Job ID = 10194828 sra ファイルのダウンロード中... Completed: 788020K bytes transferred in 14 seconds (438085K 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 40564191 spots for /home/okishinya/chipatlas/results/rn6/SRX1977118/SRR3952250.sra Written 40564191 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: 01:13:58 40564191 reads; of these: 40564191 (100.00%) were unpaired; of these: 13361546 (32.94%) aligned 0 times 15956260 (39.34%) aligned exactly 1 time 11246385 (27.72%) aligned >1 times 67.06% overall alignment rate Time searching: 01:14:01 Overall time: 01:14:01 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] 3872954 / 27202645 = 0.1424 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 02:24:08: # Command line: callpeak -t SRX1977118.bam -f BAM -g 2.15e9 -n SRX1977118.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1977118.10 # format = BAM # ChIP-seq file = ['SRX1977118.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 02:24:08: #1 read tag files... INFO @ Sat, 11 Nov 2017 02:24:08: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 02:24:08: # Command line: callpeak -t SRX1977118.bam -f BAM -g 2.15e9 -n SRX1977118.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1977118.05 # format = BAM # ChIP-seq file = ['SRX1977118.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 02:24:08: #1 read tag files... INFO @ Sat, 11 Nov 2017 02:24:08: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 02:24:08: # Command line: callpeak -t SRX1977118.bam -f BAM -g 2.15e9 -n SRX1977118.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1977118.20 # format = BAM # ChIP-seq file = ['SRX1977118.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 02:24:08: #1 read tag files... INFO @ Sat, 11 Nov 2017 02:24:08: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 02:24:18: 1000000 INFO @ Sat, 11 Nov 2017 02:24:20: 1000000 INFO @ Sat, 11 Nov 2017 02:24:20: 1000000 INFO @ Sat, 11 Nov 2017 02:24:27: 2000000 INFO @ Sat, 11 Nov 2017 02:24:28: 2000000 INFO @ Sat, 11 Nov 2017 02:24:29: 2000000 INFO @ Sat, 11 Nov 2017 02:24:36: 3000000 INFO @ Sat, 11 Nov 2017 02:24:38: 3000000 INFO @ Sat, 11 Nov 2017 02:24:39: 3000000 INFO @ Sat, 11 Nov 2017 02:24:46: 4000000 INFO @ Sat, 11 Nov 2017 02:24:47: 4000000 INFO @ Sat, 11 Nov 2017 02:24:47: 4000000 INFO @ Sat, 11 Nov 2017 02:24:55: 5000000 INFO @ Sat, 11 Nov 2017 02:24:55: 5000000 INFO @ Sat, 11 Nov 2017 02:24:56: 5000000 INFO @ Sat, 11 Nov 2017 02:25:03: 6000000 INFO @ Sat, 11 Nov 2017 02:25:06: 6000000 INFO @ Sat, 11 Nov 2017 02:25:07: 6000000 INFO @ Sat, 11 Nov 2017 02:25:10: 7000000 INFO @ Sat, 11 Nov 2017 02:25:15: 7000000 INFO @ Sat, 11 Nov 2017 02:25:16: 7000000 INFO @ Sat, 11 Nov 2017 02:25:20: 8000000 INFO @ Sat, 11 Nov 2017 02:25:23: 8000000 INFO @ Sat, 11 Nov 2017 02:25:26: 8000000 INFO @ Sat, 11 Nov 2017 02:25:30: 9000000 INFO @ Sat, 11 Nov 2017 02:25:33: 9000000 INFO @ Sat, 11 Nov 2017 02:25:36: 9000000 INFO @ Sat, 11 Nov 2017 02:25:41: 10000000 INFO @ Sat, 11 Nov 2017 02:25:42: 10000000 INFO @ Sat, 11 Nov 2017 02:25:45: 10000000 INFO @ Sat, 11 Nov 2017 02:25:48: 11000000 INFO @ Sat, 11 Nov 2017 02:25:54: 11000000 INFO @ Sat, 11 Nov 2017 02:25:55: 11000000 INFO @ Sat, 11 Nov 2017 02:25:57: 12000000 INFO @ Sat, 11 Nov 2017 02:26:04: 12000000 INFO @ Sat, 11 Nov 2017 02:26:04: 12000000 INFO @ Sat, 11 Nov 2017 02:26:06: 13000000 INFO @ Sat, 11 Nov 2017 02:26:13: 13000000 INFO @ Sat, 11 Nov 2017 02:26:14: 13000000 INFO @ Sat, 11 Nov 2017 02:26:16: 14000000 INFO @ Sat, 11 Nov 2017 02:26:21: 14000000 INFO @ Sat, 11 Nov 2017 02:26:23: 14000000 INFO @ Sat, 11 Nov 2017 02:26:25: 15000000 INFO @ Sat, 11 Nov 2017 02:26:29: 15000000 INFO @ Sat, 11 Nov 2017 02:26:32: 15000000 INFO @ Sat, 11 Nov 2017 02:26:35: 16000000 INFO @ Sat, 11 Nov 2017 02:26:39: 16000000 INFO @ Sat, 11 Nov 2017 02:26:41: 16000000 INFO @ Sat, 11 Nov 2017 02:26:44: 17000000 INFO @ Sat, 11 Nov 2017 02:26:47: 17000000 INFO @ Sat, 11 Nov 2017 02:26:49: 17000000 INFO @ Sat, 11 Nov 2017 02:26:51: 18000000 INFO @ Sat, 11 Nov 2017 02:26:58: 18000000 INFO @ Sat, 11 Nov 2017 02:26:59: 18000000 INFO @ Sat, 11 Nov 2017 02:26:59: 19000000 INFO @ Sat, 11 Nov 2017 02:27:07: 19000000 INFO @ Sat, 11 Nov 2017 02:27:07: 20000000 INFO @ Sat, 11 Nov 2017 02:27:08: 19000000 INFO @ Sat, 11 Nov 2017 02:27:15: 20000000 INFO @ Sat, 11 Nov 2017 02:27:16: 20000000 INFO @ Sat, 11 Nov 2017 02:27:17: 21000000 INFO @ Sat, 11 Nov 2017 02:27:23: 21000000 INFO @ Sat, 11 Nov 2017 02:27:26: 21000000 INFO @ Sat, 11 Nov 2017 02:27:27: 22000000 INFO @ Sat, 11 Nov 2017 02:27:30: 22000000 INFO @ Sat, 11 Nov 2017 02:27:35: 22000000 INFO @ Sat, 11 Nov 2017 02:27:37: 23000000 INFO @ Sat, 11 Nov 2017 02:27:40: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 02:27:40: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 02:27:40: #1 total tags in treatment: 23329691 INFO @ Sat, 11 Nov 2017 02:27:40: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 02:27:40: #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 02:27:41: #1 tags after filtering in treatment: 23329583 INFO @ Sat, 11 Nov 2017 02:27:41: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 02:27:41: #1 finished! INFO @ Sat, 11 Nov 2017 02:27:41: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 02:27:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 02:27:41: 23000000 INFO @ Sat, 11 Nov 2017 02:27:42: 23000000 INFO @ Sat, 11 Nov 2017 02:27:45: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 02:27:45: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 02:27:45: #1 total tags in treatment: 23329691 INFO @ Sat, 11 Nov 2017 02:27:45: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 02:27:45: #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 02:27:45: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 02:27:45: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 02:27:45: #1 total tags in treatment: 23329691 INFO @ Sat, 11 Nov 2017 02:27:45: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 02:27:45: #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 02:27:45: #2 number of paired peaks: 58962 INFO @ Sat, 11 Nov 2017 02:27:45: start model_add_line... INFO @ Sat, 11 Nov 2017 02:27:45: #1 tags after filtering in treatment: 23329583 INFO @ Sat, 11 Nov 2017 02:27:45: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 02:27:45: #1 finished! INFO @ Sat, 11 Nov 2017 02:27:45: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 02:27:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 02:27:46: start X-correlation... INFO @ Sat, 11 Nov 2017 02:27:46: end of X-cor INFO @ Sat, 11 Nov 2017 02:27:46: #2 finished! INFO @ Sat, 11 Nov 2017 02:27:46: #2 predicted fragment length is 162 bps INFO @ Sat, 11 Nov 2017 02:27:46: #2 alternative fragment length(s) may be 162 bps INFO @ Sat, 11 Nov 2017 02:27:46: #2.2 Generate R script for model : SRX1977118.10_model.r INFO @ Sat, 11 Nov 2017 02:27:46: #3 Call peaks... INFO @ Sat, 11 Nov 2017 02:27:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 02:27:46: #1 tags after filtering in treatment: 23329583 INFO @ Sat, 11 Nov 2017 02:27:46: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 02:27:46: #1 finished! INFO @ Sat, 11 Nov 2017 02:27:46: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 02:27:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 02:27:51: #2 number of paired peaks: 58962 INFO @ Sat, 11 Nov 2017 02:27:51: start model_add_line... INFO @ Sat, 11 Nov 2017 02:27:51: start X-correlation... INFO @ Sat, 11 Nov 2017 02:27:51: end of X-cor INFO @ Sat, 11 Nov 2017 02:27:51: #2 finished! INFO @ Sat, 11 Nov 2017 02:27:51: #2 predicted fragment length is 162 bps INFO @ Sat, 11 Nov 2017 02:27:51: #2 alternative fragment length(s) may be 162 bps INFO @ Sat, 11 Nov 2017 02:27:51: #2.2 Generate R script for model : SRX1977118.20_model.r INFO @ Sat, 11 Nov 2017 02:27:51: #3 Call peaks... INFO @ Sat, 11 Nov 2017 02:27:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 02:27:51: #2 number of paired peaks: 58962 INFO @ Sat, 11 Nov 2017 02:27:51: start model_add_line... INFO @ Sat, 11 Nov 2017 02:27:52: start X-correlation... INFO @ Sat, 11 Nov 2017 02:27:52: end of X-cor INFO @ Sat, 11 Nov 2017 02:27:52: #2 finished! INFO @ Sat, 11 Nov 2017 02:27:52: #2 predicted fragment length is 162 bps INFO @ Sat, 11 Nov 2017 02:27:52: #2 alternative fragment length(s) may be 162 bps INFO @ Sat, 11 Nov 2017 02:27:52: #2.2 Generate R script for model : SRX1977118.05_model.r INFO @ Sat, 11 Nov 2017 02:27:52: #3 Call peaks... INFO @ Sat, 11 Nov 2017 02:27:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 02:28:54: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 02:28:59: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 02:29:10: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 02:29:34: #4 Write output xls file... SRX1977118.10_peaks.xls INFO @ Sat, 11 Nov 2017 02:29:34: #4 Write peak in narrowPeak format file... SRX1977118.10_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 02:29:35: #4 Write summits bed file... SRX1977118.10_summits.bed INFO @ Sat, 11 Nov 2017 02:29:35: Done! pass1 - making usageList (132 chroms): 3 millis pass2 - checking and writing primary data (11416 records, 4 fields): 31 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 02:29:43: #4 Write output xls file... SRX1977118.05_peaks.xls INFO @ Sat, 11 Nov 2017 02:29:44: #4 Write peak in narrowPeak format file... SRX1977118.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 02:29:44: #4 Write summits bed file... SRX1977118.05_summits.bed INFO @ Sat, 11 Nov 2017 02:29:44: Done! pass1 - making usageList (204 chroms): 15 millis pass2 - checking and writing primary data (42627 records, 4 fields): 101 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 02:29:54: #4 Write output xls file... SRX1977118.20_peaks.xls INFO @ Sat, 11 Nov 2017 02:29:55: #4 Write peak in narrowPeak format file... SRX1977118.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 02:29:55: #4 Write summits bed file... SRX1977118.20_summits.bed INFO @ Sat, 11 Nov 2017 02:29:55: Done! pass1 - making usageList (76 chroms): 1 millis pass2 - checking and writing primary data (1627 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。