Job ID = 10194902 sra ファイルのダウンロード中... Completed: 119378K bytes transferred in 13 seconds (73066K bits/sec), in 1 file. Completed: 116693K bytes transferred in 13 seconds (68448K bits/sec), in 1 file. Completed: 196139K bytes transferred in 17 seconds (92906K bits/sec), in 1 file. Completed: 192518K bytes transferred in 16 seconds (98480K bits/sec), in 1 file. Completed: 192812K bytes transferred in 17 seconds (90304K bits/sec), in 1 file. Completed: 189963K bytes transferred in 14 seconds (110346K 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 2730919 spots for /home/okishinya/chipatlas/results/rn6/SRX2202897/SRR4319927.sra Written 2730919 spots total Written 2804832 spots for /home/okishinya/chipatlas/results/rn6/SRX2202897/SRR4319926.sra Written 2804832 spots total Written 4143328 spots for /home/okishinya/chipatlas/results/rn6/SRX2202897/SRR4319931.sra Written 4143328 spots total Written 4198070 spots for /home/okishinya/chipatlas/results/rn6/SRX2202897/SRR4319930.sra Written 4198070 spots total Written 4162407 spots for /home/okishinya/chipatlas/results/rn6/SRX2202897/SRR4319929.sra Written 4162407 spots total Written 4269042 spots for /home/okishinya/chipatlas/results/rn6/SRX2202897/SRR4319928.sra Written 4269042 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: 00:00:00 Multiseed full-index search: 00:37:23 22308598 reads; of these: 22308598 (100.00%) were unpaired; of these: 1748529 (7.84%) aligned 0 times 13872016 (62.18%) aligned exactly 1 time 6688053 (29.98%) aligned >1 times 92.16% overall alignment rate Time searching: 00:37:26 Overall time: 00:37:26 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 12 files... [bam_rmdupse_core] 7566180 / 20560069 = 0.3680 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 22:42:26: # Command line: callpeak -t SRX2202897.bam -f BAM -g 2.15e9 -n SRX2202897.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2202897.10 # format = BAM # ChIP-seq file = ['SRX2202897.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 22:42:26: #1 read tag files... INFO @ Fri, 10 Nov 2017 22:42:26: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 22:42:26: # Command line: callpeak -t SRX2202897.bam -f BAM -g 2.15e9 -n SRX2202897.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2202897.05 # format = BAM # ChIP-seq file = ['SRX2202897.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 22:42:26: #1 read tag files... INFO @ Fri, 10 Nov 2017 22:42:26: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 22:42:26: # Command line: callpeak -t SRX2202897.bam -f BAM -g 2.15e9 -n SRX2202897.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2202897.20 # format = BAM # ChIP-seq file = ['SRX2202897.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 22:42:26: #1 read tag files... INFO @ Fri, 10 Nov 2017 22:42:26: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 22:42:45: 1000000 INFO @ Fri, 10 Nov 2017 22:42:47: 1000000 INFO @ Fri, 10 Nov 2017 22:42:53: 1000000 INFO @ Fri, 10 Nov 2017 22:43:03: 2000000 INFO @ Fri, 10 Nov 2017 22:43:04: 2000000 INFO @ Fri, 10 Nov 2017 22:43:13: 2000000 INFO @ Fri, 10 Nov 2017 22:43:21: 3000000 INFO @ Fri, 10 Nov 2017 22:43:24: 3000000 INFO @ Fri, 10 Nov 2017 22:43:30: 3000000 INFO @ Fri, 10 Nov 2017 22:43:40: 4000000 INFO @ Fri, 10 Nov 2017 22:43:44: 4000000 INFO @ Fri, 10 Nov 2017 22:43:49: 4000000 INFO @ Fri, 10 Nov 2017 22:44:00: 5000000 INFO @ Fri, 10 Nov 2017 22:44:05: 5000000 INFO @ Fri, 10 Nov 2017 22:44:09: 5000000 INFO @ Fri, 10 Nov 2017 22:44:20: 6000000 INFO @ Fri, 10 Nov 2017 22:44:25: 6000000 INFO @ Fri, 10 Nov 2017 22:44:28: 6000000 INFO @ Fri, 10 Nov 2017 22:44:40: 7000000 INFO @ Fri, 10 Nov 2017 22:44:44: 7000000 INFO @ Fri, 10 Nov 2017 22:44:46: 7000000 INFO @ Fri, 10 Nov 2017 22:45:00: 8000000 INFO @ Fri, 10 Nov 2017 22:45:01: 8000000 INFO @ Fri, 10 Nov 2017 22:45:05: 8000000 INFO @ Fri, 10 Nov 2017 22:45:14: 9000000 INFO @ Fri, 10 Nov 2017 22:45:19: 9000000 INFO @ Fri, 10 Nov 2017 22:45:23: 9000000 INFO @ Fri, 10 Nov 2017 22:45:27: 10000000 INFO @ Fri, 10 Nov 2017 22:45:39: 11000000 INFO @ Fri, 10 Nov 2017 22:45:40: 10000000 INFO @ Fri, 10 Nov 2017 22:45:40: 10000000 INFO @ Fri, 10 Nov 2017 22:45:52: 12000000 INFO @ Fri, 10 Nov 2017 22:45:57: 11000000 INFO @ Fri, 10 Nov 2017 22:45:57: 11000000 INFO @ Fri, 10 Nov 2017 22:46:06: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 22:46:06: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 22:46:06: #1 total tags in treatment: 12993889 INFO @ Fri, 10 Nov 2017 22:46:06: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 22:46:06: #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 22:46:07: #1 tags after filtering in treatment: 12993722 INFO @ Fri, 10 Nov 2017 22:46:07: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 22:46:07: #1 finished! INFO @ Fri, 10 Nov 2017 22:46:07: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 22:46:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 22:46:11: #2 number of paired peaks: 41834 INFO @ Fri, 10 Nov 2017 22:46:11: start model_add_line... INFO @ Fri, 10 Nov 2017 22:46:11: start X-correlation... INFO @ Fri, 10 Nov 2017 22:46:11: end of X-cor INFO @ Fri, 10 Nov 2017 22:46:11: #2 finished! INFO @ Fri, 10 Nov 2017 22:46:11: #2 predicted fragment length is 132 bps INFO @ Fri, 10 Nov 2017 22:46:11: #2 alternative fragment length(s) may be 132 bps INFO @ Fri, 10 Nov 2017 22:46:11: #2.2 Generate R script for model : SRX2202897.20_model.r INFO @ Fri, 10 Nov 2017 22:46:12: #3 Call peaks... INFO @ Fri, 10 Nov 2017 22:46:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 22:46:13: 12000000 INFO @ Fri, 10 Nov 2017 22:46:13: 12000000 INFO @ Fri, 10 Nov 2017 22:46:29: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 22:46:29: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 22:46:29: #1 total tags in treatment: 12993889 INFO @ Fri, 10 Nov 2017 22:46:29: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 22:46:29: #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 22:46:30: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 22:46:30: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 22:46:30: #1 total tags in treatment: 12993889 INFO @ Fri, 10 Nov 2017 22:46:30: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 22:46:30: #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 22:46:30: #1 tags after filtering in treatment: 12993722 INFO @ Fri, 10 Nov 2017 22:46:30: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 22:46:30: #1 finished! INFO @ Fri, 10 Nov 2017 22:46:30: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 22:46:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 22:46:30: #1 tags after filtering in treatment: 12993722 INFO @ Fri, 10 Nov 2017 22:46:30: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 22:46:30: #1 finished! INFO @ Fri, 10 Nov 2017 22:46:30: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 22:46:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 22:46:34: #2 number of paired peaks: 41834 INFO @ Fri, 10 Nov 2017 22:46:34: start model_add_line... INFO @ Fri, 10 Nov 2017 22:46:34: start X-correlation... INFO @ Fri, 10 Nov 2017 22:46:34: end of X-cor INFO @ Fri, 10 Nov 2017 22:46:34: #2 finished! INFO @ Fri, 10 Nov 2017 22:46:34: #2 predicted fragment length is 132 bps INFO @ Fri, 10 Nov 2017 22:46:34: #2 alternative fragment length(s) may be 132 bps INFO @ Fri, 10 Nov 2017 22:46:34: #2.2 Generate R script for model : SRX2202897.10_model.r INFO @ Fri, 10 Nov 2017 22:46:34: #3 Call peaks... INFO @ Fri, 10 Nov 2017 22:46:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 22:46:34: #2 number of paired peaks: 41834 INFO @ Fri, 10 Nov 2017 22:46:34: start model_add_line... INFO @ Fri, 10 Nov 2017 22:46:34: start X-correlation... INFO @ Fri, 10 Nov 2017 22:46:34: end of X-cor INFO @ Fri, 10 Nov 2017 22:46:34: #2 finished! INFO @ Fri, 10 Nov 2017 22:46:34: #2 predicted fragment length is 132 bps INFO @ Fri, 10 Nov 2017 22:46:34: #2 alternative fragment length(s) may be 132 bps INFO @ Fri, 10 Nov 2017 22:46:34: #2.2 Generate R script for model : SRX2202897.05_model.r INFO @ Fri, 10 Nov 2017 22:46:34: #3 Call peaks... INFO @ Fri, 10 Nov 2017 22:46:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 22:47:28: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 22:47:52: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 22:47:52: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 22:48:24: #4 Write output xls file... SRX2202897.20_peaks.xls INFO @ Fri, 10 Nov 2017 22:48:24: #4 Write peak in narrowPeak format file... SRX2202897.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 22:48:24: #4 Write summits bed file... SRX2202897.20_summits.bed INFO @ Fri, 10 Nov 2017 22:48:24: Done! pass1 - making usageList (40 chroms): 2 millis pass2 - checking and writing primary data (2171 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 22:48:42: #4 Write output xls file... SRX2202897.10_peaks.xls INFO @ Fri, 10 Nov 2017 22:48:42: #4 Write output xls file... SRX2202897.05_peaks.xls INFO @ Fri, 10 Nov 2017 22:48:42: #4 Write peak in narrowPeak format file... SRX2202897.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 22:48:42: #4 Write summits bed file... SRX2202897.10_summits.bed INFO @ Fri, 10 Nov 2017 22:48:43: #4 Write peak in narrowPeak format file... SRX2202897.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 22:48:43: Done! INFO @ Fri, 10 Nov 2017 22:48:43: #4 Write summits bed file... SRX2202897.05_summits.bed pass1 - making usageList (69 chroms): 3 millis INFO @ Fri, 10 Nov 2017 22:48:43: Done! pass2 - checking and writing primary data (9583 records, 4 fields): 22 millis CompletedMACS2peakCalling pass1 - making usageList (95 chroms): 7 millis pass2 - checking and writing primary data (17991 records, 4 fields): 50 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。