Job ID = 10194849 sra ファイルのダウンロード中... Completed: 1064890K bytes transferred in 20 seconds (428673K 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 53180292 spots for /home/okishinya/chipatlas/results/rn6/SRX1977138/SRR3952270.sra Written 53180292 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: 01:25:11 53180292 reads; of these: 53180292 (100.00%) were unpaired; of these: 22365131 (42.06%) aligned 0 times 17440838 (32.80%) aligned exactly 1 time 13374323 (25.15%) aligned >1 times 57.94% overall alignment rate Time searching: 01:25:15 Overall time: 01:25:15 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 16 files... [bam_rmdupse_core] 7625729 / 30815161 = 0.2475 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 03:22:31: # Command line: callpeak -t SRX1977138.bam -f BAM -g 2.15e9 -n SRX1977138.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1977138.05 # format = BAM # ChIP-seq file = ['SRX1977138.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 03:22:31: # Command line: callpeak -t SRX1977138.bam -f BAM -g 2.15e9 -n SRX1977138.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1977138.20 # format = BAM # ChIP-seq file = ['SRX1977138.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 03:22:31: # Command line: callpeak -t SRX1977138.bam -f BAM -g 2.15e9 -n SRX1977138.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1977138.10 # format = BAM # ChIP-seq file = ['SRX1977138.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 03:22:31: #1 read tag files... INFO @ Sat, 11 Nov 2017 03:22:31: #1 read tag files... INFO @ Sat, 11 Nov 2017 03:22:31: #1 read tag files... INFO @ Sat, 11 Nov 2017 03:22:31: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 03:22:31: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 03:22:31: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 03:22:38: 1000000 INFO @ Sat, 11 Nov 2017 03:22:39: 1000000 INFO @ Sat, 11 Nov 2017 03:22:39: 1000000 INFO @ Sat, 11 Nov 2017 03:22:46: 2000000 INFO @ Sat, 11 Nov 2017 03:22:46: 2000000 INFO @ Sat, 11 Nov 2017 03:22:46: 2000000 INFO @ Sat, 11 Nov 2017 03:22:53: 3000000 INFO @ Sat, 11 Nov 2017 03:22:53: 3000000 INFO @ Sat, 11 Nov 2017 03:22:53: 3000000 INFO @ Sat, 11 Nov 2017 03:23:00: 4000000 INFO @ Sat, 11 Nov 2017 03:23:00: 4000000 INFO @ Sat, 11 Nov 2017 03:23:01: 4000000 INFO @ Sat, 11 Nov 2017 03:23:07: 5000000 INFO @ Sat, 11 Nov 2017 03:23:08: 5000000 INFO @ Sat, 11 Nov 2017 03:23:08: 5000000 INFO @ Sat, 11 Nov 2017 03:23:14: 6000000 INFO @ Sat, 11 Nov 2017 03:23:15: 6000000 INFO @ Sat, 11 Nov 2017 03:23:15: 6000000 INFO @ Sat, 11 Nov 2017 03:23:22: 7000000 INFO @ Sat, 11 Nov 2017 03:23:23: 7000000 INFO @ Sat, 11 Nov 2017 03:23:23: 7000000 INFO @ Sat, 11 Nov 2017 03:23:29: 8000000 INFO @ Sat, 11 Nov 2017 03:23:30: 8000000 INFO @ Sat, 11 Nov 2017 03:23:30: 8000000 INFO @ Sat, 11 Nov 2017 03:23:36: 9000000 INFO @ Sat, 11 Nov 2017 03:23:37: 9000000 INFO @ Sat, 11 Nov 2017 03:23:38: 9000000 INFO @ Sat, 11 Nov 2017 03:23:43: 10000000 INFO @ Sat, 11 Nov 2017 03:23:45: 10000000 INFO @ Sat, 11 Nov 2017 03:23:46: 10000000 INFO @ Sat, 11 Nov 2017 03:23:50: 11000000 INFO @ Sat, 11 Nov 2017 03:23:53: 11000000 INFO @ Sat, 11 Nov 2017 03:23:53: 11000000 INFO @ Sat, 11 Nov 2017 03:23:57: 12000000 INFO @ Sat, 11 Nov 2017 03:24:00: 12000000 INFO @ Sat, 11 Nov 2017 03:24:01: 12000000 INFO @ Sat, 11 Nov 2017 03:24:05: 13000000 INFO @ Sat, 11 Nov 2017 03:24:08: 13000000 INFO @ Sat, 11 Nov 2017 03:24:08: 13000000 INFO @ Sat, 11 Nov 2017 03:24:12: 14000000 INFO @ Sat, 11 Nov 2017 03:24:15: 14000000 INFO @ Sat, 11 Nov 2017 03:24:16: 14000000 INFO @ Sat, 11 Nov 2017 03:24:19: 15000000 INFO @ Sat, 11 Nov 2017 03:24:23: 15000000 INFO @ Sat, 11 Nov 2017 03:24:24: 15000000 INFO @ Sat, 11 Nov 2017 03:24:26: 16000000 INFO @ Sat, 11 Nov 2017 03:24:31: 16000000 INFO @ Sat, 11 Nov 2017 03:24:32: 16000000 INFO @ Sat, 11 Nov 2017 03:24:33: 17000000 INFO @ Sat, 11 Nov 2017 03:24:39: 17000000 INFO @ Sat, 11 Nov 2017 03:24:39: 17000000 INFO @ Sat, 11 Nov 2017 03:24:41: 18000000 INFO @ Sat, 11 Nov 2017 03:24:46: 18000000 INFO @ Sat, 11 Nov 2017 03:24:47: 18000000 INFO @ Sat, 11 Nov 2017 03:24:48: 19000000 INFO @ Sat, 11 Nov 2017 03:24:54: 19000000 INFO @ Sat, 11 Nov 2017 03:24:55: 20000000 INFO @ Sat, 11 Nov 2017 03:24:55: 19000000 INFO @ Sat, 11 Nov 2017 03:25:02: 20000000 INFO @ Sat, 11 Nov 2017 03:25:02: 21000000 INFO @ Sat, 11 Nov 2017 03:25:03: 20000000 INFO @ Sat, 11 Nov 2017 03:25:09: 21000000 INFO @ Sat, 11 Nov 2017 03:25:09: 22000000 INFO @ Sat, 11 Nov 2017 03:25:11: 21000000 INFO @ Sat, 11 Nov 2017 03:25:17: 23000000 INFO @ Sat, 11 Nov 2017 03:25:17: 22000000 INFO @ Sat, 11 Nov 2017 03:25:18: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 03:25:18: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 03:25:18: #1 total tags in treatment: 23189432 INFO @ Sat, 11 Nov 2017 03:25:18: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 03:25:18: #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 03:25:19: #1 tags after filtering in treatment: 23189324 INFO @ Sat, 11 Nov 2017 03:25:19: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 03:25:19: #1 finished! INFO @ Sat, 11 Nov 2017 03:25:19: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 03:25:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 03:25:19: 22000000 INFO @ Sat, 11 Nov 2017 03:25:23: #2 number of paired peaks: 47710 INFO @ Sat, 11 Nov 2017 03:25:23: start model_add_line... INFO @ Sat, 11 Nov 2017 03:25:23: start X-correlation... INFO @ Sat, 11 Nov 2017 03:25:23: end of X-cor INFO @ Sat, 11 Nov 2017 03:25:23: #2 finished! INFO @ Sat, 11 Nov 2017 03:25:23: #2 predicted fragment length is 150 bps INFO @ Sat, 11 Nov 2017 03:25:23: #2 alternative fragment length(s) may be 62,150 bps INFO @ Sat, 11 Nov 2017 03:25:23: #2.2 Generate R script for model : SRX1977138.20_model.r INFO @ Sat, 11 Nov 2017 03:25:23: #3 Call peaks... INFO @ Sat, 11 Nov 2017 03:25:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 03:25:25: 23000000 INFO @ Sat, 11 Nov 2017 03:25:26: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 03:25:26: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 03:25:26: #1 total tags in treatment: 23189432 INFO @ Sat, 11 Nov 2017 03:25:26: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 03:25:26: #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 03:25:27: #1 tags after filtering in treatment: 23189324 INFO @ Sat, 11 Nov 2017 03:25:27: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 03:25:27: #1 finished! INFO @ Sat, 11 Nov 2017 03:25:27: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 03:25:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 03:25:27: 23000000 INFO @ Sat, 11 Nov 2017 03:25:28: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 03:25:28: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 03:25:28: #1 total tags in treatment: 23189432 INFO @ Sat, 11 Nov 2017 03:25:28: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 03:25:28: #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 03:25:29: #1 tags after filtering in treatment: 23189324 INFO @ Sat, 11 Nov 2017 03:25:29: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 03:25:29: #1 finished! INFO @ Sat, 11 Nov 2017 03:25:29: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 03:25:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 03:25:31: #2 number of paired peaks: 47710 INFO @ Sat, 11 Nov 2017 03:25:31: start model_add_line... INFO @ Sat, 11 Nov 2017 03:25:31: start X-correlation... INFO @ Sat, 11 Nov 2017 03:25:31: end of X-cor INFO @ Sat, 11 Nov 2017 03:25:31: #2 finished! INFO @ Sat, 11 Nov 2017 03:25:31: #2 predicted fragment length is 150 bps INFO @ Sat, 11 Nov 2017 03:25:31: #2 alternative fragment length(s) may be 62,150 bps INFO @ Sat, 11 Nov 2017 03:25:31: #2.2 Generate R script for model : SRX1977138.10_model.r INFO @ Sat, 11 Nov 2017 03:25:31: #3 Call peaks... INFO @ Sat, 11 Nov 2017 03:25:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 03:25:33: #2 number of paired peaks: 47710 INFO @ Sat, 11 Nov 2017 03:25:33: start model_add_line... INFO @ Sat, 11 Nov 2017 03:25:34: start X-correlation... INFO @ Sat, 11 Nov 2017 03:25:34: end of X-cor INFO @ Sat, 11 Nov 2017 03:25:34: #2 finished! INFO @ Sat, 11 Nov 2017 03:25:34: #2 predicted fragment length is 150 bps INFO @ Sat, 11 Nov 2017 03:25:34: #2 alternative fragment length(s) may be 62,150 bps INFO @ Sat, 11 Nov 2017 03:25:34: #2.2 Generate R script for model : SRX1977138.05_model.r INFO @ Sat, 11 Nov 2017 03:25:34: #3 Call peaks... INFO @ Sat, 11 Nov 2017 03:25:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 03:26:24: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 03:26:30: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 03:26:34: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 03:26:56: #4 Write output xls file... SRX1977138.20_peaks.xls INFO @ Sat, 11 Nov 2017 03:26:56: #4 Write peak in narrowPeak format file... SRX1977138.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 03:26:56: #4 Write summits bed file... SRX1977138.20_summits.bed INFO @ Sat, 11 Nov 2017 03:26:56: Done! pass1 - making usageList (83 chroms): 2 millis pass2 - checking and writing primary data (2207 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 03:27:05: #4 Write output xls file... SRX1977138.10_peaks.xls INFO @ Sat, 11 Nov 2017 03:27:06: #4 Write peak in narrowPeak format file... SRX1977138.10_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 03:27:06: #4 Write summits bed file... SRX1977138.10_summits.bed INFO @ Sat, 11 Nov 2017 03:27:06: Done! pass1 - making usageList (126 chroms): 3 millis pass2 - checking and writing primary data (13057 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 03:27:07: #4 Write output xls file... SRX1977138.05_peaks.xls INFO @ Sat, 11 Nov 2017 03:27:07: #4 Write peak in narrowPeak format file... SRX1977138.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 03:27:07: #4 Write summits bed file... SRX1977138.05_summits.bed INFO @ Sat, 11 Nov 2017 03:27:07: Done! pass1 - making usageList (204 chroms): 7 millis pass2 - checking and writing primary data (37807 records, 4 fields): 51 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。