Job ID = 1293838 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 31,546,612 reads read : 31,546,612 reads written : 31,546,612 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:10:11 31546612 reads; of these: 31546612 (100.00%) were unpaired; of these: 1695928 (5.38%) aligned 0 times 21428477 (67.93%) aligned exactly 1 time 8422207 (26.70%) aligned >1 times 94.62% overall alignment rate Time searching: 00:10:11 Overall time: 00:10:11 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] 12604432 / 29850684 = 0.4222 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, 03 Jun 2019 03:00:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX128303/SRX128303.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX128303/SRX128303.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX128303/SRX128303.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX128303/SRX128303.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, 03 Jun 2019 03:00:40: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:00:40: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:00:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX128303/SRX128303.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX128303/SRX128303.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX128303/SRX128303.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX128303/SRX128303.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, 03 Jun 2019 03:00:40: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:00:40: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:00:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX128303/SRX128303.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX128303/SRX128303.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX128303/SRX128303.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX128303/SRX128303.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, 03 Jun 2019 03:00:40: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:00:40: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:00:48: 1000000 INFO @ Mon, 03 Jun 2019 03:00:48: 1000000 INFO @ Mon, 03 Jun 2019 03:00:48: 1000000 INFO @ Mon, 03 Jun 2019 03:00:57: 2000000 INFO @ Mon, 03 Jun 2019 03:00:57: 2000000 INFO @ Mon, 03 Jun 2019 03:00:57: 2000000 INFO @ Mon, 03 Jun 2019 03:01:05: 3000000 INFO @ Mon, 03 Jun 2019 03:01:05: 3000000 INFO @ Mon, 03 Jun 2019 03:01:05: 3000000 INFO @ Mon, 03 Jun 2019 03:01:13: 4000000 INFO @ Mon, 03 Jun 2019 03:01:13: 4000000 INFO @ Mon, 03 Jun 2019 03:01:13: 4000000 INFO @ Mon, 03 Jun 2019 03:01:21: 5000000 INFO @ Mon, 03 Jun 2019 03:01:21: 5000000 INFO @ Mon, 03 Jun 2019 03:01:22: 5000000 INFO @ Mon, 03 Jun 2019 03:01:28: 6000000 INFO @ Mon, 03 Jun 2019 03:01:30: 6000000 INFO @ Mon, 03 Jun 2019 03:01:30: 6000000 INFO @ Mon, 03 Jun 2019 03:01:36: 7000000 INFO @ Mon, 03 Jun 2019 03:01:38: 7000000 INFO @ Mon, 03 Jun 2019 03:01:38: 7000000 INFO @ Mon, 03 Jun 2019 03:01:44: 8000000 INFO @ Mon, 03 Jun 2019 03:01:46: 8000000 INFO @ Mon, 03 Jun 2019 03:01:46: 8000000 INFO @ Mon, 03 Jun 2019 03:01:52: 9000000 INFO @ Mon, 03 Jun 2019 03:01:54: 9000000 INFO @ Mon, 03 Jun 2019 03:01:54: 9000000 INFO @ Mon, 03 Jun 2019 03:01:59: 10000000 INFO @ Mon, 03 Jun 2019 03:02:02: 10000000 INFO @ Mon, 03 Jun 2019 03:02:02: 10000000 INFO @ Mon, 03 Jun 2019 03:02:07: 11000000 INFO @ Mon, 03 Jun 2019 03:02:09: 11000000 INFO @ Mon, 03 Jun 2019 03:02:10: 11000000 INFO @ Mon, 03 Jun 2019 03:02:14: 12000000 INFO @ Mon, 03 Jun 2019 03:02:17: 12000000 INFO @ Mon, 03 Jun 2019 03:02:18: 12000000 INFO @ Mon, 03 Jun 2019 03:02:22: 13000000 INFO @ Mon, 03 Jun 2019 03:02:24: 13000000 INFO @ Mon, 03 Jun 2019 03:02:25: 13000000 INFO @ Mon, 03 Jun 2019 03:02:29: 14000000 INFO @ Mon, 03 Jun 2019 03:02:32: 14000000 INFO @ Mon, 03 Jun 2019 03:02:33: 14000000 INFO @ Mon, 03 Jun 2019 03:02:37: 15000000 INFO @ Mon, 03 Jun 2019 03:02:39: 15000000 INFO @ Mon, 03 Jun 2019 03:02:41: 15000000 INFO @ Mon, 03 Jun 2019 03:02:44: 16000000 INFO @ Mon, 03 Jun 2019 03:02:47: 16000000 INFO @ Mon, 03 Jun 2019 03:02:49: 16000000 INFO @ Mon, 03 Jun 2019 03:02:52: 17000000 INFO @ Mon, 03 Jun 2019 03:02:54: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 03:02:54: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 03:02:54: #1 total tags in treatment: 17246252 INFO @ Mon, 03 Jun 2019 03:02:54: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:02:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 03:02:55: #1 tags after filtering in treatment: 17246252 INFO @ Mon, 03 Jun 2019 03:02:55: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:02:55: #1 finished! INFO @ Mon, 03 Jun 2019 03:02:55: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:02:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:02:55: 17000000 INFO @ Mon, 03 Jun 2019 03:02:57: #2 number of paired peaks: 2822 INFO @ Mon, 03 Jun 2019 03:02:57: start model_add_line... INFO @ Mon, 03 Jun 2019 03:02:57: start X-correlation... INFO @ Mon, 03 Jun 2019 03:02:57: end of X-cor INFO @ Mon, 03 Jun 2019 03:02:57: #2 finished! INFO @ Mon, 03 Jun 2019 03:02:57: #2 predicted fragment length is 82 bps INFO @ Mon, 03 Jun 2019 03:02:57: #2 alternative fragment length(s) may be 4,82 bps INFO @ Mon, 03 Jun 2019 03:02:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX128303/SRX128303.20_model.r INFO @ Mon, 03 Jun 2019 03:02:57: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:02:57: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:02:57: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 03:02:57: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 03:02:57: #1 total tags in treatment: 17246252 INFO @ Mon, 03 Jun 2019 03:02:57: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:02:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 03:02:57: #1 tags after filtering in treatment: 17246252 INFO @ Mon, 03 Jun 2019 03:02:57: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:02:57: #1 finished! INFO @ Mon, 03 Jun 2019 03:02:57: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:02:57: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:02:57: 17000000 INFO @ Mon, 03 Jun 2019 03:02:59: #2 number of paired peaks: 2822 INFO @ Mon, 03 Jun 2019 03:02:59: start model_add_line... INFO @ Mon, 03 Jun 2019 03:02:59: start X-correlation... INFO @ Mon, 03 Jun 2019 03:02:59: end of X-cor INFO @ Mon, 03 Jun 2019 03:02:59: #2 finished! INFO @ Mon, 03 Jun 2019 03:02:59: #2 predicted fragment length is 82 bps INFO @ Mon, 03 Jun 2019 03:02:59: #2 alternative fragment length(s) may be 4,82 bps INFO @ Mon, 03 Jun 2019 03:02:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX128303/SRX128303.10_model.r INFO @ Mon, 03 Jun 2019 03:02:59: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:02:59: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:03:00: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 03:03:00: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 03:03:00: #1 total tags in treatment: 17246252 INFO @ Mon, 03 Jun 2019 03:03:00: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:03:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 03:03:00: #1 tags after filtering in treatment: 17246252 INFO @ Mon, 03 Jun 2019 03:03:00: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:03:00: #1 finished! INFO @ Mon, 03 Jun 2019 03:03:00: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:03:00: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:03:02: #2 number of paired peaks: 2822 INFO @ Mon, 03 Jun 2019 03:03:02: start model_add_line... INFO @ Mon, 03 Jun 2019 03:03:02: start X-correlation... INFO @ Mon, 03 Jun 2019 03:03:02: end of X-cor INFO @ Mon, 03 Jun 2019 03:03:02: #2 finished! INFO @ Mon, 03 Jun 2019 03:03:02: #2 predicted fragment length is 82 bps INFO @ Mon, 03 Jun 2019 03:03:02: #2 alternative fragment length(s) may be 4,82 bps INFO @ Mon, 03 Jun 2019 03:03:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX128303/SRX128303.05_model.r INFO @ Mon, 03 Jun 2019 03:03:02: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:03:02: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:03:45: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:03:48: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:03:51: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:04:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX128303/SRX128303.20_peaks.xls INFO @ Mon, 03 Jun 2019 03:04:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX128303/SRX128303.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:04:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX128303/SRX128303.20_summits.bed INFO @ Mon, 03 Jun 2019 03:04:07: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5244 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 03:04:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX128303/SRX128303.10_peaks.xls INFO @ Mon, 03 Jun 2019 03:04:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX128303/SRX128303.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:04:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX128303/SRX128303.10_summits.bed INFO @ Mon, 03 Jun 2019 03:04:11: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (10183 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 03:04:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX128303/SRX128303.05_peaks.xls INFO @ Mon, 03 Jun 2019 03:04:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX128303/SRX128303.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:04:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX128303/SRX128303.05_summits.bed INFO @ Mon, 03 Jun 2019 03:04:16: Done! pass1 - making usageList (15 chroms): 8 millis pass2 - checking and writing primary data (16500 records, 4 fields): 21 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。