Job ID = 11192587 sra ファイルのダウンロード中... Completed: 332171K bytes transferred in 31 seconds (85184K 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 31700012 spots for /home/okishinya/chipatlas/results/rn6/SRX4014807/SRR7085056.sra Written 31700012 spots for /home/okishinya/chipatlas/results/rn6/SRX4014807/SRR7085056.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: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:33:50 31700012 reads; of these: 31700012 (100.00%) were unpaired; of these: 925047 (2.92%) aligned 0 times 27084722 (85.44%) aligned exactly 1 time 3690243 (11.64%) aligned >1 times 97.08% overall alignment rate Time searching: 00:33:52 Overall time: 00:33:52 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] 2800045 / 30774965 = 0.0910 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 11:22:53: # Command line: callpeak -t SRX4014807.bam -f BAM -g 2.15e9 -n SRX4014807.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4014807.05 # format = BAM # ChIP-seq file = ['SRX4014807.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 11:22:53: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:22:53: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:22:53: # Command line: callpeak -t SRX4014807.bam -f BAM -g 2.15e9 -n SRX4014807.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4014807.20 # format = BAM # ChIP-seq file = ['SRX4014807.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 11:22:53: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:22:53: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:22:53: # Command line: callpeak -t SRX4014807.bam -f BAM -g 2.15e9 -n SRX4014807.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4014807.10 # format = BAM # ChIP-seq file = ['SRX4014807.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 11:22:53: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:22:53: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:22:59: 1000000 INFO @ Sat, 15 Sep 2018 11:22:59: 1000000 INFO @ Sat, 15 Sep 2018 11:22:59: 1000000 INFO @ Sat, 15 Sep 2018 11:23:06: 2000000 INFO @ Sat, 15 Sep 2018 11:23:06: 2000000 INFO @ Sat, 15 Sep 2018 11:23:06: 2000000 INFO @ Sat, 15 Sep 2018 11:23:12: 3000000 INFO @ Sat, 15 Sep 2018 11:23:12: 3000000 INFO @ Sat, 15 Sep 2018 11:23:12: 3000000 INFO @ Sat, 15 Sep 2018 11:23:19: 4000000 INFO @ Sat, 15 Sep 2018 11:23:19: 4000000 INFO @ Sat, 15 Sep 2018 11:23:19: 4000000 INFO @ Sat, 15 Sep 2018 11:23:25: 5000000 INFO @ Sat, 15 Sep 2018 11:23:25: 5000000 INFO @ Sat, 15 Sep 2018 11:23:25: 5000000 INFO @ Sat, 15 Sep 2018 11:23:32: 6000000 INFO @ Sat, 15 Sep 2018 11:23:32: 6000000 INFO @ Sat, 15 Sep 2018 11:23:32: 6000000 INFO @ Sat, 15 Sep 2018 11:23:38: 7000000 INFO @ Sat, 15 Sep 2018 11:23:38: 7000000 INFO @ Sat, 15 Sep 2018 11:23:38: 7000000 INFO @ Sat, 15 Sep 2018 11:23:44: 8000000 INFO @ Sat, 15 Sep 2018 11:23:44: 8000000 INFO @ Sat, 15 Sep 2018 11:23:45: 8000000 INFO @ Sat, 15 Sep 2018 11:23:51: 9000000 INFO @ Sat, 15 Sep 2018 11:23:51: 9000000 INFO @ Sat, 15 Sep 2018 11:23:51: 9000000 INFO @ Sat, 15 Sep 2018 11:23:57: 10000000 INFO @ Sat, 15 Sep 2018 11:23:57: 10000000 INFO @ Sat, 15 Sep 2018 11:23:58: 10000000 INFO @ Sat, 15 Sep 2018 11:24:03: 11000000 INFO @ Sat, 15 Sep 2018 11:24:04: 11000000 INFO @ Sat, 15 Sep 2018 11:24:04: 11000000 INFO @ Sat, 15 Sep 2018 11:24:10: 12000000 INFO @ Sat, 15 Sep 2018 11:24:10: 12000000 INFO @ Sat, 15 Sep 2018 11:24:10: 12000000 INFO @ Sat, 15 Sep 2018 11:24:16: 13000000 INFO @ Sat, 15 Sep 2018 11:24:16: 13000000 INFO @ Sat, 15 Sep 2018 11:24:17: 13000000 INFO @ Sat, 15 Sep 2018 11:24:23: 14000000 INFO @ Sat, 15 Sep 2018 11:24:23: 14000000 INFO @ Sat, 15 Sep 2018 11:24:23: 14000000 INFO @ Sat, 15 Sep 2018 11:24:29: 15000000 INFO @ Sat, 15 Sep 2018 11:24:29: 15000000 INFO @ Sat, 15 Sep 2018 11:24:30: 15000000 INFO @ Sat, 15 Sep 2018 11:24:35: 16000000 INFO @ Sat, 15 Sep 2018 11:24:36: 16000000 INFO @ Sat, 15 Sep 2018 11:24:36: 16000000 INFO @ Sat, 15 Sep 2018 11:24:42: 17000000 INFO @ Sat, 15 Sep 2018 11:24:42: 17000000 INFO @ Sat, 15 Sep 2018 11:24:43: 17000000 INFO @ Sat, 15 Sep 2018 11:24:48: 18000000 INFO @ Sat, 15 Sep 2018 11:24:49: 18000000 INFO @ Sat, 15 Sep 2018 11:24:49: 18000000 INFO @ Sat, 15 Sep 2018 11:24:55: 19000000 INFO @ Sat, 15 Sep 2018 11:24:55: 19000000 INFO @ Sat, 15 Sep 2018 11:24:56: 19000000 INFO @ Sat, 15 Sep 2018 11:25:02: 20000000 INFO @ Sat, 15 Sep 2018 11:25:02: 20000000 INFO @ Sat, 15 Sep 2018 11:25:02: 20000000 INFO @ Sat, 15 Sep 2018 11:25:08: 21000000 INFO @ Sat, 15 Sep 2018 11:25:09: 21000000 INFO @ Sat, 15 Sep 2018 11:25:09: 21000000 INFO @ Sat, 15 Sep 2018 11:25:15: 22000000 INFO @ Sat, 15 Sep 2018 11:25:15: 22000000 INFO @ Sat, 15 Sep 2018 11:25:15: 22000000 INFO @ Sat, 15 Sep 2018 11:25:21: 23000000 INFO @ Sat, 15 Sep 2018 11:25:22: 23000000 INFO @ Sat, 15 Sep 2018 11:25:22: 23000000 INFO @ Sat, 15 Sep 2018 11:25:28: 24000000 INFO @ Sat, 15 Sep 2018 11:25:29: 24000000 INFO @ Sat, 15 Sep 2018 11:25:29: 24000000 INFO @ Sat, 15 Sep 2018 11:25:35: 25000000 INFO @ Sat, 15 Sep 2018 11:25:35: 25000000 INFO @ Sat, 15 Sep 2018 11:25:35: 25000000 INFO @ Sat, 15 Sep 2018 11:25:41: 26000000 INFO @ Sat, 15 Sep 2018 11:25:42: 26000000 INFO @ Sat, 15 Sep 2018 11:25:42: 26000000 INFO @ Sat, 15 Sep 2018 11:25:48: 27000000 INFO @ Sat, 15 Sep 2018 11:25:48: 27000000 INFO @ Sat, 15 Sep 2018 11:25:48: 27000000 INFO @ Sat, 15 Sep 2018 11:25:55: #1 tag size is determined as 75 bps INFO @ Sat, 15 Sep 2018 11:25:55: #1 tag size = 75 INFO @ Sat, 15 Sep 2018 11:25:55: #1 total tags in treatment: 27974920 INFO @ Sat, 15 Sep 2018 11:25:55: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:25:55: #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 11:25:55: #1 tag size is determined as 75 bps INFO @ Sat, 15 Sep 2018 11:25:55: #1 tag size = 75 INFO @ Sat, 15 Sep 2018 11:25:55: #1 total tags in treatment: 27974920 INFO @ Sat, 15 Sep 2018 11:25:55: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:25:55: #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 11:25:55: #1 tag size is determined as 75 bps INFO @ Sat, 15 Sep 2018 11:25:55: #1 tag size = 75 INFO @ Sat, 15 Sep 2018 11:25:55: #1 total tags in treatment: 27974920 INFO @ Sat, 15 Sep 2018 11:25:55: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:25:55: #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 11:25:55: #1 tags after filtering in treatment: 27974716 INFO @ Sat, 15 Sep 2018 11:25:55: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 11:25:55: #1 finished! INFO @ Sat, 15 Sep 2018 11:25:55: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:25:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:25:56: #1 tags after filtering in treatment: 27974716 INFO @ Sat, 15 Sep 2018 11:25:56: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 11:25:56: #1 finished! INFO @ Sat, 15 Sep 2018 11:25:56: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:25:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:25:56: #1 tags after filtering in treatment: 27974716 INFO @ Sat, 15 Sep 2018 11:25:56: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 11:25:56: #1 finished! INFO @ Sat, 15 Sep 2018 11:25:56: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:25:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:26:04: #2 number of paired peaks: 154147 INFO @ Sat, 15 Sep 2018 11:26:04: start model_add_line... INFO @ Sat, 15 Sep 2018 11:26:04: #2 number of paired peaks: 154147 INFO @ Sat, 15 Sep 2018 11:26:04: start model_add_line... INFO @ Sat, 15 Sep 2018 11:26:04: #2 number of paired peaks: 154147 INFO @ Sat, 15 Sep 2018 11:26:04: start model_add_line... INFO @ Sat, 15 Sep 2018 11:26:04: start X-correlation... INFO @ Sat, 15 Sep 2018 11:26:04: start X-correlation... INFO @ Sat, 15 Sep 2018 11:26:04: end of X-cor INFO @ Sat, 15 Sep 2018 11:26:04: end of X-cor INFO @ Sat, 15 Sep 2018 11:26:04: #2 finished! INFO @ Sat, 15 Sep 2018 11:26:04: #2 finished! INFO @ Sat, 15 Sep 2018 11:26:04: #2 predicted fragment length is 257 bps INFO @ Sat, 15 Sep 2018 11:26:04: #2 predicted fragment length is 257 bps INFO @ Sat, 15 Sep 2018 11:26:04: #2 alternative fragment length(s) may be 4,257 bps INFO @ Sat, 15 Sep 2018 11:26:04: #2 alternative fragment length(s) may be 4,257 bps INFO @ Sat, 15 Sep 2018 11:26:04: #2.2 Generate R script for model : SRX4014807.20_model.r INFO @ Sat, 15 Sep 2018 11:26:04: #2.2 Generate R script for model : SRX4014807.05_model.r INFO @ Sat, 15 Sep 2018 11:26:04: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:26:04: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:26:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:26:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:26:05: start X-correlation... INFO @ Sat, 15 Sep 2018 11:26:05: end of X-cor INFO @ Sat, 15 Sep 2018 11:26:05: #2 finished! INFO @ Sat, 15 Sep 2018 11:26:05: #2 predicted fragment length is 257 bps INFO @ Sat, 15 Sep 2018 11:26:05: #2 alternative fragment length(s) may be 4,257 bps INFO @ Sat, 15 Sep 2018 11:26:05: #2.2 Generate R script for model : SRX4014807.10_model.r INFO @ Sat, 15 Sep 2018 11:26:05: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:26:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:27:17: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:27:18: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:27:19: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:27:59: #4 Write output xls file... SRX4014807.20_peaks.xls INFO @ Sat, 15 Sep 2018 11:27:59: #4 Write peak in narrowPeak format file... SRX4014807.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:27:59: #4 Write summits bed file... SRX4014807.20_summits.bed INFO @ Sat, 15 Sep 2018 11:27:59: Done! pass1 - making usageList (50 chroms): 0 millis pass2 - checking and writing primary data (816 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 11:28:04: #4 Write output xls file... SRX4014807.10_peaks.xls INFO @ Sat, 15 Sep 2018 11:28:04: #4 Write peak in narrowPeak format file... SRX4014807.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:28:04: #4 Write summits bed file... SRX4014807.10_summits.bed INFO @ Sat, 15 Sep 2018 11:28:04: Done! pass1 - making usageList (77 chroms): 2 millis pass2 - checking and writing primary data (5477 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 11:28:04: #4 Write output xls file... SRX4014807.05_peaks.xls INFO @ Sat, 15 Sep 2018 11:28:05: #4 Write peak in narrowPeak format file... SRX4014807.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:28:05: #4 Write summits bed file... SRX4014807.05_summits.bed INFO @ Sat, 15 Sep 2018 11:28:05: Done! pass1 - making usageList (123 chroms): 4 millis pass2 - checking and writing primary data (20801 records, 4 fields): 31 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。