Job ID = 10194879 sra ファイルのダウンロード中... Completed: 134325K bytes transferred in 5 seconds (215117K bits/sec), in 1 file. Completed: 134579K bytes transferred in 6 seconds (177352K bits/sec), in 1 file. Completed: 128096K bytes transferred in 7 seconds (146867K bits/sec), in 1 file. Completed: 126488K bytes transferred in 7 seconds (131526K bits/sec), in 1 file. Completed: 144214K bytes transferred in 5 seconds (207899K bits/sec), in 1 file. Completed: 145378K bytes transferred in 7 seconds (166105K 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 2839268 spots for /home/okishinya/chipatlas/results/rn6/SRX2202874/SRR4319791.sra Written 2839268 spots total Written 2868574 spots for /home/okishinya/chipatlas/results/rn6/SRX2202874/SRR4319790.sra Written 2868574 spots total Written 2992519 spots for /home/okishinya/chipatlas/results/rn6/SRX2202874/SRR4319789.sra Written 2992519 spots total Written 2996621 spots for /home/okishinya/chipatlas/results/rn6/SRX2202874/SRR4319788.sra Written 2996621 spots total Written 3145752 spots for /home/okishinya/chipatlas/results/rn6/SRX2202874/SRR4319792.sra Written 3145752 spots total Written 3158639 spots for /home/okishinya/chipatlas/results/rn6/SRX2202874/SRR4319793.sra Written 3158639 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: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:12:07 18001373 reads; of these: 18001373 (100.00%) were unpaired; of these: 2491239 (13.84%) aligned 0 times 11763180 (65.35%) aligned exactly 1 time 3746954 (20.81%) aligned >1 times 86.16% overall alignment rate Time searching: 00:12:09 Overall time: 00:12:09 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] 4648769 / 15510134 = 0.2997 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 17:46:40: # Command line: callpeak -t SRX2202874.bam -f BAM -g 2.15e9 -n SRX2202874.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2202874.05 # format = BAM # ChIP-seq file = ['SRX2202874.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 17:46:40: #1 read tag files... INFO @ Fri, 10 Nov 2017 17:46:40: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 17:46:40: # Command line: callpeak -t SRX2202874.bam -f BAM -g 2.15e9 -n SRX2202874.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2202874.20 # format = BAM # ChIP-seq file = ['SRX2202874.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 17:46:40: #1 read tag files... INFO @ Fri, 10 Nov 2017 17:46:40: # Command line: callpeak -t SRX2202874.bam -f BAM -g 2.15e9 -n SRX2202874.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2202874.10 # format = BAM # ChIP-seq file = ['SRX2202874.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 17:46:40: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 17:46:40: #1 read tag files... INFO @ Fri, 10 Nov 2017 17:46:40: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 17:46:47: 1000000 INFO @ Fri, 10 Nov 2017 17:46:48: 1000000 INFO @ Fri, 10 Nov 2017 17:46:48: 1000000 INFO @ Fri, 10 Nov 2017 17:46:54: 2000000 INFO @ Fri, 10 Nov 2017 17:46:55: 2000000 INFO @ Fri, 10 Nov 2017 17:46:55: 2000000 INFO @ Fri, 10 Nov 2017 17:47:01: 3000000 INFO @ Fri, 10 Nov 2017 17:47:03: 3000000 INFO @ Fri, 10 Nov 2017 17:47:03: 3000000 INFO @ Fri, 10 Nov 2017 17:47:07: 4000000 INFO @ Fri, 10 Nov 2017 17:47:11: 4000000 INFO @ Fri, 10 Nov 2017 17:47:11: 4000000 INFO @ Fri, 10 Nov 2017 17:47:14: 5000000 INFO @ Fri, 10 Nov 2017 17:47:18: 5000000 INFO @ Fri, 10 Nov 2017 17:47:18: 5000000 INFO @ Fri, 10 Nov 2017 17:47:21: 6000000 INFO @ Fri, 10 Nov 2017 17:47:26: 6000000 INFO @ Fri, 10 Nov 2017 17:47:26: 6000000 INFO @ Fri, 10 Nov 2017 17:47:28: 7000000 INFO @ Fri, 10 Nov 2017 17:47:33: 7000000 INFO @ Fri, 10 Nov 2017 17:47:33: 7000000 INFO @ Fri, 10 Nov 2017 17:47:35: 8000000 INFO @ Fri, 10 Nov 2017 17:47:41: 8000000 INFO @ Fri, 10 Nov 2017 17:47:41: 8000000 INFO @ Fri, 10 Nov 2017 17:47:42: 9000000 INFO @ Fri, 10 Nov 2017 17:47:49: 9000000 INFO @ Fri, 10 Nov 2017 17:47:49: 9000000 INFO @ Fri, 10 Nov 2017 17:47:49: 10000000 INFO @ Fri, 10 Nov 2017 17:47:55: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 17:47:55: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 17:47:55: #1 total tags in treatment: 10861365 INFO @ Fri, 10 Nov 2017 17:47:55: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 17:47:55: #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 17:47:55: #1 tags after filtering in treatment: 10861186 INFO @ Fri, 10 Nov 2017 17:47:55: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 17:47:55: #1 finished! INFO @ Fri, 10 Nov 2017 17:47:55: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 17:47:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 17:47:56: 10000000 INFO @ Fri, 10 Nov 2017 17:47:56: 10000000 INFO @ Fri, 10 Nov 2017 17:47:57: #2 number of paired peaks: 27131 INFO @ Fri, 10 Nov 2017 17:47:57: start model_add_line... INFO @ Fri, 10 Nov 2017 17:47:57: start X-correlation... INFO @ Fri, 10 Nov 2017 17:47:57: end of X-cor INFO @ Fri, 10 Nov 2017 17:47:57: #2 finished! INFO @ Fri, 10 Nov 2017 17:47:58: #2 predicted fragment length is 126 bps INFO @ Fri, 10 Nov 2017 17:47:58: #2 alternative fragment length(s) may be 126,150,153 bps INFO @ Fri, 10 Nov 2017 17:47:58: #2.2 Generate R script for model : SRX2202874.05_model.r INFO @ Fri, 10 Nov 2017 17:47:58: #3 Call peaks... INFO @ Fri, 10 Nov 2017 17:47:58: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 17:48:03: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 17:48:03: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 17:48:03: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 17:48:03: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 17:48:03: #1 total tags in treatment: 10861365 INFO @ Fri, 10 Nov 2017 17:48:03: #1 total tags in treatment: 10861365 INFO @ Fri, 10 Nov 2017 17:48:03: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 17:48:03: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 17:48:03: #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 17:48:03: #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 17:48:04: #1 tags after filtering in treatment: 10861186 INFO @ Fri, 10 Nov 2017 17:48:04: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 17:48:04: #1 tags after filtering in treatment: 10861186 INFO @ Fri, 10 Nov 2017 17:48:04: #1 finished! INFO @ Fri, 10 Nov 2017 17:48:04: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 17:48:04: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 17:48:04: #1 finished! INFO @ Fri, 10 Nov 2017 17:48:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 17:48:04: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 17:48:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 17:48:06: #2 number of paired peaks: 27131 INFO @ Fri, 10 Nov 2017 17:48:06: start model_add_line... INFO @ Fri, 10 Nov 2017 17:48:06: #2 number of paired peaks: 27131 INFO @ Fri, 10 Nov 2017 17:48:06: start model_add_line... INFO @ Fri, 10 Nov 2017 17:48:06: start X-correlation... INFO @ Fri, 10 Nov 2017 17:48:06: end of X-cor INFO @ Fri, 10 Nov 2017 17:48:06: #2 finished! INFO @ Fri, 10 Nov 2017 17:48:06: #2 predicted fragment length is 126 bps INFO @ Fri, 10 Nov 2017 17:48:06: #2 alternative fragment length(s) may be 126,150,153 bps INFO @ Fri, 10 Nov 2017 17:48:06: #2.2 Generate R script for model : SRX2202874.20_model.r INFO @ Fri, 10 Nov 2017 17:48:06: #3 Call peaks... INFO @ Fri, 10 Nov 2017 17:48:06: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 17:48:06: start X-correlation... INFO @ Fri, 10 Nov 2017 17:48:06: end of X-cor INFO @ Fri, 10 Nov 2017 17:48:06: #2 finished! INFO @ Fri, 10 Nov 2017 17:48:06: #2 predicted fragment length is 126 bps INFO @ Fri, 10 Nov 2017 17:48:06: #2 alternative fragment length(s) may be 126,150,153 bps INFO @ Fri, 10 Nov 2017 17:48:06: #2.2 Generate R script for model : SRX2202874.10_model.r INFO @ Fri, 10 Nov 2017 17:48:06: #3 Call peaks... INFO @ Fri, 10 Nov 2017 17:48:06: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 17:48:26: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 17:48:33: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 17:48:33: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 17:48:41: #4 Write output xls file... SRX2202874.05_peaks.xls INFO @ Fri, 10 Nov 2017 17:48:41: #4 Write peak in narrowPeak format file... SRX2202874.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 17:48:41: #4 Write summits bed file... SRX2202874.05_summits.bed INFO @ Fri, 10 Nov 2017 17:48:41: Done! pass1 - making usageList (42 chroms): 1 millis pass2 - checking and writing primary data (1326 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 17:48:48: #4 Write output xls file... SRX2202874.10_peaks.xls INFO @ Fri, 10 Nov 2017 17:48:48: #4 Write peak in narrowPeak format file... SRX2202874.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 17:48:48: #4 Write summits bed file... SRX2202874.10_summits.bed INFO @ Fri, 10 Nov 2017 17:48:48: Done! pass1 - making usageList (36 chroms): 1 millis pass2 - checking and writing primary data (452 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 17:48:50: #4 Write output xls file... SRX2202874.20_peaks.xls INFO @ Fri, 10 Nov 2017 17:48:50: #4 Write peak in narrowPeak format file... SRX2202874.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 17:48:50: #4 Write summits bed file... SRX2202874.20_summits.bed INFO @ Fri, 10 Nov 2017 17:48:50: Done! pass1 - making usageList (26 chroms): 1 millis pass2 - checking and writing primary data (233 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。