Job ID = 10194922 sra ファイルのダウンロード中... Completed: 89844K bytes transferred in 7 seconds (99671K bits/sec), in 1 file. Completed: 87904K bytes transferred in 6 seconds (104533K bits/sec), in 1 file. Completed: 149415K bytes transferred in 10 seconds (111531K bits/sec), in 1 file. Completed: 146959K bytes transferred in 8 seconds (136254K bits/sec), in 1 file. Completed: 145540K bytes transferred in 12 seconds (94911K bits/sec), in 1 file. Completed: 143736K bytes transferred in 10 seconds (108166K 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 2066189 spots for /home/okishinya/chipatlas/results/rn6/SRX2202917/SRR4320047.sra Written 2066189 spots total Written 2120832 spots for /home/okishinya/chipatlas/results/rn6/SRX2202917/SRR4320046.sra Written 2120832 spots total Written 3146536 spots for /home/okishinya/chipatlas/results/rn6/SRX2202917/SRR4320051.sra Written 3146536 spots total Written 3186028 spots for /home/okishinya/chipatlas/results/rn6/SRX2202917/SRR4320049.sra Written 3186028 spots total Written 3181115 spots for /home/okishinya/chipatlas/results/rn6/SRX2202917/SRR4320050.sra Written 3181115 spots total Written 3259740 spots for /home/okishinya/chipatlas/results/rn6/SRX2202917/SRR4320048.sra Written 3259740 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: 00:00:01 Multiseed full-index search: 00:26:46 16960440 reads; of these: 16960440 (100.00%) were unpaired; of these: 627300 (3.70%) aligned 0 times 11394898 (67.19%) aligned exactly 1 time 4938242 (29.12%) aligned >1 times 96.30% overall alignment rate Time searching: 00:26:50 Overall time: 00:26:50 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] 8478910 / 16333140 = 0.5191 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 23:44:26: # Command line: callpeak -t SRX2202917.bam -f BAM -g 2.15e9 -n SRX2202917.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2202917.20 # format = BAM # ChIP-seq file = ['SRX2202917.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 23:44:26: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:44:26: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:44:26: # Command line: callpeak -t SRX2202917.bam -f BAM -g 2.15e9 -n SRX2202917.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2202917.05 # format = BAM # ChIP-seq file = ['SRX2202917.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 23:44:26: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:44:26: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:44:26: # Command line: callpeak -t SRX2202917.bam -f BAM -g 2.15e9 -n SRX2202917.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2202917.10 # format = BAM # ChIP-seq file = ['SRX2202917.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 23:44:26: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:44:26: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:44:33: 1000000 INFO @ Fri, 10 Nov 2017 23:44:33: 1000000 INFO @ Fri, 10 Nov 2017 23:44:34: 1000000 INFO @ Fri, 10 Nov 2017 23:44:40: 2000000 INFO @ Fri, 10 Nov 2017 23:44:40: 2000000 INFO @ Fri, 10 Nov 2017 23:44:41: 2000000 INFO @ Fri, 10 Nov 2017 23:44:47: 3000000 INFO @ Fri, 10 Nov 2017 23:44:47: 3000000 INFO @ Fri, 10 Nov 2017 23:44:49: 3000000 INFO @ Fri, 10 Nov 2017 23:44:54: 4000000 INFO @ Fri, 10 Nov 2017 23:44:54: 4000000 INFO @ Fri, 10 Nov 2017 23:44:57: 4000000 INFO @ Fri, 10 Nov 2017 23:45:01: 5000000 INFO @ Fri, 10 Nov 2017 23:45:02: 5000000 INFO @ Fri, 10 Nov 2017 23:45:05: 5000000 INFO @ Fri, 10 Nov 2017 23:45:08: 6000000 INFO @ Fri, 10 Nov 2017 23:45:09: 6000000 INFO @ Fri, 10 Nov 2017 23:45:13: 6000000 INFO @ Fri, 10 Nov 2017 23:45:15: 7000000 INFO @ Fri, 10 Nov 2017 23:45:16: 7000000 INFO @ Fri, 10 Nov 2017 23:45:21: 7000000 INFO @ Fri, 10 Nov 2017 23:45:21: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 23:45:21: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 23:45:21: #1 total tags in treatment: 7854230 INFO @ Fri, 10 Nov 2017 23:45:21: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 23:45:21: #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 23:45:22: #1 tags after filtering in treatment: 7854043 INFO @ Fri, 10 Nov 2017 23:45:22: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 23:45:22: #1 finished! INFO @ Fri, 10 Nov 2017 23:45:22: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 23:45:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 23:45:22: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 23:45:22: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 23:45:22: #1 total tags in treatment: 7854230 INFO @ Fri, 10 Nov 2017 23:45:22: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 23:45:22: #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 23:45:23: #1 tags after filtering in treatment: 7854043 INFO @ Fri, 10 Nov 2017 23:45:23: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 23:45:23: #1 finished! INFO @ Fri, 10 Nov 2017 23:45:23: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 23:45:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 23:45:25: #2 number of paired peaks: 31445 INFO @ Fri, 10 Nov 2017 23:45:25: start model_add_line... INFO @ Fri, 10 Nov 2017 23:45:25: start X-correlation... INFO @ Fri, 10 Nov 2017 23:45:25: end of X-cor INFO @ Fri, 10 Nov 2017 23:45:25: #2 finished! INFO @ Fri, 10 Nov 2017 23:45:25: #2 predicted fragment length is 167 bps INFO @ Fri, 10 Nov 2017 23:45:25: #2 alternative fragment length(s) may be 54,167,174,222 bps INFO @ Fri, 10 Nov 2017 23:45:25: #2.2 Generate R script for model : SRX2202917.05_model.r INFO @ Fri, 10 Nov 2017 23:45:25: #3 Call peaks... INFO @ Fri, 10 Nov 2017 23:45:25: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 23:45:26: #2 number of paired peaks: 31445 INFO @ Fri, 10 Nov 2017 23:45:26: start model_add_line... INFO @ Fri, 10 Nov 2017 23:45:26: start X-correlation... INFO @ Fri, 10 Nov 2017 23:45:26: end of X-cor INFO @ Fri, 10 Nov 2017 23:45:26: #2 finished! INFO @ Fri, 10 Nov 2017 23:45:26: #2 predicted fragment length is 167 bps INFO @ Fri, 10 Nov 2017 23:45:26: #2 alternative fragment length(s) may be 54,167,174,222 bps INFO @ Fri, 10 Nov 2017 23:45:26: #2.2 Generate R script for model : SRX2202917.10_model.r INFO @ Fri, 10 Nov 2017 23:45:26: #3 Call peaks... INFO @ Fri, 10 Nov 2017 23:45:26: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 23:45:28: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 23:45:28: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 23:45:28: #1 total tags in treatment: 7854230 INFO @ Fri, 10 Nov 2017 23:45:28: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 23:45:28: #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 23:45:28: #1 tags after filtering in treatment: 7854043 INFO @ Fri, 10 Nov 2017 23:45:28: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 23:45:28: #1 finished! INFO @ Fri, 10 Nov 2017 23:45:28: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 23:45:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 23:45:31: #2 number of paired peaks: 31445 INFO @ Fri, 10 Nov 2017 23:45:31: start model_add_line... INFO @ Fri, 10 Nov 2017 23:45:31: start X-correlation... INFO @ Fri, 10 Nov 2017 23:45:31: end of X-cor INFO @ Fri, 10 Nov 2017 23:45:31: #2 finished! INFO @ Fri, 10 Nov 2017 23:45:31: #2 predicted fragment length is 167 bps INFO @ Fri, 10 Nov 2017 23:45:31: #2 alternative fragment length(s) may be 54,167,174,222 bps INFO @ Fri, 10 Nov 2017 23:45:31: #2.2 Generate R script for model : SRX2202917.20_model.r INFO @ Fri, 10 Nov 2017 23:45:31: #3 Call peaks... INFO @ Fri, 10 Nov 2017 23:45:31: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 23:45:48: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 23:45:53: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 23:45:54: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 23:46:01: #4 Write output xls file... SRX2202917.05_peaks.xls INFO @ Fri, 10 Nov 2017 23:46:01: #4 Write peak in narrowPeak format file... SRX2202917.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 23:46:01: #4 Write summits bed file... SRX2202917.05_summits.bed INFO @ Fri, 10 Nov 2017 23:46:01: Done! pass1 - making usageList (42 chroms): 1 millis pass2 - checking and writing primary data (742 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 23:46:07: #4 Write output xls file... SRX2202917.20_peaks.xls INFO @ Fri, 10 Nov 2017 23:46:07: #4 Write peak in narrowPeak format file... SRX2202917.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 23:46:07: #4 Write summits bed file... SRX2202917.20_summits.bed INFO @ Fri, 10 Nov 2017 23:46:07: Done! pass1 - making usageList (26 chroms): 2 millis pass2 - checking and writing primary data (263 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 23:46:09: #4 Write output xls file... SRX2202917.10_peaks.xls INFO @ Fri, 10 Nov 2017 23:46:09: #4 Write peak in narrowPeak format file... SRX2202917.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 23:46:09: #4 Write summits bed file... SRX2202917.10_summits.bed INFO @ Fri, 10 Nov 2017 23:46:09: Done! pass1 - making usageList (37 chroms): 1 millis pass2 - checking and writing primary data (502 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。