Job ID = 10194916 sra ファイルのダウンロード中... Completed: 128666K bytes transferred in 10 seconds (100445K bits/sec), in 1 file. Completed: 217283K bytes transferred in 16 seconds (107112K bits/sec), in 1 file. Completed: 213367K bytes transferred in 9 seconds (187545K bits/sec), in 1 file. Completed: 213434K bytes transferred in 10 seconds (160477K bits/sec), in 1 file. Completed: 210431K bytes transferred in 15 seconds (113011K bits/sec), in 1 file. Completed: 131750K bytes transferred in 8 seconds (129883K 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 3011575 spots for /home/okishinya/chipatlas/results/rn6/SRX2202911/SRR4320011.sra Written 3011575 spots total Written 3096803 spots for /home/okishinya/chipatlas/results/rn6/SRX2202911/SRR4320010.sra Written 3096803 spots total Written 4588228 spots for /home/okishinya/chipatlas/results/rn6/SRX2202911/SRR4320015.sra Written 4588228 spots total Written 4612195 spots for /home/okishinya/chipatlas/results/rn6/SRX2202911/SRR4320013.sra Written 4612195 spots total Written 4644576 spots for /home/okishinya/chipatlas/results/rn6/SRX2202911/SRR4320014.sra Written 4644576 spots total Written 4727617 spots for /home/okishinya/chipatlas/results/rn6/SRX2202911/SRR4320012.sra Written 4727617 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: 00:47:46 24680994 reads; of these: 24680994 (100.00%) were unpaired; of these: 1459691 (5.91%) aligned 0 times 15796687 (64.00%) aligned exactly 1 time 7424616 (30.08%) aligned >1 times 94.09% overall alignment rate Time searching: 00:47:50 Overall time: 00:47:50 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 12 files... [bam_rmdupse_core] 3401164 / 23221303 = 0.1465 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 23:43:40: # Command line: callpeak -t SRX2202911.bam -f BAM -g 2.15e9 -n SRX2202911.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2202911.10 # format = BAM # ChIP-seq file = ['SRX2202911.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 23:43:40: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:43:40: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:43:40: # Command line: callpeak -t SRX2202911.bam -f BAM -g 2.15e9 -n SRX2202911.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2202911.20 # format = BAM # ChIP-seq file = ['SRX2202911.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 23:43:40: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:43:40: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:43:40: # Command line: callpeak -t SRX2202911.bam -f BAM -g 2.15e9 -n SRX2202911.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2202911.05 # format = BAM # ChIP-seq file = ['SRX2202911.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 23:43:40: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:43:40: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:43:58: 1000000 INFO @ Fri, 10 Nov 2017 23:44:01: 1000000 INFO @ Fri, 10 Nov 2017 23:44:03: 1000000 INFO @ Fri, 10 Nov 2017 23:44:16: 2000000 INFO @ Fri, 10 Nov 2017 23:44:24: 2000000 INFO @ Fri, 10 Nov 2017 23:44:25: 2000000 INFO @ Fri, 10 Nov 2017 23:44:33: 3000000 INFO @ Fri, 10 Nov 2017 23:44:46: 3000000 INFO @ Fri, 10 Nov 2017 23:44:50: 3000000 INFO @ Fri, 10 Nov 2017 23:44:51: 4000000 INFO @ Fri, 10 Nov 2017 23:45:07: 4000000 INFO @ Fri, 10 Nov 2017 23:45:08: 5000000 INFO @ Fri, 10 Nov 2017 23:45:16: 4000000 INFO @ Fri, 10 Nov 2017 23:45:26: 6000000 INFO @ Fri, 10 Nov 2017 23:45:28: 5000000 INFO @ Fri, 10 Nov 2017 23:45:39: 5000000 INFO @ Fri, 10 Nov 2017 23:45:43: 7000000 INFO @ Fri, 10 Nov 2017 23:45:50: 6000000 INFO @ Fri, 10 Nov 2017 23:46:00: 8000000 INFO @ Fri, 10 Nov 2017 23:46:01: 6000000 INFO @ Fri, 10 Nov 2017 23:46:14: 7000000 INFO @ Fri, 10 Nov 2017 23:46:18: 9000000 INFO @ Fri, 10 Nov 2017 23:46:24: 7000000 INFO @ Fri, 10 Nov 2017 23:46:36: 10000000 INFO @ Fri, 10 Nov 2017 23:46:36: 8000000 INFO @ Fri, 10 Nov 2017 23:46:46: 8000000 INFO @ Fri, 10 Nov 2017 23:46:54: 11000000 INFO @ Fri, 10 Nov 2017 23:46:59: 9000000 INFO @ Fri, 10 Nov 2017 23:47:07: 9000000 INFO @ Fri, 10 Nov 2017 23:47:09: 12000000 INFO @ Fri, 10 Nov 2017 23:47:23: 10000000 INFO @ Fri, 10 Nov 2017 23:47:23: 13000000 INFO @ Fri, 10 Nov 2017 23:47:28: 10000000 INFO @ Fri, 10 Nov 2017 23:47:38: 14000000 INFO @ Fri, 10 Nov 2017 23:47:47: 11000000 INFO @ Fri, 10 Nov 2017 23:47:52: 15000000 INFO @ Fri, 10 Nov 2017 23:47:52: 11000000 INFO @ Fri, 10 Nov 2017 23:48:06: 16000000 INFO @ Fri, 10 Nov 2017 23:48:09: 12000000 INFO @ Fri, 10 Nov 2017 23:48:15: 12000000 INFO @ Fri, 10 Nov 2017 23:48:19: 17000000 INFO @ Fri, 10 Nov 2017 23:48:28: 13000000 INFO @ Fri, 10 Nov 2017 23:48:33: 18000000 INFO @ Fri, 10 Nov 2017 23:48:37: 13000000 INFO @ Fri, 10 Nov 2017 23:48:47: 19000000 INFO @ Fri, 10 Nov 2017 23:48:47: 14000000 INFO @ Fri, 10 Nov 2017 23:48:57: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 23:48:57: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 23:48:57: #1 total tags in treatment: 19820139 INFO @ Fri, 10 Nov 2017 23:48:57: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 23:48:57: #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 23:48:58: #1 tags after filtering in treatment: 19820008 INFO @ Fri, 10 Nov 2017 23:48:58: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 23:48:58: #1 finished! INFO @ Fri, 10 Nov 2017 23:48:58: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 23:48:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 23:48:59: 14000000 INFO @ Fri, 10 Nov 2017 23:49:03: #2 number of paired peaks: 40069 INFO @ Fri, 10 Nov 2017 23:49:03: start model_add_line... INFO @ Fri, 10 Nov 2017 23:49:03: start X-correlation... INFO @ Fri, 10 Nov 2017 23:49:03: end of X-cor INFO @ Fri, 10 Nov 2017 23:49:03: #2 finished! INFO @ Fri, 10 Nov 2017 23:49:03: #2 predicted fragment length is 132 bps INFO @ Fri, 10 Nov 2017 23:49:03: #2 alternative fragment length(s) may be 132 bps INFO @ Fri, 10 Nov 2017 23:49:03: #2.2 Generate R script for model : SRX2202911.10_model.r INFO @ Fri, 10 Nov 2017 23:49:03: #3 Call peaks... INFO @ Fri, 10 Nov 2017 23:49:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 23:49:05: 15000000 INFO @ Fri, 10 Nov 2017 23:49:23: 15000000 INFO @ Fri, 10 Nov 2017 23:49:27: 16000000 INFO @ Fri, 10 Nov 2017 23:49:47: 16000000 INFO @ Fri, 10 Nov 2017 23:49:49: 17000000 INFO @ Fri, 10 Nov 2017 23:50:11: 17000000 INFO @ Fri, 10 Nov 2017 23:50:12: 18000000 INFO @ Fri, 10 Nov 2017 23:50:19: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 23:50:33: 18000000 INFO @ Fri, 10 Nov 2017 23:50:36: 19000000 INFO @ Fri, 10 Nov 2017 23:50:57: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 23:50:57: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 23:50:57: #1 total tags in treatment: 19820139 INFO @ Fri, 10 Nov 2017 23:50:57: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 23:50:57: #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 23:50:57: 19000000 INFO @ Fri, 10 Nov 2017 23:50:58: #1 tags after filtering in treatment: 19820008 INFO @ Fri, 10 Nov 2017 23:50:58: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 23:50:58: #1 finished! INFO @ Fri, 10 Nov 2017 23:50:58: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 23:50:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 23:51:02: #2 number of paired peaks: 40069 INFO @ Fri, 10 Nov 2017 23:51:02: start model_add_line... INFO @ Fri, 10 Nov 2017 23:51:03: start X-correlation... INFO @ Fri, 10 Nov 2017 23:51:03: end of X-cor INFO @ Fri, 10 Nov 2017 23:51:03: #2 finished! INFO @ Fri, 10 Nov 2017 23:51:03: #2 predicted fragment length is 132 bps INFO @ Fri, 10 Nov 2017 23:51:03: #2 alternative fragment length(s) may be 132 bps INFO @ Fri, 10 Nov 2017 23:51:03: #2.2 Generate R script for model : SRX2202911.05_model.r INFO @ Fri, 10 Nov 2017 23:51:03: #3 Call peaks... INFO @ Fri, 10 Nov 2017 23:51:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 23:51:07: #4 Write output xls file... SRX2202911.10_peaks.xls INFO @ Fri, 10 Nov 2017 23:51:07: #4 Write peak in narrowPeak format file... SRX2202911.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 23:51:07: #4 Write summits bed file... SRX2202911.10_summits.bed INFO @ Fri, 10 Nov 2017 23:51:07: Done! pass1 - making usageList (83 chroms): 6 millis pass2 - checking and writing primary data (13972 records, 4 fields): 31 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 23:51:17: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 23:51:17: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 23:51:17: #1 total tags in treatment: 19820139 INFO @ Fri, 10 Nov 2017 23:51:17: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 23:51:17: #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 23:51:18: #1 tags after filtering in treatment: 19820008 INFO @ Fri, 10 Nov 2017 23:51:18: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 23:51:18: #1 finished! INFO @ Fri, 10 Nov 2017 23:51:18: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 23:51:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 23:51:22: #2 number of paired peaks: 40069 INFO @ Fri, 10 Nov 2017 23:51:22: start model_add_line... INFO @ Fri, 10 Nov 2017 23:51:23: start X-correlation... INFO @ Fri, 10 Nov 2017 23:51:23: end of X-cor INFO @ Fri, 10 Nov 2017 23:51:23: #2 finished! INFO @ Fri, 10 Nov 2017 23:51:23: #2 predicted fragment length is 132 bps INFO @ Fri, 10 Nov 2017 23:51:23: #2 alternative fragment length(s) may be 132 bps INFO @ Fri, 10 Nov 2017 23:51:23: #2.2 Generate R script for model : SRX2202911.20_model.r INFO @ Fri, 10 Nov 2017 23:51:23: #3 Call peaks... INFO @ Fri, 10 Nov 2017 23:51:23: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 23:52:09: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 23:52:29: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 23:52:49: #4 Write output xls file... SRX2202911.05_peaks.xls INFO @ Fri, 10 Nov 2017 23:52:50: #4 Write peak in narrowPeak format file... SRX2202911.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 23:52:50: #4 Write summits bed file... SRX2202911.05_summits.bed INFO @ Fri, 10 Nov 2017 23:52:50: Done! pass1 - making usageList (112 chroms): 7 millis pass2 - checking and writing primary data (21425 records, 4 fields): 44 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 23:53:09: #4 Write output xls file... SRX2202911.20_peaks.xls INFO @ Fri, 10 Nov 2017 23:53:09: #4 Write peak in narrowPeak format file... SRX2202911.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 23:53:09: #4 Write summits bed file... SRX2202911.20_summits.bed INFO @ Fri, 10 Nov 2017 23:53:09: Done! pass1 - making usageList (52 chroms): 3 millis pass2 - checking and writing primary data (5693 records, 4 fields): 15 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。