Job ID = 10194926 sra ファイルのダウンロード中... Completed: 121363K bytes transferred in 9 seconds (102761K bits/sec), in 1 file. Completed: 118906K bytes transferred in 11 seconds (82392K bits/sec), in 1 file. Completed: 199681K bytes transferred in 11 seconds (137468K bits/sec), in 1 file. Completed: 196222K bytes transferred in 14 seconds (110392K bits/sec), in 1 file. Completed: 196944K bytes transferred in 11 seconds (140906K bits/sec), in 1 file. Completed: 194249K bytes transferred in 9 seconds (161911K 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 2824168 spots for /home/okishinya/chipatlas/results/rn6/SRX2202921/SRR4320070.sra Written 2824168 spots total Written 2755479 spots for /home/okishinya/chipatlas/results/rn6/SRX2202921/SRR4320071.sra Written 2755479 spots total Written 4198756 spots for /home/okishinya/chipatlas/results/rn6/SRX2202921/SRR4320075.sra Written 4198756 spots total Written 4205192 spots for /home/okishinya/chipatlas/results/rn6/SRX2202921/SRR4320073.sra Written 4205192 spots total Written 4248382 spots for /home/okishinya/chipatlas/results/rn6/SRX2202921/SRR4320074.sra Written 4248382 spots total Written 4307432 spots for /home/okishinya/chipatlas/results/rn6/SRX2202921/SRR4320072.sra Written 4307432 spots total rm: cannot remove `[DSE]RX*': No such file or directory 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: 00:00:02 Multiseed full-index search: 00:29:03 22539409 reads; of these: 22539409 (100.00%) were unpaired; of these: 1054229 (4.68%) aligned 0 times 15626195 (69.33%) aligned exactly 1 time 5858985 (25.99%) aligned >1 times 95.32% overall alignment rate Time searching: 00:29:07 Overall time: 00:29:07 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] 3975483 / 21485180 = 0.1850 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 23:55:49: # Command line: callpeak -t SRX2202921.bam -f BAM -g 2.15e9 -n SRX2202921.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2202921.05 # format = BAM # ChIP-seq file = ['SRX2202921.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 23:55:49: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:55:49: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:55:49: # Command line: callpeak -t SRX2202921.bam -f BAM -g 2.15e9 -n SRX2202921.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2202921.10 # format = BAM # ChIP-seq file = ['SRX2202921.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 23:55:49: # Command line: callpeak -t SRX2202921.bam -f BAM -g 2.15e9 -n SRX2202921.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2202921.20 # format = BAM # ChIP-seq file = ['SRX2202921.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 23:55:49: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:55:49: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:55:49: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:55:49: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:55:57: 1000000 INFO @ Fri, 10 Nov 2017 23:55:59: 1000000 INFO @ Fri, 10 Nov 2017 23:56:00: 1000000 INFO @ Fri, 10 Nov 2017 23:56:04: 2000000 INFO @ Fri, 10 Nov 2017 23:56:09: 2000000 INFO @ Fri, 10 Nov 2017 23:56:09: 2000000 INFO @ Fri, 10 Nov 2017 23:56:12: 3000000 INFO @ Fri, 10 Nov 2017 23:56:18: 3000000 INFO @ Fri, 10 Nov 2017 23:56:18: 3000000 INFO @ Fri, 10 Nov 2017 23:56:19: 4000000 INFO @ Fri, 10 Nov 2017 23:56:26: 5000000 INFO @ Fri, 10 Nov 2017 23:56:27: 4000000 INFO @ Fri, 10 Nov 2017 23:56:28: 4000000 INFO @ Fri, 10 Nov 2017 23:56:34: 6000000 INFO @ Fri, 10 Nov 2017 23:56:35: 5000000 INFO @ Fri, 10 Nov 2017 23:56:37: 5000000 INFO @ Fri, 10 Nov 2017 23:56:42: 7000000 INFO @ Fri, 10 Nov 2017 23:56:43: 6000000 INFO @ Fri, 10 Nov 2017 23:56:46: 6000000 INFO @ Fri, 10 Nov 2017 23:56:51: 7000000 INFO @ Fri, 10 Nov 2017 23:56:52: 8000000 INFO @ Fri, 10 Nov 2017 23:56:57: 7000000 INFO @ Fri, 10 Nov 2017 23:57:01: 8000000 INFO @ Fri, 10 Nov 2017 23:57:02: 9000000 INFO @ Fri, 10 Nov 2017 23:57:09: 8000000 INFO @ Fri, 10 Nov 2017 23:57:10: 9000000 INFO @ Fri, 10 Nov 2017 23:57:12: 10000000 INFO @ Fri, 10 Nov 2017 23:57:20: 10000000 INFO @ Fri, 10 Nov 2017 23:57:22: 9000000 INFO @ Fri, 10 Nov 2017 23:57:23: 11000000 INFO @ Fri, 10 Nov 2017 23:57:30: 11000000 INFO @ Fri, 10 Nov 2017 23:57:33: 12000000 INFO @ Fri, 10 Nov 2017 23:57:35: 10000000 INFO @ Fri, 10 Nov 2017 23:57:39: 12000000 INFO @ Fri, 10 Nov 2017 23:57:43: 13000000 INFO @ Fri, 10 Nov 2017 23:57:48: 11000000 INFO @ Fri, 10 Nov 2017 23:57:50: 13000000 INFO @ Fri, 10 Nov 2017 23:57:54: 14000000 INFO @ Fri, 10 Nov 2017 23:58:00: 14000000 INFO @ Fri, 10 Nov 2017 23:58:00: 12000000 INFO @ Fri, 10 Nov 2017 23:58:05: 15000000 INFO @ Fri, 10 Nov 2017 23:58:10: 15000000 INFO @ Fri, 10 Nov 2017 23:58:12: 13000000 INFO @ Fri, 10 Nov 2017 23:58:16: 16000000 INFO @ Fri, 10 Nov 2017 23:58:20: 16000000 INFO @ Fri, 10 Nov 2017 23:58:25: 14000000 INFO @ Fri, 10 Nov 2017 23:58:26: 17000000 INFO @ Fri, 10 Nov 2017 23:58:30: 17000000 INFO @ Fri, 10 Nov 2017 23:58:32: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 23:58:32: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 23:58:32: #1 total tags in treatment: 17509697 INFO @ Fri, 10 Nov 2017 23:58:32: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 23:58:32: #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 23:58:33: #1 tags after filtering in treatment: 17509516 INFO @ Fri, 10 Nov 2017 23:58:33: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 23:58:33: #1 finished! INFO @ Fri, 10 Nov 2017 23:58:33: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 23:58:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 23:58:35: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 23:58:35: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 23:58:35: #1 total tags in treatment: 17509697 INFO @ Fri, 10 Nov 2017 23:58:35: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 23:58:35: #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 23:58:36: #1 tags after filtering in treatment: 17509516 INFO @ Fri, 10 Nov 2017 23:58:36: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 23:58:36: #1 finished! INFO @ Fri, 10 Nov 2017 23:58:36: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 23:58:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 23:58:37: 15000000 INFO @ Fri, 10 Nov 2017 23:58:37: #2 number of paired peaks: 40818 INFO @ Fri, 10 Nov 2017 23:58:37: start model_add_line... INFO @ Fri, 10 Nov 2017 23:58:37: start X-correlation... INFO @ Fri, 10 Nov 2017 23:58:37: end of X-cor INFO @ Fri, 10 Nov 2017 23:58:37: #2 finished! INFO @ Fri, 10 Nov 2017 23:58:37: #2 predicted fragment length is 128 bps INFO @ Fri, 10 Nov 2017 23:58:37: #2 alternative fragment length(s) may be 128 bps INFO @ Fri, 10 Nov 2017 23:58:37: #2.2 Generate R script for model : SRX2202921.05_model.r INFO @ Fri, 10 Nov 2017 23:58:37: #3 Call peaks... INFO @ Fri, 10 Nov 2017 23:58:37: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 23:58:40: #2 number of paired peaks: 40818 INFO @ Fri, 10 Nov 2017 23:58:40: start model_add_line... INFO @ Fri, 10 Nov 2017 23:58:40: start X-correlation... INFO @ Fri, 10 Nov 2017 23:58:40: end of X-cor INFO @ Fri, 10 Nov 2017 23:58:40: #2 finished! INFO @ Fri, 10 Nov 2017 23:58:40: #2 predicted fragment length is 128 bps INFO @ Fri, 10 Nov 2017 23:58:40: #2 alternative fragment length(s) may be 128 bps INFO @ Fri, 10 Nov 2017 23:58:40: #2.2 Generate R script for model : SRX2202921.20_model.r INFO @ Fri, 10 Nov 2017 23:58:40: #3 Call peaks... INFO @ Fri, 10 Nov 2017 23:58:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 23:58:48: 16000000 INFO @ Fri, 10 Nov 2017 23:59:01: 17000000 INFO @ Fri, 10 Nov 2017 23:59:07: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 23:59:07: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 23:59:07: #1 total tags in treatment: 17509697 INFO @ Fri, 10 Nov 2017 23:59:07: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 23:59:07: #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 23:59:07: #1 tags after filtering in treatment: 17509516 INFO @ Fri, 10 Nov 2017 23:59:07: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 23:59:07: #1 finished! INFO @ Fri, 10 Nov 2017 23:59:07: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 23:59:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 23:59:11: #2 number of paired peaks: 40818 INFO @ Fri, 10 Nov 2017 23:59:11: start model_add_line... INFO @ Fri, 10 Nov 2017 23:59:12: start X-correlation... INFO @ Fri, 10 Nov 2017 23:59:12: end of X-cor INFO @ Fri, 10 Nov 2017 23:59:12: #2 finished! INFO @ Fri, 10 Nov 2017 23:59:12: #2 predicted fragment length is 128 bps INFO @ Fri, 10 Nov 2017 23:59:12: #2 alternative fragment length(s) may be 128 bps INFO @ Fri, 10 Nov 2017 23:59:12: #2.2 Generate R script for model : SRX2202921.10_model.r INFO @ Fri, 10 Nov 2017 23:59:12: #3 Call peaks... INFO @ Fri, 10 Nov 2017 23:59:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 23:59:28: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 23:59:31: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:00:02: #4 Write output xls file... SRX2202921.05_peaks.xls INFO @ Sat, 11 Nov 2017 00:00:03: #4 Write peak in narrowPeak format file... SRX2202921.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:00:03: #4 Write summits bed file... SRX2202921.05_summits.bed INFO @ Sat, 11 Nov 2017 00:00:03: Done! pass1 - making usageList (114 chroms): 7 millis pass2 - checking and writing primary data (27433 records, 4 fields): 50 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 00:00:04: #4 Write output xls file... SRX2202921.20_peaks.xls INFO @ Sat, 11 Nov 2017 00:00:04: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:00:04: #4 Write peak in narrowPeak format file... SRX2202921.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:00:04: #4 Write summits bed file... SRX2202921.20_summits.bed INFO @ Sat, 11 Nov 2017 00:00:05: Done! pass1 - making usageList (83 chroms): 6 millis pass2 - checking and writing primary data (15129 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 00:00:39: #4 Write output xls file... SRX2202921.10_peaks.xls INFO @ Sat, 11 Nov 2017 00:00:40: #4 Write peak in narrowPeak format file... SRX2202921.10_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:00:40: #4 Write summits bed file... SRX2202921.10_summits.bed INFO @ Sat, 11 Nov 2017 00:00:40: Done! pass1 - making usageList (100 chroms): 6 millis pass2 - checking and writing primary data (21500 records, 4 fields): 41 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。