Job ID = 10195033 sra ファイルのダウンロード中... Completed: 62896K bytes transferred in 4 seconds (119331K bits/sec), in 1 file. Completed: 568329K bytes transferred in 13 seconds (346759K 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 2641184 spots for /home/okishinya/chipatlas/results/rn6/SRX913502/SRR1870941.sra Written 2641184 spots total Written 17851941 spots for /home/okishinya/chipatlas/results/rn6/SRX913502/SRR1870942.sra Written 17851941 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 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: 00:00:02 Multiseed full-index search: 00:12:21 20493125 reads; of these: 20493125 (100.00%) were unpaired; of these: 2999052 (14.63%) aligned 0 times 12993384 (63.40%) aligned exactly 1 time 4500689 (21.96%) aligned >1 times 85.37% overall alignment rate Time searching: 00:12:26 Overall time: 00:12:26 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] 1578623 / 17494073 = 0.0902 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 06:56:38: # Command line: callpeak -t SRX913502.bam -f BAM -g 2.15e9 -n SRX913502.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX913502.10 # format = BAM # ChIP-seq file = ['SRX913502.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 06:56:38: # Command line: callpeak -t SRX913502.bam -f BAM -g 2.15e9 -n SRX913502.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX913502.20 # format = BAM # ChIP-seq file = ['SRX913502.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 06:56:38: # Command line: callpeak -t SRX913502.bam -f BAM -g 2.15e9 -n SRX913502.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX913502.05 # format = BAM # ChIP-seq file = ['SRX913502.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 06:56:38: #1 read tag files... INFO @ Sat, 11 Nov 2017 06:56:38: #1 read tag files... INFO @ Sat, 11 Nov 2017 06:56:38: #1 read tag files... INFO @ Sat, 11 Nov 2017 06:56:38: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 06:56:38: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 06:56:38: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 06:56:45: 1000000 INFO @ Sat, 11 Nov 2017 06:56:46: 1000000 INFO @ Sat, 11 Nov 2017 06:56:46: 1000000 INFO @ Sat, 11 Nov 2017 06:56:52: 2000000 INFO @ Sat, 11 Nov 2017 06:56:53: 2000000 INFO @ Sat, 11 Nov 2017 06:56:54: 2000000 INFO @ Sat, 11 Nov 2017 06:56:59: 3000000 INFO @ Sat, 11 Nov 2017 06:57:01: 3000000 INFO @ Sat, 11 Nov 2017 06:57:02: 3000000 INFO @ Sat, 11 Nov 2017 06:57:06: 4000000 INFO @ Sat, 11 Nov 2017 06:57:09: 4000000 INFO @ Sat, 11 Nov 2017 06:57:10: 4000000 INFO @ Sat, 11 Nov 2017 06:57:13: 5000000 INFO @ Sat, 11 Nov 2017 06:57:16: 5000000 INFO @ Sat, 11 Nov 2017 06:57:18: 5000000 INFO @ Sat, 11 Nov 2017 06:57:20: 6000000 INFO @ Sat, 11 Nov 2017 06:57:24: 6000000 INFO @ Sat, 11 Nov 2017 06:57:26: 6000000 INFO @ Sat, 11 Nov 2017 06:57:27: 7000000 INFO @ Sat, 11 Nov 2017 06:57:32: 7000000 INFO @ Sat, 11 Nov 2017 06:57:34: 8000000 INFO @ Sat, 11 Nov 2017 06:57:34: 7000000 INFO @ Sat, 11 Nov 2017 06:57:39: 8000000 INFO @ Sat, 11 Nov 2017 06:57:40: 9000000 INFO @ Sat, 11 Nov 2017 06:57:42: 8000000 INFO @ Sat, 11 Nov 2017 06:57:47: 9000000 INFO @ Sat, 11 Nov 2017 06:57:47: 10000000 INFO @ Sat, 11 Nov 2017 06:57:50: 9000000 INFO @ Sat, 11 Nov 2017 06:57:54: 11000000 INFO @ Sat, 11 Nov 2017 06:57:54: 10000000 INFO @ Sat, 11 Nov 2017 06:57:58: 10000000 INFO @ Sat, 11 Nov 2017 06:58:01: 12000000 INFO @ Sat, 11 Nov 2017 06:58:02: 11000000 INFO @ Sat, 11 Nov 2017 06:58:06: 11000000 INFO @ Sat, 11 Nov 2017 06:58:08: 13000000 INFO @ Sat, 11 Nov 2017 06:58:09: 12000000 INFO @ Sat, 11 Nov 2017 06:58:14: 12000000 INFO @ Sat, 11 Nov 2017 06:58:15: 14000000 INFO @ Sat, 11 Nov 2017 06:58:17: 13000000 INFO @ Sat, 11 Nov 2017 06:58:22: 15000000 INFO @ Sat, 11 Nov 2017 06:58:22: 13000000 INFO @ Sat, 11 Nov 2017 06:58:25: 14000000 INFO @ Sat, 11 Nov 2017 06:58:29: #1 tag size is determined as 47 bps INFO @ Sat, 11 Nov 2017 06:58:29: #1 tag size = 47 INFO @ Sat, 11 Nov 2017 06:58:29: #1 total tags in treatment: 15915450 INFO @ Sat, 11 Nov 2017 06:58:29: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 06:58:29: #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 06:58:29: #1 tags after filtering in treatment: 15915291 INFO @ Sat, 11 Nov 2017 06:58:29: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 06:58:29: #1 finished! INFO @ Sat, 11 Nov 2017 06:58:29: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 06:58:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 06:58:30: 14000000 INFO @ Sat, 11 Nov 2017 06:58:31: #2 number of paired peaks: 13040 INFO @ Sat, 11 Nov 2017 06:58:31: start model_add_line... INFO @ Sat, 11 Nov 2017 06:58:32: start X-correlation... INFO @ Sat, 11 Nov 2017 06:58:32: end of X-cor INFO @ Sat, 11 Nov 2017 06:58:32: #2 finished! INFO @ Sat, 11 Nov 2017 06:58:32: #2 predicted fragment length is 95 bps INFO @ Sat, 11 Nov 2017 06:58:32: #2 alternative fragment length(s) may be 95 bps INFO @ Sat, 11 Nov 2017 06:58:32: #2.2 Generate R script for model : SRX913502.05_model.r INFO @ Sat, 11 Nov 2017 06:58:32: #3 Call peaks... INFO @ Sat, 11 Nov 2017 06:58:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 06:58:32: 15000000 INFO @ Sat, 11 Nov 2017 06:58:38: 15000000 INFO @ Sat, 11 Nov 2017 06:58:39: #1 tag size is determined as 47 bps INFO @ Sat, 11 Nov 2017 06:58:39: #1 tag size = 47 INFO @ Sat, 11 Nov 2017 06:58:39: #1 total tags in treatment: 15915450 INFO @ Sat, 11 Nov 2017 06:58:39: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 06:58:39: #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 06:58:40: #1 tags after filtering in treatment: 15915291 INFO @ Sat, 11 Nov 2017 06:58:40: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 06:58:40: #1 finished! INFO @ Sat, 11 Nov 2017 06:58:40: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 06:58:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 06:58:42: #2 number of paired peaks: 13040 INFO @ Sat, 11 Nov 2017 06:58:42: start model_add_line... INFO @ Sat, 11 Nov 2017 06:58:42: start X-correlation... INFO @ Sat, 11 Nov 2017 06:58:42: end of X-cor INFO @ Sat, 11 Nov 2017 06:58:42: #2 finished! INFO @ Sat, 11 Nov 2017 06:58:42: #2 predicted fragment length is 95 bps INFO @ Sat, 11 Nov 2017 06:58:42: #2 alternative fragment length(s) may be 95 bps INFO @ Sat, 11 Nov 2017 06:58:42: #2.2 Generate R script for model : SRX913502.20_model.r INFO @ Sat, 11 Nov 2017 06:58:42: #3 Call peaks... INFO @ Sat, 11 Nov 2017 06:58:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 06:58:45: #1 tag size is determined as 47 bps INFO @ Sat, 11 Nov 2017 06:58:45: #1 tag size = 47 INFO @ Sat, 11 Nov 2017 06:58:45: #1 total tags in treatment: 15915450 INFO @ Sat, 11 Nov 2017 06:58:45: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 06:58:45: #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 06:58:45: #1 tags after filtering in treatment: 15915291 INFO @ Sat, 11 Nov 2017 06:58:45: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 06:58:45: #1 finished! INFO @ Sat, 11 Nov 2017 06:58:45: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 06:58:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 06:58:48: #2 number of paired peaks: 13040 INFO @ Sat, 11 Nov 2017 06:58:48: start model_add_line... INFO @ Sat, 11 Nov 2017 06:58:48: start X-correlation... INFO @ Sat, 11 Nov 2017 06:58:48: end of X-cor INFO @ Sat, 11 Nov 2017 06:58:48: #2 finished! INFO @ Sat, 11 Nov 2017 06:58:48: #2 predicted fragment length is 95 bps INFO @ Sat, 11 Nov 2017 06:58:48: #2 alternative fragment length(s) may be 95 bps INFO @ Sat, 11 Nov 2017 06:58:48: #2.2 Generate R script for model : SRX913502.10_model.r INFO @ Sat, 11 Nov 2017 06:58:48: #3 Call peaks... INFO @ Sat, 11 Nov 2017 06:58:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 06:59:09: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 06:59:21: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 06:59:26: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 06:59:30: #4 Write output xls file... SRX913502.05_peaks.xls INFO @ Sat, 11 Nov 2017 06:59:30: #4 Write peak in narrowPeak format file... SRX913502.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 06:59:30: #4 Write summits bed file... SRX913502.05_summits.bed INFO @ Sat, 11 Nov 2017 06:59:30: Done! pass1 - making usageList (41 chroms): 1 millis pass2 - checking and writing primary data (633 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 06:59:43: #4 Write output xls file... SRX913502.20_peaks.xls INFO @ Sat, 11 Nov 2017 06:59:43: #4 Write peak in narrowPeak format file... SRX913502.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 06:59:43: #4 Write summits bed file... SRX913502.20_summits.bed INFO @ Sat, 11 Nov 2017 06:59:43: Done! pass1 - making usageList (19 chroms): 1 millis pass2 - checking and writing primary data (85 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 06:59:47: #4 Write output xls file... SRX913502.10_peaks.xls INFO @ Sat, 11 Nov 2017 06:59:47: #4 Write peak in narrowPeak format file... SRX913502.10_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 06:59:47: #4 Write summits bed file... SRX913502.10_summits.bed INFO @ Sat, 11 Nov 2017 06:59:47: Done! pass1 - making usageList (33 chroms): 1 millis pass2 - checking and writing primary data (283 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。