Job ID = 2590659 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 17,095,829 reads read : 34,191,658 reads written : 17,095,829 reads 0-length : 17,095,829 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: 00:06:01 17095829 reads; of these: 17095829 (100.00%) were unpaired; of these: 1851212 (10.83%) aligned 0 times 11589956 (67.79%) aligned exactly 1 time 3654661 (21.38%) aligned >1 times 89.17% overall alignment rate Time searching: 00:06:01 Overall time: 00:06:01 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] 6365531 / 15244617 = 0.4176 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 23:10:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011010/SRX5011010.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011010/SRX5011010.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011010/SRX5011010.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011010/SRX5011010.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 23:10:36: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:10:36: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:10:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011010/SRX5011010.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011010/SRX5011010.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011010/SRX5011010.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011010/SRX5011010.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 23:10:37: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:10:37: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:10:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011010/SRX5011010.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011010/SRX5011010.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011010/SRX5011010.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011010/SRX5011010.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 23:10:38: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:10:38: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:10:43: 1000000 INFO @ Mon, 12 Aug 2019 23:10:47: 1000000 INFO @ Mon, 12 Aug 2019 23:10:47: 1000000 INFO @ Mon, 12 Aug 2019 23:10:51: 2000000 INFO @ Mon, 12 Aug 2019 23:10:55: 2000000 INFO @ Mon, 12 Aug 2019 23:10:58: 2000000 INFO @ Mon, 12 Aug 2019 23:10:59: 3000000 INFO @ Mon, 12 Aug 2019 23:11:04: 3000000 INFO @ Mon, 12 Aug 2019 23:11:08: 4000000 INFO @ Mon, 12 Aug 2019 23:11:08: 3000000 INFO @ Mon, 12 Aug 2019 23:11:12: 4000000 INFO @ Mon, 12 Aug 2019 23:11:15: 5000000 INFO @ Mon, 12 Aug 2019 23:11:18: 4000000 INFO @ Mon, 12 Aug 2019 23:11:21: 5000000 INFO @ Mon, 12 Aug 2019 23:11:23: 6000000 INFO @ Mon, 12 Aug 2019 23:11:28: 5000000 INFO @ Mon, 12 Aug 2019 23:11:29: 6000000 INFO @ Mon, 12 Aug 2019 23:11:30: 7000000 INFO @ Mon, 12 Aug 2019 23:11:38: 8000000 INFO @ Mon, 12 Aug 2019 23:11:38: 7000000 INFO @ Mon, 12 Aug 2019 23:11:39: 6000000 INFO @ Mon, 12 Aug 2019 23:11:44: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:11:44: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:11:44: #1 total tags in treatment: 8879086 INFO @ Mon, 12 Aug 2019 23:11:44: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:11:44: #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 23:11:45: #1 tags after filtering in treatment: 8879086 INFO @ Mon, 12 Aug 2019 23:11:45: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:11:45: #1 finished! INFO @ Mon, 12 Aug 2019 23:11:45: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:11:45: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:11:45: #2 number of paired peaks: 1682 INFO @ Mon, 12 Aug 2019 23:11:45: start model_add_line... INFO @ Mon, 12 Aug 2019 23:11:46: start X-correlation... INFO @ Mon, 12 Aug 2019 23:11:46: end of X-cor INFO @ Mon, 12 Aug 2019 23:11:46: #2 finished! INFO @ Mon, 12 Aug 2019 23:11:46: #2 predicted fragment length is 177 bps INFO @ Mon, 12 Aug 2019 23:11:46: #2 alternative fragment length(s) may be 177 bps INFO @ Mon, 12 Aug 2019 23:11:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011010/SRX5011010.05_model.r INFO @ Mon, 12 Aug 2019 23:11:46: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:11:46: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:11:46: 8000000 INFO @ Mon, 12 Aug 2019 23:11:49: 7000000 INFO @ Mon, 12 Aug 2019 23:11:54: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:11:54: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:11:54: #1 total tags in treatment: 8879086 INFO @ Mon, 12 Aug 2019 23:11:54: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:11:54: #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 23:11:54: #1 tags after filtering in treatment: 8879086 INFO @ Mon, 12 Aug 2019 23:11:54: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:11:54: #1 finished! INFO @ Mon, 12 Aug 2019 23:11:54: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:11:54: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:11:55: #2 number of paired peaks: 1682 INFO @ Mon, 12 Aug 2019 23:11:55: start model_add_line... INFO @ Mon, 12 Aug 2019 23:11:55: start X-correlation... INFO @ Mon, 12 Aug 2019 23:11:55: end of X-cor INFO @ Mon, 12 Aug 2019 23:11:55: #2 finished! INFO @ Mon, 12 Aug 2019 23:11:55: #2 predicted fragment length is 177 bps INFO @ Mon, 12 Aug 2019 23:11:55: #2 alternative fragment length(s) may be 177 bps INFO @ Mon, 12 Aug 2019 23:11:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011010/SRX5011010.20_model.r INFO @ Mon, 12 Aug 2019 23:11:55: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:11:55: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:11:59: 8000000 INFO @ Mon, 12 Aug 2019 23:12:08: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:12:08: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:12:08: #1 total tags in treatment: 8879086 INFO @ Mon, 12 Aug 2019 23:12:08: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:12:08: #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 23:12:08: #1 tags after filtering in treatment: 8879086 INFO @ Mon, 12 Aug 2019 23:12:08: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:12:08: #1 finished! INFO @ Mon, 12 Aug 2019 23:12:08: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:12:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:12:09: #2 number of paired peaks: 1682 INFO @ Mon, 12 Aug 2019 23:12:09: start model_add_line... INFO @ Mon, 12 Aug 2019 23:12:09: start X-correlation... INFO @ Mon, 12 Aug 2019 23:12:09: end of X-cor INFO @ Mon, 12 Aug 2019 23:12:09: #2 finished! INFO @ Mon, 12 Aug 2019 23:12:09: #2 predicted fragment length is 177 bps INFO @ Mon, 12 Aug 2019 23:12:09: #2 alternative fragment length(s) may be 177 bps INFO @ Mon, 12 Aug 2019 23:12:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011010/SRX5011010.10_model.r INFO @ Mon, 12 Aug 2019 23:12:09: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:12:09: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:12:13: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:12:22: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:12:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011010/SRX5011010.05_peaks.xls INFO @ Mon, 12 Aug 2019 23:12:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011010/SRX5011010.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:12:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011010/SRX5011010.05_summits.bed INFO @ Mon, 12 Aug 2019 23:12:26: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9536 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:12:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011010/SRX5011010.20_peaks.xls INFO @ Mon, 12 Aug 2019 23:12:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011010/SRX5011010.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:12:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011010/SRX5011010.20_summits.bed INFO @ Mon, 12 Aug 2019 23:12:35: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2841 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:12:36: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:12:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011010/SRX5011010.10_peaks.xls INFO @ Mon, 12 Aug 2019 23:12:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011010/SRX5011010.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:12:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011010/SRX5011010.10_summits.bed INFO @ Mon, 12 Aug 2019 23:12:50: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (5971 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。