Job ID = 10194842 sra ファイルのダウンロード中... Completed: 1461880K bytes transferred in 32 seconds (371699K 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 71217611 spots for /home/okishinya/chipatlas/results/rn6/SRX1977131/SRR3952263.sra Written 71217611 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 rm: cannot remove `[DSE]RR*.fastq': 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: 02:05:37 71217611 reads; of these: 71217611 (100.00%) were unpaired; of these: 9688371 (13.60%) aligned 0 times 29426540 (41.32%) aligned exactly 1 time 32102700 (45.08%) aligned >1 times 86.40% overall alignment rate Time searching: 02:05:40 Overall time: 02:05:40 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 28 files... [bam_rmdupse_core] 8823483 / 61529240 = 0.1434 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 04:12:07: # Command line: callpeak -t SRX1977131.bam -f BAM -g 2.15e9 -n SRX1977131.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1977131.05 # format = BAM # ChIP-seq file = ['SRX1977131.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 04:12:07: #1 read tag files... INFO @ Sat, 11 Nov 2017 04:12:07: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 04:12:07: # Command line: callpeak -t SRX1977131.bam -f BAM -g 2.15e9 -n SRX1977131.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1977131.20 # format = BAM # ChIP-seq file = ['SRX1977131.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 04:12:07: #1 read tag files... INFO @ Sat, 11 Nov 2017 04:12:07: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 04:12:07: # Command line: callpeak -t SRX1977131.bam -f BAM -g 2.15e9 -n SRX1977131.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1977131.10 # format = BAM # ChIP-seq file = ['SRX1977131.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 04:12:07: #1 read tag files... INFO @ Sat, 11 Nov 2017 04:12:07: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 04:12:14: 1000000 INFO @ Sat, 11 Nov 2017 04:12:14: 1000000 INFO @ Sat, 11 Nov 2017 04:12:14: 1000000 INFO @ Sat, 11 Nov 2017 04:12:21: 2000000 INFO @ Sat, 11 Nov 2017 04:12:21: 2000000 INFO @ Sat, 11 Nov 2017 04:12:21: 2000000 INFO @ Sat, 11 Nov 2017 04:12:28: 3000000 INFO @ Sat, 11 Nov 2017 04:12:28: 3000000 INFO @ Sat, 11 Nov 2017 04:12:28: 3000000 INFO @ Sat, 11 Nov 2017 04:12:35: 4000000 INFO @ Sat, 11 Nov 2017 04:12:35: 4000000 INFO @ Sat, 11 Nov 2017 04:12:35: 4000000 INFO @ Sat, 11 Nov 2017 04:12:42: 5000000 INFO @ Sat, 11 Nov 2017 04:12:42: 5000000 INFO @ Sat, 11 Nov 2017 04:12:42: 5000000 INFO @ Sat, 11 Nov 2017 04:12:49: 6000000 INFO @ Sat, 11 Nov 2017 04:12:49: 6000000 INFO @ Sat, 11 Nov 2017 04:12:50: 6000000 INFO @ Sat, 11 Nov 2017 04:12:56: 7000000 INFO @ Sat, 11 Nov 2017 04:12:56: 7000000 INFO @ Sat, 11 Nov 2017 04:12:57: 7000000 INFO @ Sat, 11 Nov 2017 04:13:03: 8000000 INFO @ Sat, 11 Nov 2017 04:13:04: 8000000 INFO @ Sat, 11 Nov 2017 04:13:04: 8000000 INFO @ Sat, 11 Nov 2017 04:13:10: 9000000 INFO @ Sat, 11 Nov 2017 04:13:11: 9000000 INFO @ Sat, 11 Nov 2017 04:13:11: 9000000 INFO @ Sat, 11 Nov 2017 04:13:16: 10000000 INFO @ Sat, 11 Nov 2017 04:13:18: 10000000 INFO @ Sat, 11 Nov 2017 04:13:18: 10000000 INFO @ Sat, 11 Nov 2017 04:13:23: 11000000 INFO @ Sat, 11 Nov 2017 04:13:25: 11000000 INFO @ Sat, 11 Nov 2017 04:13:25: 11000000 INFO @ Sat, 11 Nov 2017 04:13:30: 12000000 INFO @ Sat, 11 Nov 2017 04:13:32: 12000000 INFO @ Sat, 11 Nov 2017 04:13:33: 12000000 INFO @ Sat, 11 Nov 2017 04:13:37: 13000000 INFO @ Sat, 11 Nov 2017 04:13:39: 13000000 INFO @ Sat, 11 Nov 2017 04:13:40: 13000000 INFO @ Sat, 11 Nov 2017 04:13:44: 14000000 INFO @ Sat, 11 Nov 2017 04:13:46: 14000000 INFO @ Sat, 11 Nov 2017 04:13:47: 14000000 INFO @ Sat, 11 Nov 2017 04:13:51: 15000000 INFO @ Sat, 11 Nov 2017 04:13:54: 15000000 INFO @ Sat, 11 Nov 2017 04:13:54: 15000000 INFO @ Sat, 11 Nov 2017 04:13:58: 16000000 INFO @ Sat, 11 Nov 2017 04:14:01: 16000000 INFO @ Sat, 11 Nov 2017 04:14:01: 16000000 INFO @ Sat, 11 Nov 2017 04:14:05: 17000000 INFO @ Sat, 11 Nov 2017 04:14:08: 17000000 INFO @ Sat, 11 Nov 2017 04:14:08: 17000000 INFO @ Sat, 11 Nov 2017 04:14:12: 18000000 INFO @ Sat, 11 Nov 2017 04:14:15: 18000000 INFO @ Sat, 11 Nov 2017 04:14:15: 18000000 INFO @ Sat, 11 Nov 2017 04:14:18: 19000000 INFO @ Sat, 11 Nov 2017 04:14:22: 19000000 INFO @ Sat, 11 Nov 2017 04:14:22: 19000000 INFO @ Sat, 11 Nov 2017 04:14:25: 20000000 INFO @ Sat, 11 Nov 2017 04:14:29: 20000000 INFO @ Sat, 11 Nov 2017 04:14:29: 20000000 INFO @ Sat, 11 Nov 2017 04:14:32: 21000000 INFO @ Sat, 11 Nov 2017 04:14:36: 21000000 INFO @ Sat, 11 Nov 2017 04:14:37: 21000000 INFO @ Sat, 11 Nov 2017 04:14:39: 22000000 INFO @ Sat, 11 Nov 2017 04:14:43: 22000000 INFO @ Sat, 11 Nov 2017 04:14:44: 22000000 INFO @ Sat, 11 Nov 2017 04:14:46: 23000000 INFO @ Sat, 11 Nov 2017 04:14:51: 23000000 INFO @ Sat, 11 Nov 2017 04:14:51: 23000000 INFO @ Sat, 11 Nov 2017 04:14:53: 24000000 INFO @ Sat, 11 Nov 2017 04:14:58: 24000000 INFO @ Sat, 11 Nov 2017 04:14:58: 24000000 INFO @ Sat, 11 Nov 2017 04:15:00: 25000000 INFO @ Sat, 11 Nov 2017 04:15:05: 25000000 INFO @ Sat, 11 Nov 2017 04:15:05: 25000000 INFO @ Sat, 11 Nov 2017 04:15:07: 26000000 INFO @ Sat, 11 Nov 2017 04:15:12: 26000000 INFO @ Sat, 11 Nov 2017 04:15:12: 26000000 INFO @ Sat, 11 Nov 2017 04:15:14: 27000000 INFO @ Sat, 11 Nov 2017 04:15:19: 27000000 INFO @ Sat, 11 Nov 2017 04:15:19: 27000000 INFO @ Sat, 11 Nov 2017 04:15:21: 28000000 INFO @ Sat, 11 Nov 2017 04:15:26: 28000000 INFO @ Sat, 11 Nov 2017 04:15:26: 28000000 INFO @ Sat, 11 Nov 2017 04:15:28: 29000000 INFO @ Sat, 11 Nov 2017 04:15:34: 29000000 INFO @ Sat, 11 Nov 2017 04:15:34: 29000000 INFO @ Sat, 11 Nov 2017 04:15:36: 30000000 INFO @ Sat, 11 Nov 2017 04:15:41: 30000000 INFO @ Sat, 11 Nov 2017 04:15:41: 30000000 INFO @ Sat, 11 Nov 2017 04:15:43: 31000000 INFO @ Sat, 11 Nov 2017 04:15:48: 31000000 INFO @ Sat, 11 Nov 2017 04:15:48: 31000000 INFO @ Sat, 11 Nov 2017 04:15:50: 32000000 INFO @ Sat, 11 Nov 2017 04:15:55: 32000000 INFO @ Sat, 11 Nov 2017 04:15:56: 32000000 INFO @ Sat, 11 Nov 2017 04:15:57: 33000000 INFO @ Sat, 11 Nov 2017 04:16:02: 33000000 INFO @ Sat, 11 Nov 2017 04:16:03: 33000000 INFO @ Sat, 11 Nov 2017 04:16:04: 34000000 INFO @ Sat, 11 Nov 2017 04:16:09: 34000000 INFO @ Sat, 11 Nov 2017 04:16:10: 34000000 INFO @ Sat, 11 Nov 2017 04:16:11: 35000000 INFO @ Sat, 11 Nov 2017 04:16:16: 35000000 INFO @ Sat, 11 Nov 2017 04:16:17: 35000000 INFO @ Sat, 11 Nov 2017 04:16:18: 36000000 INFO @ Sat, 11 Nov 2017 04:16:23: 36000000 INFO @ Sat, 11 Nov 2017 04:16:25: 36000000 INFO @ Sat, 11 Nov 2017 04:16:25: 37000000 INFO @ Sat, 11 Nov 2017 04:16:30: 37000000 INFO @ Sat, 11 Nov 2017 04:16:32: 37000000 INFO @ Sat, 11 Nov 2017 04:16:33: 38000000 INFO @ Sat, 11 Nov 2017 04:16:37: 38000000 INFO @ Sat, 11 Nov 2017 04:16:39: 38000000 INFO @ Sat, 11 Nov 2017 04:16:40: 39000000 INFO @ Sat, 11 Nov 2017 04:16:44: 39000000 INFO @ Sat, 11 Nov 2017 04:16:47: 39000000 INFO @ Sat, 11 Nov 2017 04:16:47: 40000000 INFO @ Sat, 11 Nov 2017 04:16:51: 40000000 INFO @ Sat, 11 Nov 2017 04:16:54: 40000000 INFO @ Sat, 11 Nov 2017 04:16:54: 41000000 INFO @ Sat, 11 Nov 2017 04:16:58: 41000000 INFO @ Sat, 11 Nov 2017 04:17:01: 41000000 INFO @ Sat, 11 Nov 2017 04:17:01: 42000000 INFO @ Sat, 11 Nov 2017 04:17:05: 42000000 INFO @ Sat, 11 Nov 2017 04:17:08: 42000000 INFO @ Sat, 11 Nov 2017 04:17:08: 43000000 INFO @ Sat, 11 Nov 2017 04:17:12: 43000000 INFO @ Sat, 11 Nov 2017 04:17:16: 44000000 INFO @ Sat, 11 Nov 2017 04:17:16: 43000000 INFO @ Sat, 11 Nov 2017 04:17:19: 44000000 INFO @ Sat, 11 Nov 2017 04:17:23: 45000000 INFO @ Sat, 11 Nov 2017 04:17:23: 44000000 INFO @ Sat, 11 Nov 2017 04:17:26: 45000000 INFO @ Sat, 11 Nov 2017 04:17:30: 46000000 INFO @ Sat, 11 Nov 2017 04:17:30: 45000000 INFO @ Sat, 11 Nov 2017 04:17:33: 46000000 INFO @ Sat, 11 Nov 2017 04:17:37: 47000000 INFO @ Sat, 11 Nov 2017 04:17:38: 46000000 INFO @ Sat, 11 Nov 2017 04:17:40: 47000000 INFO @ Sat, 11 Nov 2017 04:17:44: 48000000 INFO @ Sat, 11 Nov 2017 04:17:45: 47000000 INFO @ Sat, 11 Nov 2017 04:17:47: 48000000 INFO @ Sat, 11 Nov 2017 04:17:51: 49000000 INFO @ Sat, 11 Nov 2017 04:17:52: 48000000 INFO @ Sat, 11 Nov 2017 04:17:54: 49000000 INFO @ Sat, 11 Nov 2017 04:17:59: 50000000 INFO @ Sat, 11 Nov 2017 04:18:00: 49000000 INFO @ Sat, 11 Nov 2017 04:18:01: 50000000 INFO @ Sat, 11 Nov 2017 04:18:06: 51000000 INFO @ Sat, 11 Nov 2017 04:18:07: 50000000 INFO @ Sat, 11 Nov 2017 04:18:08: 51000000 INFO @ Sat, 11 Nov 2017 04:18:13: 52000000 INFO @ Sat, 11 Nov 2017 04:18:14: 51000000 INFO @ Sat, 11 Nov 2017 04:18:15: 52000000 INFO @ Sat, 11 Nov 2017 04:18:19: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 04:18:19: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 04:18:19: #1 total tags in treatment: 52705757 INFO @ Sat, 11 Nov 2017 04:18:19: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 04:18:19: #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 04:18:20: #1 tags after filtering in treatment: 52705705 INFO @ Sat, 11 Nov 2017 04:18:20: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 04:18:20: #1 finished! INFO @ Sat, 11 Nov 2017 04:18:20: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 04:18:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 04:18:20: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 04:18:20: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 04:18:20: #1 total tags in treatment: 52705757 INFO @ Sat, 11 Nov 2017 04:18:20: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 04:18:20: #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 04:18:21: 52000000 INFO @ Sat, 11 Nov 2017 04:18:22: #1 tags after filtering in treatment: 52705705 INFO @ Sat, 11 Nov 2017 04:18:22: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 04:18:22: #1 finished! INFO @ Sat, 11 Nov 2017 04:18:22: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 04:18:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 04:18:27: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 04:18:27: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 04:18:27: #1 total tags in treatment: 52705757 INFO @ Sat, 11 Nov 2017 04:18:27: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 04:18:27: #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 04:18:27: #2 number of paired peaks: 45973 INFO @ Sat, 11 Nov 2017 04:18:27: start model_add_line... INFO @ Sat, 11 Nov 2017 04:18:28: start X-correlation... INFO @ Sat, 11 Nov 2017 04:18:28: end of X-cor INFO @ Sat, 11 Nov 2017 04:18:28: #2 finished! INFO @ Sat, 11 Nov 2017 04:18:28: #2 predicted fragment length is 176 bps INFO @ Sat, 11 Nov 2017 04:18:28: #2 alternative fragment length(s) may be 176 bps INFO @ Sat, 11 Nov 2017 04:18:28: #2.2 Generate R script for model : SRX1977131.20_model.r INFO @ Sat, 11 Nov 2017 04:18:28: #3 Call peaks... INFO @ Sat, 11 Nov 2017 04:18:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 04:18:28: #1 tags after filtering in treatment: 52705705 INFO @ Sat, 11 Nov 2017 04:18:28: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 04:18:28: #1 finished! INFO @ Sat, 11 Nov 2017 04:18:28: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 04:18:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 04:18:29: #2 number of paired peaks: 45973 INFO @ Sat, 11 Nov 2017 04:18:29: start model_add_line... INFO @ Sat, 11 Nov 2017 04:18:30: start X-correlation... INFO @ Sat, 11 Nov 2017 04:18:30: end of X-cor INFO @ Sat, 11 Nov 2017 04:18:30: #2 finished! INFO @ Sat, 11 Nov 2017 04:18:30: #2 predicted fragment length is 176 bps INFO @ Sat, 11 Nov 2017 04:18:30: #2 alternative fragment length(s) may be 176 bps INFO @ Sat, 11 Nov 2017 04:18:30: #2.2 Generate R script for model : SRX1977131.10_model.r INFO @ Sat, 11 Nov 2017 04:18:30: #3 Call peaks... INFO @ Sat, 11 Nov 2017 04:18:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 04:18:35: #2 number of paired peaks: 45973 INFO @ Sat, 11 Nov 2017 04:18:35: start model_add_line... INFO @ Sat, 11 Nov 2017 04:18:36: start X-correlation... INFO @ Sat, 11 Nov 2017 04:18:36: end of X-cor INFO @ Sat, 11 Nov 2017 04:18:36: #2 finished! INFO @ Sat, 11 Nov 2017 04:18:36: #2 predicted fragment length is 176 bps INFO @ Sat, 11 Nov 2017 04:18:36: #2 alternative fragment length(s) may be 176 bps INFO @ Sat, 11 Nov 2017 04:18:36: #2.2 Generate R script for model : SRX1977131.05_model.r INFO @ Sat, 11 Nov 2017 04:18:36: #3 Call peaks... INFO @ Sat, 11 Nov 2017 04:18:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 04:20:43: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 04:20:45: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 04:20:52: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 04:22:06: #4 Write output xls file... SRX1977131.05_peaks.xls INFO @ Sat, 11 Nov 2017 04:22:07: #4 Write output xls file... SRX1977131.20_peaks.xls INFO @ Sat, 11 Nov 2017 04:22:07: #4 Write peak in narrowPeak format file... SRX1977131.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 04:22:07: #4 Write summits bed file... SRX1977131.20_summits.bed INFO @ Sat, 11 Nov 2017 04:22:07: Done! pass1 - making usageList (106 chroms): 3 millis pass2 - checking and writing primary data (13103 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 04:22:07: #4 Write peak in narrowPeak format file... SRX1977131.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 04:22:08: #4 Write summits bed file... SRX1977131.05_summits.bed INFO @ Sat, 11 Nov 2017 04:22:09: Done! INFO @ Sat, 11 Nov 2017 04:22:10: #4 Write output xls file... SRX1977131.10_peaks.xls INFO @ Sat, 11 Nov 2017 04:22:10: #4 Write peak in narrowPeak format file... SRX1977131.10_peaks.narrowPeak pass1 - making usageList (286 chroms): 20 millis pass2 - checking and writing primary data (116923 records, 4 fields): 142 millis INFO @ Sat, 11 Nov 2017 04:22:10: #4 Write summits bed file... SRX1977131.10_summits.bed CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 04:22:11: Done! pass1 - making usageList (199 chroms): 9 millis pass2 - checking and writing primary data (49913 records, 4 fields): 64 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。