Job ID = 2590585 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 22,998,454 reads read : 45,996,908 reads written : 22,998,454 reads 0-length : 22,998,454 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: 00:07:16 22998454 reads; of these: 22998454 (100.00%) were unpaired; of these: 509388 (2.21%) aligned 0 times 18237979 (79.30%) aligned exactly 1 time 4251087 (18.48%) aligned >1 times 97.79% overall alignment rate Time searching: 00:07:16 Overall time: 00:07:16 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 12 files... [bam_rmdupse_core] 7575235 / 22489066 = 0.3368 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 @ Mon, 12 Aug 2019 22:47:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4923178/SRX4923178.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4923178/SRX4923178.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4923178/SRX4923178.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4923178/SRX4923178.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 @ Mon, 12 Aug 2019 22:47:12: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:47:12: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:47:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4923178/SRX4923178.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4923178/SRX4923178.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4923178/SRX4923178.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4923178/SRX4923178.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 @ Mon, 12 Aug 2019 22:47:13: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:47:13: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:47:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4923178/SRX4923178.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4923178/SRX4923178.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4923178/SRX4923178.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4923178/SRX4923178.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 @ Mon, 12 Aug 2019 22:47:14: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:47:14: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:47:21: 1000000 INFO @ Mon, 12 Aug 2019 22:47:24: 1000000 INFO @ Mon, 12 Aug 2019 22:47:26: 1000000 INFO @ Mon, 12 Aug 2019 22:47:31: 2000000 INFO @ Mon, 12 Aug 2019 22:47:33: 2000000 INFO @ Mon, 12 Aug 2019 22:47:38: 2000000 INFO @ Mon, 12 Aug 2019 22:47:40: 3000000 INFO @ Mon, 12 Aug 2019 22:47:43: 3000000 INFO @ Mon, 12 Aug 2019 22:47:49: 3000000 INFO @ Mon, 12 Aug 2019 22:47:50: 4000000 INFO @ Mon, 12 Aug 2019 22:47:52: 4000000 INFO @ Mon, 12 Aug 2019 22:47:58: 5000000 INFO @ Mon, 12 Aug 2019 22:48:00: 5000000 INFO @ Mon, 12 Aug 2019 22:48:00: 4000000 INFO @ Mon, 12 Aug 2019 22:48:06: 6000000 INFO @ Mon, 12 Aug 2019 22:48:08: 6000000 INFO @ Mon, 12 Aug 2019 22:48:11: 5000000 INFO @ Mon, 12 Aug 2019 22:48:14: 7000000 INFO @ Mon, 12 Aug 2019 22:48:16: 7000000 INFO @ Mon, 12 Aug 2019 22:48:21: 6000000 INFO @ Mon, 12 Aug 2019 22:48:22: 8000000 INFO @ Mon, 12 Aug 2019 22:48:23: 8000000 INFO @ Mon, 12 Aug 2019 22:48:30: 9000000 INFO @ Mon, 12 Aug 2019 22:48:31: 9000000 INFO @ Mon, 12 Aug 2019 22:48:32: 7000000 INFO @ Mon, 12 Aug 2019 22:48:38: 10000000 INFO @ Mon, 12 Aug 2019 22:48:39: 10000000 INFO @ Mon, 12 Aug 2019 22:48:43: 8000000 INFO @ Mon, 12 Aug 2019 22:48:45: 11000000 INFO @ Mon, 12 Aug 2019 22:48:47: 11000000 INFO @ Mon, 12 Aug 2019 22:48:53: 9000000 INFO @ Mon, 12 Aug 2019 22:48:54: 12000000 INFO @ Mon, 12 Aug 2019 22:48:55: 12000000 INFO @ Mon, 12 Aug 2019 22:49:02: 13000000 INFO @ Mon, 12 Aug 2019 22:49:03: 13000000 INFO @ Mon, 12 Aug 2019 22:49:04: 10000000 INFO @ Mon, 12 Aug 2019 22:49:10: 14000000 INFO @ Mon, 12 Aug 2019 22:49:11: 14000000 INFO @ Mon, 12 Aug 2019 22:49:15: 11000000 INFO @ Mon, 12 Aug 2019 22:49:17: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 22:49:17: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 22:49:17: #1 total tags in treatment: 14913831 INFO @ Mon, 12 Aug 2019 22:49:17: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:49:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 22:49:17: #1 tags after filtering in treatment: 14913831 INFO @ Mon, 12 Aug 2019 22:49:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:49:17: #1 finished! INFO @ Mon, 12 Aug 2019 22:49:17: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:49:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:49:19: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 22:49:19: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 22:49:19: #1 total tags in treatment: 14913831 INFO @ Mon, 12 Aug 2019 22:49:19: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:49:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 22:49:19: #1 tags after filtering in treatment: 14913831 INFO @ Mon, 12 Aug 2019 22:49:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:49:19: #1 finished! INFO @ Mon, 12 Aug 2019 22:49:19: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:49:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:49:20: #2 number of paired peaks: 8581 INFO @ Mon, 12 Aug 2019 22:49:20: start model_add_line... INFO @ Mon, 12 Aug 2019 22:49:20: start X-correlation... INFO @ Mon, 12 Aug 2019 22:49:20: end of X-cor INFO @ Mon, 12 Aug 2019 22:49:20: #2 finished! INFO @ Mon, 12 Aug 2019 22:49:20: #2 predicted fragment length is 139 bps INFO @ Mon, 12 Aug 2019 22:49:20: #2 alternative fragment length(s) may be 139 bps INFO @ Mon, 12 Aug 2019 22:49:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4923178/SRX4923178.05_model.r INFO @ Mon, 12 Aug 2019 22:49:20: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:49:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:49:21: #2 number of paired peaks: 8581 INFO @ Mon, 12 Aug 2019 22:49:21: start model_add_line... INFO @ Mon, 12 Aug 2019 22:49:21: start X-correlation... INFO @ Mon, 12 Aug 2019 22:49:21: end of X-cor INFO @ Mon, 12 Aug 2019 22:49:21: #2 finished! INFO @ Mon, 12 Aug 2019 22:49:21: #2 predicted fragment length is 139 bps INFO @ Mon, 12 Aug 2019 22:49:21: #2 alternative fragment length(s) may be 139 bps INFO @ Mon, 12 Aug 2019 22:49:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4923178/SRX4923178.10_model.r INFO @ Mon, 12 Aug 2019 22:49:21: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:49:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:49:25: 12000000 INFO @ Mon, 12 Aug 2019 22:49:36: 13000000 INFO @ Mon, 12 Aug 2019 22:49:46: 14000000 INFO @ Mon, 12 Aug 2019 22:49:55: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 22:49:55: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 22:49:55: #1 total tags in treatment: 14913831 INFO @ Mon, 12 Aug 2019 22:49:55: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:49:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 22:49:56: #1 tags after filtering in treatment: 14913831 INFO @ Mon, 12 Aug 2019 22:49:56: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:49:56: #1 finished! INFO @ Mon, 12 Aug 2019 22:49:56: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:49:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:49:58: #2 number of paired peaks: 8581 INFO @ Mon, 12 Aug 2019 22:49:58: start model_add_line... INFO @ Mon, 12 Aug 2019 22:49:58: start X-correlation... INFO @ Mon, 12 Aug 2019 22:49:58: end of X-cor INFO @ Mon, 12 Aug 2019 22:49:58: #2 finished! INFO @ Mon, 12 Aug 2019 22:49:58: #2 predicted fragment length is 139 bps INFO @ Mon, 12 Aug 2019 22:49:58: #2 alternative fragment length(s) may be 139 bps INFO @ Mon, 12 Aug 2019 22:49:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4923178/SRX4923178.20_model.r INFO @ Mon, 12 Aug 2019 22:49:58: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:49:58: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:50:06: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:50:07: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:50:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4923178/SRX4923178.05_peaks.xls INFO @ Mon, 12 Aug 2019 22:50:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4923178/SRX4923178.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:50:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4923178/SRX4923178.05_summits.bed INFO @ Mon, 12 Aug 2019 22:50:26: Done! pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (9570 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:50:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4923178/SRX4923178.10_peaks.xls INFO @ Mon, 12 Aug 2019 22:50:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4923178/SRX4923178.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:50:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4923178/SRX4923178.10_summits.bed INFO @ Mon, 12 Aug 2019 22:50:27: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (8467 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:50:45: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:51:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4923178/SRX4923178.20_peaks.xls INFO @ Mon, 12 Aug 2019 22:51:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4923178/SRX4923178.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:51:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4923178/SRX4923178.20_summits.bed INFO @ Mon, 12 Aug 2019 22:51:06: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (7135 records, 4 fields): 17 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。