Job ID = 10194886 sra ファイルのダウンロード中... Completed: 217529K bytes transferred in 9 seconds (184082K bits/sec), in 1 file. Completed: 218308K bytes transferred in 7 seconds (229998K bits/sec), in 1 file. Completed: 207260K bytes transferred in 6 seconds (246001K bits/sec), in 1 file. Completed: 204312K bytes transferred in 8 seconds (188193K bits/sec), in 1 file. Completed: 245811K bytes transferred in 9 seconds (212918K bits/sec), in 1 file. Completed: 249028K bytes transferred in 10 seconds (185607K 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 4619067 spots for /home/okishinya/chipatlas/results/rn6/SRX2202881/SRR4319833.sra Written 4619067 spots total Written 4675087 spots for /home/okishinya/chipatlas/results/rn6/SRX2202881/SRR4319832.sra Written 4675087 spots total Written 4888899 spots for /home/okishinya/chipatlas/results/rn6/SRX2202881/SRR4319831.sra Written 4888899 spots total Written 4888469 spots for /home/okishinya/chipatlas/results/rn6/SRX2202881/SRR4319830.sra Written 4888469 spots total Written 5404294 spots for /home/okishinya/chipatlas/results/rn6/SRX2202881/SRR4319834.sra Written 5404294 spots total Written 5454436 spots for /home/okishinya/chipatlas/results/rn6/SRX2202881/SRR4319835.sra Written 5454436 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: 00:21:49 29930252 reads; of these: 29930252 (100.00%) were unpaired; of these: 2339483 (7.82%) aligned 0 times 20836952 (69.62%) aligned exactly 1 time 6753817 (22.57%) aligned >1 times 92.18% overall alignment rate Time searching: 00:21:53 Overall time: 00:21:53 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] 3803304 / 27590769 = 0.1378 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 18:17:34: # Command line: callpeak -t SRX2202881.bam -f BAM -g 2.15e9 -n SRX2202881.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2202881.10 # format = BAM # ChIP-seq file = ['SRX2202881.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 18:17:34: # Command line: callpeak -t SRX2202881.bam -f BAM -g 2.15e9 -n SRX2202881.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2202881.20 # format = BAM # ChIP-seq file = ['SRX2202881.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 18:17:34: # Command line: callpeak -t SRX2202881.bam -f BAM -g 2.15e9 -n SRX2202881.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2202881.05 # format = BAM # ChIP-seq file = ['SRX2202881.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 18:17:34: #1 read tag files... INFO @ Fri, 10 Nov 2017 18:17:34: #1 read tag files... INFO @ Fri, 10 Nov 2017 18:17:34: #1 read tag files... INFO @ Fri, 10 Nov 2017 18:17:34: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 18:17:34: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 18:17:34: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 18:17:41: 1000000 INFO @ Fri, 10 Nov 2017 18:17:42: 1000000 INFO @ Fri, 10 Nov 2017 18:17:42: 1000000 INFO @ Fri, 10 Nov 2017 18:17:48: 2000000 INFO @ Fri, 10 Nov 2017 18:17:49: 2000000 INFO @ Fri, 10 Nov 2017 18:17:49: 2000000 INFO @ Fri, 10 Nov 2017 18:17:54: 3000000 INFO @ Fri, 10 Nov 2017 18:17:56: 3000000 INFO @ Fri, 10 Nov 2017 18:17:56: 3000000 INFO @ Fri, 10 Nov 2017 18:18:01: 4000000 INFO @ Fri, 10 Nov 2017 18:18:03: 4000000 INFO @ Fri, 10 Nov 2017 18:18:03: 4000000 INFO @ Fri, 10 Nov 2017 18:18:08: 5000000 INFO @ Fri, 10 Nov 2017 18:18:09: 5000000 INFO @ Fri, 10 Nov 2017 18:18:11: 5000000 INFO @ Fri, 10 Nov 2017 18:18:15: 6000000 INFO @ Fri, 10 Nov 2017 18:18:16: 6000000 INFO @ Fri, 10 Nov 2017 18:18:18: 6000000 INFO @ Fri, 10 Nov 2017 18:18:22: 7000000 INFO @ Fri, 10 Nov 2017 18:18:23: 7000000 INFO @ Fri, 10 Nov 2017 18:18:25: 7000000 INFO @ Fri, 10 Nov 2017 18:18:29: 8000000 INFO @ Fri, 10 Nov 2017 18:18:30: 8000000 INFO @ Fri, 10 Nov 2017 18:18:33: 8000000 INFO @ Fri, 10 Nov 2017 18:18:36: 9000000 INFO @ Fri, 10 Nov 2017 18:18:36: 9000000 INFO @ Fri, 10 Nov 2017 18:18:40: 9000000 INFO @ Fri, 10 Nov 2017 18:18:43: 10000000 INFO @ Fri, 10 Nov 2017 18:18:43: 10000000 INFO @ Fri, 10 Nov 2017 18:18:47: 10000000 INFO @ Fri, 10 Nov 2017 18:18:50: 11000000 INFO @ Fri, 10 Nov 2017 18:18:50: 11000000 INFO @ Fri, 10 Nov 2017 18:18:54: 11000000 INFO @ Fri, 10 Nov 2017 18:18:56: 12000000 INFO @ Fri, 10 Nov 2017 18:18:57: 12000000 INFO @ Fri, 10 Nov 2017 18:19:01: 12000000 INFO @ Fri, 10 Nov 2017 18:19:03: 13000000 INFO @ Fri, 10 Nov 2017 18:19:04: 13000000 INFO @ Fri, 10 Nov 2017 18:19:09: 13000000 INFO @ Fri, 10 Nov 2017 18:19:10: 14000000 INFO @ Fri, 10 Nov 2017 18:19:11: 14000000 INFO @ Fri, 10 Nov 2017 18:19:16: 14000000 INFO @ Fri, 10 Nov 2017 18:19:16: 15000000 INFO @ Fri, 10 Nov 2017 18:19:18: 15000000 INFO @ Fri, 10 Nov 2017 18:19:23: 16000000 INFO @ Fri, 10 Nov 2017 18:19:23: 15000000 INFO @ Fri, 10 Nov 2017 18:19:25: 16000000 INFO @ Fri, 10 Nov 2017 18:19:30: 17000000 INFO @ Fri, 10 Nov 2017 18:19:30: 16000000 INFO @ Fri, 10 Nov 2017 18:19:32: 17000000 INFO @ Fri, 10 Nov 2017 18:19:37: 18000000 INFO @ Fri, 10 Nov 2017 18:19:38: 17000000 INFO @ Fri, 10 Nov 2017 18:19:39: 18000000 INFO @ Fri, 10 Nov 2017 18:19:44: 19000000 INFO @ Fri, 10 Nov 2017 18:19:45: 18000000 INFO @ Fri, 10 Nov 2017 18:19:46: 19000000 INFO @ Fri, 10 Nov 2017 18:19:51: 20000000 INFO @ Fri, 10 Nov 2017 18:19:53: 20000000 INFO @ Fri, 10 Nov 2017 18:19:53: 19000000 INFO @ Fri, 10 Nov 2017 18:19:58: 21000000 INFO @ Fri, 10 Nov 2017 18:19:59: 21000000 INFO @ Fri, 10 Nov 2017 18:20:00: 20000000 INFO @ Fri, 10 Nov 2017 18:20:06: 22000000 INFO @ Fri, 10 Nov 2017 18:20:06: 22000000 INFO @ Fri, 10 Nov 2017 18:20:08: 21000000 INFO @ Fri, 10 Nov 2017 18:20:13: 23000000 INFO @ Fri, 10 Nov 2017 18:20:13: 23000000 INFO @ Fri, 10 Nov 2017 18:20:15: 22000000 INFO @ Fri, 10 Nov 2017 18:20:18: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 18:20:18: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 18:20:18: #1 total tags in treatment: 23787465 INFO @ Fri, 10 Nov 2017 18:20:18: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 18:20:18: #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 18:20:19: #1 tags after filtering in treatment: 23787336 INFO @ Fri, 10 Nov 2017 18:20:19: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 18:20:19: #1 finished! INFO @ Fri, 10 Nov 2017 18:20:19: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 18:20:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 18:20:19: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 18:20:19: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 18:20:19: #1 total tags in treatment: 23787465 INFO @ Fri, 10 Nov 2017 18:20:19: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 18:20:19: #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 18:20:20: #1 tags after filtering in treatment: 23787336 INFO @ Fri, 10 Nov 2017 18:20:20: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 18:20:20: #1 finished! INFO @ Fri, 10 Nov 2017 18:20:20: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 18:20:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 18:20:22: #2 number of paired peaks: 22840 INFO @ Fri, 10 Nov 2017 18:20:22: start model_add_line... INFO @ Fri, 10 Nov 2017 18:20:22: start X-correlation... INFO @ Fri, 10 Nov 2017 18:20:22: end of X-cor INFO @ Fri, 10 Nov 2017 18:20:22: #2 finished! INFO @ Fri, 10 Nov 2017 18:20:22: #2 predicted fragment length is 124 bps INFO @ Fri, 10 Nov 2017 18:20:22: #2 alternative fragment length(s) may be 124 bps INFO @ Fri, 10 Nov 2017 18:20:22: #2.2 Generate R script for model : SRX2202881.10_model.r INFO @ Fri, 10 Nov 2017 18:20:22: #3 Call peaks... INFO @ Fri, 10 Nov 2017 18:20:22: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 18:20:22: 23000000 INFO @ Fri, 10 Nov 2017 18:20:23: #2 number of paired peaks: 22840 INFO @ Fri, 10 Nov 2017 18:20:23: start model_add_line... INFO @ Fri, 10 Nov 2017 18:20:23: start X-correlation... INFO @ Fri, 10 Nov 2017 18:20:23: end of X-cor INFO @ Fri, 10 Nov 2017 18:20:23: #2 finished! INFO @ Fri, 10 Nov 2017 18:20:23: #2 predicted fragment length is 124 bps INFO @ Fri, 10 Nov 2017 18:20:23: #2 alternative fragment length(s) may be 124 bps INFO @ Fri, 10 Nov 2017 18:20:23: #2.2 Generate R script for model : SRX2202881.05_model.r INFO @ Fri, 10 Nov 2017 18:20:23: #3 Call peaks... INFO @ Fri, 10 Nov 2017 18:20:23: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 18:20:28: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 18:20:28: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 18:20:28: #1 total tags in treatment: 23787465 INFO @ Fri, 10 Nov 2017 18:20:28: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 18:20:28: #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 18:20:29: #1 tags after filtering in treatment: 23787336 INFO @ Fri, 10 Nov 2017 18:20:29: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 18:20:29: #1 finished! INFO @ Fri, 10 Nov 2017 18:20:29: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 18:20:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 18:20:32: #2 number of paired peaks: 22840 INFO @ Fri, 10 Nov 2017 18:20:32: start model_add_line... INFO @ Fri, 10 Nov 2017 18:20:32: start X-correlation... INFO @ Fri, 10 Nov 2017 18:20:32: end of X-cor INFO @ Fri, 10 Nov 2017 18:20:32: #2 finished! INFO @ Fri, 10 Nov 2017 18:20:32: #2 predicted fragment length is 124 bps INFO @ Fri, 10 Nov 2017 18:20:32: #2 alternative fragment length(s) may be 124 bps INFO @ Fri, 10 Nov 2017 18:20:32: #2.2 Generate R script for model : SRX2202881.20_model.r INFO @ Fri, 10 Nov 2017 18:20:32: #3 Call peaks... INFO @ Fri, 10 Nov 2017 18:20:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 18:21:20: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 18:21:23: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 18:21:32: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 18:21:56: #4 Write output xls file... SRX2202881.10_peaks.xls INFO @ Fri, 10 Nov 2017 18:21:56: #4 Write peak in narrowPeak format file... SRX2202881.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 18:21:56: #4 Write summits bed file... SRX2202881.10_summits.bed INFO @ Fri, 10 Nov 2017 18:21:56: Done! pass1 - making usageList (40 chroms): 1 millis pass2 - checking and writing primary data (782 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 18:22:00: #4 Write output xls file... SRX2202881.05_peaks.xls INFO @ Fri, 10 Nov 2017 18:22:00: #4 Write peak in narrowPeak format file... SRX2202881.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 18:22:00: #4 Write summits bed file... SRX2202881.05_summits.bed INFO @ Fri, 10 Nov 2017 18:22:00: Done! pass1 - making usageList (54 chroms): 2 millis pass2 - checking and writing primary data (3616 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 18:22:07: #4 Write output xls file... SRX2202881.20_peaks.xls INFO @ Fri, 10 Nov 2017 18:22:07: #4 Write peak in narrowPeak format file... SRX2202881.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 18:22:07: #4 Write summits bed file... SRX2202881.20_summits.bed INFO @ Fri, 10 Nov 2017 18:22:07: Done! pass1 - making usageList (33 chroms): 0 millis pass2 - checking and writing primary data (363 records, 4 fields): 210 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。