Job ID = 4178459 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 42,375,457 reads read : 84,750,914 reads written : 42,375,457 reads 0-length : 42,375,457 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 00:08:19 42375457 reads; of these: 42375457 (100.00%) were unpaired; of these: 22839553 (53.90%) aligned 0 times 15158768 (35.77%) aligned exactly 1 time 4377136 (10.33%) aligned >1 times 46.10% overall alignment rate Time searching: 00:08:19 Overall time: 00:08:19 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] 13683796 / 19535904 = 0.7004 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 12:46:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5232775/SRX5232775.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5232775/SRX5232775.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5232775/SRX5232775.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5232775/SRX5232775.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 @ Thu, 05 Dec 2019 12:46:28: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:46:28: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:46:34: 1000000 INFO @ Thu, 05 Dec 2019 12:46:39: 2000000 INFO @ Thu, 05 Dec 2019 12:46:45: 3000000 INFO @ Thu, 05 Dec 2019 12:46:50: 4000000 INFO @ Thu, 05 Dec 2019 12:46:56: 5000000 INFO @ Thu, 05 Dec 2019 12:46:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5232775/SRX5232775.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5232775/SRX5232775.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5232775/SRX5232775.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5232775/SRX5232775.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 @ Thu, 05 Dec 2019 12:46:58: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:46:58: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:47:01: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:47:01: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:47:01: #1 total tags in treatment: 5852108 INFO @ Thu, 05 Dec 2019 12:47:01: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:47:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:47:02: #1 tags after filtering in treatment: 5852108 INFO @ Thu, 05 Dec 2019 12:47:02: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:47:02: #1 finished! INFO @ Thu, 05 Dec 2019 12:47:02: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:47:02: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:47:02: #2 number of paired peaks: 1791 INFO @ Thu, 05 Dec 2019 12:47:02: start model_add_line... INFO @ Thu, 05 Dec 2019 12:47:02: start X-correlation... INFO @ Thu, 05 Dec 2019 12:47:02: end of X-cor INFO @ Thu, 05 Dec 2019 12:47:02: #2 finished! INFO @ Thu, 05 Dec 2019 12:47:02: #2 predicted fragment length is 124 bps INFO @ Thu, 05 Dec 2019 12:47:02: #2 alternative fragment length(s) may be 124 bps INFO @ Thu, 05 Dec 2019 12:47:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5232775/SRX5232775.05_model.r INFO @ Thu, 05 Dec 2019 12:47:02: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:47:02: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:47:04: 1000000 INFO @ Thu, 05 Dec 2019 12:47:10: 2000000 INFO @ Thu, 05 Dec 2019 12:47:14: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:47:15: 3000000 INFO @ Thu, 05 Dec 2019 12:47:21: 4000000 INFO @ Thu, 05 Dec 2019 12:47:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5232775/SRX5232775.05_peaks.xls INFO @ Thu, 05 Dec 2019 12:47:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5232775/SRX5232775.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:47:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5232775/SRX5232775.05_summits.bed INFO @ Thu, 05 Dec 2019 12:47:23: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4168 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換中... INFO @ Thu, 05 Dec 2019 12:47:27: 5000000 INFO @ Thu, 05 Dec 2019 12:47:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5232775/SRX5232775.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5232775/SRX5232775.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5232775/SRX5232775.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5232775/SRX5232775.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 @ Thu, 05 Dec 2019 12:47:28: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:47:28: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:47:32: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:47:32: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:47:32: #1 total tags in treatment: 5852108 INFO @ Thu, 05 Dec 2019 12:47:32: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:47:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:47:32: #1 tags after filtering in treatment: 5852108 INFO @ Thu, 05 Dec 2019 12:47:32: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:47:32: #1 finished! INFO @ Thu, 05 Dec 2019 12:47:32: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:47:32: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:47:32: #2 number of paired peaks: 1791 INFO @ Thu, 05 Dec 2019 12:47:32: start model_add_line... INFO @ Thu, 05 Dec 2019 12:47:32: start X-correlation... INFO @ Thu, 05 Dec 2019 12:47:32: end of X-cor INFO @ Thu, 05 Dec 2019 12:47:32: #2 finished! INFO @ Thu, 05 Dec 2019 12:47:32: #2 predicted fragment length is 124 bps INFO @ Thu, 05 Dec 2019 12:47:32: #2 alternative fragment length(s) may be 124 bps INFO @ Thu, 05 Dec 2019 12:47:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5232775/SRX5232775.10_model.r INFO @ Thu, 05 Dec 2019 12:47:32: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:47:32: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:47:34: 1000000 INFO @ Thu, 05 Dec 2019 12:47:40: 2000000 INFO @ Thu, 05 Dec 2019 12:47:45: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:47:45: 3000000 INFO @ Thu, 05 Dec 2019 12:47:51: 4000000 INFO @ Thu, 05 Dec 2019 12:47:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5232775/SRX5232775.10_peaks.xls INFO @ Thu, 05 Dec 2019 12:47:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5232775/SRX5232775.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:47:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5232775/SRX5232775.10_summits.bed INFO @ Thu, 05 Dec 2019 12:47:52: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3086 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:47:57: 5000000 INFO @ Thu, 05 Dec 2019 12:48:02: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:48:02: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:48:02: #1 total tags in treatment: 5852108 INFO @ Thu, 05 Dec 2019 12:48:02: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:48:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:48:02: #1 tags after filtering in treatment: 5852108 INFO @ Thu, 05 Dec 2019 12:48:02: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:48:02: #1 finished! INFO @ Thu, 05 Dec 2019 12:48:02: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:48:02: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:48:02: #2 number of paired peaks: 1791 INFO @ Thu, 05 Dec 2019 12:48:02: start model_add_line... INFO @ Thu, 05 Dec 2019 12:48:02: start X-correlation... INFO @ Thu, 05 Dec 2019 12:48:02: end of X-cor INFO @ Thu, 05 Dec 2019 12:48:02: #2 finished! INFO @ Thu, 05 Dec 2019 12:48:02: #2 predicted fragment length is 124 bps INFO @ Thu, 05 Dec 2019 12:48:02: #2 alternative fragment length(s) may be 124 bps INFO @ Thu, 05 Dec 2019 12:48:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5232775/SRX5232775.20_model.r INFO @ Thu, 05 Dec 2019 12:48:02: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:48:02: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:48:14: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:48:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5232775/SRX5232775.20_peaks.xls INFO @ Thu, 05 Dec 2019 12:48:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5232775/SRX5232775.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:48:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5232775/SRX5232775.20_summits.bed INFO @ Thu, 05 Dec 2019 12:48:22: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (2204 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。