Job ID = 11192559 sra ファイルのダウンロード中... Completed: 1383903K bytes transferred in 14 seconds (781965K 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 43568274 spots for /home/okishinya/chipatlas/results/rn6/SRX2226573/SRR4374823.sra Written 43568274 spots for /home/okishinya/chipatlas/results/rn6/SRX2226573/SRR4374823.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: 00:00:00 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:25:32 43568274 reads; of these: 43568274 (100.00%) were unpaired; of these: 10410508 (23.89%) aligned 0 times 26685832 (61.25%) aligned exactly 1 time 6471934 (14.85%) aligned >1 times 76.11% overall alignment rate Time searching: 00:25:35 Overall time: 00:25:35 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] 18833772 / 33157766 = 0.5680 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 09:23:07: # Command line: callpeak -t SRX2226573.bam -f BAM -g 2.15e9 -n SRX2226573.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2226573.10 # format = BAM # ChIP-seq file = ['SRX2226573.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 09:23:07: # Command line: callpeak -t SRX2226573.bam -f BAM -g 2.15e9 -n SRX2226573.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2226573.05 # format = BAM # ChIP-seq file = ['SRX2226573.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 09:23:07: # Command line: callpeak -t SRX2226573.bam -f BAM -g 2.15e9 -n SRX2226573.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2226573.20 # format = BAM # ChIP-seq file = ['SRX2226573.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 09:23:07: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:23:07: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:23:07: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:23:07: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:23:07: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:23:07: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:23:15: 1000000 INFO @ Sat, 15 Sep 2018 09:23:15: 1000000 INFO @ Sat, 15 Sep 2018 09:23:16: 1000000 INFO @ Sat, 15 Sep 2018 09:23:22: 2000000 INFO @ Sat, 15 Sep 2018 09:23:23: 2000000 INFO @ Sat, 15 Sep 2018 09:23:24: 2000000 INFO @ Sat, 15 Sep 2018 09:23:30: 3000000 INFO @ Sat, 15 Sep 2018 09:23:31: 3000000 INFO @ Sat, 15 Sep 2018 09:23:32: 3000000 INFO @ Sat, 15 Sep 2018 09:23:38: 4000000 INFO @ Sat, 15 Sep 2018 09:23:39: 4000000 INFO @ Sat, 15 Sep 2018 09:23:41: 4000000 INFO @ Sat, 15 Sep 2018 09:23:46: 5000000 INFO @ Sat, 15 Sep 2018 09:23:47: 5000000 INFO @ Sat, 15 Sep 2018 09:23:49: 5000000 INFO @ Sat, 15 Sep 2018 09:23:55: 6000000 INFO @ Sat, 15 Sep 2018 09:23:56: 6000000 INFO @ Sat, 15 Sep 2018 09:23:57: 6000000 INFO @ Sat, 15 Sep 2018 09:24:04: 7000000 INFO @ Sat, 15 Sep 2018 09:24:06: 7000000 INFO @ Sat, 15 Sep 2018 09:24:06: 7000000 INFO @ Sat, 15 Sep 2018 09:24:13: 8000000 INFO @ Sat, 15 Sep 2018 09:24:14: 8000000 INFO @ Sat, 15 Sep 2018 09:24:15: 8000000 INFO @ Sat, 15 Sep 2018 09:24:22: 9000000 INFO @ Sat, 15 Sep 2018 09:24:22: 9000000 INFO @ Sat, 15 Sep 2018 09:24:24: 9000000 INFO @ Sat, 15 Sep 2018 09:24:31: 10000000 INFO @ Sat, 15 Sep 2018 09:24:31: 10000000 INFO @ Sat, 15 Sep 2018 09:24:34: 10000000 INFO @ Sat, 15 Sep 2018 09:24:39: 11000000 INFO @ Sat, 15 Sep 2018 09:24:40: 11000000 INFO @ Sat, 15 Sep 2018 09:24:43: 11000000 INFO @ Sat, 15 Sep 2018 09:24:47: 12000000 INFO @ Sat, 15 Sep 2018 09:24:50: 12000000 INFO @ Sat, 15 Sep 2018 09:24:53: 12000000 INFO @ Sat, 15 Sep 2018 09:24:55: 13000000 INFO @ Sat, 15 Sep 2018 09:24:59: 13000000 INFO @ Sat, 15 Sep 2018 09:25:02: 13000000 INFO @ Sat, 15 Sep 2018 09:25:03: 14000000 INFO @ Sat, 15 Sep 2018 09:25:06: #1 tag size is determined as 50 bps INFO @ Sat, 15 Sep 2018 09:25:06: #1 tag size = 50 INFO @ Sat, 15 Sep 2018 09:25:06: #1 total tags in treatment: 14323994 INFO @ Sat, 15 Sep 2018 09:25:06: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:25:06: #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 09:25:06: #1 tags after filtering in treatment: 14323821 INFO @ Sat, 15 Sep 2018 09:25:06: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 09:25:06: #1 finished! INFO @ Sat, 15 Sep 2018 09:25:06: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:25:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:25:08: 14000000 INFO @ Sat, 15 Sep 2018 09:25:09: #2 number of paired peaks: 41691 INFO @ Sat, 15 Sep 2018 09:25:09: start model_add_line... INFO @ Sat, 15 Sep 2018 09:25:10: start X-correlation... INFO @ Sat, 15 Sep 2018 09:25:10: end of X-cor INFO @ Sat, 15 Sep 2018 09:25:10: #2 finished! INFO @ Sat, 15 Sep 2018 09:25:10: #2 predicted fragment length is 215 bps INFO @ Sat, 15 Sep 2018 09:25:10: #2 alternative fragment length(s) may be 215 bps INFO @ Sat, 15 Sep 2018 09:25:10: #2.2 Generate R script for model : SRX2226573.10_model.r INFO @ Sat, 15 Sep 2018 09:25:10: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:25:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:25:11: #1 tag size is determined as 50 bps INFO @ Sat, 15 Sep 2018 09:25:11: #1 tag size = 50 INFO @ Sat, 15 Sep 2018 09:25:11: #1 total tags in treatment: 14323994 INFO @ Sat, 15 Sep 2018 09:25:11: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:25:11: #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 09:25:11: 14000000 INFO @ Sat, 15 Sep 2018 09:25:12: #1 tags after filtering in treatment: 14323821 INFO @ Sat, 15 Sep 2018 09:25:12: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 09:25:12: #1 finished! INFO @ Sat, 15 Sep 2018 09:25:12: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:25:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:25:14: #1 tag size is determined as 50 bps INFO @ Sat, 15 Sep 2018 09:25:14: #1 tag size = 50 INFO @ Sat, 15 Sep 2018 09:25:14: #1 total tags in treatment: 14323994 INFO @ Sat, 15 Sep 2018 09:25:14: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:25:14: #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 09:25:14: #1 tags after filtering in treatment: 14323821 INFO @ Sat, 15 Sep 2018 09:25:14: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 09:25:14: #1 finished! INFO @ Sat, 15 Sep 2018 09:25:14: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:25:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:25:15: #2 number of paired peaks: 41691 INFO @ Sat, 15 Sep 2018 09:25:15: start model_add_line... INFO @ Sat, 15 Sep 2018 09:25:15: start X-correlation... INFO @ Sat, 15 Sep 2018 09:25:15: end of X-cor INFO @ Sat, 15 Sep 2018 09:25:15: #2 finished! INFO @ Sat, 15 Sep 2018 09:25:15: #2 predicted fragment length is 215 bps INFO @ Sat, 15 Sep 2018 09:25:15: #2 alternative fragment length(s) may be 215 bps INFO @ Sat, 15 Sep 2018 09:25:15: #2.2 Generate R script for model : SRX2226573.05_model.r INFO @ Sat, 15 Sep 2018 09:25:15: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:25:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:25:17: #2 number of paired peaks: 41691 INFO @ Sat, 15 Sep 2018 09:25:17: start model_add_line... INFO @ Sat, 15 Sep 2018 09:25:18: start X-correlation... INFO @ Sat, 15 Sep 2018 09:25:18: end of X-cor INFO @ Sat, 15 Sep 2018 09:25:18: #2 finished! INFO @ Sat, 15 Sep 2018 09:25:18: #2 predicted fragment length is 215 bps INFO @ Sat, 15 Sep 2018 09:25:18: #2 alternative fragment length(s) may be 215 bps INFO @ Sat, 15 Sep 2018 09:25:18: #2.2 Generate R script for model : SRX2226573.20_model.r INFO @ Sat, 15 Sep 2018 09:25:18: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:25:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:25:50: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:25:55: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:25:56: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:26:16: #4 Write output xls file... SRX2226573.10_peaks.xls INFO @ Sat, 15 Sep 2018 09:26:16: #4 Write peak in narrowPeak format file... SRX2226573.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:26:16: #4 Write summits bed file... SRX2226573.10_summits.bed INFO @ Sat, 15 Sep 2018 09:26:16: Done! pass1 - making usageList (91 chroms): 3 millis pass2 - checking and writing primary data (11615 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 09:26:18: #4 Write output xls file... SRX2226573.20_peaks.xls INFO @ Sat, 15 Sep 2018 09:26:18: #4 Write peak in narrowPeak format file... SRX2226573.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:26:18: #4 Write summits bed file... SRX2226573.20_summits.bed INFO @ Sat, 15 Sep 2018 09:26:18: Done! pass1 - making usageList (68 chroms): 10 millis pass2 - checking and writing primary data (8157 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 09:26:19: #4 Write output xls file... SRX2226573.05_peaks.xls INFO @ Sat, 15 Sep 2018 09:26:19: #4 Write peak in narrowPeak format file... SRX2226573.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:26:19: #4 Write summits bed file... SRX2226573.05_summits.bed INFO @ Sat, 15 Sep 2018 09:26:19: Done! pass1 - making usageList (117 chroms): 3 millis pass2 - checking and writing primary data (16569 records, 4 fields): 25 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。