Job ID = 9370020 sra ファイルのダウンロード中... Completed: 2160734K bytes transferred in 137 seconds (128309K bits/sec), in 1 file, 2 directories. 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 63135631 spots for /home/okishinya/chipatlas/results/ce10/SRX2710281/SRR5418735.sra Written 63135631 spots total 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: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:56:25 63135631 reads; of these: 63135631 (100.00%) were unpaired; of these: 6484455 (10.27%) aligned 0 times 24281728 (38.46%) aligned exactly 1 time 32369448 (51.27%) aligned >1 times 89.73% overall alignment rate Time searching: 00:56:26 Overall time: 00:56:26 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 24 files... [bam_rmdupse_core] 39750104 / 56651176 = 0.7017 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, 04 Aug 2017 13:20:59: # Command line: callpeak -t SRX2710281.bam -f BAM -g ce -n SRX2710281.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2710281.10 # format = BAM # ChIP-seq file = ['SRX2710281.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 04 Aug 2017 13:20:59: #1 read tag files... INFO @ Fri, 04 Aug 2017 13:20:59: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 13:20:59: # Command line: callpeak -t SRX2710281.bam -f BAM -g ce -n SRX2710281.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2710281.20 # format = BAM # ChIP-seq file = ['SRX2710281.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 04 Aug 2017 13:20:59: #1 read tag files... INFO @ Fri, 04 Aug 2017 13:20:59: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 13:20:59: # Command line: callpeak -t SRX2710281.bam -f BAM -g ce -n SRX2710281.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2710281.05 # format = BAM # ChIP-seq file = ['SRX2710281.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 04 Aug 2017 13:20:59: #1 read tag files... INFO @ Fri, 04 Aug 2017 13:20:59: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 13:21:11: 1000000 INFO @ Fri, 04 Aug 2017 13:21:12: 1000000 INFO @ Fri, 04 Aug 2017 13:21:16: 1000000 INFO @ Fri, 04 Aug 2017 13:21:22: 2000000 INFO @ Fri, 04 Aug 2017 13:21:24: 2000000 INFO @ Fri, 04 Aug 2017 13:21:34: 3000000 INFO @ Fri, 04 Aug 2017 13:21:34: 3000000 INFO @ Fri, 04 Aug 2017 13:21:37: 2000000 INFO @ Fri, 04 Aug 2017 13:21:46: 4000000 INFO @ Fri, 04 Aug 2017 13:21:47: 4000000 INFO @ Fri, 04 Aug 2017 13:21:51: 3000000 INFO @ Fri, 04 Aug 2017 13:22:00: 5000000 INFO @ Fri, 04 Aug 2017 13:22:04: 4000000 INFO @ Fri, 04 Aug 2017 13:22:05: 5000000 INFO @ Fri, 04 Aug 2017 13:22:13: 6000000 INFO @ Fri, 04 Aug 2017 13:22:18: 5000000 INFO @ Fri, 04 Aug 2017 13:22:20: 6000000 INFO @ Fri, 04 Aug 2017 13:22:27: 7000000 INFO @ Fri, 04 Aug 2017 13:22:31: 6000000 INFO @ Fri, 04 Aug 2017 13:22:36: 7000000 INFO @ Fri, 04 Aug 2017 13:22:45: 8000000 INFO @ Fri, 04 Aug 2017 13:22:45: 7000000 INFO @ Fri, 04 Aug 2017 13:22:56: 8000000 INFO @ Fri, 04 Aug 2017 13:23:00: 8000000 INFO @ Fri, 04 Aug 2017 13:23:02: 9000000 INFO @ Fri, 04 Aug 2017 13:23:09: 9000000 INFO @ Fri, 04 Aug 2017 13:23:14: 9000000 INFO @ Fri, 04 Aug 2017 13:23:16: 10000000 INFO @ Fri, 04 Aug 2017 13:23:20: 10000000 INFO @ Fri, 04 Aug 2017 13:23:30: 10000000 INFO @ Fri, 04 Aug 2017 13:23:33: 11000000 INFO @ Fri, 04 Aug 2017 13:23:35: 11000000 INFO @ Fri, 04 Aug 2017 13:23:47: 11000000 INFO @ Fri, 04 Aug 2017 13:23:47: 12000000 INFO @ Fri, 04 Aug 2017 13:23:55: 12000000 INFO @ Fri, 04 Aug 2017 13:23:59: 13000000 INFO @ Fri, 04 Aug 2017 13:24:09: 12000000 INFO @ Fri, 04 Aug 2017 13:24:12: 14000000 INFO @ Fri, 04 Aug 2017 13:24:15: 13000000 INFO @ Fri, 04 Aug 2017 13:24:25: 15000000 INFO @ Fri, 04 Aug 2017 13:24:26: 13000000 INFO @ Fri, 04 Aug 2017 13:24:29: 14000000 INFO @ Fri, 04 Aug 2017 13:24:36: 16000000 INFO @ Fri, 04 Aug 2017 13:24:40: 14000000 INFO @ Fri, 04 Aug 2017 13:24:40: 15000000 INFO @ Fri, 04 Aug 2017 13:24:46: #1 tag size is determined as 50 bps INFO @ Fri, 04 Aug 2017 13:24:46: #1 tag size = 50 INFO @ Fri, 04 Aug 2017 13:24:46: #1 total tags in treatment: 16901072 INFO @ Fri, 04 Aug 2017 13:24:46: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 13:24:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 13:24:47: #1 tags after filtering in treatment: 16901072 INFO @ Fri, 04 Aug 2017 13:24:47: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 Aug 2017 13:24:47: #1 finished! INFO @ Fri, 04 Aug 2017 13:24:47: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 13:24:47: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 13:24:49: #2 number of paired peaks: 1395 INFO @ Fri, 04 Aug 2017 13:24:49: start model_add_line... INFO @ Fri, 04 Aug 2017 13:24:49: start X-correlation... INFO @ Fri, 04 Aug 2017 13:24:49: end of X-cor INFO @ Fri, 04 Aug 2017 13:24:49: #2 finished! INFO @ Fri, 04 Aug 2017 13:24:49: #2 predicted fragment length is 106 bps INFO @ Fri, 04 Aug 2017 13:24:49: #2 alternative fragment length(s) may be 4,106 bps INFO @ Fri, 04 Aug 2017 13:24:49: #2.2 Generate R script for model : SRX2710281.10_model.r INFO @ Fri, 04 Aug 2017 13:24:49: #3 Call peaks... INFO @ Fri, 04 Aug 2017 13:24:49: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 13:24:51: 16000000 INFO @ Fri, 04 Aug 2017 13:24:53: 15000000 INFO @ Fri, 04 Aug 2017 13:25:04: #1 tag size is determined as 50 bps INFO @ Fri, 04 Aug 2017 13:25:04: #1 tag size = 50 INFO @ Fri, 04 Aug 2017 13:25:04: #1 total tags in treatment: 16901072 INFO @ Fri, 04 Aug 2017 13:25:04: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 13:25:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 13:25:05: #1 tags after filtering in treatment: 16901072 INFO @ Fri, 04 Aug 2017 13:25:05: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 Aug 2017 13:25:05: #1 finished! INFO @ Fri, 04 Aug 2017 13:25:05: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 13:25:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 13:25:08: 16000000 INFO @ Fri, 04 Aug 2017 13:25:08: #2 number of paired peaks: 1395 INFO @ Fri, 04 Aug 2017 13:25:08: start model_add_line... INFO @ Fri, 04 Aug 2017 13:25:08: start X-correlation... INFO @ Fri, 04 Aug 2017 13:25:08: end of X-cor INFO @ Fri, 04 Aug 2017 13:25:08: #2 finished! INFO @ Fri, 04 Aug 2017 13:25:08: #2 predicted fragment length is 106 bps INFO @ Fri, 04 Aug 2017 13:25:08: #2 alternative fragment length(s) may be 4,106 bps INFO @ Fri, 04 Aug 2017 13:25:08: #2.2 Generate R script for model : SRX2710281.20_model.r INFO @ Fri, 04 Aug 2017 13:25:08: #3 Call peaks... INFO @ Fri, 04 Aug 2017 13:25:08: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 13:25:24: #1 tag size is determined as 50 bps INFO @ Fri, 04 Aug 2017 13:25:24: #1 tag size = 50 INFO @ Fri, 04 Aug 2017 13:25:24: #1 total tags in treatment: 16901072 INFO @ Fri, 04 Aug 2017 13:25:24: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 13:25:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 13:25:25: #1 tags after filtering in treatment: 16901072 INFO @ Fri, 04 Aug 2017 13:25:25: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 Aug 2017 13:25:25: #1 finished! INFO @ Fri, 04 Aug 2017 13:25:25: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 13:25:25: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 13:25:27: #2 number of paired peaks: 1395 INFO @ Fri, 04 Aug 2017 13:25:27: start model_add_line... INFO @ Fri, 04 Aug 2017 13:25:27: start X-correlation... INFO @ Fri, 04 Aug 2017 13:25:27: end of X-cor INFO @ Fri, 04 Aug 2017 13:25:27: #2 finished! INFO @ Fri, 04 Aug 2017 13:25:27: #2 predicted fragment length is 106 bps INFO @ Fri, 04 Aug 2017 13:25:27: #2 alternative fragment length(s) may be 4,106 bps INFO @ Fri, 04 Aug 2017 13:25:27: #2.2 Generate R script for model : SRX2710281.05_model.r INFO @ Fri, 04 Aug 2017 13:25:27: #3 Call peaks... INFO @ Fri, 04 Aug 2017 13:25:27: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 13:26:14: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 13:26:24: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 13:26:45: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 13:27:01: #4 Write output xls file... SRX2710281.10_peaks.xls INFO @ Fri, 04 Aug 2017 13:27:01: #4 Write peak in narrowPeak format file... SRX2710281.10_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 13:27:01: #4 Write summits bed file... SRX2710281.10_summits.bed INFO @ Fri, 04 Aug 2017 13:27:01: Done! INFO @ Fri, 04 Aug 2017 13:27:01: #4 Write output xls file... SRX2710281.20_peaks.xls INFO @ Fri, 04 Aug 2017 13:27:01: #4 Write peak in narrowPeak format file... SRX2710281.20_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 13:27:01: #4 Write summits bed file... SRX2710281.20_summits.bed INFO @ Fri, 04 Aug 2017 13:27:02: Done! pass1 - making usageList (7 chroms): 5 millis pass2 - checking and writing primary data (16416 records, 4 fields): 46 millis CompletedMACS2peakCalling pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (9106 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 13:27:23: #4 Write output xls file... SRX2710281.05_peaks.xls INFO @ Fri, 04 Aug 2017 13:27:23: #4 Write peak in narrowPeak format file... SRX2710281.05_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 13:27:23: #4 Write summits bed file... SRX2710281.05_summits.bed INFO @ Fri, 04 Aug 2017 13:27:24: Done! pass1 - making usageList (7 chroms): 7 millis pass2 - checking and writing primary data (24524 records, 4 fields): 76 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。