Job ID = 11632681 sra ファイルのダウンロード中... Completed: 761962K bytes transferred in 20 seconds (311221K 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 43274128 spots for /home/okishinya/chipatlas/results/rn6/SRX3360119/SRR6253225.sra Written 43274128 spots for /home/okishinya/chipatlas/results/rn6/SRX3360119/SRR6253225.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: 00:00:00 Time loading mirror index: 00:00:03 Multiseed full-index search: 00:20:00 43274128 reads; of these: 43274128 (100.00%) were unpaired; of these: 13781533 (31.85%) aligned 0 times 24852280 (57.43%) aligned exactly 1 time 4640315 (10.72%) aligned >1 times 68.15% overall alignment rate Time searching: 00:20:04 Overall time: 00:20:04 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] 7192159 / 29492595 = 0.2439 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 07:24:15: # Command line: callpeak -t SRX3360119.bam -f BAM -g 2.15e9 -n SRX3360119.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3360119.10 # format = BAM # ChIP-seq file = ['SRX3360119.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 07:24:15: # Command line: callpeak -t SRX3360119.bam -f BAM -g 2.15e9 -n SRX3360119.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3360119.05 # format = BAM # ChIP-seq file = ['SRX3360119.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 07:24:15: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:24:15: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:24:15: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:24:15: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:24:15: # Command line: callpeak -t SRX3360119.bam -f BAM -g 2.15e9 -n SRX3360119.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3360119.20 # format = BAM # ChIP-seq file = ['SRX3360119.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 07:24:15: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:24:15: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:24:23: 1000000 INFO @ Fri, 15 Feb 2019 07:24:23: 1000000 INFO @ Fri, 15 Feb 2019 07:24:23: 1000000 INFO @ Fri, 15 Feb 2019 07:24:30: 2000000 INFO @ Fri, 15 Feb 2019 07:24:31: 2000000 INFO @ Fri, 15 Feb 2019 07:24:31: 2000000 INFO @ Fri, 15 Feb 2019 07:24:37: 3000000 INFO @ Fri, 15 Feb 2019 07:24:39: 3000000 INFO @ Fri, 15 Feb 2019 07:24:39: 3000000 INFO @ Fri, 15 Feb 2019 07:24:45: 4000000 INFO @ Fri, 15 Feb 2019 07:24:47: 4000000 INFO @ Fri, 15 Feb 2019 07:24:47: 4000000 INFO @ Fri, 15 Feb 2019 07:24:52: 5000000 INFO @ Fri, 15 Feb 2019 07:24:55: 5000000 INFO @ Fri, 15 Feb 2019 07:24:55: 5000000 INFO @ Fri, 15 Feb 2019 07:25:00: 6000000 INFO @ Fri, 15 Feb 2019 07:25:03: 6000000 INFO @ Fri, 15 Feb 2019 07:25:03: 6000000 INFO @ Fri, 15 Feb 2019 07:25:07: 7000000 INFO @ Fri, 15 Feb 2019 07:25:11: 7000000 INFO @ Fri, 15 Feb 2019 07:25:11: 7000000 INFO @ Fri, 15 Feb 2019 07:25:15: 8000000 INFO @ Fri, 15 Feb 2019 07:25:19: 8000000 INFO @ Fri, 15 Feb 2019 07:25:19: 8000000 INFO @ Fri, 15 Feb 2019 07:25:23: 9000000 INFO @ Fri, 15 Feb 2019 07:25:27: 9000000 INFO @ Fri, 15 Feb 2019 07:25:27: 9000000 INFO @ Fri, 15 Feb 2019 07:25:30: 10000000 INFO @ Fri, 15 Feb 2019 07:25:35: 10000000 INFO @ Fri, 15 Feb 2019 07:25:35: 10000000 INFO @ Fri, 15 Feb 2019 07:25:38: 11000000 INFO @ Fri, 15 Feb 2019 07:25:43: 11000000 INFO @ Fri, 15 Feb 2019 07:25:43: 11000000 INFO @ Fri, 15 Feb 2019 07:25:46: 12000000 INFO @ Fri, 15 Feb 2019 07:25:51: 12000000 INFO @ Fri, 15 Feb 2019 07:25:51: 12000000 INFO @ Fri, 15 Feb 2019 07:25:54: 13000000 INFO @ Fri, 15 Feb 2019 07:25:59: 13000000 INFO @ Fri, 15 Feb 2019 07:25:59: 13000000 INFO @ Fri, 15 Feb 2019 07:26:01: 14000000 INFO @ Fri, 15 Feb 2019 07:26:07: 14000000 INFO @ Fri, 15 Feb 2019 07:26:07: 14000000 INFO @ Fri, 15 Feb 2019 07:26:09: 15000000 INFO @ Fri, 15 Feb 2019 07:26:15: 15000000 INFO @ Fri, 15 Feb 2019 07:26:15: 15000000 INFO @ Fri, 15 Feb 2019 07:26:17: 16000000 INFO @ Fri, 15 Feb 2019 07:26:23: 16000000 INFO @ Fri, 15 Feb 2019 07:26:23: 16000000 INFO @ Fri, 15 Feb 2019 07:26:25: 17000000 INFO @ Fri, 15 Feb 2019 07:26:31: 17000000 INFO @ Fri, 15 Feb 2019 07:26:31: 17000000 INFO @ Fri, 15 Feb 2019 07:26:32: 18000000 INFO @ Fri, 15 Feb 2019 07:26:39: 18000000 INFO @ Fri, 15 Feb 2019 07:26:39: 18000000 INFO @ Fri, 15 Feb 2019 07:26:40: 19000000 INFO @ Fri, 15 Feb 2019 07:26:47: 19000000 INFO @ Fri, 15 Feb 2019 07:26:47: 19000000 INFO @ Fri, 15 Feb 2019 07:26:48: 20000000 INFO @ Fri, 15 Feb 2019 07:26:55: 20000000 INFO @ Fri, 15 Feb 2019 07:26:55: 20000000 INFO @ Fri, 15 Feb 2019 07:26:56: 21000000 INFO @ Fri, 15 Feb 2019 07:27:03: 21000000 INFO @ Fri, 15 Feb 2019 07:27:03: 21000000 INFO @ Fri, 15 Feb 2019 07:27:04: 22000000 INFO @ Fri, 15 Feb 2019 07:27:07: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 07:27:07: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 07:27:07: #1 total tags in treatment: 22300436 INFO @ Fri, 15 Feb 2019 07:27:07: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:27:07: #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 07:27:07: #1 tags after filtering in treatment: 22300245 INFO @ Fri, 15 Feb 2019 07:27:07: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:27:07: #1 finished! INFO @ Fri, 15 Feb 2019 07:27:07: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:27:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:27:11: 22000000 INFO @ Fri, 15 Feb 2019 07:27:11: 22000000 INFO @ Fri, 15 Feb 2019 07:27:12: #2 number of paired peaks: 41675 INFO @ Fri, 15 Feb 2019 07:27:12: start model_add_line... INFO @ Fri, 15 Feb 2019 07:27:12: start X-correlation... INFO @ Fri, 15 Feb 2019 07:27:12: end of X-cor INFO @ Fri, 15 Feb 2019 07:27:12: #2 finished! INFO @ Fri, 15 Feb 2019 07:27:12: #2 predicted fragment length is 161 bps INFO @ Fri, 15 Feb 2019 07:27:12: #2 alternative fragment length(s) may be 161 bps INFO @ Fri, 15 Feb 2019 07:27:12: #2.2 Generate R script for model : SRX3360119.05_model.r INFO @ Fri, 15 Feb 2019 07:27:12: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:27:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:27:14: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 07:27:14: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 07:27:14: #1 total tags in treatment: 22300436 INFO @ Fri, 15 Feb 2019 07:27:14: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:27:14: #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 07:27:14: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 07:27:14: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 07:27:14: #1 total tags in treatment: 22300436 INFO @ Fri, 15 Feb 2019 07:27:14: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:27:14: #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 07:27:14: #1 tags after filtering in treatment: 22300245 INFO @ Fri, 15 Feb 2019 07:27:14: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:27:14: #1 finished! INFO @ Fri, 15 Feb 2019 07:27:14: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:27:14: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:27:14: #1 tags after filtering in treatment: 22300245 INFO @ Fri, 15 Feb 2019 07:27:14: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:27:14: #1 finished! INFO @ Fri, 15 Feb 2019 07:27:14: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:27:14: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:27:19: #2 number of paired peaks: 41675 INFO @ Fri, 15 Feb 2019 07:27:19: start model_add_line... INFO @ Fri, 15 Feb 2019 07:27:19: #2 number of paired peaks: 41675 INFO @ Fri, 15 Feb 2019 07:27:19: start model_add_line... INFO @ Fri, 15 Feb 2019 07:27:19: start X-correlation... INFO @ Fri, 15 Feb 2019 07:27:19: end of X-cor INFO @ Fri, 15 Feb 2019 07:27:19: #2 finished! INFO @ Fri, 15 Feb 2019 07:27:19: #2 predicted fragment length is 161 bps INFO @ Fri, 15 Feb 2019 07:27:19: #2 alternative fragment length(s) may be 161 bps INFO @ Fri, 15 Feb 2019 07:27:19: #2.2 Generate R script for model : SRX3360119.10_model.r INFO @ Fri, 15 Feb 2019 07:27:19: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:27:19: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:27:19: start X-correlation... INFO @ Fri, 15 Feb 2019 07:27:19: end of X-cor INFO @ Fri, 15 Feb 2019 07:27:19: #2 finished! INFO @ Fri, 15 Feb 2019 07:27:19: #2 predicted fragment length is 161 bps INFO @ Fri, 15 Feb 2019 07:27:19: #2 alternative fragment length(s) may be 161 bps INFO @ Fri, 15 Feb 2019 07:27:19: #2.2 Generate R script for model : SRX3360119.20_model.r INFO @ Fri, 15 Feb 2019 07:27:19: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:27:19: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:28:12: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:28:18: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:28:19: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:28:47: #4 Write output xls file... SRX3360119.05_peaks.xls INFO @ Fri, 15 Feb 2019 07:28:47: #4 Write peak in narrowPeak format file... SRX3360119.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:28:48: #4 Write summits bed file... SRX3360119.05_summits.bed INFO @ Fri, 15 Feb 2019 07:28:48: Done! pass1 - making usageList (140 chroms): 10 millis pass2 - checking and writing primary data (33229 records, 4 fields): 48 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 07:28:51: #4 Write output xls file... SRX3360119.20_peaks.xls INFO @ Fri, 15 Feb 2019 07:28:51: #4 Write peak in narrowPeak format file... SRX3360119.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:28:51: #4 Write summits bed file... SRX3360119.20_summits.bed INFO @ Fri, 15 Feb 2019 07:28:51: Done! pass1 - making usageList (108 chroms): 7 millis pass2 - checking and writing primary data (22768 records, 4 fields): 35 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 07:28:55: #4 Write output xls file... SRX3360119.10_peaks.xls INFO @ Fri, 15 Feb 2019 07:28:55: #4 Write peak in narrowPeak format file... SRX3360119.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:28:55: #4 Write summits bed file... SRX3360119.10_summits.bed INFO @ Fri, 15 Feb 2019 07:28:55: Done! pass1 - making usageList (126 chroms): 8 millis pass2 - checking and writing primary data (28453 records, 4 fields): 41 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。