Job ID = 10194869 sra ファイルのダウンロード中... Completed: 144645K bytes transferred in 6 seconds (182375K bits/sec), in 1 file. Completed: 145549K bytes transferred in 7 seconds (164191K bits/sec), in 1 file. Completed: 137379K bytes transferred in 6 seconds (164458K bits/sec), in 1 file. Completed: 135464K bytes transferred in 6 seconds (178485K bits/sec), in 1 file. Completed: 164568K bytes transferred in 5 seconds (233798K bits/sec), in 1 file. Completed: 166934K bytes transferred in 7 seconds (193269K 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 3096672 spots for /home/okishinya/chipatlas/results/rn6/SRX2202865/SRR4319736.sra Written 3096672 spots total Written 3060310 spots for /home/okishinya/chipatlas/results/rn6/SRX2202865/SRR4319737.sra Written 3060310 spots total Written 3256746 spots for /home/okishinya/chipatlas/results/rn6/SRX2202865/SRR4319735.sra Written 3247551 spots for /home/okishinya/chipatlas/results/rn6/SRX2202865/SRR4319734.sra Written 3256746 spots total Written 3247551 spots total Written 3611597 spots for /home/okishinya/chipatlas/results/rn6/SRX2202865/SRR4319738.sra Written 3611597 spots total Written 3648226 spots for /home/okishinya/chipatlas/results/rn6/SRX2202865/SRR4319739.sra Written 3648226 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: 00:00:00 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:14:38 19921102 reads; of these: 19921102 (100.00%) were unpaired; of these: 925749 (4.65%) aligned 0 times 14518163 (72.88%) aligned exactly 1 time 4477190 (22.47%) aligned >1 times 95.35% overall alignment rate Time searching: 00:14:40 Overall time: 00:14:40 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] 2206980 / 18995353 = 0.1162 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 17:38:09: # Command line: callpeak -t SRX2202865.bam -f BAM -g 2.15e9 -n SRX2202865.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2202865.10 # format = BAM # ChIP-seq file = ['SRX2202865.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 17:38:09: # Command line: callpeak -t SRX2202865.bam -f BAM -g 2.15e9 -n SRX2202865.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2202865.20 # format = BAM # ChIP-seq file = ['SRX2202865.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 17:38:09: # Command line: callpeak -t SRX2202865.bam -f BAM -g 2.15e9 -n SRX2202865.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2202865.05 # format = BAM # ChIP-seq file = ['SRX2202865.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 17:38:09: #1 read tag files... INFO @ Fri, 10 Nov 2017 17:38:09: #1 read tag files... INFO @ Fri, 10 Nov 2017 17:38:09: #1 read tag files... INFO @ Fri, 10 Nov 2017 17:38:09: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 17:38:09: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 17:38:09: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 17:38:17: 1000000 INFO @ Fri, 10 Nov 2017 17:38:17: 1000000 INFO @ Fri, 10 Nov 2017 17:38:17: 1000000 INFO @ Fri, 10 Nov 2017 17:38:24: 2000000 INFO @ Fri, 10 Nov 2017 17:38:25: 2000000 INFO @ Fri, 10 Nov 2017 17:38:25: 2000000 INFO @ Fri, 10 Nov 2017 17:38:30: 3000000 INFO @ Fri, 10 Nov 2017 17:38:32: 3000000 INFO @ Fri, 10 Nov 2017 17:38:32: 3000000 INFO @ Fri, 10 Nov 2017 17:38:37: 4000000 INFO @ Fri, 10 Nov 2017 17:38:40: 4000000 INFO @ Fri, 10 Nov 2017 17:38:40: 4000000 INFO @ Fri, 10 Nov 2017 17:38:44: 5000000 INFO @ Fri, 10 Nov 2017 17:38:47: 5000000 INFO @ Fri, 10 Nov 2017 17:38:47: 5000000 INFO @ Fri, 10 Nov 2017 17:38:51: 6000000 INFO @ Fri, 10 Nov 2017 17:38:55: 6000000 INFO @ Fri, 10 Nov 2017 17:38:55: 6000000 INFO @ Fri, 10 Nov 2017 17:38:58: 7000000 INFO @ Fri, 10 Nov 2017 17:39:02: 7000000 INFO @ Fri, 10 Nov 2017 17:39:02: 7000000 INFO @ Fri, 10 Nov 2017 17:39:05: 8000000 INFO @ Fri, 10 Nov 2017 17:39:10: 8000000 INFO @ Fri, 10 Nov 2017 17:39:10: 8000000 INFO @ Fri, 10 Nov 2017 17:39:13: 9000000 INFO @ Fri, 10 Nov 2017 17:39:17: 9000000 INFO @ Fri, 10 Nov 2017 17:39:18: 9000000 INFO @ Fri, 10 Nov 2017 17:39:20: 10000000 INFO @ Fri, 10 Nov 2017 17:39:24: 10000000 INFO @ Fri, 10 Nov 2017 17:39:25: 10000000 INFO @ Fri, 10 Nov 2017 17:39:27: 11000000 INFO @ Fri, 10 Nov 2017 17:39:31: 11000000 INFO @ Fri, 10 Nov 2017 17:39:33: 11000000 INFO @ Fri, 10 Nov 2017 17:39:35: 12000000 INFO @ Fri, 10 Nov 2017 17:39:39: 12000000 INFO @ Fri, 10 Nov 2017 17:39:40: 12000000 INFO @ Fri, 10 Nov 2017 17:39:42: 13000000 INFO @ Fri, 10 Nov 2017 17:39:46: 13000000 INFO @ Fri, 10 Nov 2017 17:39:48: 13000000 INFO @ Fri, 10 Nov 2017 17:39:50: 14000000 INFO @ Fri, 10 Nov 2017 17:39:53: 14000000 INFO @ Fri, 10 Nov 2017 17:39:56: 14000000 INFO @ Fri, 10 Nov 2017 17:39:57: 15000000 INFO @ Fri, 10 Nov 2017 17:40:02: 15000000 INFO @ Fri, 10 Nov 2017 17:40:05: 15000000 INFO @ Fri, 10 Nov 2017 17:40:05: 16000000 INFO @ Fri, 10 Nov 2017 17:40:11: 16000000 INFO @ Fri, 10 Nov 2017 17:40:12: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 17:40:12: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 17:40:12: #1 total tags in treatment: 16788373 INFO @ Fri, 10 Nov 2017 17:40:12: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 17:40:12: #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 17:40:12: #1 tags after filtering in treatment: 16788202 INFO @ Fri, 10 Nov 2017 17:40:12: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 17:40:12: #1 finished! INFO @ Fri, 10 Nov 2017 17:40:12: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 17:40:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 17:40:14: 16000000 INFO @ Fri, 10 Nov 2017 17:40:15: #2 number of paired peaks: 28466 INFO @ Fri, 10 Nov 2017 17:40:15: start model_add_line... INFO @ Fri, 10 Nov 2017 17:40:15: start X-correlation... INFO @ Fri, 10 Nov 2017 17:40:15: end of X-cor INFO @ Fri, 10 Nov 2017 17:40:15: #2 finished! INFO @ Fri, 10 Nov 2017 17:40:15: #2 predicted fragment length is 157 bps INFO @ Fri, 10 Nov 2017 17:40:15: #2 alternative fragment length(s) may be 157 bps INFO @ Fri, 10 Nov 2017 17:40:15: #2.2 Generate R script for model : SRX2202865.05_model.r INFO @ Fri, 10 Nov 2017 17:40:15: #3 Call peaks... INFO @ Fri, 10 Nov 2017 17:40:15: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 17:40:17: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 17:40:17: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 17:40:17: #1 total tags in treatment: 16788373 INFO @ Fri, 10 Nov 2017 17:40:17: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 17:40:17: #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 17:40:18: #1 tags after filtering in treatment: 16788202 INFO @ Fri, 10 Nov 2017 17:40:18: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 17:40:18: #1 finished! INFO @ Fri, 10 Nov 2017 17:40:18: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 17:40:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 17:40:20: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 17:40:20: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 17:40:20: #1 total tags in treatment: 16788373 INFO @ Fri, 10 Nov 2017 17:40:20: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 17:40:20: #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 17:40:20: #1 tags after filtering in treatment: 16788202 INFO @ Fri, 10 Nov 2017 17:40:20: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 17:40:20: #1 finished! INFO @ Fri, 10 Nov 2017 17:40:20: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 17:40:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 17:40:20: #2 number of paired peaks: 28466 INFO @ Fri, 10 Nov 2017 17:40:20: start model_add_line... INFO @ Fri, 10 Nov 2017 17:40:21: start X-correlation... INFO @ Fri, 10 Nov 2017 17:40:21: end of X-cor INFO @ Fri, 10 Nov 2017 17:40:21: #2 finished! INFO @ Fri, 10 Nov 2017 17:40:21: #2 predicted fragment length is 157 bps INFO @ Fri, 10 Nov 2017 17:40:21: #2 alternative fragment length(s) may be 157 bps INFO @ Fri, 10 Nov 2017 17:40:21: #2.2 Generate R script for model : SRX2202865.10_model.r INFO @ Fri, 10 Nov 2017 17:40:21: #3 Call peaks... INFO @ Fri, 10 Nov 2017 17:40:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 17:40:23: #2 number of paired peaks: 28466 INFO @ Fri, 10 Nov 2017 17:40:23: start model_add_line... INFO @ Fri, 10 Nov 2017 17:40:23: start X-correlation... INFO @ Fri, 10 Nov 2017 17:40:23: end of X-cor INFO @ Fri, 10 Nov 2017 17:40:23: #2 finished! INFO @ Fri, 10 Nov 2017 17:40:23: #2 predicted fragment length is 157 bps INFO @ Fri, 10 Nov 2017 17:40:23: #2 alternative fragment length(s) may be 157 bps INFO @ Fri, 10 Nov 2017 17:40:23: #2.2 Generate R script for model : SRX2202865.20_model.r INFO @ Fri, 10 Nov 2017 17:40:23: #3 Call peaks... INFO @ Fri, 10 Nov 2017 17:40:23: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 17:40:56: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 17:41:01: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 17:41:04: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 17:41:21: #4 Write output xls file... SRX2202865.05_peaks.xls INFO @ Fri, 10 Nov 2017 17:41:21: #4 Write peak in narrowPeak format file... SRX2202865.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 17:41:21: #4 Write summits bed file... SRX2202865.05_summits.bed INFO @ Fri, 10 Nov 2017 17:41:21: Done! pass1 - making usageList (48 chroms): 1 millis pass2 - checking and writing primary data (3813 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 17:41:25: #4 Write output xls file... SRX2202865.10_peaks.xls INFO @ Fri, 10 Nov 2017 17:41:25: #4 Write peak in narrowPeak format file... SRX2202865.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 17:41:25: #4 Write summits bed file... SRX2202865.10_summits.bed INFO @ Fri, 10 Nov 2017 17:41:25: Done! pass1 - making usageList (39 chroms): 1 millis pass2 - checking and writing primary data (640 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 17:41:29: #4 Write output xls file... SRX2202865.20_peaks.xls INFO @ Fri, 10 Nov 2017 17:41:29: #4 Write peak in narrowPeak format file... SRX2202865.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 17:41:29: #4 Write summits bed file... SRX2202865.20_summits.bed INFO @ Fri, 10 Nov 2017 17:41:29: Done! pass1 - making usageList (29 chroms): 1 millis pass2 - checking and writing primary data (277 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。