Job ID = 10194781 sra ファイルのダウンロード中... Completed: 792658K bytes transferred in 9 seconds (707293K 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 34061992 spots for /home/okishinya/chipatlas/results/rn6/SRX1774913/SRR3544945.sra Written 34061992 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: 00:27:28 34061992 reads; of these: 34061992 (100.00%) were unpaired; of these: 1004713 (2.95%) aligned 0 times 25499432 (74.86%) aligned exactly 1 time 7557847 (22.19%) aligned >1 times 97.05% overall alignment rate Time searching: 00:27:30 Overall time: 00:27:30 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] 14194100 / 33057279 = 0.4294 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 17:30:28: # Command line: callpeak -t SRX1774913.bam -f BAM -g 2.15e9 -n SRX1774913.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1774913.10 # format = BAM # ChIP-seq file = ['SRX1774913.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 17:30:28: #1 read tag files... INFO @ Fri, 10 Nov 2017 17:30:28: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 17:30:28: # Command line: callpeak -t SRX1774913.bam -f BAM -g 2.15e9 -n SRX1774913.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1774913.20 # format = BAM # ChIP-seq file = ['SRX1774913.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 17:30:28: #1 read tag files... INFO @ Fri, 10 Nov 2017 17:30:28: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 17:30:28: # Command line: callpeak -t SRX1774913.bam -f BAM -g 2.15e9 -n SRX1774913.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1774913.05 # format = BAM # ChIP-seq file = ['SRX1774913.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 17:30:28: #1 read tag files... INFO @ Fri, 10 Nov 2017 17:30:28: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 17:30:36: 1000000 INFO @ Fri, 10 Nov 2017 17:30:36: 1000000 INFO @ Fri, 10 Nov 2017 17:30:36: 1000000 INFO @ Fri, 10 Nov 2017 17:30:43: 2000000 INFO @ Fri, 10 Nov 2017 17:30:44: 2000000 INFO @ Fri, 10 Nov 2017 17:30:44: 2000000 INFO @ Fri, 10 Nov 2017 17:30:51: 3000000 INFO @ Fri, 10 Nov 2017 17:30:51: 3000000 INFO @ Fri, 10 Nov 2017 17:30:51: 3000000 INFO @ Fri, 10 Nov 2017 17:30:59: 4000000 INFO @ Fri, 10 Nov 2017 17:30:59: 4000000 INFO @ Fri, 10 Nov 2017 17:30:59: 4000000 INFO @ Fri, 10 Nov 2017 17:31:07: 5000000 INFO @ Fri, 10 Nov 2017 17:31:07: 5000000 INFO @ Fri, 10 Nov 2017 17:31:07: 5000000 INFO @ Fri, 10 Nov 2017 17:31:15: 6000000 INFO @ Fri, 10 Nov 2017 17:31:15: 6000000 INFO @ Fri, 10 Nov 2017 17:31:15: 6000000 INFO @ Fri, 10 Nov 2017 17:31:22: 7000000 INFO @ Fri, 10 Nov 2017 17:31:23: 7000000 INFO @ Fri, 10 Nov 2017 17:31:23: 7000000 INFO @ Fri, 10 Nov 2017 17:31:30: 8000000 INFO @ Fri, 10 Nov 2017 17:31:31: 8000000 INFO @ Fri, 10 Nov 2017 17:31:31: 8000000 INFO @ Fri, 10 Nov 2017 17:31:37: 9000000 INFO @ Fri, 10 Nov 2017 17:31:38: 9000000 INFO @ Fri, 10 Nov 2017 17:31:38: 9000000 INFO @ Fri, 10 Nov 2017 17:31:43: 10000000 INFO @ Fri, 10 Nov 2017 17:31:45: 10000000 INFO @ Fri, 10 Nov 2017 17:31:45: 10000000 INFO @ Fri, 10 Nov 2017 17:31:50: 11000000 INFO @ Fri, 10 Nov 2017 17:31:52: 11000000 INFO @ Fri, 10 Nov 2017 17:31:52: 11000000 INFO @ Fri, 10 Nov 2017 17:31:56: 12000000 INFO @ Fri, 10 Nov 2017 17:31:59: 12000000 INFO @ Fri, 10 Nov 2017 17:31:59: 12000000 INFO @ Fri, 10 Nov 2017 17:32:03: 13000000 INFO @ Fri, 10 Nov 2017 17:32:06: 13000000 INFO @ Fri, 10 Nov 2017 17:32:06: 13000000 INFO @ Fri, 10 Nov 2017 17:32:09: 14000000 INFO @ Fri, 10 Nov 2017 17:32:13: 14000000 INFO @ Fri, 10 Nov 2017 17:32:13: 14000000 INFO @ Fri, 10 Nov 2017 17:32:16: 15000000 INFO @ Fri, 10 Nov 2017 17:32:21: 15000000 INFO @ Fri, 10 Nov 2017 17:32:21: 15000000 INFO @ Fri, 10 Nov 2017 17:32:23: 16000000 INFO @ Fri, 10 Nov 2017 17:32:28: 16000000 INFO @ Fri, 10 Nov 2017 17:32:28: 16000000 INFO @ Fri, 10 Nov 2017 17:32:29: 17000000 INFO @ Fri, 10 Nov 2017 17:32:35: 17000000 INFO @ Fri, 10 Nov 2017 17:32:35: 17000000 INFO @ Fri, 10 Nov 2017 17:32:36: 18000000 INFO @ Fri, 10 Nov 2017 17:32:42: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 17:32:42: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 17:32:42: #1 total tags in treatment: 18863179 INFO @ Fri, 10 Nov 2017 17:32:42: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 17:32:42: #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 17:32:42: 18000000 INFO @ Fri, 10 Nov 2017 17:32:42: 18000000 INFO @ Fri, 10 Nov 2017 17:32:42: #1 tags after filtering in treatment: 18863051 INFO @ Fri, 10 Nov 2017 17:32:42: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 17:32:42: #1 finished! INFO @ Fri, 10 Nov 2017 17:32:42: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 17:32:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 17:32:45: #2 number of paired peaks: 12376 INFO @ Fri, 10 Nov 2017 17:32:45: start model_add_line... INFO @ Fri, 10 Nov 2017 17:32:45: start X-correlation... INFO @ Fri, 10 Nov 2017 17:32:45: end of X-cor INFO @ Fri, 10 Nov 2017 17:32:45: #2 finished! INFO @ Fri, 10 Nov 2017 17:32:45: #2 predicted fragment length is 146 bps INFO @ Fri, 10 Nov 2017 17:32:45: #2 alternative fragment length(s) may be 146 bps INFO @ Fri, 10 Nov 2017 17:32:45: #2.2 Generate R script for model : SRX1774913.05_model.r INFO @ Fri, 10 Nov 2017 17:32:45: #3 Call peaks... INFO @ Fri, 10 Nov 2017 17:32:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 17:32:48: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 17:32:48: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 17:32:48: #1 total tags in treatment: 18863179 INFO @ Fri, 10 Nov 2017 17:32:48: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 17:32:48: #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 17:32:48: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 17:32:48: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 17:32:48: #1 total tags in treatment: 18863179 INFO @ Fri, 10 Nov 2017 17:32:48: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 17:32:48: #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 17:32:49: #1 tags after filtering in treatment: 18863051 INFO @ Fri, 10 Nov 2017 17:32:49: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 17:32:49: #1 finished! INFO @ Fri, 10 Nov 2017 17:32:49: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 17:32:49: #1 tags after filtering in treatment: 18863051 INFO @ Fri, 10 Nov 2017 17:32:49: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 17:32:49: #1 finished! INFO @ Fri, 10 Nov 2017 17:32:49: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 17:32:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 17:32:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 17:32:51: #2 number of paired peaks: 12376 INFO @ Fri, 10 Nov 2017 17:32:51: start model_add_line... INFO @ Fri, 10 Nov 2017 17:32:51: start X-correlation... INFO @ Fri, 10 Nov 2017 17:32:51: end of X-cor INFO @ Fri, 10 Nov 2017 17:32:51: #2 finished! INFO @ Fri, 10 Nov 2017 17:32:51: #2 predicted fragment length is 146 bps INFO @ Fri, 10 Nov 2017 17:32:51: #2 alternative fragment length(s) may be 146 bps INFO @ Fri, 10 Nov 2017 17:32:51: #2.2 Generate R script for model : SRX1774913.10_model.r INFO @ Fri, 10 Nov 2017 17:32:51: #3 Call peaks... INFO @ Fri, 10 Nov 2017 17:32:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 17:32:51: #2 number of paired peaks: 12376 INFO @ Fri, 10 Nov 2017 17:32:51: start model_add_line... INFO @ Fri, 10 Nov 2017 17:32:52: start X-correlation... INFO @ Fri, 10 Nov 2017 17:32:52: end of X-cor INFO @ Fri, 10 Nov 2017 17:32:52: #2 finished! INFO @ Fri, 10 Nov 2017 17:32:52: #2 predicted fragment length is 146 bps INFO @ Fri, 10 Nov 2017 17:32:52: #2 alternative fragment length(s) may be 146 bps INFO @ Fri, 10 Nov 2017 17:32:52: #2.2 Generate R script for model : SRX1774913.20_model.r INFO @ Fri, 10 Nov 2017 17:32:52: #3 Call peaks... INFO @ Fri, 10 Nov 2017 17:32:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 17:33:33: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 17:33:36: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 17:33:38: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 17:33:59: #4 Write output xls file... SRX1774913.05_peaks.xls INFO @ Fri, 10 Nov 2017 17:33:59: #4 Write peak in narrowPeak format file... SRX1774913.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 17:33:59: #4 Write summits bed file... SRX1774913.05_summits.bed INFO @ Fri, 10 Nov 2017 17:33:59: Done! pass1 - making usageList (52 chroms): 1 millis pass2 - checking and writing primary data (2777 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 17:34:05: #4 Write output xls file... SRX1774913.10_peaks.xls INFO @ Fri, 10 Nov 2017 17:34:05: #4 Write peak in narrowPeak format file... SRX1774913.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 17:34:05: #4 Write summits bed file... SRX1774913.10_summits.bed INFO @ Fri, 10 Nov 2017 17:34:05: Done! pass1 - making usageList (35 chroms): 1 millis pass2 - checking and writing primary data (1239 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 17:34:05: #4 Write output xls file... SRX1774913.20_peaks.xls INFO @ Fri, 10 Nov 2017 17:34:05: #4 Write peak in narrowPeak format file... SRX1774913.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 17:34:05: #4 Write summits bed file... SRX1774913.20_summits.bed INFO @ Fri, 10 Nov 2017 17:34:05: Done! pass1 - making usageList (30 chroms): 1 millis pass2 - checking and writing primary data (510 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。