Job ID = 10194917 sra ファイルのダウンロード中... Completed: 104426K bytes transferred in 7 seconds (107244K bits/sec), in 1 file. Completed: 102132K bytes transferred in 8 seconds (102441K bits/sec), in 1 file. Completed: 171053K bytes transferred in 12 seconds (110711K bits/sec), in 1 file. Completed: 168228K bytes transferred in 10 seconds (126851K bits/sec), in 1 file. Completed: 167814K bytes transferred in 12 seconds (113492K bits/sec), in 1 file. Completed: 165499K bytes transferred in 7 seconds (186558K 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 2371646 spots for /home/okishinya/chipatlas/results/rn6/SRX2202912/SRR4320017.sra Written 2371646 spots total Written 2434889 spots for /home/okishinya/chipatlas/results/rn6/SRX2202912/SRR4320016.sra Written 2434889 spots total Written 3586055 spots for /home/okishinya/chipatlas/results/rn6/SRX2202912/SRR4320021.sra Written 3586055 spots total Written 3615388 spots for /home/okishinya/chipatlas/results/rn6/SRX2202912/SRR4320019.sra Written 3615388 spots total Written 3629657 spots for /home/okishinya/chipatlas/results/rn6/SRX2202912/SRR4320020.sra Written 3629657 spots total Written 3698695 spots for /home/okishinya/chipatlas/results/rn6/SRX2202912/SRR4320018.sra Written 3698695 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: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:40:13 19336330 reads; of these: 19336330 (100.00%) were unpaired; of these: 712400 (3.68%) aligned 0 times 13089639 (67.69%) aligned exactly 1 time 5534291 (28.62%) aligned >1 times 96.32% overall alignment rate Time searching: 00:40:16 Overall time: 00:40:16 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] 1661783 / 18623930 = 0.0892 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 23:41:30: # Command line: callpeak -t SRX2202912.bam -f BAM -g 2.15e9 -n SRX2202912.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2202912.05 # format = BAM # ChIP-seq file = ['SRX2202912.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 23:41:30: # Command line: callpeak -t SRX2202912.bam -f BAM -g 2.15e9 -n SRX2202912.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2202912.20 # format = BAM # ChIP-seq file = ['SRX2202912.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 23:41:30: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:41:30: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:41:30: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:41:30: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:41:30: # Command line: callpeak -t SRX2202912.bam -f BAM -g 2.15e9 -n SRX2202912.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2202912.10 # format = BAM # ChIP-seq file = ['SRX2202912.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 23:41:30: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:41:30: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:41:44: 1000000 INFO @ Fri, 10 Nov 2017 23:41:46: 1000000 INFO @ Fri, 10 Nov 2017 23:41:46: 1000000 INFO @ Fri, 10 Nov 2017 23:41:59: 2000000 INFO @ Fri, 10 Nov 2017 23:42:02: 2000000 INFO @ Fri, 10 Nov 2017 23:42:02: 2000000 INFO @ Fri, 10 Nov 2017 23:42:15: 3000000 INFO @ Fri, 10 Nov 2017 23:42:16: 3000000 INFO @ Fri, 10 Nov 2017 23:42:18: 3000000 INFO @ Fri, 10 Nov 2017 23:42:29: 4000000 INFO @ Fri, 10 Nov 2017 23:42:31: 4000000 INFO @ Fri, 10 Nov 2017 23:42:37: 4000000 INFO @ Fri, 10 Nov 2017 23:42:45: 5000000 INFO @ Fri, 10 Nov 2017 23:42:46: 5000000 INFO @ Fri, 10 Nov 2017 23:42:55: 5000000 INFO @ Fri, 10 Nov 2017 23:43:00: 6000000 INFO @ Fri, 10 Nov 2017 23:43:01: 6000000 INFO @ Fri, 10 Nov 2017 23:43:14: 6000000 INFO @ Fri, 10 Nov 2017 23:43:14: 7000000 INFO @ Fri, 10 Nov 2017 23:43:15: 7000000 INFO @ Fri, 10 Nov 2017 23:43:28: 8000000 INFO @ Fri, 10 Nov 2017 23:43:29: 8000000 INFO @ Fri, 10 Nov 2017 23:43:33: 7000000 INFO @ Fri, 10 Nov 2017 23:43:42: 9000000 INFO @ Fri, 10 Nov 2017 23:43:46: 9000000 INFO @ Fri, 10 Nov 2017 23:43:51: 8000000 INFO @ Fri, 10 Nov 2017 23:43:56: 10000000 INFO @ Fri, 10 Nov 2017 23:44:03: 10000000 INFO @ Fri, 10 Nov 2017 23:44:10: 9000000 INFO @ Fri, 10 Nov 2017 23:44:11: 11000000 INFO @ Fri, 10 Nov 2017 23:44:20: 11000000 INFO @ Fri, 10 Nov 2017 23:44:25: 12000000 INFO @ Fri, 10 Nov 2017 23:44:29: 10000000 INFO @ Fri, 10 Nov 2017 23:44:36: 12000000 INFO @ Fri, 10 Nov 2017 23:44:40: 13000000 INFO @ Fri, 10 Nov 2017 23:44:47: 11000000 INFO @ Fri, 10 Nov 2017 23:44:52: 13000000 INFO @ Fri, 10 Nov 2017 23:44:56: 14000000 INFO @ Fri, 10 Nov 2017 23:45:06: 12000000 INFO @ Fri, 10 Nov 2017 23:45:09: 14000000 INFO @ Fri, 10 Nov 2017 23:45:11: 15000000 INFO @ Fri, 10 Nov 2017 23:45:25: 13000000 INFO @ Fri, 10 Nov 2017 23:45:26: 15000000 INFO @ Fri, 10 Nov 2017 23:45:27: 16000000 INFO @ Fri, 10 Nov 2017 23:45:43: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 23:45:43: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 23:45:43: #1 total tags in treatment: 16962147 INFO @ Fri, 10 Nov 2017 23:45:43: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 23:45:43: #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 23:45:43: #1 tags after filtering in treatment: 16961987 INFO @ Fri, 10 Nov 2017 23:45:43: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 23:45:43: #1 finished! INFO @ Fri, 10 Nov 2017 23:45:43: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 23:45:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 23:45:44: 14000000 INFO @ Fri, 10 Nov 2017 23:45:47: 16000000 INFO @ Fri, 10 Nov 2017 23:45:47: #2 number of paired peaks: 33362 INFO @ Fri, 10 Nov 2017 23:45:47: start model_add_line... INFO @ Fri, 10 Nov 2017 23:45:47: start X-correlation... INFO @ Fri, 10 Nov 2017 23:45:47: end of X-cor INFO @ Fri, 10 Nov 2017 23:45:47: #2 finished! INFO @ Fri, 10 Nov 2017 23:45:47: #2 predicted fragment length is 125 bps INFO @ Fri, 10 Nov 2017 23:45:47: #2 alternative fragment length(s) may be 125 bps INFO @ Fri, 10 Nov 2017 23:45:47: #2.2 Generate R script for model : SRX2202912.05_model.r INFO @ Fri, 10 Nov 2017 23:45:47: #3 Call peaks... INFO @ Fri, 10 Nov 2017 23:45:47: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 23:46:04: 15000000 INFO @ Fri, 10 Nov 2017 23:46:08: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 23:46:08: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 23:46:08: #1 total tags in treatment: 16962147 INFO @ Fri, 10 Nov 2017 23:46:08: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 23:46:08: #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 23:46:09: #1 tags after filtering in treatment: 16961987 INFO @ Fri, 10 Nov 2017 23:46:09: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 23:46:09: #1 finished! INFO @ Fri, 10 Nov 2017 23:46:09: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 23:46:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 23:46:12: #2 number of paired peaks: 33362 INFO @ Fri, 10 Nov 2017 23:46:12: start model_add_line... INFO @ Fri, 10 Nov 2017 23:46:13: start X-correlation... INFO @ Fri, 10 Nov 2017 23:46:13: end of X-cor INFO @ Fri, 10 Nov 2017 23:46:13: #2 finished! INFO @ Fri, 10 Nov 2017 23:46:13: #2 predicted fragment length is 125 bps INFO @ Fri, 10 Nov 2017 23:46:13: #2 alternative fragment length(s) may be 125 bps INFO @ Fri, 10 Nov 2017 23:46:13: #2.2 Generate R script for model : SRX2202912.20_model.r INFO @ Fri, 10 Nov 2017 23:46:13: #3 Call peaks... INFO @ Fri, 10 Nov 2017 23:46:13: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 23:46:23: 16000000 INFO @ Fri, 10 Nov 2017 23:46:41: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 23:46:43: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 23:46:43: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 23:46:43: #1 total tags in treatment: 16962147 INFO @ Fri, 10 Nov 2017 23:46:43: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 23:46:43: #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 23:46:43: #1 tags after filtering in treatment: 16961987 INFO @ Fri, 10 Nov 2017 23:46:43: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 23:46:43: #1 finished! INFO @ Fri, 10 Nov 2017 23:46:43: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 23:46:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 23:46:47: #2 number of paired peaks: 33362 INFO @ Fri, 10 Nov 2017 23:46:47: start model_add_line... INFO @ Fri, 10 Nov 2017 23:46:47: start X-correlation... INFO @ Fri, 10 Nov 2017 23:46:47: end of X-cor INFO @ Fri, 10 Nov 2017 23:46:47: #2 finished! INFO @ Fri, 10 Nov 2017 23:46:47: #2 predicted fragment length is 125 bps INFO @ Fri, 10 Nov 2017 23:46:47: #2 alternative fragment length(s) may be 125 bps INFO @ Fri, 10 Nov 2017 23:46:47: #2.2 Generate R script for model : SRX2202912.10_model.r INFO @ Fri, 10 Nov 2017 23:46:47: #3 Call peaks... INFO @ Fri, 10 Nov 2017 23:46:47: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 23:47:07: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 23:47:15: #4 Write output xls file... SRX2202912.05_peaks.xls INFO @ Fri, 10 Nov 2017 23:47:15: #4 Write peak in narrowPeak format file... SRX2202912.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 23:47:15: #4 Write summits bed file... SRX2202912.05_summits.bed INFO @ Fri, 10 Nov 2017 23:47:15: Done! pass1 - making usageList (88 chroms): 6 millis pass2 - checking and writing primary data (17357 records, 4 fields): 35 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 23:47:42: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 23:47:45: #4 Write output xls file... SRX2202912.20_peaks.xls INFO @ Fri, 10 Nov 2017 23:47:45: #4 Write peak in narrowPeak format file... SRX2202912.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 23:47:45: #4 Write summits bed file... SRX2202912.20_summits.bed INFO @ Fri, 10 Nov 2017 23:47:45: Done! pass1 - making usageList (40 chroms): 2 millis pass2 - checking and writing primary data (1904 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 23:48:15: #4 Write output xls file... SRX2202912.10_peaks.xls INFO @ Fri, 10 Nov 2017 23:48:15: #4 Write peak in narrowPeak format file... SRX2202912.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 23:48:15: #4 Write summits bed file... SRX2202912.10_summits.bed INFO @ Fri, 10 Nov 2017 23:48:15: Done! pass1 - making usageList (62 chroms): 4 millis pass2 - checking and writing primary data (9461 records, 4 fields): 21 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。