Job ID = 11192576 sra ファイルのダウンロード中... Completed: 1259089K bytes transferred in 13 seconds (753540K 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 38949054 spots for /home/okishinya/chipatlas/results/rn6/SRX2226588/SRR4374838.sra Written 38949054 spots for /home/okishinya/chipatlas/results/rn6/SRX2226588/SRR4374838.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: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:18:33 38949054 reads; of these: 38949054 (100.00%) were unpaired; of these: 16021068 (41.13%) aligned 0 times 17613139 (45.22%) aligned exactly 1 time 5314847 (13.65%) aligned >1 times 58.87% overall alignment rate Time searching: 00:18:36 Overall time: 00:18:36 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] 6970858 / 22927986 = 0.3040 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, 15 Sep 2018 09:27:59: # Command line: callpeak -t SRX2226588.bam -f BAM -g 2.15e9 -n SRX2226588.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2226588.05 # format = BAM # ChIP-seq file = ['SRX2226588.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, 15 Sep 2018 09:27:59: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:27:59: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:27:59: # Command line: callpeak -t SRX2226588.bam -f BAM -g 2.15e9 -n SRX2226588.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2226588.20 # format = BAM # ChIP-seq file = ['SRX2226588.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, 15 Sep 2018 09:27:59: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:27:59: # Command line: callpeak -t SRX2226588.bam -f BAM -g 2.15e9 -n SRX2226588.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2226588.10 # format = BAM # ChIP-seq file = ['SRX2226588.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, 15 Sep 2018 09:27:59: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:27:59: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:27:59: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:28:06: 1000000 INFO @ Sat, 15 Sep 2018 09:28:06: 1000000 INFO @ Sat, 15 Sep 2018 09:28:06: 1000000 INFO @ Sat, 15 Sep 2018 09:28:12: 2000000 INFO @ Sat, 15 Sep 2018 09:28:12: 2000000 INFO @ Sat, 15 Sep 2018 09:28:12: 2000000 INFO @ Sat, 15 Sep 2018 09:28:18: 3000000 INFO @ Sat, 15 Sep 2018 09:28:18: 3000000 INFO @ Sat, 15 Sep 2018 09:28:19: 3000000 INFO @ Sat, 15 Sep 2018 09:28:24: 4000000 INFO @ Sat, 15 Sep 2018 09:28:25: 4000000 INFO @ Sat, 15 Sep 2018 09:28:25: 4000000 INFO @ Sat, 15 Sep 2018 09:28:31: 5000000 INFO @ Sat, 15 Sep 2018 09:28:31: 5000000 INFO @ Sat, 15 Sep 2018 09:28:32: 5000000 INFO @ Sat, 15 Sep 2018 09:28:37: 6000000 INFO @ Sat, 15 Sep 2018 09:28:38: 6000000 INFO @ Sat, 15 Sep 2018 09:28:38: 6000000 INFO @ Sat, 15 Sep 2018 09:28:44: 7000000 INFO @ Sat, 15 Sep 2018 09:28:44: 7000000 INFO @ Sat, 15 Sep 2018 09:28:45: 7000000 INFO @ Sat, 15 Sep 2018 09:28:50: 8000000 INFO @ Sat, 15 Sep 2018 09:28:51: 8000000 INFO @ Sat, 15 Sep 2018 09:28:51: 8000000 INFO @ Sat, 15 Sep 2018 09:28:56: 9000000 INFO @ Sat, 15 Sep 2018 09:28:57: 9000000 INFO @ Sat, 15 Sep 2018 09:28:58: 9000000 INFO @ Sat, 15 Sep 2018 09:29:03: 10000000 INFO @ Sat, 15 Sep 2018 09:29:03: 10000000 INFO @ Sat, 15 Sep 2018 09:29:04: 10000000 INFO @ Sat, 15 Sep 2018 09:29:09: 11000000 INFO @ Sat, 15 Sep 2018 09:29:10: 11000000 INFO @ Sat, 15 Sep 2018 09:29:11: 11000000 INFO @ Sat, 15 Sep 2018 09:29:15: 12000000 INFO @ Sat, 15 Sep 2018 09:29:16: 12000000 INFO @ Sat, 15 Sep 2018 09:29:18: 12000000 INFO @ Sat, 15 Sep 2018 09:29:22: 13000000 INFO @ Sat, 15 Sep 2018 09:29:22: 13000000 INFO @ Sat, 15 Sep 2018 09:29:24: 13000000 INFO @ Sat, 15 Sep 2018 09:29:28: 14000000 INFO @ Sat, 15 Sep 2018 09:29:28: 14000000 INFO @ Sat, 15 Sep 2018 09:29:31: 14000000 INFO @ Sat, 15 Sep 2018 09:29:35: 15000000 INFO @ Sat, 15 Sep 2018 09:29:35: 15000000 INFO @ Sat, 15 Sep 2018 09:29:38: 15000000 INFO @ Sat, 15 Sep 2018 09:29:41: #1 tag size is determined as 50 bps INFO @ Sat, 15 Sep 2018 09:29:41: #1 tag size = 50 INFO @ Sat, 15 Sep 2018 09:29:41: #1 total tags in treatment: 15957128 INFO @ Sat, 15 Sep 2018 09:29:41: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:29:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 09:29:41: #1 tag size is determined as 50 bps INFO @ Sat, 15 Sep 2018 09:29:41: #1 tag size = 50 INFO @ Sat, 15 Sep 2018 09:29:41: #1 total tags in treatment: 15957128 INFO @ Sat, 15 Sep 2018 09:29:41: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:29:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 09:29:42: #1 tags after filtering in treatment: 15956976 INFO @ Sat, 15 Sep 2018 09:29:42: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 09:29:42: #1 finished! INFO @ Sat, 15 Sep 2018 09:29:42: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:29:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:29:42: #1 tags after filtering in treatment: 15956976 INFO @ Sat, 15 Sep 2018 09:29:42: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 09:29:42: #1 finished! INFO @ Sat, 15 Sep 2018 09:29:42: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:29:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:29:44: #2 number of paired peaks: 30327 INFO @ Sat, 15 Sep 2018 09:29:44: start model_add_line... INFO @ Sat, 15 Sep 2018 09:29:44: #1 tag size is determined as 50 bps INFO @ Sat, 15 Sep 2018 09:29:44: #1 tag size = 50 INFO @ Sat, 15 Sep 2018 09:29:44: #1 total tags in treatment: 15957128 INFO @ Sat, 15 Sep 2018 09:29:44: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:29:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 09:29:44: #2 number of paired peaks: 30327 INFO @ Sat, 15 Sep 2018 09:29:44: start model_add_line... INFO @ Sat, 15 Sep 2018 09:29:44: start X-correlation... INFO @ Sat, 15 Sep 2018 09:29:45: end of X-cor INFO @ Sat, 15 Sep 2018 09:29:45: #2 finished! INFO @ Sat, 15 Sep 2018 09:29:45: #2 predicted fragment length is 132 bps INFO @ Sat, 15 Sep 2018 09:29:45: #2 alternative fragment length(s) may be 132 bps INFO @ Sat, 15 Sep 2018 09:29:45: #2.2 Generate R script for model : SRX2226588.10_model.r INFO @ Sat, 15 Sep 2018 09:29:45: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:29:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:29:45: start X-correlation... INFO @ Sat, 15 Sep 2018 09:29:45: end of X-cor INFO @ Sat, 15 Sep 2018 09:29:45: #2 finished! INFO @ Sat, 15 Sep 2018 09:29:45: #2 predicted fragment length is 132 bps INFO @ Sat, 15 Sep 2018 09:29:45: #2 alternative fragment length(s) may be 132 bps INFO @ Sat, 15 Sep 2018 09:29:45: #2.2 Generate R script for model : SRX2226588.20_model.r INFO @ Sat, 15 Sep 2018 09:29:45: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:29:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:29:45: #1 tags after filtering in treatment: 15956976 INFO @ Sat, 15 Sep 2018 09:29:45: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 09:29:45: #1 finished! INFO @ Sat, 15 Sep 2018 09:29:45: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:29:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:29:47: #2 number of paired peaks: 30327 INFO @ Sat, 15 Sep 2018 09:29:47: start model_add_line... INFO @ Sat, 15 Sep 2018 09:29:48: start X-correlation... INFO @ Sat, 15 Sep 2018 09:29:48: end of X-cor INFO @ Sat, 15 Sep 2018 09:29:48: #2 finished! INFO @ Sat, 15 Sep 2018 09:29:48: #2 predicted fragment length is 132 bps INFO @ Sat, 15 Sep 2018 09:29:48: #2 alternative fragment length(s) may be 132 bps INFO @ Sat, 15 Sep 2018 09:29:48: #2.2 Generate R script for model : SRX2226588.05_model.r INFO @ Sat, 15 Sep 2018 09:29:48: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:29:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:30:23: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:30:24: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:30:26: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:30:44: #4 Write output xls file... SRX2226588.20_peaks.xls INFO @ Sat, 15 Sep 2018 09:30:44: #4 Write peak in narrowPeak format file... SRX2226588.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:30:44: #4 Write summits bed file... SRX2226588.20_summits.bed INFO @ Sat, 15 Sep 2018 09:30:44: Done! pass1 - making usageList (60 chroms): 1 millis pass2 - checking and writing primary data (2285 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 09:30:47: #4 Write output xls file... SRX2226588.10_peaks.xls INFO @ Sat, 15 Sep 2018 09:30:47: #4 Write peak in narrowPeak format file... SRX2226588.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:30:47: #4 Write summits bed file... SRX2226588.10_summits.bed INFO @ Sat, 15 Sep 2018 09:30:47: Done! pass1 - making usageList (75 chroms): 1 millis pass2 - checking and writing primary data (4515 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 09:30:48: #4 Write output xls file... SRX2226588.05_peaks.xls INFO @ Sat, 15 Sep 2018 09:30:48: #4 Write peak in narrowPeak format file... SRX2226588.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:30:48: #4 Write summits bed file... SRX2226588.05_summits.bed INFO @ Sat, 15 Sep 2018 09:30:48: Done! pass1 - making usageList (98 chroms): 2 millis pass2 - checking and writing primary data (8724 records, 4 fields): 15 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。