feb 2019 06:37:04: 4000000 INFO @ Fri, 15 Feb 2019 06:37:06: 4000000 INFO @ Fri, 15 Feb 2019 06:37:10: 5000000 INFO @ Fri, 15 Feb 2019 06:37:11: 5000000 INFO @ Fri, 15 Feb 2019 06:37:13: 5000000 INFO @ Fri, 15 Feb 2019 06:37:16: 6000000 INFO @ Fri, 15 Feb 2019 06:37:18: 6000000 INFO @ Fri, 15 Feb 2019 06:37:21: 6000000 INFO @ Fri, 15 Feb 2019 06:37:22: 7000000 INFO @ Fri, 15 Feb 2019 06:37:25: 7000000 INFO @ Fri, 15 Feb 2019 06:37:28: 7000000 INFO @ Fri, 15 Feb 2019 06:37:29: 8000000 INFO @ Fri, 15 Feb 2019 06:37:31: 8000000 INFO @ Fri, 15 Feb 2019 06:37:35: 9000000 INFO @ Fri, 15 Feb 2019 06:37:35: 8000000 INFO @ Fri, 15 Feb 2019 06:37:38: 9000000 INFO @ Fri, 15 Feb 2019 06:37:41: 10000000 INFO @ Fri, 15 Feb 2019 06:37:43: 9000000 INFO @ Fri, 15 Feb 2019 06:37:45: 10000000 INFO @ Fri, 15 Feb 2019 06:37:48: 11000000 INFO @ Fri, 15 Feb 2019 06:37:50: 10000000 INFO @ Fri, 15 Feb 2019 06:37:52: 11000000 INFO @ Fri, 15 Feb 2019 06:37:54: 12000000 INFO @ Fri, 15 Feb 2019 06:37:57: 11000000 INFO @ Fri, 15 Feb 2019 06:37:58: 12000000 INFO @ Fri, 15 Feb 2019 06:38:01: 13000000 INFO @ Fri, 15 Feb 2019 06:38:05: 12000000 INFO @ Fri, 15 Feb 2019 06:38:05: 13000000 INFO @ Fri, 15 Feb 2019 06:38:07: 14000000 INFO @ Fri, 15 Feb 2019 06:38:12: 13000000 INFO @ Fri, 15 Feb 2019 06:38:12: 14000000 INFO @ Fri, 15 Feb 2019 06:38:14: 15000000 INFO @ Fri, 15 Feb 2019 06:38:17: #1 tag size is determined as 44 bps INFO @ Fri, 15 Feb 2019 06:38:17: #1 tag size = 44 INFO @ Fri, 15 Feb 2019 06:38:17: #1 total tags in treatment: 15451259 INFO @ Fri, 15 Feb 2019 06:38:17: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 06:38:17: #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 06:38:17: #1 tags after filtering in treatment: 15451114 INFO @ Fri, 15 Feb 2019 06:38:17: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 06:38:17: #1 finished! INFO @ Fri, 15 Feb 2019 06:38:17: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 06:38:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 06:38:19: 15000000 INFO @ Fri, 15 Feb 2019 06:38:19: 14000000 INFO @ Fri, 15 Feb 2019 06:38:20: #2 number of paired peaks: 45019 INFO @ Fri, 15 Feb 2019 06:38:20: start model_add_line... INFO @ Fri, 15 Feb 2019 06:38:20: start X-correlation... INFO @ Fri, 15 Feb 2019 06:38:20: end of X-cor INFO @ Fri, 15 Feb 2019 06:38:20: #2 finished! INFO @ Fri, 15 Feb 2019 06:38:20: #2 predicted fragment length is 135 bps INFO @ Fri, 15 Feb 2019 06:38:20: #2 alternative fragment length(s) may be 135 bps INFO @ Fri, 15 Feb 2019 06:38:20: #2.2 Generate R script for model : SRX3782459.20_model.r INFO @ Fri, 15 Feb 2019 06:38:20: #3 Call peaks... INFO @ Fri, 15 Feb 2019 06:38:20: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 06:38:22: #1 tag size is determined as 44 bps INFO @ Fri, 15 Feb 2019 06:38:22: #1 tag size = 44 INFO @ Fri, 15 Feb 2019 06:38:22: #1 total tags in treatment: 15451259 INFO @ Fri, 15 Feb 2019 06:38:22: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 06:38:22: #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 06:38:23: #1 tags after filtering in treatment: 15451114 INFO @ Fri, 15 Feb 2019 06:38:23: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 06:38:23: #1 finished! INFO @ Fri, 15 Feb 2019 06:38:23: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 06:38:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 06:38:26: #2 number of paired peaks: 45019 INFO @ Fri, 15 Feb 2019 06:38:26: start model_add_line... INFO @ Fri, 15 Feb 2019 06:38:26: 15000000 INFO @ Fri, 15 Feb 2019 06:38:26: start X-correlation... INFO @ Fri, 15 Feb 2019 06:38:26: end of X-cor INFO @ Fri, 15 Feb 2019 06:38:26: #2 finished! INFO @ Fri, 15 Feb 2019 06:38:26: #2 predicted fragment length is 135 bps INFO @ Fri, 15 Feb 2019 06:38:26: #2 alternative fragment length(s) may be 135 bps INFO @ Fri, 15 Feb 2019 06:38:26: #2.2 Generate R script for model : SRX3782459.10_model.r INFO @ Fri, 15 Feb 2019 06:38:26: #3 Call peaks... INFO @ Fri, 15 Feb 2019 06:38:26: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 06:38:29: #1 tag size is determined as 44 bps INFO @ Fri, 15 Feb 2019 06:38:29: #1 tag size = 44 INFO @ Fri, 15 Feb 2019 06:38:29: #1 total tags in treatment: 15451259 INFO @ Fri, 15 Feb 2019 06:38:29: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 06:38:29: #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 06:38:30: #1 tags after filtering in treatment: 15451114 INFO @ Fri, 15 Feb 2019 06:38:30: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 06:38:30: #1 finished! INFO @ Fri, 15 Feb 2019 06:38:30: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 06:38:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 06:38:33: #2 number of paired peaks: 45019 INFO @ Fri, 15 Feb 2019 06:38:33: start model_add_line... INFO @ Fri, 15 Feb 2019 06:38:33: start X-correlation... INFO @ Fri, 15 Feb 2019 06:38:33: end of X-cor INFO @ Fri, 15 Feb 2019 06:38:33: #2 finished! INFO @ Fri, 15 Feb 2019 06:38:33: #2 predicted fragment length is 135 bps INFO @ Fri, 15 Feb 2019 06:38:33: #2 alternative fragment length(s) may be 135 bps INFO @ Fri, 15 Feb 2019 06:38:33: #2.2 Generate R script for model : SRX3782459.05_model.r INFO @ Fri, 15 Feb 2019 06:38:33: #3 Call peaks... INFO @ Fri, 15 Feb 2019 06:38:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 06:38:58: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 06:39:06: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 06:39:12: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 06:39:21: #4 Write output xls file... SRX3782459.20_peaks.xls INFO @ Fri, 15 Feb 2019 06:39:21: #4 Write peak in narrowPeak format file... SRX3782459.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 06:39:21: #4 Write summits bed file... SRX3782459.20_summits.bed INFO @ Fri, 15 Feb 2019 06:39:21: Done! pass1 - making usageList (31 chroms): 4 millis pass2 - checking and writing primary data (358 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 06:39:27: #4 Write output xls file... SRX3782459.10_peaks.xls INFO @ Fri, 15 Feb 2019 06:39:27: #4 Write peak in narrowPeak format file... SRX3782459.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 06:39:27: #4 Write summits bed file... SRX3782459.10_summits.bed INFO @ Fri, 15 Feb 2019 06:39:27: Done! pass1 - making usageList (48 chroms): 4 millis pass2 - checking and writing primary data (881 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 06:39:37: #4 Write output xls file... SRX3782459.05_peaks.xls INFO @ Fri, 15 Feb 2019 06:39:37: #4 Write peak in narrowPeak format file... SRX3782459.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 06:39:37: #4 Write summits bed file... SRX3782459.05_summits.bed INFO @ Fri, 15 Feb 2019 06:39:37: Done! pass1 - making usageList (90 chroms): 6 millis pass2 - checking and writing primary data (5961 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。