Job ID = 10194945 sra ファイルのダウンロード中... Completed: 770322K bytes transferred in 11 seconds (546914K 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 20664657 spots for /home/okishinya/chipatlas/results/rn6/SRX2568198/SRR5264110.sra Written 20664657 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: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:46:39 20664657 reads; of these: 20664657 (100.00%) were unpaired; of these: 813861 (3.94%) aligned 0 times 17016899 (82.35%) aligned exactly 1 time 2833897 (13.71%) aligned >1 times 96.06% overall alignment rate Time searching: 00:46:44 Overall time: 00:46:44 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] 1449911 / 19850796 = 0.0730 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, 11 Nov 2017 01:01:08: # Command line: callpeak -t SRX2568198.bam -f BAM -g 2.15e9 -n SRX2568198.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2568198.20 # format = BAM # ChIP-seq file = ['SRX2568198.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, 11 Nov 2017 01:01:08: #1 read tag files... INFO @ Sat, 11 Nov 2017 01:01:08: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 01:01:08: # Command line: callpeak -t SRX2568198.bam -f BAM -g 2.15e9 -n SRX2568198.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2568198.05 # format = BAM # ChIP-seq file = ['SRX2568198.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, 11 Nov 2017 01:01:08: #1 read tag files... INFO @ Sat, 11 Nov 2017 01:01:08: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 01:01:08: # Command line: callpeak -t SRX2568198.bam -f BAM -g 2.15e9 -n SRX2568198.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2568198.10 # format = BAM # ChIP-seq file = ['SRX2568198.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, 11 Nov 2017 01:01:08: #1 read tag files... INFO @ Sat, 11 Nov 2017 01:01:08: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 01:01:18: 1000000 INFO @ Sat, 11 Nov 2017 01:01:21: 1000000 INFO @ Sat, 11 Nov 2017 01:01:23: 1000000 INFO @ Sat, 11 Nov 2017 01:01:28: 2000000 INFO @ Sat, 11 Nov 2017 01:01:32: 2000000 INFO @ Sat, 11 Nov 2017 01:01:35: 2000000 INFO @ Sat, 11 Nov 2017 01:01:38: 3000000 INFO @ Sat, 11 Nov 2017 01:01:45: 3000000 INFO @ Sat, 11 Nov 2017 01:01:48: 4000000 INFO @ Sat, 11 Nov 2017 01:01:50: 3000000 INFO @ Sat, 11 Nov 2017 01:01:57: 4000000 INFO @ Sat, 11 Nov 2017 01:01:58: 5000000 INFO @ Sat, 11 Nov 2017 01:02:01: 4000000 INFO @ Sat, 11 Nov 2017 01:02:07: 5000000 INFO @ Sat, 11 Nov 2017 01:02:09: 6000000 INFO @ Sat, 11 Nov 2017 01:02:12: 5000000 INFO @ Sat, 11 Nov 2017 01:02:17: 6000000 INFO @ Sat, 11 Nov 2017 01:02:18: 7000000 INFO @ Sat, 11 Nov 2017 01:02:23: 6000000 INFO @ Sat, 11 Nov 2017 01:02:27: 7000000 INFO @ Sat, 11 Nov 2017 01:02:28: 8000000 INFO @ Sat, 11 Nov 2017 01:02:35: 7000000 INFO @ Sat, 11 Nov 2017 01:02:40: 8000000 INFO @ Sat, 11 Nov 2017 01:02:41: 9000000 INFO @ Sat, 11 Nov 2017 01:02:46: 8000000 INFO @ Sat, 11 Nov 2017 01:02:53: 9000000 INFO @ Sat, 11 Nov 2017 01:02:54: 10000000 INFO @ Sat, 11 Nov 2017 01:02:58: 9000000 INFO @ Sat, 11 Nov 2017 01:03:05: 11000000 INFO @ Sat, 11 Nov 2017 01:03:06: 10000000 INFO @ Sat, 11 Nov 2017 01:03:09: 10000000 INFO @ Sat, 11 Nov 2017 01:03:17: 12000000 INFO @ Sat, 11 Nov 2017 01:03:19: 11000000 INFO @ Sat, 11 Nov 2017 01:03:20: 11000000 INFO @ Sat, 11 Nov 2017 01:03:27: 13000000 INFO @ Sat, 11 Nov 2017 01:03:30: 12000000 INFO @ Sat, 11 Nov 2017 01:03:35: 12000000 INFO @ Sat, 11 Nov 2017 01:03:39: 14000000 INFO @ Sat, 11 Nov 2017 01:03:41: 13000000 INFO @ Sat, 11 Nov 2017 01:03:48: 13000000 INFO @ Sat, 11 Nov 2017 01:03:51: 15000000 INFO @ Sat, 11 Nov 2017 01:03:51: 14000000 INFO @ Sat, 11 Nov 2017 01:04:01: 15000000 INFO @ Sat, 11 Nov 2017 01:04:02: 14000000 INFO @ Sat, 11 Nov 2017 01:04:05: 16000000 INFO @ Sat, 11 Nov 2017 01:04:12: 16000000 INFO @ Sat, 11 Nov 2017 01:04:17: 15000000 INFO @ Sat, 11 Nov 2017 01:04:20: 17000000 INFO @ Sat, 11 Nov 2017 01:04:22: 17000000 INFO @ Sat, 11 Nov 2017 01:04:33: 18000000 INFO @ Sat, 11 Nov 2017 01:04:33: 16000000 INFO @ Sat, 11 Nov 2017 01:04:36: 18000000 INFO @ Sat, 11 Nov 2017 01:04:37: #1 tag size is determined as 75 bps INFO @ Sat, 11 Nov 2017 01:04:37: #1 tag size = 75 INFO @ Sat, 11 Nov 2017 01:04:37: #1 total tags in treatment: 18400885 INFO @ Sat, 11 Nov 2017 01:04:37: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 01:04:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 01:04:38: #1 tags after filtering in treatment: 18400658 INFO @ Sat, 11 Nov 2017 01:04:38: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 01:04:38: #1 finished! INFO @ Sat, 11 Nov 2017 01:04:38: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 01:04:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 01:04:42: #1 tag size is determined as 75 bps INFO @ Sat, 11 Nov 2017 01:04:42: #1 tag size = 75 INFO @ Sat, 11 Nov 2017 01:04:42: #1 total tags in treatment: 18400885 INFO @ Sat, 11 Nov 2017 01:04:42: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 01:04:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 01:04:43: #1 tags after filtering in treatment: 18400658 INFO @ Sat, 11 Nov 2017 01:04:43: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 01:04:43: #1 finished! INFO @ Sat, 11 Nov 2017 01:04:43: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 01:04:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 01:04:44: #2 number of paired peaks: 83248 INFO @ Sat, 11 Nov 2017 01:04:44: start model_add_line... INFO @ Sat, 11 Nov 2017 01:04:44: start X-correlation... INFO @ Sat, 11 Nov 2017 01:04:44: end of X-cor INFO @ Sat, 11 Nov 2017 01:04:44: #2 finished! INFO @ Sat, 11 Nov 2017 01:04:44: #2 predicted fragment length is 185 bps INFO @ Sat, 11 Nov 2017 01:04:44: #2 alternative fragment length(s) may be 185 bps INFO @ Sat, 11 Nov 2017 01:04:44: #2.2 Generate R script for model : SRX2568198.05_model.r INFO @ Sat, 11 Nov 2017 01:04:44: #3 Call peaks... INFO @ Sat, 11 Nov 2017 01:04:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 01:04:46: 17000000 INFO @ Sat, 11 Nov 2017 01:04:48: #2 number of paired peaks: 83248 INFO @ Sat, 11 Nov 2017 01:04:48: start model_add_line... INFO @ Sat, 11 Nov 2017 01:04:49: start X-correlation... INFO @ Sat, 11 Nov 2017 01:04:49: end of X-cor INFO @ Sat, 11 Nov 2017 01:04:49: #2 finished! INFO @ Sat, 11 Nov 2017 01:04:49: #2 predicted fragment length is 185 bps INFO @ Sat, 11 Nov 2017 01:04:49: #2 alternative fragment length(s) may be 185 bps INFO @ Sat, 11 Nov 2017 01:04:49: #2.2 Generate R script for model : SRX2568198.20_model.r INFO @ Sat, 11 Nov 2017 01:04:49: #3 Call peaks... INFO @ Sat, 11 Nov 2017 01:04:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 01:04:58: 18000000 INFO @ Sat, 11 Nov 2017 01:05:04: #1 tag size is determined as 75 bps INFO @ Sat, 11 Nov 2017 01:05:04: #1 tag size = 75 INFO @ Sat, 11 Nov 2017 01:05:04: #1 total tags in treatment: 18400885 INFO @ Sat, 11 Nov 2017 01:05:04: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 01:05:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 01:05:04: #1 tags after filtering in treatment: 18400658 INFO @ Sat, 11 Nov 2017 01:05:04: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 01:05:04: #1 finished! INFO @ Sat, 11 Nov 2017 01:05:04: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 01:05:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 01:05:10: #2 number of paired peaks: 83248 INFO @ Sat, 11 Nov 2017 01:05:10: start model_add_line... INFO @ Sat, 11 Nov 2017 01:05:10: start X-correlation... INFO @ Sat, 11 Nov 2017 01:05:11: end of X-cor INFO @ Sat, 11 Nov 2017 01:05:11: #2 finished! INFO @ Sat, 11 Nov 2017 01:05:11: #2 predicted fragment length is 185 bps INFO @ Sat, 11 Nov 2017 01:05:11: #2 alternative fragment length(s) may be 185 bps INFO @ Sat, 11 Nov 2017 01:05:11: #2.2 Generate R script for model : SRX2568198.10_model.r INFO @ Sat, 11 Nov 2017 01:05:11: #3 Call peaks... INFO @ Sat, 11 Nov 2017 01:05:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 01:05:44: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 01:05:48: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 01:06:10: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 01:06:20: #4 Write output xls file... SRX2568198.05_peaks.xls INFO @ Sat, 11 Nov 2017 01:06:20: #4 Write peak in narrowPeak format file... SRX2568198.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 01:06:20: #4 Write summits bed file... SRX2568198.05_summits.bed INFO @ Sat, 11 Nov 2017 01:06:20: Done! pass1 - making usageList (101 chroms): 8 millis pass2 - checking and writing primary data (31015 records, 4 fields): 50 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 01:06:23: #4 Write output xls file... SRX2568198.20_peaks.xls INFO @ Sat, 11 Nov 2017 01:06:23: #4 Write peak in narrowPeak format file... SRX2568198.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 01:06:23: #4 Write summits bed file... SRX2568198.20_summits.bed INFO @ Sat, 11 Nov 2017 01:06:23: Done! pass1 - making usageList (44 chroms): 2 millis pass2 - checking and writing primary data (7309 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 01:06:54: #4 Write output xls file... SRX2568198.10_peaks.xls INFO @ Sat, 11 Nov 2017 01:06:55: #4 Write peak in narrowPeak format file... SRX2568198.10_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 01:06:55: #4 Write summits bed file... SRX2568198.10_summits.bed INFO @ Sat, 11 Nov 2017 01:06:55: Done! pass1 - making usageList (76 chroms): 5 millis pass2 - checking and writing primary data (18550 records, 4 fields): 32 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。