Job ID = 10194935 sra ファイルのダウンロード中... Completed: 676688K bytes transferred in 10 seconds (507531K bits/sec), in 1 file. Completed: 625026K bytes transferred in 10 seconds (502702K 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 30382286 spots for /home/okishinya/chipatlas/results/rn6/SRX2512945/SRR5197458.sra Written 30382286 spots total Written 31781014 spots for /home/okishinya/chipatlas/results/rn6/SRX2512945/SRR5197459.sra Written 31781014 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: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:52:40 62163300 reads; of these: 62163300 (100.00%) were unpaired; of these: 19716139 (31.72%) aligned 0 times 28172192 (45.32%) aligned exactly 1 time 14274969 (22.96%) aligned >1 times 68.28% overall alignment rate Time searching: 00:52:44 Overall time: 00:52:44 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] 6325921 / 42447161 = 0.1490 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 00:54:11: # Command line: callpeak -t SRX2512945.bam -f BAM -g 2.15e9 -n SRX2512945.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2512945.10 # format = BAM # ChIP-seq file = ['SRX2512945.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 00:54:11: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:54:11: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:54:11: # Command line: callpeak -t SRX2512945.bam -f BAM -g 2.15e9 -n SRX2512945.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2512945.05 # format = BAM # ChIP-seq file = ['SRX2512945.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 00:54:11: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:54:11: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:54:11: # Command line: callpeak -t SRX2512945.bam -f BAM -g 2.15e9 -n SRX2512945.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2512945.20 # format = BAM # ChIP-seq file = ['SRX2512945.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 00:54:11: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:54:11: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:54:19: 1000000 INFO @ Sat, 11 Nov 2017 00:54:20: 1000000 INFO @ Sat, 11 Nov 2017 00:54:20: 1000000 INFO @ Sat, 11 Nov 2017 00:54:27: 2000000 INFO @ Sat, 11 Nov 2017 00:54:28: 2000000 INFO @ Sat, 11 Nov 2017 00:54:28: 2000000 INFO @ Sat, 11 Nov 2017 00:54:34: 3000000 INFO @ Sat, 11 Nov 2017 00:54:36: 3000000 INFO @ Sat, 11 Nov 2017 00:54:36: 3000000 INFO @ Sat, 11 Nov 2017 00:54:41: 4000000 INFO @ Sat, 11 Nov 2017 00:54:43: 4000000 INFO @ Sat, 11 Nov 2017 00:54:43: 4000000 INFO @ Sat, 11 Nov 2017 00:54:48: 5000000 INFO @ Sat, 11 Nov 2017 00:54:50: 5000000 INFO @ Sat, 11 Nov 2017 00:54:50: 5000000 INFO @ Sat, 11 Nov 2017 00:54:55: 6000000 INFO @ Sat, 11 Nov 2017 00:54:58: 6000000 INFO @ Sat, 11 Nov 2017 00:54:58: 6000000 INFO @ Sat, 11 Nov 2017 00:55:02: 7000000 INFO @ Sat, 11 Nov 2017 00:55:05: 7000000 INFO @ Sat, 11 Nov 2017 00:55:06: 7000000 INFO @ Sat, 11 Nov 2017 00:55:09: 8000000 INFO @ Sat, 11 Nov 2017 00:55:13: 8000000 INFO @ Sat, 11 Nov 2017 00:55:13: 8000000 INFO @ Sat, 11 Nov 2017 00:55:16: 9000000 INFO @ Sat, 11 Nov 2017 00:55:22: 9000000 INFO @ Sat, 11 Nov 2017 00:55:23: 9000000 INFO @ Sat, 11 Nov 2017 00:55:25: 10000000 INFO @ Sat, 11 Nov 2017 00:55:30: 10000000 INFO @ Sat, 11 Nov 2017 00:55:31: 10000000 INFO @ Sat, 11 Nov 2017 00:55:33: 11000000 INFO @ Sat, 11 Nov 2017 00:55:37: 11000000 INFO @ Sat, 11 Nov 2017 00:55:38: 11000000 INFO @ Sat, 11 Nov 2017 00:55:40: 12000000 INFO @ Sat, 11 Nov 2017 00:55:44: 12000000 INFO @ Sat, 11 Nov 2017 00:55:46: 12000000 INFO @ Sat, 11 Nov 2017 00:55:47: 13000000 INFO @ Sat, 11 Nov 2017 00:55:51: 13000000 INFO @ Sat, 11 Nov 2017 00:55:53: 13000000 INFO @ Sat, 11 Nov 2017 00:55:54: 14000000 INFO @ Sat, 11 Nov 2017 00:55:58: 14000000 INFO @ Sat, 11 Nov 2017 00:56:00: 14000000 INFO @ Sat, 11 Nov 2017 00:56:01: 15000000 INFO @ Sat, 11 Nov 2017 00:56:06: 15000000 INFO @ Sat, 11 Nov 2017 00:56:07: 15000000 INFO @ Sat, 11 Nov 2017 00:56:08: 16000000 INFO @ Sat, 11 Nov 2017 00:56:16: 16000000 INFO @ Sat, 11 Nov 2017 00:56:19: 16000000 INFO @ Sat, 11 Nov 2017 00:56:21: 17000000 INFO @ Sat, 11 Nov 2017 00:56:29: 17000000 INFO @ Sat, 11 Nov 2017 00:56:31: 17000000 INFO @ Sat, 11 Nov 2017 00:56:34: 18000000 INFO @ Sat, 11 Nov 2017 00:56:37: 18000000 INFO @ Sat, 11 Nov 2017 00:56:39: 18000000 INFO @ Sat, 11 Nov 2017 00:56:45: 19000000 INFO @ Sat, 11 Nov 2017 00:56:45: 19000000 INFO @ Sat, 11 Nov 2017 00:56:47: 19000000 INFO @ Sat, 11 Nov 2017 00:56:54: 20000000 INFO @ Sat, 11 Nov 2017 00:56:54: 20000000 INFO @ Sat, 11 Nov 2017 00:56:54: 20000000 INFO @ Sat, 11 Nov 2017 00:57:02: 21000000 INFO @ Sat, 11 Nov 2017 00:57:03: 21000000 INFO @ Sat, 11 Nov 2017 00:57:04: 21000000 INFO @ Sat, 11 Nov 2017 00:57:09: 22000000 INFO @ Sat, 11 Nov 2017 00:57:13: 22000000 INFO @ Sat, 11 Nov 2017 00:57:14: 22000000 INFO @ Sat, 11 Nov 2017 00:57:22: 23000000 INFO @ Sat, 11 Nov 2017 00:57:26: 23000000 INFO @ Sat, 11 Nov 2017 00:57:27: 23000000 INFO @ Sat, 11 Nov 2017 00:57:34: 24000000 INFO @ Sat, 11 Nov 2017 00:57:36: 24000000 INFO @ Sat, 11 Nov 2017 00:57:36: 24000000 INFO @ Sat, 11 Nov 2017 00:57:43: 25000000 INFO @ Sat, 11 Nov 2017 00:57:44: 25000000 INFO @ Sat, 11 Nov 2017 00:57:45: 25000000 INFO @ Sat, 11 Nov 2017 00:57:50: 26000000 INFO @ Sat, 11 Nov 2017 00:57:53: 26000000 INFO @ Sat, 11 Nov 2017 00:57:54: 26000000 INFO @ Sat, 11 Nov 2017 00:57:57: 27000000 INFO @ Sat, 11 Nov 2017 00:58:01: 27000000 INFO @ Sat, 11 Nov 2017 00:58:02: 27000000 INFO @ Sat, 11 Nov 2017 00:58:04: 28000000 INFO @ Sat, 11 Nov 2017 00:58:08: 28000000 INFO @ Sat, 11 Nov 2017 00:58:10: 28000000 INFO @ Sat, 11 Nov 2017 00:58:12: 29000000 INFO @ Sat, 11 Nov 2017 00:58:17: 29000000 INFO @ Sat, 11 Nov 2017 00:58:18: 29000000 INFO @ Sat, 11 Nov 2017 00:58:20: 30000000 INFO @ Sat, 11 Nov 2017 00:58:26: 30000000 INFO @ Sat, 11 Nov 2017 00:58:27: 30000000 INFO @ Sat, 11 Nov 2017 00:58:28: 31000000 INFO @ Sat, 11 Nov 2017 00:58:35: 31000000 INFO @ Sat, 11 Nov 2017 00:58:36: 31000000 INFO @ Sat, 11 Nov 2017 00:58:36: 32000000 INFO @ Sat, 11 Nov 2017 00:58:43: 32000000 INFO @ Sat, 11 Nov 2017 00:58:44: 33000000 INFO @ Sat, 11 Nov 2017 00:58:44: 32000000 INFO @ Sat, 11 Nov 2017 00:58:51: 34000000 INFO @ Sat, 11 Nov 2017 00:58:52: 33000000 INFO @ Sat, 11 Nov 2017 00:58:53: 33000000 INFO @ Sat, 11 Nov 2017 00:58:59: 35000000 INFO @ Sat, 11 Nov 2017 00:59:01: 34000000 INFO @ Sat, 11 Nov 2017 00:59:01: 34000000 INFO @ Sat, 11 Nov 2017 00:59:07: 36000000 INFO @ Sat, 11 Nov 2017 00:59:09: #1 tag size is determined as 36 bps INFO @ Sat, 11 Nov 2017 00:59:09: #1 tag size = 36 INFO @ Sat, 11 Nov 2017 00:59:09: #1 total tags in treatment: 36121240 INFO @ Sat, 11 Nov 2017 00:59:09: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:59:09: #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 00:59:10: 35000000 INFO @ Sat, 11 Nov 2017 00:59:10: #1 tags after filtering in treatment: 36121177 INFO @ Sat, 11 Nov 2017 00:59:10: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:59:10: #1 finished! INFO @ Sat, 11 Nov 2017 00:59:10: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:59:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:59:10: 35000000 INFO @ Sat, 11 Nov 2017 00:59:14: #2 number of paired peaks: 10297 INFO @ Sat, 11 Nov 2017 00:59:14: start model_add_line... INFO @ Sat, 11 Nov 2017 00:59:15: start X-correlation... INFO @ Sat, 11 Nov 2017 00:59:15: end of X-cor INFO @ Sat, 11 Nov 2017 00:59:15: #2 finished! INFO @ Sat, 11 Nov 2017 00:59:15: #2 predicted fragment length is 136 bps INFO @ Sat, 11 Nov 2017 00:59:15: #2 alternative fragment length(s) may be 136 bps INFO @ Sat, 11 Nov 2017 00:59:15: #2.2 Generate R script for model : SRX2512945.10_model.r INFO @ Sat, 11 Nov 2017 00:59:15: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:59:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 00:59:17: 36000000 INFO @ Sat, 11 Nov 2017 00:59:18: #1 tag size is determined as 36 bps INFO @ Sat, 11 Nov 2017 00:59:18: #1 tag size = 36 INFO @ Sat, 11 Nov 2017 00:59:18: #1 total tags in treatment: 36121240 INFO @ Sat, 11 Nov 2017 00:59:18: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:59:18: #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 00:59:19: 36000000 INFO @ Sat, 11 Nov 2017 00:59:20: #1 tags after filtering in treatment: 36121177 INFO @ Sat, 11 Nov 2017 00:59:20: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:59:20: #1 finished! INFO @ Sat, 11 Nov 2017 00:59:20: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:59:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:59:21: #1 tag size is determined as 36 bps INFO @ Sat, 11 Nov 2017 00:59:21: #1 tag size = 36 INFO @ Sat, 11 Nov 2017 00:59:21: #1 total tags in treatment: 36121240 INFO @ Sat, 11 Nov 2017 00:59:21: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:59:21: #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 00:59:22: #1 tags after filtering in treatment: 36121177 INFO @ Sat, 11 Nov 2017 00:59:22: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:59:22: #1 finished! INFO @ Sat, 11 Nov 2017 00:59:22: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:59:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:59:24: #2 number of paired peaks: 10297 INFO @ Sat, 11 Nov 2017 00:59:24: start model_add_line... INFO @ Sat, 11 Nov 2017 00:59:25: start X-correlation... INFO @ Sat, 11 Nov 2017 00:59:25: end of X-cor INFO @ Sat, 11 Nov 2017 00:59:25: #2 finished! INFO @ Sat, 11 Nov 2017 00:59:25: #2 predicted fragment length is 136 bps INFO @ Sat, 11 Nov 2017 00:59:25: #2 alternative fragment length(s) may be 136 bps INFO @ Sat, 11 Nov 2017 00:59:25: #2.2 Generate R script for model : SRX2512945.20_model.r INFO @ Sat, 11 Nov 2017 00:59:25: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:59:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 00:59:27: #2 number of paired peaks: 10297 INFO @ Sat, 11 Nov 2017 00:59:27: start model_add_line... INFO @ Sat, 11 Nov 2017 00:59:28: start X-correlation... INFO @ Sat, 11 Nov 2017 00:59:28: end of X-cor INFO @ Sat, 11 Nov 2017 00:59:28: #2 finished! INFO @ Sat, 11 Nov 2017 00:59:28: #2 predicted fragment length is 136 bps INFO @ Sat, 11 Nov 2017 00:59:28: #2 alternative fragment length(s) may be 136 bps INFO @ Sat, 11 Nov 2017 00:59:28: #2.2 Generate R script for model : SRX2512945.05_model.r INFO @ Sat, 11 Nov 2017 00:59:28: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:59:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 01:01:00: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 01:01:12: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 01:01:13: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 01:02:02: #4 Write output xls file... SRX2512945.10_peaks.xls INFO @ Sat, 11 Nov 2017 01:02:02: #4 Write peak in narrowPeak format file... SRX2512945.10_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 01:02:02: #4 Write summits bed file... SRX2512945.10_summits.bed INFO @ Sat, 11 Nov 2017 01:02:02: Done! pass1 - making usageList (80 chroms): 2 millis pass2 - checking and writing primary data (3921 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 01:02:16: #4 Write output xls file... SRX2512945.20_peaks.xls INFO @ Sat, 11 Nov 2017 01:02:16: #4 Write peak in narrowPeak format file... SRX2512945.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 01:02:16: #4 Write summits bed file... SRX2512945.20_summits.bed INFO @ Sat, 11 Nov 2017 01:02:16: Done! pass1 - making usageList (64 chroms): 2 millis pass2 - checking and writing primary data (1627 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 01:02:18: #4 Write output xls file... SRX2512945.05_peaks.xls INFO @ Sat, 11 Nov 2017 01:02:18: #4 Write peak in narrowPeak format file... SRX2512945.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 01:02:18: #4 Write summits bed file... SRX2512945.05_summits.bed INFO @ Sat, 11 Nov 2017 01:02:18: Done! pass1 - making usageList (108 chroms): 4 millis pass2 - checking and writing primary data (9374 records, 4 fields): 22 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。