Job ID = 10194925 sra ファイルのダウンロード中... Completed: 167924K bytes transferred in 12 seconds (109543K bits/sec), in 1 file. Completed: 164628K bytes transferred in 14 seconds (92066K bits/sec), in 1 file. Completed: 265754K bytes transferred in 18 seconds (119571K bits/sec), in 1 file. Completed: 262953K bytes transferred in 13 seconds (161111K bits/sec), in 1 file. Completed: 259907K bytes transferred in 14 seconds (147331K bits/sec), in 1 file. Completed: 257268K bytes transferred in 11 seconds (186768K 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 3876821 spots for /home/okishinya/chipatlas/results/rn6/SRX2202920/SRR4320065.sra Written 3876821 spots total Written 3966907 spots for /home/okishinya/chipatlas/results/rn6/SRX2202920/SRR4320064.sra Written 3966907 spots total Written 5643509 spots for /home/okishinya/chipatlas/results/rn6/SRX2202920/SRR4320069.sra Written 5643509 spots total Written 5692523 spots for /home/okishinya/chipatlas/results/rn6/SRX2202920/SRR4320068.sra Written 5692523 spots total Written 5717706 spots for /home/okishinya/chipatlas/results/rn6/SRX2202920/SRR4320067.sra Written 5717706 spots total Written 5820963 spots for /home/okishinya/chipatlas/results/rn6/SRX2202920/SRR4320066.sra Written 5820963 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: 00:38:53 30718429 reads; of these: 30718429 (100.00%) were unpaired; of these: 11024451 (35.89%) aligned 0 times 13883181 (45.19%) aligned exactly 1 time 5810797 (18.92%) aligned >1 times 64.11% overall alignment rate Time searching: 00:38:58 Overall time: 00:38:58 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] 3113322 / 19693978 = 0.1581 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 @ Sat, 11 Nov 2017 00:04:15: # Command line: callpeak -t SRX2202920.bam -f BAM -g 2.15e9 -n SRX2202920.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2202920.10 # format = BAM # ChIP-seq file = ['SRX2202920.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 @ Sat, 11 Nov 2017 00:04:15: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:04:15: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:04:15: # Command line: callpeak -t SRX2202920.bam -f BAM -g 2.15e9 -n SRX2202920.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2202920.05 # format = BAM # ChIP-seq file = ['SRX2202920.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 @ Sat, 11 Nov 2017 00:04:15: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:04:15: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:04:15: # Command line: callpeak -t SRX2202920.bam -f BAM -g 2.15e9 -n SRX2202920.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2202920.20 # format = BAM # ChIP-seq file = ['SRX2202920.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 @ Sat, 11 Nov 2017 00:04:15: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:04:15: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:04:23: 1000000 INFO @ Sat, 11 Nov 2017 00:04:30: 1000000 INFO @ Sat, 11 Nov 2017 00:04:32: 2000000 INFO @ Sat, 11 Nov 2017 00:04:34: 1000000 INFO @ Sat, 11 Nov 2017 00:04:42: 3000000 INFO @ Sat, 11 Nov 2017 00:04:45: 2000000 INFO @ Sat, 11 Nov 2017 00:04:49: 2000000 INFO @ Sat, 11 Nov 2017 00:04:55: 4000000 INFO @ Sat, 11 Nov 2017 00:05:02: 3000000 INFO @ Sat, 11 Nov 2017 00:05:07: 3000000 INFO @ Sat, 11 Nov 2017 00:05:08: 5000000 INFO @ Sat, 11 Nov 2017 00:05:16: 4000000 INFO @ Sat, 11 Nov 2017 00:05:21: 6000000 INFO @ Sat, 11 Nov 2017 00:05:25: 4000000 INFO @ Sat, 11 Nov 2017 00:05:31: 5000000 INFO @ Sat, 11 Nov 2017 00:05:34: 7000000 INFO @ Sat, 11 Nov 2017 00:05:43: 5000000 INFO @ Sat, 11 Nov 2017 00:05:46: 6000000 INFO @ Sat, 11 Nov 2017 00:05:47: 8000000 INFO @ Sat, 11 Nov 2017 00:06:01: 9000000 INFO @ Sat, 11 Nov 2017 00:06:01: 6000000 INFO @ Sat, 11 Nov 2017 00:06:02: 7000000 INFO @ Sat, 11 Nov 2017 00:06:14: 10000000 INFO @ Sat, 11 Nov 2017 00:06:17: 8000000 INFO @ Sat, 11 Nov 2017 00:06:19: 7000000 INFO @ Sat, 11 Nov 2017 00:06:26: 11000000 INFO @ Sat, 11 Nov 2017 00:06:31: 9000000 INFO @ Sat, 11 Nov 2017 00:06:35: 8000000 INFO @ Sat, 11 Nov 2017 00:06:38: 12000000 INFO @ Sat, 11 Nov 2017 00:06:45: 10000000 INFO @ Sat, 11 Nov 2017 00:06:50: 13000000 INFO @ Sat, 11 Nov 2017 00:06:52: 9000000 INFO @ Sat, 11 Nov 2017 00:06:59: 11000000 INFO @ Sat, 11 Nov 2017 00:07:01: 14000000 INFO @ Sat, 11 Nov 2017 00:07:08: 10000000 INFO @ Sat, 11 Nov 2017 00:07:12: 12000000 INFO @ Sat, 11 Nov 2017 00:07:13: 15000000 INFO @ Sat, 11 Nov 2017 00:07:24: 13000000 INFO @ Sat, 11 Nov 2017 00:07:24: 11000000 INFO @ Sat, 11 Nov 2017 00:07:24: 16000000 INFO @ Sat, 11 Nov 2017 00:07:31: #1 tag size is determined as 50 bps INFO @ Sat, 11 Nov 2017 00:07:31: #1 tag size = 50 INFO @ Sat, 11 Nov 2017 00:07:31: #1 total tags in treatment: 16580656 INFO @ Sat, 11 Nov 2017 00:07:31: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:07:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 00:07:32: #1 tags after filtering in treatment: 16580491 INFO @ Sat, 11 Nov 2017 00:07:32: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:07:32: #1 finished! INFO @ Sat, 11 Nov 2017 00:07:32: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:07:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:07:35: #2 number of paired peaks: 24064 INFO @ Sat, 11 Nov 2017 00:07:35: start model_add_line... INFO @ Sat, 11 Nov 2017 00:07:36: start X-correlation... INFO @ Sat, 11 Nov 2017 00:07:36: end of X-cor INFO @ Sat, 11 Nov 2017 00:07:36: #2 finished! INFO @ Sat, 11 Nov 2017 00:07:36: #2 predicted fragment length is 109 bps INFO @ Sat, 11 Nov 2017 00:07:36: #2 alternative fragment length(s) may be 109 bps INFO @ Sat, 11 Nov 2017 00:07:36: #2.2 Generate R script for model : SRX2202920.20_model.r INFO @ Sat, 11 Nov 2017 00:07:36: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:07:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 00:07:37: 14000000 INFO @ Sat, 11 Nov 2017 00:07:39: 12000000 INFO @ Sat, 11 Nov 2017 00:07:49: 15000000 INFO @ Sat, 11 Nov 2017 00:07:54: 13000000 INFO @ Sat, 11 Nov 2017 00:08:01: 16000000 INFO @ Sat, 11 Nov 2017 00:08:08: #1 tag size is determined as 50 bps INFO @ Sat, 11 Nov 2017 00:08:08: #1 tag size = 50 INFO @ Sat, 11 Nov 2017 00:08:08: #1 total tags in treatment: 16580656 INFO @ Sat, 11 Nov 2017 00:08:08: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:08:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 00:08:09: #1 tags after filtering in treatment: 16580491 INFO @ Sat, 11 Nov 2017 00:08:09: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:08:09: #1 finished! INFO @ Sat, 11 Nov 2017 00:08:09: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:08:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:08:10: 14000000 INFO @ Sat, 11 Nov 2017 00:08:12: #2 number of paired peaks: 24064 INFO @ Sat, 11 Nov 2017 00:08:12: start model_add_line... INFO @ Sat, 11 Nov 2017 00:08:12: start X-correlation... INFO @ Sat, 11 Nov 2017 00:08:12: end of X-cor INFO @ Sat, 11 Nov 2017 00:08:12: #2 finished! INFO @ Sat, 11 Nov 2017 00:08:12: #2 predicted fragment length is 109 bps INFO @ Sat, 11 Nov 2017 00:08:12: #2 alternative fragment length(s) may be 109 bps INFO @ Sat, 11 Nov 2017 00:08:12: #2.2 Generate R script for model : SRX2202920.05_model.r INFO @ Sat, 11 Nov 2017 00:08:12: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:08:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 00:08:27: 15000000 INFO @ Sat, 11 Nov 2017 00:08:29: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:08:44: 16000000 INFO @ Sat, 11 Nov 2017 00:08:53: #1 tag size is determined as 50 bps INFO @ Sat, 11 Nov 2017 00:08:53: #1 tag size = 50 INFO @ Sat, 11 Nov 2017 00:08:53: #1 total tags in treatment: 16580656 INFO @ Sat, 11 Nov 2017 00:08:53: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:08:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 00:08:54: #1 tags after filtering in treatment: 16580491 INFO @ Sat, 11 Nov 2017 00:08:54: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:08:54: #1 finished! INFO @ Sat, 11 Nov 2017 00:08:54: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:08:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:08:57: #2 number of paired peaks: 24064 INFO @ Sat, 11 Nov 2017 00:08:57: start model_add_line... INFO @ Sat, 11 Nov 2017 00:08:57: start X-correlation... INFO @ Sat, 11 Nov 2017 00:08:57: end of X-cor INFO @ Sat, 11 Nov 2017 00:08:57: #2 finished! INFO @ Sat, 11 Nov 2017 00:08:57: #2 predicted fragment length is 109 bps INFO @ Sat, 11 Nov 2017 00:08:57: #2 alternative fragment length(s) may be 109 bps INFO @ Sat, 11 Nov 2017 00:08:57: #2.2 Generate R script for model : SRX2202920.10_model.r INFO @ Sat, 11 Nov 2017 00:08:57: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:08:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 00:09:02: #4 Write output xls file... SRX2202920.20_peaks.xls INFO @ Sat, 11 Nov 2017 00:09:02: #4 Write peak in narrowPeak format file... SRX2202920.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:09:02: #4 Write summits bed file... SRX2202920.20_summits.bed INFO @ Sat, 11 Nov 2017 00:09:02: Done! pass1 - making usageList (34 chroms): 1 millis pass2 - checking and writing primary data (415 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 00:09:04: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:09:36: #4 Write output xls file... SRX2202920.05_peaks.xls INFO @ Sat, 11 Nov 2017 00:09:36: #4 Write peak in narrowPeak format file... SRX2202920.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:09:36: #4 Write summits bed file... SRX2202920.05_summits.bed INFO @ Sat, 11 Nov 2017 00:09:36: Done! pass1 - making usageList (69 chroms): 3 millis pass2 - checking and writing primary data (8457 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 00:09:51: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:10:22: #4 Write output xls file... SRX2202920.10_peaks.xls INFO @ Sat, 11 Nov 2017 00:10:22: #4 Write peak in narrowPeak format file... SRX2202920.10_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:10:22: #4 Write summits bed file... SRX2202920.10_summits.bed INFO @ Sat, 11 Nov 2017 00:10:22: Done! pass1 - making usageList (45 chroms): 1 millis pass2 - checking and writing primary data (1741 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。