Job ID = 10194743 sra ファイルのダウンロード中... Completed: 392201K bytes transferred in 6 seconds (525862K 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 15177374 spots for /home/okishinya/chipatlas/results/rn6/SRX1068232/SRR2073191.sra Written 15177374 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: 00:00:00 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:15:41 15177374 reads; of these: 15177374 (100.00%) were unpaired; of these: 297723 (1.96%) aligned 0 times 12860336 (84.73%) aligned exactly 1 time 2019315 (13.30%) aligned >1 times 98.04% overall alignment rate Time searching: 00:15:43 Overall time: 00:15:43 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] 658079 / 14879651 = 0.0442 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, 10 Nov 2017 23:50:37: # Command line: callpeak -t SRX1068232.bam -f BAM -g 2.15e9 -n SRX1068232.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1068232.10 # format = BAM # ChIP-seq file = ['SRX1068232.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, 10 Nov 2017 23:50:37: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:50:37: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:50:37: # Command line: callpeak -t SRX1068232.bam -f BAM -g 2.15e9 -n SRX1068232.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1068232.20 # format = BAM # ChIP-seq file = ['SRX1068232.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, 10 Nov 2017 23:50:37: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:50:37: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:50:37: # Command line: callpeak -t SRX1068232.bam -f BAM -g 2.15e9 -n SRX1068232.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1068232.05 # format = BAM # ChIP-seq file = ['SRX1068232.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, 10 Nov 2017 23:50:37: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:50:37: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:50:44: 1000000 INFO @ Fri, 10 Nov 2017 23:50:44: 1000000 INFO @ Fri, 10 Nov 2017 23:50:44: 1000000 INFO @ Fri, 10 Nov 2017 23:50:50: 2000000 INFO @ Fri, 10 Nov 2017 23:50:50: 2000000 INFO @ Fri, 10 Nov 2017 23:50:51: 2000000 INFO @ Fri, 10 Nov 2017 23:50:57: 3000000 INFO @ Fri, 10 Nov 2017 23:50:57: 3000000 INFO @ Fri, 10 Nov 2017 23:50:57: 3000000 INFO @ Fri, 10 Nov 2017 23:51:03: 4000000 INFO @ Fri, 10 Nov 2017 23:51:04: 4000000 INFO @ Fri, 10 Nov 2017 23:51:04: 4000000 INFO @ Fri, 10 Nov 2017 23:51:10: 5000000 INFO @ Fri, 10 Nov 2017 23:51:10: 5000000 INFO @ Fri, 10 Nov 2017 23:51:11: 5000000 INFO @ Fri, 10 Nov 2017 23:51:16: 6000000 INFO @ Fri, 10 Nov 2017 23:51:17: 6000000 INFO @ Fri, 10 Nov 2017 23:51:18: 6000000 INFO @ Fri, 10 Nov 2017 23:51:23: 7000000 INFO @ Fri, 10 Nov 2017 23:51:24: 7000000 INFO @ Fri, 10 Nov 2017 23:51:24: 7000000 INFO @ Fri, 10 Nov 2017 23:51:30: 8000000 INFO @ Fri, 10 Nov 2017 23:51:31: 8000000 INFO @ Fri, 10 Nov 2017 23:51:31: 8000000 INFO @ Fri, 10 Nov 2017 23:51:36: 9000000 INFO @ Fri, 10 Nov 2017 23:51:37: 9000000 INFO @ Fri, 10 Nov 2017 23:51:38: 9000000 INFO @ Fri, 10 Nov 2017 23:51:43: 10000000 INFO @ Fri, 10 Nov 2017 23:51:44: 10000000 INFO @ Fri, 10 Nov 2017 23:51:45: 10000000 INFO @ Fri, 10 Nov 2017 23:51:50: 11000000 INFO @ Fri, 10 Nov 2017 23:51:51: 11000000 INFO @ Fri, 10 Nov 2017 23:51:51: 11000000 INFO @ Fri, 10 Nov 2017 23:51:56: 12000000 INFO @ Fri, 10 Nov 2017 23:51:58: 12000000 INFO @ Fri, 10 Nov 2017 23:51:58: 12000000 INFO @ Fri, 10 Nov 2017 23:52:03: 13000000 INFO @ Fri, 10 Nov 2017 23:52:04: 13000000 INFO @ Fri, 10 Nov 2017 23:52:05: 13000000 INFO @ Fri, 10 Nov 2017 23:52:10: 14000000 INFO @ Fri, 10 Nov 2017 23:52:11: #1 tag size is determined as 64 bps INFO @ Fri, 10 Nov 2017 23:52:11: #1 tag size = 64 INFO @ Fri, 10 Nov 2017 23:52:11: #1 total tags in treatment: 14221572 INFO @ Fri, 10 Nov 2017 23:52:11: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 23:52:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 23:52:11: 14000000 INFO @ Fri, 10 Nov 2017 23:52:11: 14000000 INFO @ Fri, 10 Nov 2017 23:52:12: #1 tags after filtering in treatment: 14221319 INFO @ Fri, 10 Nov 2017 23:52:12: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 23:52:12: #1 finished! INFO @ Fri, 10 Nov 2017 23:52:12: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 23:52:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 23:52:13: #1 tag size is determined as 64 bps INFO @ Fri, 10 Nov 2017 23:52:13: #1 tag size = 64 INFO @ Fri, 10 Nov 2017 23:52:13: #1 total tags in treatment: 14221572 INFO @ Fri, 10 Nov 2017 23:52:13: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 23:52:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 23:52:13: #1 tag size is determined as 64 bps INFO @ Fri, 10 Nov 2017 23:52:13: #1 tag size = 64 INFO @ Fri, 10 Nov 2017 23:52:13: #1 total tags in treatment: 14221572 INFO @ Fri, 10 Nov 2017 23:52:13: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 23:52:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 23:52:13: #1 tags after filtering in treatment: 14221319 INFO @ Fri, 10 Nov 2017 23:52:13: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 23:52:13: #1 finished! INFO @ Fri, 10 Nov 2017 23:52:13: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 23:52:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 23:52:13: #1 tags after filtering in treatment: 14221319 INFO @ Fri, 10 Nov 2017 23:52:13: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 23:52:13: #1 finished! INFO @ Fri, 10 Nov 2017 23:52:13: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 23:52:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 23:52:17: #2 number of paired peaks: 126099 INFO @ Fri, 10 Nov 2017 23:52:17: start model_add_line... INFO @ Fri, 10 Nov 2017 23:52:17: start X-correlation... INFO @ Fri, 10 Nov 2017 23:52:17: end of X-cor INFO @ Fri, 10 Nov 2017 23:52:17: #2 finished! INFO @ Fri, 10 Nov 2017 23:52:17: #2 predicted fragment length is 288 bps INFO @ Fri, 10 Nov 2017 23:52:17: #2 alternative fragment length(s) may be 288 bps INFO @ Fri, 10 Nov 2017 23:52:17: #2.2 Generate R script for model : SRX1068232.05_model.r INFO @ Fri, 10 Nov 2017 23:52:17: #3 Call peaks... INFO @ Fri, 10 Nov 2017 23:52:17: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 23:52:19: #2 number of paired peaks: 126099 INFO @ Fri, 10 Nov 2017 23:52:19: start model_add_line... INFO @ Fri, 10 Nov 2017 23:52:19: #2 number of paired peaks: 126099 INFO @ Fri, 10 Nov 2017 23:52:19: start model_add_line... INFO @ Fri, 10 Nov 2017 23:52:19: start X-correlation... INFO @ Fri, 10 Nov 2017 23:52:19: end of X-cor INFO @ Fri, 10 Nov 2017 23:52:19: #2 finished! INFO @ Fri, 10 Nov 2017 23:52:19: #2 predicted fragment length is 288 bps INFO @ Fri, 10 Nov 2017 23:52:19: #2 alternative fragment length(s) may be 288 bps INFO @ Fri, 10 Nov 2017 23:52:19: #2.2 Generate R script for model : SRX1068232.20_model.r INFO @ Fri, 10 Nov 2017 23:52:19: #3 Call peaks... INFO @ Fri, 10 Nov 2017 23:52:19: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 23:52:19: start X-correlation... INFO @ Fri, 10 Nov 2017 23:52:19: end of X-cor INFO @ Fri, 10 Nov 2017 23:52:19: #2 finished! INFO @ Fri, 10 Nov 2017 23:52:19: #2 predicted fragment length is 288 bps INFO @ Fri, 10 Nov 2017 23:52:19: #2 alternative fragment length(s) may be 288 bps INFO @ Fri, 10 Nov 2017 23:52:19: #2.2 Generate R script for model : SRX1068232.10_model.r INFO @ Fri, 10 Nov 2017 23:52:19: #3 Call peaks... INFO @ Fri, 10 Nov 2017 23:52:19: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 23:52:55: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 23:52:55: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 23:52:56: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 23:53:17: #4 Write output xls file... SRX1068232.20_peaks.xls INFO @ Fri, 10 Nov 2017 23:53:17: #4 Write peak in narrowPeak format file... SRX1068232.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 23:53:17: #4 Write summits bed file... SRX1068232.20_summits.bed INFO @ Fri, 10 Nov 2017 23:53:17: Done! pass1 - making usageList (19 chroms): 0 millis pass2 - checking and writing primary data (226 records, 4 fields): 31 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 23:53:17: #4 Write output xls file... SRX1068232.10_peaks.xls INFO @ Fri, 10 Nov 2017 23:53:17: #4 Write peak in narrowPeak format file... SRX1068232.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 23:53:17: #4 Write summits bed file... SRX1068232.10_summits.bed INFO @ Fri, 10 Nov 2017 23:53:17: Done! pass1 - making usageList (29 chroms): 2 millis pass2 - checking and writing primary data (3349 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 23:53:20: #4 Write output xls file... SRX1068232.05_peaks.xls INFO @ Fri, 10 Nov 2017 23:53:20: #4 Write peak in narrowPeak format file... SRX1068232.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 23:53:20: #4 Write summits bed file... SRX1068232.05_summits.bed INFO @ Fri, 10 Nov 2017 23:53:20: Done! pass1 - making usageList (63 chroms): 4 millis pass2 - checking and writing primary data (19807 records, 4 fields): 24 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。