Job ID = 11293659 sra ファイルのダウンロード中... Completed: 273184K bytes transferred in 7 seconds (319460K 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... Read 13046291 spots for /home/okishinya/chipatlas/results/dm3/SRX3873748/SRR6927813.sra Written 13046291 spots for /home/okishinya/chipatlas/results/dm3/SRX3873748/SRR6927813.sra 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: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:46 13046291 reads; of these: 13046291 (100.00%) were unpaired; of these: 1649131 (12.64%) aligned 0 times 9474701 (72.62%) aligned exactly 1 time 1922459 (14.74%) aligned >1 times 87.36% overall alignment rate Time searching: 00:03:46 Overall time: 00:03:46 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 2788621 / 11397160 = 0.2447 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 @ Sun, 04 Nov 2018 17:53:59: # Command line: callpeak -t SRX3873748.bam -f BAM -g dm -n SRX3873748.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3873748.20 # format = BAM # ChIP-seq file = ['SRX3873748.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 04 Nov 2018 17:53:59: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:53:59: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:53:59: # Command line: callpeak -t SRX3873748.bam -f BAM -g dm -n SRX3873748.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3873748.10 # format = BAM # ChIP-seq file = ['SRX3873748.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 04 Nov 2018 17:53:59: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:53:59: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:53:59: # Command line: callpeak -t SRX3873748.bam -f BAM -g dm -n SRX3873748.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3873748.05 # format = BAM # ChIP-seq file = ['SRX3873748.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 04 Nov 2018 17:53:59: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:53:59: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:54:05: 1000000 INFO @ Sun, 04 Nov 2018 17:54:06: 1000000 INFO @ Sun, 04 Nov 2018 17:54:06: 1000000 INFO @ Sun, 04 Nov 2018 17:54:12: 2000000 INFO @ Sun, 04 Nov 2018 17:54:12: 2000000 INFO @ Sun, 04 Nov 2018 17:54:13: 2000000 INFO @ Sun, 04 Nov 2018 17:54:19: 3000000 INFO @ Sun, 04 Nov 2018 17:54:19: 3000000 INFO @ Sun, 04 Nov 2018 17:54:20: 3000000 INFO @ Sun, 04 Nov 2018 17:54:26: 4000000 INFO @ Sun, 04 Nov 2018 17:54:26: 4000000 INFO @ Sun, 04 Nov 2018 17:54:27: 4000000 INFO @ Sun, 04 Nov 2018 17:54:33: 5000000 INFO @ Sun, 04 Nov 2018 17:54:33: 5000000 INFO @ Sun, 04 Nov 2018 17:54:35: 5000000 INFO @ Sun, 04 Nov 2018 17:54:40: 6000000 INFO @ Sun, 04 Nov 2018 17:54:40: 6000000 INFO @ Sun, 04 Nov 2018 17:54:42: 6000000 INFO @ Sun, 04 Nov 2018 17:54:47: 7000000 INFO @ Sun, 04 Nov 2018 17:54:47: 7000000 INFO @ Sun, 04 Nov 2018 17:54:50: 7000000 INFO @ Sun, 04 Nov 2018 17:54:54: 8000000 INFO @ Sun, 04 Nov 2018 17:54:54: 8000000 INFO @ Sun, 04 Nov 2018 17:54:57: 8000000 INFO @ Sun, 04 Nov 2018 17:54:58: #1 tag size is determined as 50 bps INFO @ Sun, 04 Nov 2018 17:54:58: #1 tag size = 50 INFO @ Sun, 04 Nov 2018 17:54:58: #1 total tags in treatment: 8608539 INFO @ Sun, 04 Nov 2018 17:54:58: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 17:54:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Nov 2018 17:54:58: #1 tags after filtering in treatment: 8608539 INFO @ Sun, 04 Nov 2018 17:54:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 17:54:58: #1 finished! INFO @ Sun, 04 Nov 2018 17:54:58: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 17:54:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 17:54:58: #1 tag size is determined as 50 bps INFO @ Sun, 04 Nov 2018 17:54:58: #1 tag size = 50 INFO @ Sun, 04 Nov 2018 17:54:58: #1 total tags in treatment: 8608539 INFO @ Sun, 04 Nov 2018 17:54:58: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 17:54:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Nov 2018 17:54:59: #1 tags after filtering in treatment: 8608539 INFO @ Sun, 04 Nov 2018 17:54:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 17:54:59: #1 finished! INFO @ Sun, 04 Nov 2018 17:54:59: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 17:54:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 17:54:59: #2 number of paired peaks: 7570 INFO @ Sun, 04 Nov 2018 17:54:59: start model_add_line... INFO @ Sun, 04 Nov 2018 17:55:00: start X-correlation... INFO @ Sun, 04 Nov 2018 17:55:00: end of X-cor INFO @ Sun, 04 Nov 2018 17:55:00: #2 finished! INFO @ Sun, 04 Nov 2018 17:55:00: #2 predicted fragment length is 173 bps INFO @ Sun, 04 Nov 2018 17:55:00: #2 alternative fragment length(s) may be 173 bps INFO @ Sun, 04 Nov 2018 17:55:00: #2.2 Generate R script for model : SRX3873748.20_model.r INFO @ Sun, 04 Nov 2018 17:55:00: #3 Call peaks... INFO @ Sun, 04 Nov 2018 17:55:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 17:55:00: #2 number of paired peaks: 7570 INFO @ Sun, 04 Nov 2018 17:55:00: start model_add_line... INFO @ Sun, 04 Nov 2018 17:55:00: start X-correlation... INFO @ Sun, 04 Nov 2018 17:55:00: end of X-cor INFO @ Sun, 04 Nov 2018 17:55:00: #2 finished! INFO @ Sun, 04 Nov 2018 17:55:00: #2 predicted fragment length is 173 bps INFO @ Sun, 04 Nov 2018 17:55:00: #2 alternative fragment length(s) may be 173 bps INFO @ Sun, 04 Nov 2018 17:55:00: #2.2 Generate R script for model : SRX3873748.05_model.r INFO @ Sun, 04 Nov 2018 17:55:00: #3 Call peaks... INFO @ Sun, 04 Nov 2018 17:55:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 17:55:01: #1 tag size is determined as 50 bps INFO @ Sun, 04 Nov 2018 17:55:01: #1 tag size = 50 INFO @ Sun, 04 Nov 2018 17:55:01: #1 total tags in treatment: 8608539 INFO @ Sun, 04 Nov 2018 17:55:01: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 17:55:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Nov 2018 17:55:01: #1 tags after filtering in treatment: 8608539 INFO @ Sun, 04 Nov 2018 17:55:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 17:55:01: #1 finished! INFO @ Sun, 04 Nov 2018 17:55:01: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 17:55:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 17:55:02: #2 number of paired peaks: 7570 INFO @ Sun, 04 Nov 2018 17:55:02: start model_add_line... INFO @ Sun, 04 Nov 2018 17:55:03: start X-correlation... INFO @ Sun, 04 Nov 2018 17:55:03: end of X-cor INFO @ Sun, 04 Nov 2018 17:55:03: #2 finished! INFO @ Sun, 04 Nov 2018 17:55:03: #2 predicted fragment length is 173 bps INFO @ Sun, 04 Nov 2018 17:55:03: #2 alternative fragment length(s) may be 173 bps INFO @ Sun, 04 Nov 2018 17:55:03: #2.2 Generate R script for model : SRX3873748.10_model.r INFO @ Sun, 04 Nov 2018 17:55:03: #3 Call peaks... INFO @ Sun, 04 Nov 2018 17:55:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 17:55:28: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 17:55:29: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 17:55:35: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 17:55:41: #4 Write output xls file... SRX3873748.20_peaks.xls INFO @ Sun, 04 Nov 2018 17:55:41: #4 Write peak in narrowPeak format file... SRX3873748.20_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 17:55:41: #4 Write summits bed file... SRX3873748.20_summits.bed INFO @ Sun, 04 Nov 2018 17:55:41: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4662 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 04 Nov 2018 17:55:41: #4 Write output xls file... SRX3873748.05_peaks.xls INFO @ Sun, 04 Nov 2018 17:55:41: #4 Write peak in narrowPeak format file... SRX3873748.05_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 17:55:42: #4 Write summits bed file... SRX3873748.05_summits.bed INFO @ Sun, 04 Nov 2018 17:55:42: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8859 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 04 Nov 2018 17:55:47: #4 Write output xls file... SRX3873748.10_peaks.xls INFO @ Sun, 04 Nov 2018 17:55:47: #4 Write peak in narrowPeak format file... SRX3873748.10_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 17:55:47: #4 Write summits bed file... SRX3873748.10_summits.bed INFO @ Sun, 04 Nov 2018 17:55:47: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6871 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。