Job ID = 10608871 sra ファイルのダウンロード中... Completed: 727068K bytes transferred in 51 seconds (116652K 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... Written 15545030 spots for /home/okishinya/chipatlas/results/rn6/SRX2727606/SRR5437669.sra Written 15545030 spots total 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: 00:23:29 15545030 reads; of these: 15545030 (100.00%) were unpaired; of these: 605527 (3.90%) aligned 0 times 13062050 (84.03%) aligned exactly 1 time 1877453 (12.08%) aligned >1 times 96.10% overall alignment rate Time searching: 00:23:32 Overall time: 00:23:32 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 8 files... [bam_rmdupse_core] 823127 / 14939503 = 0.0551 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 @ Thu, 03 May 2018 22:46:50: # Command line: callpeak -t SRX2727606.bam -f BAM -g 2.15e9 -n SRX2727606.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2727606.20 # format = BAM # ChIP-seq file = ['SRX2727606.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 @ Thu, 03 May 2018 22:46:50: #1 read tag files... INFO @ Thu, 03 May 2018 22:46:50: #1 read treatment tags... INFO @ Thu, 03 May 2018 22:46:50: # Command line: callpeak -t SRX2727606.bam -f BAM -g 2.15e9 -n SRX2727606.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2727606.10 # format = BAM # ChIP-seq file = ['SRX2727606.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 @ Thu, 03 May 2018 22:46:50: #1 read tag files... INFO @ Thu, 03 May 2018 22:46:50: #1 read treatment tags... INFO @ Thu, 03 May 2018 22:46:50: # Command line: callpeak -t SRX2727606.bam -f BAM -g 2.15e9 -n SRX2727606.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2727606.05 # format = BAM # ChIP-seq file = ['SRX2727606.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 @ Thu, 03 May 2018 22:46:50: #1 read tag files... INFO @ Thu, 03 May 2018 22:46:50: #1 read treatment tags... INFO @ Thu, 03 May 2018 22:46:57: 1000000 INFO @ Thu, 03 May 2018 22:46:58: 1000000 INFO @ Thu, 03 May 2018 22:46:58: 1000000 INFO @ Thu, 03 May 2018 22:47:05: 2000000 INFO @ Thu, 03 May 2018 22:47:05: 2000000 INFO @ Thu, 03 May 2018 22:47:05: 2000000 INFO @ Thu, 03 May 2018 22:47:13: 3000000 INFO @ Thu, 03 May 2018 22:47:13: 3000000 INFO @ Thu, 03 May 2018 22:47:13: 3000000 INFO @ Thu, 03 May 2018 22:47:20: 4000000 INFO @ Thu, 03 May 2018 22:47:20: 4000000 INFO @ Thu, 03 May 2018 22:47:21: 4000000 INFO @ Thu, 03 May 2018 22:47:28: 5000000 INFO @ Thu, 03 May 2018 22:47:28: 5000000 INFO @ Thu, 03 May 2018 22:47:29: 5000000 INFO @ Thu, 03 May 2018 22:47:36: 6000000 INFO @ Thu, 03 May 2018 22:47:36: 6000000 INFO @ Thu, 03 May 2018 22:47:37: 6000000 INFO @ Thu, 03 May 2018 22:47:44: 7000000 INFO @ Thu, 03 May 2018 22:47:44: 7000000 INFO @ Thu, 03 May 2018 22:47:45: 7000000 INFO @ Thu, 03 May 2018 22:47:51: 8000000 INFO @ Thu, 03 May 2018 22:47:52: 8000000 INFO @ Thu, 03 May 2018 22:47:53: 8000000 INFO @ Thu, 03 May 2018 22:47:59: 9000000 INFO @ Thu, 03 May 2018 22:48:00: 9000000 INFO @ Thu, 03 May 2018 22:48:01: 9000000 INFO @ Thu, 03 May 2018 22:48:07: 10000000 INFO @ Thu, 03 May 2018 22:48:07: 10000000 INFO @ Thu, 03 May 2018 22:48:09: 10000000 INFO @ Thu, 03 May 2018 22:48:14: 11000000 INFO @ Thu, 03 May 2018 22:48:15: 11000000 INFO @ Thu, 03 May 2018 22:48:17: 11000000 INFO @ Thu, 03 May 2018 22:48:22: 12000000 INFO @ Thu, 03 May 2018 22:48:23: 12000000 INFO @ Thu, 03 May 2018 22:48:25: 12000000 INFO @ Thu, 03 May 2018 22:48:29: 13000000 INFO @ Thu, 03 May 2018 22:48:31: 13000000 INFO @ Thu, 03 May 2018 22:48:34: 13000000 INFO @ Thu, 03 May 2018 22:48:37: 14000000 INFO @ Thu, 03 May 2018 22:48:38: #1 tag size is determined as 100 bps INFO @ Thu, 03 May 2018 22:48:38: #1 tag size = 100 INFO @ Thu, 03 May 2018 22:48:38: #1 total tags in treatment: 14116376 INFO @ Thu, 03 May 2018 22:48:38: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 22:48:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 03 May 2018 22:48:39: #1 tags after filtering in treatment: 14116139 INFO @ Thu, 03 May 2018 22:48:39: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 03 May 2018 22:48:39: #1 finished! INFO @ Thu, 03 May 2018 22:48:39: #2 Build Peak Model... INFO @ Thu, 03 May 2018 22:48:39: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 22:48:39: 14000000 INFO @ Thu, 03 May 2018 22:48:40: #1 tag size is determined as 100 bps INFO @ Thu, 03 May 2018 22:48:40: #1 tag size = 100 INFO @ Thu, 03 May 2018 22:48:40: #1 total tags in treatment: 14116376 INFO @ Thu, 03 May 2018 22:48:40: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 22:48:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 03 May 2018 22:48:40: #1 tags after filtering in treatment: 14116139 INFO @ Thu, 03 May 2018 22:48:40: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 03 May 2018 22:48:40: #1 finished! INFO @ Thu, 03 May 2018 22:48:40: #2 Build Peak Model... INFO @ Thu, 03 May 2018 22:48:40: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 22:48:42: 14000000 INFO @ Thu, 03 May 2018 22:48:43: #1 tag size is determined as 100 bps INFO @ Thu, 03 May 2018 22:48:43: #1 tag size = 100 INFO @ Thu, 03 May 2018 22:48:43: #1 total tags in treatment: 14116376 INFO @ Thu, 03 May 2018 22:48:43: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 22:48:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 03 May 2018 22:48:43: #1 tags after filtering in treatment: 14116139 INFO @ Thu, 03 May 2018 22:48:43: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 03 May 2018 22:48:43: #1 finished! INFO @ Thu, 03 May 2018 22:48:43: #2 Build Peak Model... INFO @ Thu, 03 May 2018 22:48:43: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 22:48:43: #2 number of paired peaks: 97799 INFO @ Thu, 03 May 2018 22:48:43: start model_add_line... INFO @ Thu, 03 May 2018 22:48:44: start X-correlation... INFO @ Thu, 03 May 2018 22:48:44: end of X-cor INFO @ Thu, 03 May 2018 22:48:44: #2 finished! INFO @ Thu, 03 May 2018 22:48:44: #2 predicted fragment length is 214 bps INFO @ Thu, 03 May 2018 22:48:44: #2 alternative fragment length(s) may be 214 bps INFO @ Thu, 03 May 2018 22:48:44: #2.2 Generate R script for model : SRX2727606.20_model.r INFO @ Thu, 03 May 2018 22:48:44: #3 Call peaks... INFO @ Thu, 03 May 2018 22:48:44: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 03 May 2018 22:48:45: #2 number of paired peaks: 97799 INFO @ Thu, 03 May 2018 22:48:45: start model_add_line... INFO @ Thu, 03 May 2018 22:48:45: start X-correlation... INFO @ Thu, 03 May 2018 22:48:45: end of X-cor INFO @ Thu, 03 May 2018 22:48:45: #2 finished! INFO @ Thu, 03 May 2018 22:48:45: #2 predicted fragment length is 214 bps INFO @ Thu, 03 May 2018 22:48:45: #2 alternative fragment length(s) may be 214 bps INFO @ Thu, 03 May 2018 22:48:45: #2.2 Generate R script for model : SRX2727606.05_model.r INFO @ Thu, 03 May 2018 22:48:45: #3 Call peaks... INFO @ Thu, 03 May 2018 22:48:45: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 03 May 2018 22:48:48: #2 number of paired peaks: 97799 INFO @ Thu, 03 May 2018 22:48:48: start model_add_line... INFO @ Thu, 03 May 2018 22:48:48: start X-correlation... INFO @ Thu, 03 May 2018 22:48:48: end of X-cor INFO @ Thu, 03 May 2018 22:48:48: #2 finished! INFO @ Thu, 03 May 2018 22:48:48: #2 predicted fragment length is 214 bps INFO @ Thu, 03 May 2018 22:48:48: #2 alternative fragment length(s) may be 214 bps INFO @ Thu, 03 May 2018 22:48:48: #2.2 Generate R script for model : SRX2727606.10_model.r INFO @ Thu, 03 May 2018 22:48:48: #3 Call peaks... INFO @ Thu, 03 May 2018 22:48:48: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 03 May 2018 22:49:21: #3 Call peaks for each chromosome... INFO @ Thu, 03 May 2018 22:49:21: #3 Call peaks for each chromosome... INFO @ Thu, 03 May 2018 22:49:25: #3 Call peaks for each chromosome... INFO @ Thu, 03 May 2018 22:49:43: #4 Write output xls file... SRX2727606.20_peaks.xls INFO @ Thu, 03 May 2018 22:49:43: #4 Write peak in narrowPeak format file... SRX2727606.20_peaks.narrowPeak INFO @ Thu, 03 May 2018 22:49:43: #4 Write summits bed file... SRX2727606.20_summits.bed INFO @ Thu, 03 May 2018 22:49:43: Done! pass1 - making usageList (54 chroms): 2 millis pass2 - checking and writing primary data (7360 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Thu, 03 May 2018 22:49:44: #4 Write output xls file... SRX2727606.05_peaks.xls INFO @ Thu, 03 May 2018 22:49:45: #4 Write peak in narrowPeak format file... SRX2727606.05_peaks.narrowPeak INFO @ Thu, 03 May 2018 22:49:45: #4 Write summits bed file... SRX2727606.05_summits.bed INFO @ Thu, 03 May 2018 22:49:45: Done! pass1 - making usageList (109 chroms): 7 millis pass2 - checking and writing primary data (34176 records, 4 fields): 43 millis CompletedMACS2peakCalling INFO @ Thu, 03 May 2018 22:49:48: #4 Write output xls file... SRX2727606.10_peaks.xls INFO @ Thu, 03 May 2018 22:49:48: #4 Write peak in narrowPeak format file... SRX2727606.10_peaks.narrowPeak INFO @ Thu, 03 May 2018 22:49:48: #4 Write summits bed file... SRX2727606.10_summits.bed INFO @ Thu, 03 May 2018 22:49:48: Done! pass1 - making usageList (81 chroms): 4 millis pass2 - checking and writing primary data (19824 records, 4 fields): 26 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。