Job ID = 11192556 sra ファイルのダウンロード中... Completed: 958980K bytes transferred in 10 seconds (735674K 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 30154183 spots for /home/okishinya/chipatlas/results/rn6/SRX2226570/SRR4374820.sra Written 30154183 spots for /home/okishinya/chipatlas/results/rn6/SRX2226570/SRR4374820.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: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:18:52 30154183 reads; of these: 30154183 (100.00%) were unpaired; of these: 4238702 (14.06%) aligned 0 times 20216719 (67.04%) aligned exactly 1 time 5698762 (18.90%) aligned >1 times 85.94% overall alignment rate Time searching: 00:18:56 Overall time: 00:18:56 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] 12816658 / 25915481 = 0.4946 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 09:10:13: # Command line: callpeak -t SRX2226570.bam -f BAM -g 2.15e9 -n SRX2226570.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2226570.05 # format = BAM # ChIP-seq file = ['SRX2226570.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 09:10:13: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:10:13: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:10:13: # Command line: callpeak -t SRX2226570.bam -f BAM -g 2.15e9 -n SRX2226570.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2226570.20 # format = BAM # ChIP-seq file = ['SRX2226570.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 09:10:13: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:10:13: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:10:13: # Command line: callpeak -t SRX2226570.bam -f BAM -g 2.15e9 -n SRX2226570.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2226570.10 # format = BAM # ChIP-seq file = ['SRX2226570.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 09:10:13: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:10:13: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:10:21: 1000000 INFO @ Sat, 15 Sep 2018 09:10:21: 1000000 INFO @ Sat, 15 Sep 2018 09:10:21: 1000000 INFO @ Sat, 15 Sep 2018 09:10:29: 2000000 INFO @ Sat, 15 Sep 2018 09:10:30: 2000000 INFO @ Sat, 15 Sep 2018 09:10:30: 2000000 INFO @ Sat, 15 Sep 2018 09:10:37: 3000000 INFO @ Sat, 15 Sep 2018 09:10:38: 3000000 INFO @ Sat, 15 Sep 2018 09:10:38: 3000000 INFO @ Sat, 15 Sep 2018 09:10:44: 4000000 INFO @ Sat, 15 Sep 2018 09:10:47: 4000000 INFO @ Sat, 15 Sep 2018 09:10:47: 4000000 INFO @ Sat, 15 Sep 2018 09:10:52: 5000000 INFO @ Sat, 15 Sep 2018 09:10:55: 5000000 INFO @ Sat, 15 Sep 2018 09:10:55: 5000000 INFO @ Sat, 15 Sep 2018 09:10:59: 6000000 INFO @ Sat, 15 Sep 2018 09:11:04: 6000000 INFO @ Sat, 15 Sep 2018 09:11:04: 6000000 INFO @ Sat, 15 Sep 2018 09:11:07: 7000000 INFO @ Sat, 15 Sep 2018 09:11:13: 7000000 INFO @ Sat, 15 Sep 2018 09:11:13: 7000000 INFO @ Sat, 15 Sep 2018 09:11:15: 8000000 INFO @ Sat, 15 Sep 2018 09:11:21: 8000000 INFO @ Sat, 15 Sep 2018 09:11:21: 8000000 INFO @ Sat, 15 Sep 2018 09:11:22: 9000000 INFO @ Sat, 15 Sep 2018 09:11:30: 10000000 INFO @ Sat, 15 Sep 2018 09:11:30: 9000000 INFO @ Sat, 15 Sep 2018 09:11:30: 9000000 INFO @ Sat, 15 Sep 2018 09:11:37: 11000000 INFO @ Sat, 15 Sep 2018 09:11:39: 10000000 INFO @ Sat, 15 Sep 2018 09:11:39: 10000000 INFO @ Sat, 15 Sep 2018 09:11:45: 12000000 INFO @ Sat, 15 Sep 2018 09:11:47: 11000000 INFO @ Sat, 15 Sep 2018 09:11:47: 11000000 INFO @ Sat, 15 Sep 2018 09:11:53: 13000000 INFO @ Sat, 15 Sep 2018 09:11:53: #1 tag size is determined as 50 bps INFO @ Sat, 15 Sep 2018 09:11:53: #1 tag size = 50 INFO @ Sat, 15 Sep 2018 09:11:53: #1 total tags in treatment: 13098823 INFO @ Sat, 15 Sep 2018 09:11:53: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:11:53: #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 09:11:54: #1 tags after filtering in treatment: 13098665 INFO @ Sat, 15 Sep 2018 09:11:54: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 09:11:54: #1 finished! INFO @ Sat, 15 Sep 2018 09:11:54: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:11:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:11:56: 12000000 INFO @ Sat, 15 Sep 2018 09:11:56: 12000000 INFO @ Sat, 15 Sep 2018 09:11:57: #2 number of paired peaks: 40994 INFO @ Sat, 15 Sep 2018 09:11:57: start model_add_line... INFO @ Sat, 15 Sep 2018 09:11:57: start X-correlation... INFO @ Sat, 15 Sep 2018 09:11:57: end of X-cor INFO @ Sat, 15 Sep 2018 09:11:57: #2 finished! INFO @ Sat, 15 Sep 2018 09:11:57: #2 predicted fragment length is 221 bps INFO @ Sat, 15 Sep 2018 09:11:57: #2 alternative fragment length(s) may be 221 bps INFO @ Sat, 15 Sep 2018 09:11:57: #2.2 Generate R script for model : SRX2226570.10_model.r INFO @ Sat, 15 Sep 2018 09:11:57: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:11:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:12:05: 13000000 INFO @ Sat, 15 Sep 2018 09:12:05: 13000000 INFO @ Sat, 15 Sep 2018 09:12:06: #1 tag size is determined as 50 bps INFO @ Sat, 15 Sep 2018 09:12:06: #1 tag size = 50 INFO @ Sat, 15 Sep 2018 09:12:06: #1 total tags in treatment: 13098823 INFO @ Sat, 15 Sep 2018 09:12:06: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:12:06: #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 09:12:06: #1 tag size is determined as 50 bps INFO @ Sat, 15 Sep 2018 09:12:06: #1 tag size = 50 INFO @ Sat, 15 Sep 2018 09:12:06: #1 total tags in treatment: 13098823 INFO @ Sat, 15 Sep 2018 09:12:06: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:12:06: #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 09:12:06: #1 tags after filtering in treatment: 13098665 INFO @ Sat, 15 Sep 2018 09:12:06: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 09:12:06: #1 finished! INFO @ Sat, 15 Sep 2018 09:12:06: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:12:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:12:06: #1 tags after filtering in treatment: 13098665 INFO @ Sat, 15 Sep 2018 09:12:06: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 09:12:06: #1 finished! INFO @ Sat, 15 Sep 2018 09:12:06: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:12:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:12:09: #2 number of paired peaks: 40994 INFO @ Sat, 15 Sep 2018 09:12:09: start model_add_line... INFO @ Sat, 15 Sep 2018 09:12:09: #2 number of paired peaks: 40994 INFO @ Sat, 15 Sep 2018 09:12:09: start model_add_line... INFO @ Sat, 15 Sep 2018 09:12:09: start X-correlation... INFO @ Sat, 15 Sep 2018 09:12:09: end of X-cor INFO @ Sat, 15 Sep 2018 09:12:09: #2 finished! INFO @ Sat, 15 Sep 2018 09:12:09: #2 predicted fragment length is 221 bps INFO @ Sat, 15 Sep 2018 09:12:09: #2 alternative fragment length(s) may be 221 bps INFO @ Sat, 15 Sep 2018 09:12:09: #2.2 Generate R script for model : SRX2226570.05_model.r INFO @ Sat, 15 Sep 2018 09:12:09: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:12:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:12:09: start X-correlation... INFO @ Sat, 15 Sep 2018 09:12:09: end of X-cor INFO @ Sat, 15 Sep 2018 09:12:09: #2 finished! INFO @ Sat, 15 Sep 2018 09:12:09: #2 predicted fragment length is 221 bps INFO @ Sat, 15 Sep 2018 09:12:09: #2 alternative fragment length(s) may be 221 bps INFO @ Sat, 15 Sep 2018 09:12:09: #2.2 Generate R script for model : SRX2226570.20_model.r INFO @ Sat, 15 Sep 2018 09:12:09: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:12:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:12:34: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:12:41: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:12:43: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:12:52: #4 Write output xls file... SRX2226570.10_peaks.xls INFO @ Sat, 15 Sep 2018 09:12:52: #4 Write peak in narrowPeak format file... SRX2226570.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:12:53: #4 Write summits bed file... SRX2226570.10_summits.bed INFO @ Sat, 15 Sep 2018 09:12:53: Done! pass1 - making usageList (53 chroms): 2 millis pass2 - checking and writing primary data (3578 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 09:13:00: #4 Write output xls file... SRX2226570.20_peaks.xls INFO @ Sat, 15 Sep 2018 09:13:00: #4 Write peak in narrowPeak format file... SRX2226570.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:13:00: #4 Write summits bed file... SRX2226570.20_summits.bed INFO @ Sat, 15 Sep 2018 09:13:00: Done! pass1 - making usageList (35 chroms): 1 millis pass2 - checking and writing primary data (1140 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 09:13:02: #4 Write output xls file... SRX2226570.05_peaks.xls INFO @ Sat, 15 Sep 2018 09:13:02: #4 Write peak in narrowPeak format file... SRX2226570.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:13:02: #4 Write summits bed file... SRX2226570.05_summits.bed INFO @ Sat, 15 Sep 2018 09:13:02: Done! pass1 - making usageList (70 chroms): 2 millis pass2 - checking and writing primary data (9097 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。